{"entity": "researcher", "timestamp": "2026-08-08T19:07:01.966Z", "family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "affiliations": ["Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.", "Center for Biosustainability, Danish Technical University, Copenhagen, Denmark."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c"}}, "publications": [{"entity": "publication", "iuid": "3c879540016f423ca84894bb30eae1b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c879540016f423ca84894bb30eae1b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c879540016f423ca84894bb30eae1b5"}}, "title": "Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.", "authors": [{"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Meng", "given": "Lingqi", "initials": "L"}, {"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Ji", "given": "Boyu", "initials": "B"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Oktem", "given": "Ece Ozdemir", "initials": "EO"}, {"family": "Sayman", "given": "Dila", "initials": "D"}, {"family": "Karaca", "given": "Ramazan", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Neurobiol. Dis.", "issn": "1095-953X", "volume": "225", "pages": "107424", "issn-l": "0969-9961"}, "abstract": "While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.", "doi": "10.1016/j.nbd.2026.107424", "pmid": "42069091", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0969-9961(26)00169-5"}], "notes": [], "created": "2026-05-11T11:43:55.203Z", "modified": "2026-06-30T09:59:57.743Z"}, {"entity": "publication", "iuid": "01a6b1a78bb54a8f8e4c51b7ca9f3d9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01a6b1a78bb54a8f8e4c51b7ca9f3d9b"}}, "title": "Longitudinal protein profiling of blood during childhood into early adulthood.", "authors": [{"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Bueno \u00c1lvez", "given": "Mar\u00eda", "initials": "M", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Kebede Merid", "given": "Simon", "initials": "S"}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}], "type": "journal article", "published": "2026-04-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Proteomic research enhances our understanding of health- and disease-related biological processes. Protein profiling during healthy childhood provides important insights into normal physiological development. We longitudinally measured 5416 plasma proteins at four follow-ups during childhood (4-, 8-, 16 years) and early adulthood (24 years) in 100 randomly selected subjects participating in a population-based Swedish cohort, using Olink Explore HT. In total, 3509 proteins were included in the analysis. 54% of the proteins were found to be associated with age, and we observed several protein trajectories from childhood to adulthood based on clustering. In addition to proteins involved in bone, teeth and cartilage formation, we identified differences in proteins involved in neural function, drug metabolism, and hormonal control. There were pronounced sex-related differences in protein levels, particularly at follow-ups 16 and 24, characterized by, for example, growth, response to stimuli and regulation of catabolic processes. We demonstrate dynamic age- and sex-related changes in protein levels during the first two decades of life. Our study results may serve as an important resource in understanding human physiological development, disease etiology, and for future protein biomarker research.", "doi": "10.1038/s41467-026-72095-3", "pmid": "42020385", "labels": {"NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13102979"}, {"db": "pii", "key": "10.1038/s41467-026-72095-3"}], "notes": [], "created": "2026-04-28T06:03:05.109Z", "modified": "2026-04-28T06:03:05.659Z"}, {"entity": "publication", "iuid": "8f8dca39f51246e399479b7a8829b62d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f8dca39f51246e399479b7a8829b62d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f8dca39f51246e399479b7a8829b62d"}}, "title": "Plasma protein profiling predicts cancer in patients with non-specific symptoms.", "authors": [{"family": "Wannberg", "given": "Fredrika", "initials": "F", "orcid": "0009-0001-8505-3122", "researcher": {"href": "https://publications.scilifelab.se/researcher/15572474779e45a7a64e439cca882a73.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Qvick", "given": "Alvida", "initials": "A", "orcid": "0000-0001-6688-947X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4be159eaa724d22982b7b1e24e9ba79.json"}}, {"family": "Pongracz", "given": "Tamas", "initials": "T", "orcid": "0000-0002-8089-4352", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bdf2f1b85954a1b872b59339838fa57.json"}}, {"family": "Aguilera", "given": "Katherina", "initials": "K"}, {"family": "Adolfsson", "given": "Emma", "initials": "E", "orcid": "0000-0002-7954-0696", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c790fe832ec4bf68608578c0c9d4552.json"}}, {"family": "Essehorn", "given": "Louise", "initials": "L"}, {"family": "Gordon", "given": "Max", "initials": "M", "orcid": "0000-0002-8080-5815", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f1f5ca4e2a4f17bf9454cd7b5a259d.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Helenius", "given": "Gisela", "initials": "G"}, {"family": "Hjalmar", "given": "Viktoria", "initials": "V"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Rosell", "given": "Axel", "initials": "A", "orcid": "0000-0001-6280-0562", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcddaba7a96a406b994756ab71427baf.json"}}, {"family": "Th\u00e5lin", "given": "Charlotte", "initials": "C", "orcid": "0009-0008-9471-3234", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a1c3368c5314543bb4b2204f2938159.json"}}], "type": "journal article", "published": "2025-12-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "pages": "151", "issn-l": "2041-1723"}, "abstract": "Cancer detection is challenging, especially in patients with diffuse symptoms that overlap with non-malignant conditions. Here we show that plasma protein profiling can identify cancer among patients with non-specific symptoms. Using proximity extension assay-based proteomics of 1463 plasma proteins from 456 patients presenting with non-specific symptoms sampled prior to cancer diagnostic work-up and diagnosis, we identify 29 proteins associated with new cancer diagnoses. We develop a model able to stratify 160 cancer cases and 296 non-cancer cases with an area under the curve of 0.80, maintaining performance (0.82) in an independent replication cohort of 238 patients. The model also distinguishes cancer from autoimmune, inflammatory and infectious diseases. Designed as a triage tool, our model based on a blood test could help prioritize patients at higher cancer risk for rapid and highly sensitive diagnostic modalities such as positron emission tomography-computed tomography. These findings emphasize the potential of blood proteome profiling to support timely diagnosis and transform clinical medicine.", "doi": "10.1038/s41467-025-67688-3", "pmid": "41457066", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics \u00d6rebro": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12774938"}, {"db": "pii", "key": "10.1038/s41467-025-67688-3"}], "notes": [], "created": "2026-01-09T16:47:14.250Z", "modified": "2026-03-05T09:10:04.784Z"}, {"entity": "publication", "iuid": "62196b2aeaf64cffbdc15583c03cd12a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62196b2aeaf64cffbdc15583c03cd12a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62196b2aeaf64cffbdc15583c03cd12a"}}, "title": "Deciphering the determinants of recombinant protein expression across the human secretome.", "authors": [{"family": "Masson", "given": "Helen O", "initials": "HO"}, {"family": "Di Giusto", "given": "Pablo", "initials": "P", "orcid": "0000-0003-1024-1222", "researcher": {"href": "https://publications.scilifelab.se/researcher/443c70edc8054e5c972eea27e8e71883.json"}}, {"family": "Kuo", "given": "Chih-Chung", "initials": "CC"}, {"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4c6c276dd64fe2abe27da888cd0925.json"}}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Sievertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Grassi", "given": "Luigi", "initials": "L", "orcid": "0000-0002-6308-7540", "researcher": {"href": "https://publications.scilifelab.se/researcher/c006b891dedd483e8f01756f73fd6fb0.json"}}, {"family": "Robasky", "given": "Kimberly", "initials": "K", "orcid": "0000-0002-0090-8698", "researcher": {"href": "https://publications.scilifelab.se/researcher/16439af864534d3bb025acbb1edb933b.json"}}, {"family": "Hsieh", "given": "Chen-Lin", "initials": "CL", "orcid": "0009-0000-9239-8711", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7175e63f7d84a99ac3a2f0b1c49cf88.json"}}, {"family": "Hatton", "given": "Diane", "initials": "D", "orcid": "0000-0002-6600-021X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a947736bdbe4177a909782cea719df8.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Lewis", "given": "Nathan E", "initials": "NE", "orcid": "0000-0001-7700-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8b8fb6dee874a178dd5c9d10d280982.json"}}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "41", "pages": "e2506036122", "issn-l": "0027-8424"}, "abstract": "Protein secretion is an essential process of mammalian cells. In biomanufacturing, this process can be optimized to enhance production yields and biotherapeutic quality. While cell line engineering and bioprocess optimization have yielded high protein titers for some recombinant proteins, many remain difficult to express. Here, we investigated factors influencing protein expression in Chinese hamster ovary (CHO) cells, expressing 2,135 Human Secretome Project proteins. While the abundance of mRNA from recombinant proteins explained less than 1% of observed variation in secretion titers, analysis of 218 biochemical and biophysical descriptors uncovered intrinsic protein features that account for ~15% of secretion variability, pinpointing key drivers such as molecular weight, cysteine content, and N-linked glycosylation, and establishing a roadmap for rational design of difficult-to-express proteins. We subsequently analyzed RNA-Seq data from 95 CHO cell cultures, each expressing a distinct recombinant protein, spanning a wide range of titers. Host cell transcriptomic signatures showed strong correlations with titer, thereby providing insights into cellular processes that covary with expression. Cells failing to produce proteins exhibited increased ubiquitin-mediated proteasomal degradation, including ER-associated degradation; whereas high-producing cells demonstrated enhanced lipid metabolism and a stronger response to oxidative stress, suggesting these factors may support successful recombinant protein productions. Together, using this resource, we quantified the contributions of various protein and cellular factors that correlate with the expression of diverse recombinant human proteins in a heterologous host, thereby providing insights for next-generation CHO cell engineering.", "doi": "10.1073/pnas.2506036122", "pmid": "41055974", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2109099"}, {"db": "pmc", "key": "PMC12541331"}], "notes": [], "created": "2025-11-21T09:55:14.036Z", "modified": "2025-11-21T09:55:15.142Z"}, {"entity": "publication", "iuid": "20400326c0944ebda6e786a24f339e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20400326c0944ebda6e786a24f339e26"}}, "title": "A human pan-disease blood atlas of the circulating proteome.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S", "orcid": "0000-0003-2910-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/648c9ed3483a4eb8a1d228cf7e59f6a7.json"}}, {"family": "Kenrick", "given": "Josefin", "initials": "J", "orcid": "0000-0002-0110-5192", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83beb37b7bc4e0aa84106bea7c6e0d0.json"}}, {"family": "Johansson", "given": "Emil", "initials": "E", "orcid": "0009-0003-1250-0678", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d953dd65ab24e8ab08aee7e7f101702.json"}}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2025-10-09", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": null, "issue": null, "pages": "eadx2678"}, "abstract": "The human blood proteome provides a holistic readout of health states through the assessment of thousands of circulating proteins. Here, we present a pan-disease resource to enable the study of diverse disease phenotypes within a harmonized proteomics dataset. By profiling protein concentrations across 59 diseases and healthy cohorts, we identified proteins associated with age, sex, and BMI, as well as disease-specific signatures. This study highlights shared and distinct protein patterns across conditions, demonstrating the power of a unified proteomics approach to uncover biological insights. The dataset, covering 8,262 individuals and up to 5,416 proteins, serves as an online resource for exploring disease-specific protein profiles and advancing precision medicine research.", "doi": "10.1126/science.adx2678", "pmid": "41066540", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Affinity Proteomics Uppsala": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-10-10T10:37:22.942Z", "modified": "2025-11-07T07:45:07.446Z"}, {"entity": "publication", "iuid": "bdbfa9803d4f4b56abcf611c35836e4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdbfa9803d4f4b56abcf611c35836e4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdbfa9803d4f4b56abcf611c35836e4b"}}, "title": "A spatiotemporal atlas of human spermatogenesis", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F"}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L"}, {"family": "Gustavsson", "given": "Jonas", "initials": "J"}, {"family": "Miranda", "given": "Gisele", "initials": "G"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Stukenborg", "given": "Jan Bernd", "initials": "JB"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "posted-content", "published": "2025-01-17", "journal": {"title": "res sq", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.21203/rs.3.rs-5594800/v1", "pmid": null, "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-25T12:59:38.185Z", "modified": "2025-12-22T07:55:55.559Z"}, {"entity": "publication", "iuid": "e20232eba3084478a0d4cb3b52b4a953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e20232eba3084478a0d4cb3b52b4a953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e20232eba3084478a0d4cb3b52b4a953"}}, "title": "Transient colonizing microbes promote gut dysbiosis and functional impairment.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Meslier", "given": "Victoria", "initials": "V", "orcid": "0000-0003-2699-0092", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cd1d7bc18954f988d1e3f5200e124eb.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Etienne-Mesmin", "given": "Lucie", "initials": "L", "orcid": "0000-0001-6104-6043", "researcher": {"href": "https://publications.scilifelab.se/researcher/51e9e5819e4e43b08593df4c66c1f0b3.json"}}, {"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5b77f5a5b98479db82a0790affe0a46.json"}}, {"family": "Plaza O\u00f1ate", "given": "Florian", "initials": "F", "orcid": "0000-0001-6036-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2a015ed8dd47f29f37ef700ccf65d0.json"}}, {"family": "Cai", "given": "Haizhuang", "initials": "H"}, {"family": "Le Chatelier", "given": "Emmanuelle", "initials": "E", "orcid": "0000-0002-2724-0536", "researcher": {"href": "https://publications.scilifelab.se/researcher/99c1ea4535d24ffca619adc5e54b5e80.json"}}, {"family": "Pons", "given": "Nicolas", "initials": "N"}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Lee", "given": "Doheon", "initials": "D", "orcid": "0000-0001-9070-4316", "researcher": {"href": "https://publications.scilifelab.se/researcher/766833afa7534fb68e04525078040b65.json"}}, {"family": "Proctor", "given": "Gordon", "initials": "G", "orcid": "0000-0002-5684-841X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d55a1e72dd9444239c5054ccf7876be3.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Blanquet-Diot", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0003-0692-8726", "researcher": {"href": "https://publications.scilifelab.se/researcher/0689cb23d6fa472aab4623c4c8e611db.json"}}, {"family": "Moyes", "given": "David", "initials": "D", "orcid": "0000-0002-1657-918X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6f9404ad0b420bb54962af7f9ff2f5.json"}}, {"family": "Almeida", "given": "Mathieu", "initials": "M", "orcid": "0000-0003-4971-0049", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cbbdb8b00b84a33a862ef1f8f030555.json"}}, {"family": "Ehrlich", "given": "S Dusko", "initials": "SD"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}], "type": "journal article", "published": "2024-09-08", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "10", "issue": "1", "pages": "80", "issn-l": "2055-5008"}, "abstract": "Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.", "doi": "10.1038/s41522-024-00561-1", "pmid": "39245657", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11381545"}, {"db": "pii", "key": "10.1038/s41522-024-00561-1"}], "notes": [], "created": "2024-11-25T10:18:41.173Z", "modified": "2025-02-28T14:15:02.782Z"}, {"entity": "publication", "iuid": "ba3c714d56ff4d3b8e49041ac8d4d503", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba3c714d56ff4d3b8e49041ac8d4d503.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba3c714d56ff4d3b8e49041ac8d4d503"}}, "title": "Global compositional and functional states of the human gut microbiome in health and disease.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Portlock", "given": "Theo", "initials": "T"}, {"family": "Le Chatelier", "given": "Emmanuelle", "initials": "E"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "O\u00f1ate", "given": "Florian Plaza", "initials": "FP"}, {"family": "Pons", "given": "Nicolas", "initials": "N"}, {"family": "Begum", "given": "Neelu", "initials": "N"}, {"family": "Harzandi", "given": "Azadeh", "initials": "A"}, {"family": "Proffitt", "given": "Ceri", "initials": "C"}, {"family": "Rosario", "given": "Dorines", "initials": "D"}, {"family": "Vaga", "given": "Stefania", "initials": "S"}, {"family": "Park", "given": "Junseok", "initials": "J", "orcid": "0000-0003-2312-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5b77f5a5b98479db82a0790affe0a46.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Edwards", "given": "Lindsey A", "initials": "LA"}, {"family": "Lombard", "given": "Vincent", "initials": "V"}, {"family": "Gauthier", "given": "Franck", "initials": "F"}, {"family": "Steves", "given": "Claire J", "initials": "CJ"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D", "orcid": "0000-0003-4186-3788", "researcher": {"href": "https://publications.scilifelab.se/researcher/561bb3d0b1314243850d7094b2ca9b1b.json"}}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Lee", "given": "Doheon", "initials": "D"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Shawcross", "given": "Debbie L", "initials": "DL"}, {"family": "Proctor", "given": "Gordon", "initials": "G"}, {"family": "Almeida", "given": "Mathieu", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Moyes", "given": "David L", "initials": "DL"}, {"family": "Ehrlich", "given": "Stanislav Dusko", "initials": "SD"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}], "type": "journal article", "published": "2024-07-23", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "34", "issue": "6", "pages": "967-978", "issn-l": "1088-9051"}, "abstract": "The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.", "doi": "10.1101/gr.278637.123", "pmid": "39038849", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11293553"}, {"db": "pii", "key": "gr.278637.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2024-11-25T10:26:17.522Z", "modified": "2025-02-28T14:19:39.101Z"}, {"entity": "publication", "iuid": "7344de1a6fea4d8e8b4e7972f2c93e6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7344de1a6fea4d8e8b4e7972f2c93e6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7344de1a6fea4d8e8b4e7972f2c93e6f"}}, "title": "The development of blood protein profiles in extremely preterm infants follows a stereotypic evolution pattern.", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "Brusselaers", "given": "Nele", "initials": "N", "orcid": "0000-0003-0137-447X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb44146e4e943a589f38cd31beae2a0.json"}}, {"family": "Wackernagel", "given": "Dirk", "initials": "D"}, {"family": "Sj\u00f6bom", "given": "Ulrika", "initials": "U"}, {"family": "S\u00e4vman", "given": "Karin", "initials": "K"}, {"family": "Hansen Pupp", "given": "Ingrid", "initials": "I"}, {"family": "Ley", "given": "David", "initials": "D"}, {"family": "Nilsson", "given": "Anders K", "initials": "AK", "orcid": "0000-0003-3631-0783", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7c743e9c8e4acc985b22d1a3b4827d.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hellstr\u00f6m", "given": "Ann", "initials": "A", "orcid": "0000-0002-9259-1244", "researcher": {"href": "https://publications.scilifelab.se/researcher/59eda2822ead4300a3ebfa8e80e4e191.json"}}], "type": "journal article", "published": "2023-08-02", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "3", "issue": "1", "pages": "107", "issn-l": null}, "abstract": "Preterm birth is the leading cause of neonatal mortality and morbidity. Early diagnosis and interventions are critical to improving the clinical outcomes of extremely premature infants. Blood protein profiling during the first months of life in preterm infants can shed light on the role of early extrauterine development and provide an increased understanding of maturation after extremely preterm birth and the underlying mechanisms of prematurity-related disorders.\n\nWe have investigated the blood protein profiles during the first months of life in preterm infants on the role of early extrauterine development. The blood protein levels were analyzed using next generation blood profiling on 1335 serum samples, collected longitudinally at nine time points from birth to full-term from 182 extremely preterm infants.\n\nThe protein analysis reveals evident predestined serum evolution patterns common for all included infants. The majority of the variations in blood protein expression are associated with the postnatal age of the preterm infants rather than any other factors. There is a uniform protein pattern on postnatal day 1 and after 30 weeks postmenstrual age (PMA), independent of gestational age (GA). However, during the first month of life, GA had a significant impact on protein variability.\n\nThe unified pattern of protein development for all included infants suggests an age-dependent stereotypic development of blood proteins after birth. This knowledge should be considered in neonatal settings and might alter the clinical approach within neonatology, where PMA is today the most dominant age variable.", "doi": "10.1038/s43856-023-00338-1", "pmid": "37532738", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10397184"}, {"db": "pii", "key": "10.1038/s43856-023-00338-1"}], "notes": [], "created": "2023-08-10T09:21:14.958Z", "modified": "2023-08-10T09:21:15.252Z"}, {"entity": "publication", "iuid": "bd7e4686333d489495edae6e2cb9e54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd7e4686333d489495edae6e2cb9e54a"}}, "title": "Next generation pan-cancer blood proteome profiling using proximity extension assay.", "authors": [{"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Lundin", "given": "Emma", "initials": "E", "orcid": "0009-0000-7711-1962", "researcher": {"href": "https://publications.scilifelab.se/researcher/06761839da88443e9098d9562810fb7f.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N", "orcid": "0000-0002-7835-4357", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1b2d0ce6ea452b82a35c603a073eb1.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Lindman", "given": "Henrik", "initials": "H"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Hesselager", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9613-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/978fc6fea7d54f5b81a8b5a87efa083a.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enblad", "given": "Malin", "initials": "M", "orcid": "0000-0001-5900-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e801966db544e6286fb2b4037980dba.json"}}, {"family": "Simonson", "given": "Oscar E", "initials": "OE", "orcid": "0000-0002-3552-5558", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a52b4426da84787aeb56b8d6232ba87.json"}}, {"family": "H\u00e4ggman", "given": "Michael", "initials": "M"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "\u00c5berg", "given": "Mikael", "initials": "M", "orcid": "0000-0002-7858-8233", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fa86e9aeaa43ea9547e48b4f3f24e3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4308"}, "abstract": "A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.", "doi": "10.1038/s41467-023-39765-y", "pmid": "37463882", "labels": {"Affinity Proteomics Uppsala": "Collaborative", "NGI Proteomics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354027"}, {"db": "pii", "key": "10.1038/s41467-023-39765-y"}], "notes": [], "created": "2023-11-29T19:16:18.991Z", "modified": "2024-01-16T13:48:32.880Z"}, {"entity": "publication", "iuid": "98a5bddd23b947cea68672bd1c9a6590", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98a5bddd23b947cea68672bd1c9a6590.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98a5bddd23b947cea68672bd1c9a6590"}}, "title": "Identification of Endothelial Proteins in Plasma Associated With Cardiovascular Risk Factors.", "authors": [{"family": "Iglesias", "given": "Maria J", "initials": "MJ", "orcid": "0000-0003-4122-1945", "researcher": {"href": "https://publications.scilifelab.se/researcher/adccb07f0a744e648516bd7b672d70be.json"}}, {"family": "Kruse", "given": "Larissa D", "initials": "LD", "orcid": "0000-0002-2015-2293", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4ee3a7110024de786807442fd68fd73.json"}}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Enge", "given": "Linnea", "initials": "L"}, {"family": "Dusart", "given": "Philip", "initials": "P", "orcid": "0000-0003-2747-3214", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dffee863552446eb498f96e04a0fe4d.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Renn\u00e9", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4594-5975", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc8b1c2969a74aa8bdc4a8ca8bee335a.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Bergstrom", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Butler", "given": "Lynn M", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Arterioscler. Thromb. Vasc. Biol.", "issn": "1524-4636", "volume": "41", "issue": "12", "pages": "2990-3004", "issn-l": "1079-5642"}, "abstract": "Endothelial cell (EC) dysfunction is a well-established response to cardiovascular disease risk factors, such as smoking and obesity. Risk factor exposure can modify EC signaling and behavior, leading to arterial and venous disease development. Here, we aimed to identify biomarker panels for the assessment of EC dysfunction, which could be useful for risk stratification or to monitor treatment response. Approach and Results: We used affinity proteomics to identify EC proteins circulating in plasma that were associated with cardiovascular disease risk factor exposure. Two hundred sixteen proteins, which we previously predicted to be EC-enriched across vascular beds, were measured in plasma samples (N=1005) from the population-based SCAPIS (Swedish Cardiopulmonary Bioimage Study) pilot. Thirty-eight of these proteins were associated with body mass index, total cholesterol, low-density lipoprotein, smoking, hypertension, or diabetes. Sex-specific analysis revealed that associations predominantly observed in female- or male-only samples were most frequently with the risk factors body mass index, or total cholesterol and smoking, respectively. We show a relationship between individual cardiovascular disease risk, calculated with the Framingham risk score, and the corresponding biomarker profiles.\n\nEC proteins in plasma could reflect vascular health status.", "doi": "10.1161/ATVBAHA.121.316779", "pmid": "34706560", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8608011"}], "notes": [], "created": "2021-12-06T08:11:54.132Z", "modified": "2021-12-06T08:12:09.738Z"}, {"entity": "publication", "iuid": "49f178b8e80b4b5fa88aeada66e2e92e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49f178b8e80b4b5fa88aeada66e2e92e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49f178b8e80b4b5fa88aeada66e2e92e"}}, "title": "Immunoglobulin A Autoreactivity toward Brain Enriched and Apoptosis-Regulating Proteins in Saliva of Athletes after Acute Concussion and Subconcussive Impacts.", "authors": [{"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Petricoin", "given": "Emanuel F", "initials": "EF"}, {"family": "Cortes", "given": "Nelson", "initials": "N"}, {"family": "Bowman", "given": "Thomas G", "initials": "TG"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Caswell", "given": "Shane V", "initials": "SV"}], "type": "journal article", "published": "2021-09-01", "journal": {"title": "J. Neurotrauma", "issn": "1557-9042", "volume": "38", "issue": "17", "pages": "2373-2383", "issn-l": "0897-7151"}, "abstract": "The diagnosis and management of concussion is hindered by its diverse clinical presentation and assessment tools reliant on subjectively experienced symptoms. The biomechanical threshold of concussion is also not well understood, and asymptomatic concussion or \"subconcussive impacts\" of variable magnitudes are common in contact sports. Concerns have risen because athletes returning to activity too soon have an increased risk of prolonged recovery or long-term adverse health consequences. To date, little is understood on a molecular level regarding concussion and subconcussive impacts. Recent research suggests that neuroinflammatory mechanisms may serve an important role subsequent to concussion and possibly to subconcussive impacts. These studies suggest that autoantibodies may be a valuable tool for detection of acute concussion and monitoring for changes caused by cumulative exposure to subconcussive impacts. Hence, we aimed to profile the immunoglobulin (Ig)A autoantibody repertoire in saliva by screening a unique sport-related head trauma biobank. Saliva samples (n = 167) were donated by male and female participants enrolled in either the concussion (24-48 h post-injury) or subconcussion (non-concussed participants having moderate or high cumulative subconcussive impact exposure) cohorts. Study design included discovery and verification phases. Discovery aimed to identify new candidate autoimmune targets of IgA. Verification tested whether concussion and subconcussion cohorts increased IgA reactivity and whether cohorts showed similarities. The results show a significant increase in the prevalence of IgA toward protein fragments representing 5-hydroxytryptamine receptor 1A (HTR1A), serine/arginine repetitive matrix 4 (SRRM4) and FAS (tumor necrosis factor receptor superfamily member 6) after concussion and subconcussion. These results may suggest that concussion and subconcussion induce similar physiological effects, especially in terms of immune response. Our study demonstrates that saliva is a potential biofluid for autoantibody detection in concussion and subconcussion. After rigorous confirmation in much larger independent study sets, a validated salivary autoantibody assay could provide a non-subjective quantitative means of assessing concussive and subconcussive events.", "doi": "10.1089/neu.2020.7375", "pmid": "33858214", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-04-17T20:45:31.849Z", "modified": "2021-11-10T12:24:41.204Z"}, {"entity": "publication", "iuid": "cef437ec472748d99c04192947b80bd4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cef437ec472748d99c04192947b80bd4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cef437ec472748d99c04192947b80bd4"}}, "title": "Genome-scale metabolic network reconstruction of model animals as a platform for translational research.", "authors": [{"family": "Wang", "given": "Hao", "initials": "H", "orcid": "0000-0001-7475-0136", "researcher": {"href": "https://publications.scilifelab.se/researcher/836b4fbf7ebd4f80abc84465c8f29a2e.json"}}, {"family": "Robinson", "given": "Jonathan L", "initials": "JL", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/b70b6d9b64fd45e882c4108aded013d4.json"}}, {"family": "Kocabas", "given": "Pinar", "initials": "P", "orcid": "0000-0001-9788-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/c89eb03e619945a2a2058179b0d0e310.json"}}, {"family": "Gustafsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-5072-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5fda1ac79e49c185ba6f4dfcdff5fc.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Cholley", "given": "Pierre-Etienne", "initials": "PE"}, {"family": "Huang", "given": "Shan", "initials": "S"}, {"family": "Gobom", "given": "Johan", "initials": "J"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Uhlen", "given": "Mattias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2021-07-27", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "30", "pages": "e2102344118", "issn-l": "0027-8424"}, "abstract": "Genome-scale metabolic models (GEMs) are used extensively for analysis of mechanisms underlying human diseases and metabolic malfunctions. However, the lack of comprehensive and high-quality GEMs for model organisms restricts translational utilization of omics data accumulating from the use of various disease models. Here we present a unified platform of GEMs that covers five major model animals, including Mouse1 (Mus musculus), Rat1 (Rattus norvegicus), Zebrafish1 (Danio rerio), Fruitfly1 (Drosophila melanogaster), and Worm1 (Caenorhabditis elegans). These GEMs represent the most comprehensive coverage of the metabolic network by considering both orthology-based pathways and species-specific reactions. All GEMs can be interactively queried via the accompanying web portal Metabolic Atlas. Specifically, through integrative analysis of Mouse1 with RNA-sequencing data from brain tissues of transgenic mice we identified a coordinated up-regulation of lysosomal GM2 ganglioside and peptide degradation pathways which appears to be a signature metabolic alteration in Alzheimer's disease (AD) mouse models with a phenotype of amyloid precursor protein overexpression. This metabolic shift was further validated with proteomics data from transgenic mice and cerebrospinal fluid samples from human patients. The elevated lysosomal enzymes thus hold potential to be used as a biomarker for early diagnosis of AD. Taken together, we foresee that this evolving open-source platform will serve as an important resource to facilitate the development of systems medicines and translational biomedical applications.", "doi": "10.1073/pnas.2102344118", "pmid": "34282017", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Systems Biology": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "2102344118"}, {"db": "pmc", "key": "PMC8325244"}], "notes": [], "created": "2021-08-19T08:56:58.316Z", "modified": "2024-01-16T13:48:39.079Z"}, {"entity": "publication", "iuid": "9ece3f643ded46e68cafc8c075b59335", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ece3f643ded46e68cafc8c075b59335.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ece3f643ded46e68cafc8c075b59335"}}, "title": "High Amounts of SARS-CoV-2 Precede Sickness Among Asymptomatic Health Care Workers.", "authors": [{"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Elfstr\u00f6m", "given": "K Miriam", "initials": "KM"}, {"family": "Blomqvist", "given": "Jonas", "initials": "J"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Nordqvist-Kleppe", "given": "Sara", "initials": "S"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Falk", "given": "August Jernbom", "initials": "AJ"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Hultin", "given": "Emilie", "initials": "E"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Pimenoff", "given": "Ville N", "initials": "VN"}, {"family": "Hassan", "given": "Sadaf", "initials": "S"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hedhammar", "given": "My", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Mattsson", "given": "Johan", "initials": "J"}, {"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Lundgren", "given": "Kalle Conneryd", "initials": "KC"}], "type": "journal article", "published": "2021-07-02", "journal": {"title": "J. Infect. Dis.", "issn": "1537-6613", "volume": "224", "issue": "1", "pages": "14-20", "issn-l": "0022-1899"}, "abstract": "Whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity among asymptomatic subjects reflects past or future disease may be difficult to ascertain.\n\nWe tested 9449 employees at Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the results to sick leave records, and determined associations with past or future sick leave using multinomial logistic regression.\n\nSubjects with high amounts of SARS-CoV-2 virus, indicated by polymerase chain reaction (PCR) cycle threshold (Ct) value, had the highest risk for sick leave in the 2 weeks after testing (odds ratio [OR], 11.97; 95% confidence interval [CI], 6.29-22.80) whereas subjects with low amounts of virus had the highest risk for sick leave in the 3 weeks before testing (OR, 6.31; 95% CI, 4.38-9.08). Only 2.5% of employees were SARS-CoV-2 positive while 10.5% were positive by serology and 1.2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR, 1.06; 95% CI, .71-1.57).\n\nHigh amounts of SARS-CoV-2 virus, as determined using PCR Ct values, was associated with development of sickness in the next few weeks. Results support the concept that PCR Ct may be informative when testing for SARS-CoV-2. Clinical Trials Registration. NCT04411576.", "doi": "10.1093/infdis/jiab099", "pmid": "33580261", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "6134453"}, {"db": "pmc", "key": "PMC7928785"}, {"db": "ClinicalTrials.gov", "key": "NCT04411576"}], "notes": [], "created": "2021-02-14T17:57:35.852Z", "modified": "2021-11-10T12:26:59.324Z"}, {"entity": "publication", "iuid": "cee69667064f4aa186925651c58a42f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cee69667064f4aa186925651c58a42f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cee69667064f4aa186925651c58a42f9"}}, "title": "A single-cell type transcriptomics map of human tissues.", "authors": [{"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L", "orcid": "0000-0001-9333-0110", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f441a799324599953796b467abf95c.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Digre", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1145-6700", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83918be53c64470a67ab23170b86b11.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Dusart", "given": "Philip", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c15b68f3b7f4188b9927c011d586efd.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications.scilifelab.se/researcher/480be47a6ccd4f9ebc66d718997a3462.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aad9ec706674ed6ab358a445ba1989d.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "31", "pages": "eabh2169", "issn-l": "2375-2548"}, "abstract": "Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.", "doi": "10.1126/sciadv.abh2169", "pmid": "34321199", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7/31/eabh2169"}, {"db": "pmc", "key": "PMC8318366"}], "notes": [], "created": "2021-08-27T07:22:02.009Z", "modified": "2024-01-16T13:48:39.387Z"}, {"entity": "publication", "iuid": "ee18e674971a4b5f89d31d1203a60cda", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee18e674971a4b5f89d31d1203a60cda.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee18e674971a4b5f89d31d1203a60cda"}}, "title": "Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy", "authors": [{"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Andersson", "given": "Morgan", "initials": "M"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Levin", "given": "Mattias", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "van Hage", "given": "Marianne", "initials": "M"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2021-03-00", "journal": {"title": "Journal of Allergy and Clinical Immunology", "issn": "1085-8725", "issn-l": "0091-6749", "volume": "147", "issue": "3", "pages": "1077-1086"}, "abstract": "The interaction of allergens and allergen-specific IgE initiates the allergic cascade after crosslinking of receptors on effector cells. Antibodies of other isotypes may modulate such a reaction. Receptor crosslinking requires binding of antibodies to multiple epitopes on the allergen. Limited information is available on the complexity of the epitope structure of most allergens.\n\nWe sought to allow description of the complexity of IgE, IgG4, and IgG epitope recognition at a global, allergome-wide level during allergen-specific immunotherapy (AIT).\n\nWe generated an allergome-wide microarray comprising 731 allergens in the form of more than 172,000 overlapping 16-mer peptides. Allergen recognition by IgE, IgG4, and IgG was examined in serum samples collected from subjects undergoing AIT against pollen allergy.\n\nExtensive induction of linear peptide-specific Phl p 1- and Bet v 1-specific humoral immunity was demonstrated in subjects undergoing a 3-year-long AIT against grass and birch pollen allergy, respectively. Epitope profiles differed between subjects but were largely established already after 1 year of AIT, suggesting that dominant allergen-specific antibody clones remained as important contributors to humoral immunity following their initial establishment during the early phase of AIT. Complex, subject-specific patterns of allergen isoform and group cross-reactivities in the repertoires were observed, patterns that may indicate different levels of protection against different allergen sources.\n\nThe study highlights the complexity and subject-specific nature of allergen epitopes recognized following AIT. We envisage that epitope deconvolution will be an important aspect of future efforts to describe and analyze the outcomes of AIT in a personalized manner.", "doi": "10.1016/j.jaci.2020.08.002", "pmid": "32791163", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0091-6749(20)31108-8"}], "notes": [], "created": "2020-08-20T06:07:25.147Z", "modified": "2023-06-19T11:55:27.568Z"}, {"entity": "publication", "iuid": "9d68ff8c44864ab9b8cc705ce6dd407f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d68ff8c44864ab9b8cc705ce6dd407f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d68ff8c44864ab9b8cc705ce6dd407f"}}, "title": "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications.scilifelab.se/researcher/a08eb47d3b0f427da9402d89cee67df8.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Shutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b9ccd9ae84cdfbcb663591f39a77b.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "590", "issue": "7847", "pages": "649-654"}, "abstract": "The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.", "doi": "10.1038/s41586-021-03232-9", "pmid": "33627808", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Spatial Proteomics": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03232-9"}], "notes": [], "created": "2021-03-01T07:10:50.117Z", "modified": "2021-12-09T13:57:57.891Z"}, {"entity": "publication", "iuid": "08a17073dc0447268b3875a07b479e0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08a17073dc0447268b3875a07b479e0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08a17073dc0447268b3875a07b479e0b"}}, "title": "Longitudinal plasma protein profiling of newly diagnosed type 2 diabetes.", "authors": [{"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Bj\u00f6rnson", "given": "Elias", "initials": "E"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Schmidt", "given": "Caroline", "initials": "C"}, {"family": "Lundqvist", "given": "Annika", "initials": "A"}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Jansson", "given": "Per-Anders", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "issn-l": "2352-3964", "volume": "63", "issue": null, "pages": "103147"}, "abstract": "Comprehensive proteomics profiling may offer new insights into the dysregulated metabolic milieu of type 2 diabetes, and in the future, serve as a useful tool for personalized medicine. This calls for a better understanding of circulating protein patterns at the early stage of type 2 diabetes as well as the dynamics of protein patterns during changes in metabolic status.\r\n\r\nTo elucidate the systemic alterations in early-stage diabetes and to investigate the effects on the proteome during metabolic improvement, we measured 974 circulating proteins in 52 newly diagnosed, treatment-na\u00efve type 2 diabetes subjects at baseline and after 1 and 3 months of guideline-based diabetes treatment, while comparing their protein profiles to that of 94 subjects without diabetes.\r\n\r\nEarly stage type 2 diabetes was associated with distinct protein patterns, reflecting key metabolic syndrome features including insulin resistance, adiposity, hyperglycemia and liver steatosis. The protein profiles at baseline were attenuated during guideline-based diabetes treatment and several plasma proteins associated with metformin medication independently of metabolic variables, such as circulating EPCAM.\r\n\r\nThe results advance our knowledge about the biochemical manifestations of type 2 diabetes and suggest that comprehensive protein profiling may serve as a useful tool for metabolic phenotyping and for elucidating the biological effects of diabetes treatments.\r\n\r\nThis work was supported by the Swedish Heart and Lung Foundation, the Swedish Research Council, the Erling Persson Foundation, the Knut and Alice Wallenberg Foundation, and the Swedish state under the agreement between the Swedish government and the county councils (ALF-agreement).", "doi": "10.1016/j.ebiom.2020.103147", "pmid": "33279861", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2352-3964(20)30523-5"}, {"db": "pmc", "key": "PMC7718461"}], "notes": [], "created": "2020-12-10T19:03:51.943Z", "modified": "2021-12-09T13:40:41.874Z"}, {"entity": "publication", "iuid": "c54fad9a92ff45be90b06c461c2854cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c54fad9a92ff45be90b06c461c2854cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c54fad9a92ff45be90b06c461c2854cb"}}, "title": "Exploring autoantibody signatures in brain tissue from patients with severe mental illness.", "authors": [{"family": "Just", "given": "David", "initials": "D", "orcid": "0000-0001-6126-2256", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f687d3a9cf4400932c75510807c764.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-0056-1313", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d155273b5b54e61b773f263e4f2ce9b.json"}}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications.scilifelab.se/researcher/38efa44f5ed64192b432d6384584f00d.json"}}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA", "orcid": "0000-0003-1861-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ebb5b73b9a42498192d35aea2d92c5.json"}}, {"family": "Rajkowska", "given": "Grazyna", "initials": "G", "orcid": "0000-0002-4348-4688", "researcher": {"href": "https://publications.scilifelab.se/researcher/4122635fead74359983624753ee365ff.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Cunningham", "given": "Janet L", "initials": "JL", "orcid": "0000-0001-7876-7779", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab30dd6c6874bc7a227a8699c4a7085.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Carlstr\u00f6m", "given": "Eva Lindholm", "initials": "EL", "orcid": "0000-0001-8055-7826", "researcher": {"href": "https://publications.scilifelab.se/researcher/c433744d926b450097e71784b8bcc27c.json"}}], "type": "journal article", "published": "2020-11-18", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "10", "issue": "1", "pages": "401", "issn-l": "2158-3188"}, "abstract": "In recent years, studies have shown higher prevalence of autoantibodies in patients with schizophrenia compared to healthy individuals. This study applies an untargeted and a targeted affinity proteomics approach to explore and characterize the autoantibody repertoire in brain tissues from 73 subjects diagnosed with schizophrenia and 52 control subjects with no psychiatric or neurological disorders. Selected brain tissue lysates were first explored for IgG reactivity on planar microarrays composed of 11,520 protein fragments representing 10,820 unique proteins. Based on these results of ours and other previous studies of autoantibodies related to psychosis, we selected 226 fragments with an average length of 80 amino acids, representing 127 unique proteins. Tissue-based analysis of IgG reactivities using antigen suspension bead arrays was performed in a multiplex and parallel fashion for all 125 subjects. Among the detected autoantigens, higher IgG reactivity in subjects with schizophrenia, as compared to psychiatrically healthy subjects, was found against the glutamate ionotropic receptor NMDA type subunit 2D (anti-GluN2D). In a separate cohort with serum samples from 395 young adults with a wider spectrum of psychiatric disorders, higher levels of serum autoantibodies targeting GluN2D were found when compared to 102 control individuals. By further validating GluN2D and additional potential autoantigens, we will seek insights into how these are associated with severe mental illnesses.", "doi": "10.1038/s41398-020-01079-8", "pmid": "33208725", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-020-01079-8"}, {"db": "pmc", "key": "PMC7676257"}], "notes": [], "created": "2020-11-19T10:26:29.658Z", "modified": "2021-11-10T12:45:09.790Z"}, {"entity": "publication", "iuid": "3b8d1f21730c444f9488bdde02b7966a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b8d1f21730c444f9488bdde02b7966a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b8d1f21730c444f9488bdde02b7966a"}}, "title": "A high-stringency blueprint of the human proteome.", "authors": [{"family": "Adhikari", "given": "Subash", "initials": "S"}, {"family": "Nice", "given": "Edouard C", "initials": "EC"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Lane", "given": "Lydie", "initials": "L", "orcid": "0000-0002-9818-3030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0992244993b4f0799f58c63f39a5c5e.json"}}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Pennington", "given": "Stephen R", "initials": "SR"}, {"family": "Paik", "given": "Young-Ki", "initials": "YK"}, {"family": "Overall", "given": "Christopher M", "initials": "CM", "orcid": "0000-0001-5844-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f770b082f2447fd96e1daab1b1bc4f1.json"}}, {"family": "Corrales", "given": "Fernando J", "initials": "FJ"}, {"family": "Cristea", "given": "Ileana M", "initials": "IM"}, {"family": "Van Eyk", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0001-9050-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e860403a0224d588958a9c588688ff6.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Chan", "given": "Daniel W", "initials": "DW"}, {"family": "Bairoch", "given": "Amos", "initials": "A"}, {"family": "Waddington", "given": "James C", "initials": "JC"}, {"family": "Justice", "given": "Joshua L", "initials": "JL"}, {"family": "LaBaer", "given": "Joshua", "initials": "J"}, {"family": "Rodriguez", "given": "Henry", "initials": "H"}, {"family": "He", "given": "Fuchu", "initials": "F"}, {"family": "Kostrzewa", "given": "Markus", "initials": "M"}, {"family": "Ping", "given": "Peipei", "initials": "P"}, {"family": "Gundry", "given": "Rebekah L", "initials": "RL", "orcid": "0000-0002-9263-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/60163f86086644e9a74a7793d886dd3e.json"}}, {"family": "Stewart", "given": "Peter", "initials": "P"}, {"family": "Srivastava", "given": "Sanjeeva", "initials": "S"}, {"family": "Srivastava", "given": "Sudhir", "initials": "S"}, {"family": "Nogueira", "given": "Fabio C S", "initials": "FCS"}, {"family": "Domont", "given": "Gilberto B", "initials": "GB"}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16eb301087cd46c5b12bdb276fdf561b.json"}}, {"family": "Lam", "given": "Maggie P Y", "initials": "MPY"}, {"family": "Wennersten", "given": "Sara", "initials": "S"}, {"family": "Vizcaino", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df36c9559504428a42edba7ba33ec08.json"}}, {"family": "Wilkins", "given": "Marc", "initials": "M", "orcid": "0000-0002-5700-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/98c5bc0757d145d692312da866ebf51a.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N", "orcid": "0000-0001-8385-3655", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6377e04591748fc9450eaff4d41acff.json"}}, {"family": "Marko-Varga", "given": "Gyorgy", "initials": "G"}, {"family": "Weintraub", "given": "Susan T", "initials": "ST"}, {"family": "Pineau", "given": "Charles", "initials": "C"}, {"family": "Kusebauch", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-6162-7577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b4bcdb047c4b1fa84e513ea0eddd5e.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL", "orcid": "0000-0002-3216-9447", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aaa7d54f7de41cf915b47e8037c15cf.json"}}, {"family": "Ahn", "given": "Seong Beom", "initials": "SB"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Snyder", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2594af48f3d45e68983030873c06cf5.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications.scilifelab.se/researcher/9222eeba13464c618695f91ea8764abb.json"}}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}], "type": "journal article", "published": "2020-10-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5301", "issn-l": "2041-1723"}, "abstract": "The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.", "doi": "10.1038/s41467-020-19045-9", "pmid": "33067450", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19045-9"}, {"db": "pmc", "key": "PMC7568584"}], "notes": [], "created": "2020-12-10T19:07:09.284Z", "modified": "2021-11-10T12:46:20.338Z"}, {"entity": "publication", "iuid": "bb0b805b5429464ab0bddbb9a6f7787e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb0b805b5429464ab0bddbb9a6f7787e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb0b805b5429464ab0bddbb9a6f7787e"}}, "title": "Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.", "authors": [{"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Chen", "given": "Xu", "initials": "X"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Lee", "given": "Woojoo", "initials": "W"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Kotol", "given": "David", "initials": "D", "orcid": "0000-0002-5388-3826", "researcher": {"href": "https://publications.scilifelab.se/researcher/085cca6e87fb4639b720b0e5c8c1da2a.json"}}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE", "orcid": "0000-0001-6201-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1156f987764218af202efbd76c31fd.json"}}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd1197769804dd48b9de86f11340ef2.json"}}, {"family": "Hall", "given": "Per", "initials": "P", "orcid": "0000-0002-5640-9126", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e177f5d95f34b148064662f34ef6660.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S"}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "3", "issue": "10", "pages": "e202000817"}, "abstract": "Despite recognizing aging as a common risk factor of many human diseases, little is known about its molecular traits. To identify age-associated proteins circulating in human blood, we screened 156 individuals aged 50-92 using exploratory and multiplexed affinity proteomics assays. Profiling eight additional study sets (N = 3,987), performing antibody validation, and conducting a meta-analysis revealed a consistent age association (P = 6.61 \u00d7 10-6) for circulating histidine-rich glycoprotein (HRG). Sequence variants of HRG influenced how the protein was recognized in the immunoassays. Indeed, only the HRG profiles affected by rs9898 were associated with age and predicted the risk of mortality (HR = 1.25 per SD; 95% CI = 1.12-1.39; P = 6.45 \u00d7 10-5) during a follow-up period of 8.5 yr after blood sampling (IQR = 7.7-9.3 yr). Our affinity proteomics analysis found associations between the particular molecular traits of circulating HRG with age and all-cause mortality. The distinct profiles of this multipurpose protein could serve as an accessible and informative indicator of the physiological processes related to biological aging.", "doi": "10.26508/lsa.202000817", "pmid": "32737166", "labels": {"Autoimmunity and Serology Profiling": "Service", "Affinity Proteomics Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3/10/e202000817"}, {"db": "pmc", "key": "PMC7409555"}], "notes": [], "created": "2020-08-21T08:30:48.217Z", "modified": "2024-01-16T13:48:41.646Z"}, {"entity": "publication", "iuid": "043ab27fa61944e99a7e279442373b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/043ab27fa61944e99a7e279442373b57"}}, "title": "Integration of molecular profiles in a longitudinal wellness profiling cohort.", "authors": [{"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Koistinen", "given": "Ina Schuppe", "initials": "IS"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Olsson", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-9730-1915", "researcher": {"href": "https://publications.scilifelab.se/researcher/2460963d77ee4eee9409fbd8c257d910.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/514fbe8cab5e4f25afa33fcd3e0523b5.json"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Stenlund", "given": "Hans", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Olin", "given": "Axel", "initials": "A", "orcid": "0000-0002-1161-4476", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dfb8efde80a4a508c93714729259aba.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Danielsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6959-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e346ce0d514179baea3c97b615e665.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Jansson", "given": "Per-Anders", "initials": "PA"}, {"family": "Anger\u00e5s", "given": "Oskar", "initials": "O"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4871-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/1689878e0c5542d08d3e2d5043a6ce5c.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4289-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbc3ade3079e4265ad42ed1be485bc24.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}], "type": "journal article", "published": "2020-09-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "4487"}, "abstract": "An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.", "doi": "10.1038/s41467-020-18148-7", "pmid": "32900998", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative", "Cellular Immunomonitoring": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-18148-7"}, {"db": "pmc", "key": "PMC7479148"}], "notes": [], "created": "2020-09-10T05:17:29.818Z", "modified": "2025-10-17T13:03:16.662Z"}, {"entity": "publication", "iuid": "8cf987b082774293badf953bb6306328", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cf987b082774293badf953bb6306328.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cf987b082774293badf953bb6306328"}}, "title": "Human Immune System Variation during 1 Year.", "authors": [{"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Muhammad", "given": "Sayyed Auwn", "initials": "SA", "orcid": "0000-0002-6664-1607", "researcher": {"href": "https://publications.scilifelab.se/researcher/b78cfcefd650480dabe7b6473caf66f3.json"}}, {"family": "Olin", "given": "Axel", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2020-07-21", "journal": {"title": "Cell Rep", "issn": "2211-1247", "issn-l": null, "volume": "32", "issue": "3", "pages": "107923"}, "abstract": "The human immune system varies extensively between individuals, but variation within individuals over time has not been well characterized. Systems-level analyses allow for simultaneous quantification of many interacting immune system components and the inference of global regulatory principles. Here, we present a longitudinal, systems-level analysis in 99 healthy adults 50 to 65 years of age and sampled every third month for 1 year. We describe the structure of interindividual variation and characterize extreme phenotypes along a principal curve. From coordinated measurement fluctuations, we infer relationships between 115 immune cell populations and 750 plasma proteins constituting the blood immune system. While most individuals have stable immune systems, the degree of longitudinal variability is an individual feature. The most variable individuals, in the absence of overt infections, exhibited differences in markers of metabolic health suggestive of a possible link between metabolic and immunologic homeostatic regulation.", "doi": "10.1016/j.celrep.2020.107923", "pmid": "32697987", "labels": {"Affinity Proteomics Stockholm": "Service", "Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(20)30904-9"}], "notes": [], "created": "2020-07-21T20:58:52.991Z", "modified": "2024-01-16T13:48:42.124Z"}, {"entity": "publication", "iuid": "13e1498d084a4f158e6801550ebd42a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13e1498d084a4f158e6801550ebd42a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13e1498d084a4f158e6801550ebd42a1"}}, "title": "Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling.", "authors": [{"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8603-8293", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66c199ece143a6ab15222d8b55e3ea.json"}}, {"family": "Thomas", "given": "Cecilia Engel", "initials": "CE"}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca04d9b9132747efb7db0efb6e34756a.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Dale", "given": "Matilda", "initials": "M", "orcid": "0000-0002-5788-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/59306e7e902048829efb30599ee3d2b1.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "issn-l": "2352-3964", "volume": "57", "issue": null, "pages": "102854"}, "abstract": "Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate.\n\nTo provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals' short-term health trajectories.\n\nWe found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed that 49% of the protein profiles were stable over one year. We also identified eight networks of proteins in which 11-242 proteins covaried over time. For each participant, there were unique protein profiles of which some could be explained by associations to genetic variants.\n\nThis observational and non-interventional study identifyed noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. To enable more personal hence precise assessments of health states, longitudinal profiling of circulating proteomes can provide a valuable component for precision medicine approaches.\n\nThis work was supported by the Erling Persson Foundation, the Swedish Heart and Lung Foundation, the Knut and Alice Wallenberg Foundation, Science for Life Laboratory, and the Swedish Research Council.", "doi": "10.1016/j.ebiom.2020.102854", "pmid": "32629387", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2352-3964(20)30229-2"}, {"db": "pmc", "key": "PMC7334812"}], "notes": [], "created": "2020-12-10T19:03:42.215Z", "modified": "2021-11-10T12:49:49.689Z"}, {"entity": "publication", "iuid": "870f001b1e924bc3b362c4ae5d683273", "links": {"self": {"href": "https://publications.scilifelab.se/publication/870f001b1e924bc3b362c4ae5d683273.json"}, "display": {"href": "https://publications.scilifelab.se/publication/870f001b1e924bc3b362c4ae5d683273"}}, "title": "Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.", "authors": [{"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Karlsson", "given": "Max J", "initials": "MJ"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Genome Med", "issn": "1756-994X", "issn-l": "1756-994X", "volume": "12", "issue": "1", "pages": "53"}, "abstract": "The human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors to determine the specific protein levels in individuals and to gain a deeper insight of the importance of genetic architecture related to the individual variability of plasma levels of proteins during adult life.\n\nWe have combined whole-genome sequencing, multiplex plasma protein profiling, and extensive clinical phenotyping in a longitudinal 2-year wellness study of 101 healthy individuals with repeated sampling. Analyses of genetic and non-genetic associations related to the variability of blood levels of proteins in these individuals were performed.\n\nThe analyses showed that each individual has a unique protein profile, and we report on the intra-individual as well as inter-individual variation for 794 plasma proteins. A genome-wide association study (GWAS) using 7.3 million genetic variants identified by whole-genome sequencing revealed 144 independent variants across 107 proteins that showed strong association (P < 6 \u00d7 10-11) between genetics and the inter-individual variability on protein levels. Many proteins not reported before were identified (67 out of 107) with individual plasma level affected by genetics. Our longitudinal analysis further demonstrates that these levels are stable during the 2-year study period. The variability of protein profiles as a consequence of environmental factors was also analyzed with focus on the effects of weight loss and infections.\n\nWe show that the adult blood levels of many proteins are determined at birth by genetics, which is important for efforts aimed to understand the relationship between plasma proteome profiles and human biology and disease.", "doi": "10.1186/s13073-020-00755-0", "pmid": "32576278", "labels": {"Affinity Proteomics Stockholm": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13073-020-00755-0"}, {"db": "pmc", "key": "PMC7310558"}], "notes": [], "created": "2020-12-10T19:03:45.805Z", "modified": "2024-01-16T13:48:42.348Z"}, {"entity": "publication", "iuid": "d64c9f1bb86044c88061329283767e2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d64c9f1bb86044c88061329283767e2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d64c9f1bb86044c88061329283767e2e"}}, "title": "Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J", "orcid": "0000-0002-3908-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a88350afba45fb8200786904bf51ca.json"}}, {"family": "\u00d6ijerstedt", "given": "Linn", "initials": "L"}, {"family": "Ullgren", "given": "Abbe", "initials": "A"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Graff", "given": "Caroline", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Transl Neurodegener", "issn": "2047-9158", "volume": "9", "issue": "1", "pages": "27", "issn-l": null}, "abstract": "The clinical presentations of frontotemporal dementia (FTD) are diverse and overlap with other neurological disorders. There are, as of today, no biomarkers in clinical practice for diagnosing the disorders. Here, we aimed to find protein markers in cerebrospinal fluid (CSF) from patients with FTD, presymptomatic mutation carriers and non-carriers.\n\nAntibody suspension bead arrays were used to analyse 328 proteins in CSF from patients with behavioural variant FTD (bvFTD, n = 16) and progressive primary aphasia (PPA, n = 13), as well as presymptomatic mutation carriers (PMC, n = 16) and non-carriers (NC, n = 8). A total of 492 antibodies were used to measure protein levels by direct labelling of the CSF samples. The findings were further examined in an independent cohort including 13 FTD patients, 79 patients with Alzheimer's disease and 18 healthy controls.\n\nWe found significantly altered protein levels in CSF from FTD patients compared to unaffected individuals (PMC and NC) for 26 proteins. The analysis show patterns of separation between unaffected individuals and FTD patients, especially for those with a clinical diagnosis of bvFTD. The most statistically significant differences in protein levels were found for VGF, TN-R, NPTXR, TMEM132D, PDYN and NF-M. Patients with FTD were found to have higher levels of TN-R and NF-M, and lower levels of VGF, NPTXR, TMEM132D and PDYN, compared to unaffected individuals. The main findings were reproduced in the independent cohort.\n\nIn this pilot study, we show a separation of FTD patients from unaffected individuals based on protein levels in CSF. Further investigation is required to explore the CSF profiles in larger cohorts, but the results presented here has the potential to enable future clinical utilization of these potential biomarkers within FTD.", "doi": "10.1186/s40035-020-00198-y", "pmid": "32576262", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40035-020-00198-y"}, {"db": "pmc", "key": "PMC7310563"}], "notes": [], "created": "2021-01-08T16:29:12.262Z", "modified": "2024-01-16T13:48:42.365Z"}, {"entity": "publication", "iuid": "b44914598864495388f1d615d5e95c2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b44914598864495388f1d615d5e95c2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b44914598864495388f1d615d5e95c2b"}}, "title": "Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.", "authors": [{"family": "Larsson", "given": "Ida", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2020-04-17", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "11", "issue": null, "pages": "381", "issn-l": "1664-8021"}, "abstract": "Glioblastoma (GBM) is an aggressive type of brain cancer with a poor prognosis for affected patients. The current line of treatment only gives the patients a survival time of on average 15 months. In this work, we use genome-scale metabolic models (GEMs) together with other systems biology tools to examine the global transcriptomics-data of GBM-patients obtained from The Cancer Genome Atlas (TCGA). We reveal the molecular mechanisms underlying GBM and identify potential therapeutic targets for effective treatment of patients. The work presented consists of two main parts. The first part stratifies the patients into two groups, high and low survival, and compares their gene expression. The second part uses GBM and healthy brain tissue GEMs to simulate gene knockout in a GBM cell model to find potential therapeutic targets and predict their side effect in healthy brain tissue. We (1) find that genes upregulated in the patients with low survival are linked to various stages of the glioma invasion process, and (2) identify five essential genes for GBM, whose inhibition is non-toxic to healthy brain tissue, therefore promising to investigate further as therapeutic targets.", "doi": "10.3389/fgene.2020.00381", "pmid": "32362913", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7181968"}], "notes": [], "created": "2020-07-08T13:04:35.735Z", "modified": "2024-01-16T13:48:42.598Z"}, {"entity": "publication", "iuid": "f4135a8deebe4537aedfb6f14b11712e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4135a8deebe4537aedfb6f14b11712e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4135a8deebe4537aedfb6f14b11712e"}}, "title": "The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.", "authors": [{"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Bjornson", "given": "Elias", "initials": "E"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf47745ed3454f3c819cf6414f140ff0.json"}}, {"family": "Lovric", "given": "Alen", "initials": "A"}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications.scilifelab.se/researcher/480be47a6ccd4f9ebc66d718997a3462.json"}}, {"family": "Juszczak", "given": "Kajetan", "initials": "K"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Kim", "given": "Jung Tae", "initials": "JT"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0001-9993-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/28c1f37dc6cc4ed98c8e8eb1a621fa2c.json"}}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "MR"}, {"family": "Bosley", "given": "Jim", "initials": "J"}, {"family": "Marschall", "given": "Hanns-Ulrich", "initials": "HU"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "volume": "16", "issue": "4", "pages": "e9495", "issn-l": "1744-4292"}, "abstract": "The prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase dramatically, and there is no approved medication for its treatment. Recently, we predicted the underlying molecular mechanisms involved in the progression of NAFLD using network analysis and identified metabolic cofactors that might be beneficial as supplements to decrease human liver fat. Here, we first assessed the tolerability of the combined metabolic cofactors including l-serine, N-acetyl-l-cysteine (NAC), nicotinamide riboside (NR), and l-carnitine by performing a 7-day rat toxicology study. Second, we performed a human calibration study by supplementing combined metabolic cofactors and a control study to study the kinetics of these metabolites in the plasma of healthy subjects with and without supplementation. We measured clinical parameters and observed no immediate side effects. Next, we generated plasma metabolomics and inflammatory protein markers data to reveal the acute changes associated with the supplementation of the metabolic cofactors. We also integrated metabolomics data using personalized genome-scale metabolic modeling and observed that such supplementation significantly affects the global human lipid, amino acid, and antioxidant metabolism. Finally, we predicted blood concentrations of these compounds during daily long-term supplementation by generating an ordinary differential equation model and liver concentrations of serine by generating a pharmacokinetic model and finally adjusted the doses of individual metabolic cofactors for future human clinical trials.", "doi": "10.15252/msb.209495", "pmid": "32337855", "labels": {"Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7184219"}], "notes": [], "created": "2020-12-10T16:30:05.091Z", "modified": "2024-01-16T13:48:42.677Z"}, {"entity": "publication", "iuid": "36235e9dc3c244d7a5646615de05fe18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36235e9dc3c244d7a5646615de05fe18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36235e9dc3c244d7a5646615de05fe18"}}, "title": "An atlas of human metabolism.", "authors": [{"family": "Robinson", "given": "Jonathan L", "initials": "JL", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/b70b6d9b64fd45e882c4108aded013d4.json"}}, {"family": "Kocaba\u015f", "given": "P\u0131nar", "initials": "P", "orcid": "0000-0001-9788-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/c89eb03e619945a2a2058179b0d0e310.json"}}, {"family": "Wang", "given": "Hao", "initials": "H", "orcid": "0000-0001-7475-0136", "researcher": {"href": "https://publications.scilifelab.se/researcher/836b4fbf7ebd4f80abc84465c8f29a2e.json"}}, {"family": "Cholley", "given": "Pierre-Etienne", "initials": "PE"}, {"family": "Cook", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5534-8600", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0b42774a1e4e0580dde05e95fcb1fc.json"}}, {"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications.scilifelab.se/researcher/44da161dba604c9e803a4af303277083.json"}}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Ferreira", "given": "Raphael", "initials": "R", "orcid": "0000-0001-9881-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e97f22759cd4e008d9b6473f52865e5.json"}}, {"family": "Domenzain", "given": "Iv\u00e1n", "initials": "I", "orcid": "0000-0002-5322-2040", "researcher": {"href": "https://publications.scilifelab.se/researcher/3793e87625584ee2a31301297263a12a.json"}}, {"family": "Billa", "given": "Virinchi", "initials": "V"}, {"family": "Limeta", "given": "Angelo", "initials": "A"}, {"family": "Hedin", "given": "Alex", "initials": "A", "orcid": "0000-0002-0829-2496", "researcher": {"href": "https://publications.scilifelab.se/researcher/88756d4d3b894ab288141af7b9c9b052.json"}}, {"family": "Gustafsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-5072-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5fda1ac79e49c185ba6f4dfcdff5fc.json"}}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df361f8014144e79479631fcbffad53.json"}}, {"family": "Svensson", "given": "L Thomas", "initials": "LT", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO", "orcid": "0000-0003-2357-6785", "researcher": {"href": "https://publications.scilifelab.se/researcher/b72eed29485a433cb85e260ee38dc894.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2020-03-24", "journal": {"title": "Sci Signal", "issn": "1937-9145", "issn-l": "1945-0877", "volume": "13", "issue": "624", "pages": null}, "abstract": "Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.", "doi": "10.1126/scisignal.aaz1482", "pmid": "32209698", "labels": {"Systems Biology": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pii", "key": "13/624/eaaz1482"}, {"db": "pmc", "key": "PMC7331181"}, {"db": "mid", "key": "NIHMS1590510"}], "notes": [], "created": "2020-12-10T11:11:44.807Z", "modified": "2021-11-10T12:52:52.282Z"}, {"entity": "publication", "iuid": "bb89d24bf5de4738810b72a84a0ad0b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb89d24bf5de4738810b72a84a0ad0b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb89d24bf5de4738810b72a84a0ad0b6"}}, "title": "An atlas of the protein-coding genes in the human, pig, and mouse brain.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications.scilifelab.se/researcher/38efa44f5ed64192b432d6384584f00d.json"}}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Limiszewska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0003-1601-8195", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e7b9e0e376422491d8bd1d76d6f774.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F", "orcid": "0000-0002-3750-9308", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e8c8f511fef466dafd7d704e17d2e30.json"}}, {"family": "Huang", "given": "Jinrong", "initials": "J", "orcid": "0000-0001-8085-9939", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a7eea9544b457b8b058c98e0f4ee94.json"}}, {"family": "Du", "given": "Yutao", "initials": "Y"}, {"family": "Lin", "given": "Lin", "initials": "L", "orcid": "0000-0002-7546-4948", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6436e2b14cd4a629aeebed48b3ae0a9.json"}}, {"family": "Dong", "given": "Zhanying", "initials": "Z"}, {"family": "Yang", "given": "Ling", "initials": "L", "orcid": "0000-0002-5425-8256", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e150be60a3740b89511174e0fd8fa6e.json"}}, {"family": "Liu", "given": "Xin", "initials": "X", "orcid": "0000-0003-3256-2940", "researcher": {"href": "https://publications.scilifelab.se/researcher/b130e21a82a94eb7acd0333f3e62b6ba.json"}}, {"family": "Jiang", "given": "Hui", "initials": "H"}, {"family": "Xu", "given": "Xun", "initials": "X", "orcid": "0000-0002-5338-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/c96e82115f8d493ea665e5dfe2a374e9.json"}}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Yang", "given": "Huanming", "initials": "H", "orcid": "0000-0003-1703-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/6575b8191e414162b52d26df8d9af26a.json"}}, {"family": "Bolund", "given": "Lars", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aad9ec706674ed6ab358a445ba1989d.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}], "type": "comparative study", "published": "2020-03-06", "journal": {"title": "Science", "issn": "1095-9203", "volume": "367", "issue": "6482", "pages": "eaay5947", "issn-l": "0036-8075"}, "abstract": "The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.", "doi": "10.1126/science.aay5947", "pmid": "32139519", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "367/6482/eaay5947"}], "notes": [], "created": "2020-12-07T16:26:57.513Z", "modified": "2024-01-16T13:48:42.811Z"}, {"entity": "publication", "iuid": "da6ca856685141ae9efbd6bfc317bff0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da6ca856685141ae9efbd6bfc317bff0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da6ca856685141ae9efbd6bfc317bff0"}}, "title": "A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf47745ed3454f3c819cf6414f140ff0.json"}}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6015314c4c04ee08d7e4358cfb55b9f.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23dc2e614784017b08cb2d8f6b60ded.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2019-12-20", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "366", "issue": "6472", "pages": null}, "abstract": "Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs.", "doi": "10.1126/science.aax9198", "pmid": "31857451", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "366/6472/eaax9198"}], "notes": [], "created": "2019-12-21T09:40:14.331Z", "modified": "2024-01-16T13:48:43.274Z"}, {"entity": "publication", "iuid": "63ec6f126e6a4e21a793a3b2389b0ecd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63ec6f126e6a4e21a793a3b2389b0ecd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63ec6f126e6a4e21a793a3b2389b0ecd"}}, "title": "Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.", "authors": [{"family": "Pineau", "given": "Charles", "initials": "C", "orcid": "0000-0002-7461-5433", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc849989e84465185d831c58b49e682.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Chen", "given": "Shuqi", "initials": "S"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}], "type": "journal article", "published": "2019-12-06", "journal": {"volume": "18", "issn": "1535-3907", "issue": "12", "pages": "4215-4230", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "One of the most complex organs in the human body is the testis, where spermatogenesis takes place. This physiological process involves thousands of genes and proteins that are activated and repressed, making testis the organ with the highest number of tissue-specific genes. However, the function of a large proportion of the corresponding proteins remains unknown and testis harbors many missing proteins (MPs), defined as products of protein-coding genes that lack experimental mass spectrometry evidence. Here, an integrated omics approach was used for exploring the cell type-specific protein expression of genes with an elevated expression in testis. By combining genome-wide transcriptomics analysis with immunohistochemistry, more than 500 proteins with distinct testicular protein expression patterns were identified, and these were selected for in-depth characterization of their in situ expression in eight different testicular cell types. The cell type-specific protein expression patterns allowed us to identify six distinct clusters of expression at different stages of spermatogenesis. The analysis highlighted numerous poorly characterized proteins in each of these clusters whose expression overlapped with that of known proteins involved in spermatogenesis, including 85 proteins with an unknown function and 60 proteins that previously have been classified as MPs. Furthermore, we were able to characterize the in situ distribution of several proteins that previously lacked spatial information and cell type-specific expression within the testis. The testis elevated expression levels both at the RNA and protein levels suggest that these proteins are related to testis-specific functions. In summary, the study demonstrates the power of combining genome-wide transcriptomics analysis with antibody-based protein profiling to explore the cell type-specific expression of both well-known proteins and MPs. The analyzed proteins constitute important targets for further testis-specific research in male reproductive disorders.", "doi": "10.1021/acs.jproteome.9b00351", "pmid": "31429579", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-08T16:47:43.388Z", "modified": "2021-07-08T13:44:33.313Z"}, {"entity": "publication", "iuid": "3e566b52c0814a2186badf96a7dcb3be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e566b52c0814a2186badf96a7dcb3be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e566b52c0814a2186badf96a7dcb3be"}}, "title": "The human secretome", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Svensson", "given": "Anne Sophie", "initials": "AS"}, {"family": "Scheffel", "given": "Julia", "initials": "J"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Ekblad", "given": "Siri", "initials": "S"}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M"}, {"family": "Kanje", "given": "Sara", "initials": "S"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Volk", "given": "Anna Luisa", "initials": "AL"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Dodig-Crnkovic", "given": "Tea", "initials": "T"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS"}, {"family": "Hong", "given": "Mun Gwan", "initials": "MG"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Robinson", "given": "Jonathan", "initials": "J"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Sullivan", "given": "Devin", "initials": "D"}, {"family": "Thul", "given": "Peter", "initials": "P"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2019-11-26", "journal": {"title": "Sci. Signal.", "issn": "1945-0877", "issn-l": "1945-0877", "volume": "12", "issue": "609", "pages": "eaaz0274"}, "abstract": "The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.", "doi": "10.1126/scisignal.aaz0274", "pmid": "31772123", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Spatial Proteomics": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-03T08:34:48.430Z", "modified": "2021-12-09T13:59:58.034Z"}, {"entity": "publication", "iuid": "c4121567e5bb46d5bfee7bf4443780a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4121567e5bb46d5bfee7bf4443780a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4121567e5bb46d5bfee7bf4443780a2"}}, "title": "Multiplexed analysis of the secretin-like GPCR-RAMP interactome.", "authors": [{"family": "Lorenzen", "given": "Emily", "initials": "E", "orcid": "0000-0002-0008-0966", "researcher": {"href": "https://publications.scilifelab.se/researcher/e009a3686e804b808372ef5cd3eabaf3.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Kotliar", "given": "Ilana B", "initials": "IB", "orcid": "0000-0001-9533-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf97aaf7767453a9a165e6198fda679.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Ceraudo", "given": "Emilie", "initials": "E", "orcid": "0000-0001-6563-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/58ba695a85a84fe2a7986ea3f3eff4ab.json"}}, {"family": "Vaughan", "given": "Roger D", "initials": "RD"}, {"family": "Uhl\u00e8n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Huber", "given": "Thomas", "initials": "T", "orcid": "0000-0002-1844-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f730be20f6dd4b8db1756bfed4aa1170.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sakmar", "given": "Thomas P", "initials": "TP", "orcid": "0000-0002-2836-8953", "researcher": {"href": "https://publications.scilifelab.se/researcher/1130157044664f8b994b94e3b199cc30.json"}}], "type": "journal article", "published": "2019-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "5", "issue": "9", "pages": "eaaw2778", "issn-l": "2375-2548"}, "abstract": "Receptor activity-modifying proteins (RAMPs) have been shown to modulate the functions of several G protein-coupled receptors (GPCRs), but potential direct interactions among the three known RAMPs and hundreds of GPCRs have never been investigated. Focusing mainly on the secretin-like family of GPCRs, we engineered epitope-tagged GPCRs and RAMPs, and developed a multiplexed suspension bead array (SBA) immunoassay to detect GPCR-RAMP complexes from detergent-solubilized lysates. Using 64 antibodies raised against the native proteins and 4 antibodies targeting the epitope tags, we mapped the interactions among 23 GPCRs and 3 RAMPs. We validated nearly all previously reported secretin-like GPCR-RAMP interactions, and also found previously unidentified RAMP interactions with additional secretin-like GPCRs, chemokine receptors, and orphan receptors. The results provide a complete interactome of secretin-like GPCRs with RAMPs. The SBA strategy will be useful to search for additional GPCR-RAMP complexes and other interacting membrane protein pairs in cell lines and tissues.", "doi": "10.1126/sciadv.aaw2778", "pmid": "31555726", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "aaw2778"}, {"db": "pmc", "key": "PMC6750928"}], "notes": [], "created": "2020-01-08T10:24:44.506Z", "modified": "2021-07-08T12:07:33.919Z"}, {"entity": "publication", "iuid": "258308396bfd46d4a0e8e2cb27558cd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/258308396bfd46d4a0e8e2cb27558cd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/258308396bfd46d4a0e8e2cb27558cd1"}}, "title": "Systematic Development of Sandwich Immunoassays for the Plasma Secretome.", "authors": [{"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS", "orcid": "0000-0003-1664-8875", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca04d9b9132747efb7db0efb6e34756a.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A"}, {"family": "Iglesias", "given": "MariaJesus", "initials": "M"}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Dale", "given": "Matilda", "initials": "M"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2019-08-00", "journal": {"title": "Proteomics", "issn": "1615-9861", "volume": "19", "issue": "15", "pages": "e1900008", "issn-l": "1615-9853"}, "abstract": "The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, \u22481800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.", "doi": "10.1002/pmic.201900008", "pmid": "31278833", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T10:38:13.224Z", "modified": "2021-07-08T13:44:33.106Z"}, {"entity": "publication", "iuid": "9dbe3bf19fd34984889399769e724b95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dbe3bf19fd34984889399769e724b95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dbe3bf19fd34984889399769e724b95"}}, "title": "Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Svensson", "given": "Anne-Sophie", "initials": "AS"}, {"family": "Bostr\u00f6m", "given": "Tove", "initials": "T"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2019-07-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "7", "pages": "2706-2718", "issn-l": "1535-3893"}, "abstract": "The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (\u226460 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.", "doi": "10.1021/acs.jproteome.8b00924", "pmid": "31094526", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-08T14:57:52.618Z", "modified": "2021-07-08T13:44:33.481Z"}, {"entity": "publication", "iuid": "cca3260cc4224306b9f2b254e6b95349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cca3260cc4224306b9f2b254e6b95349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cca3260cc4224306b9f2b254e6b95349"}}, "title": "Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.", "authors": [{"family": "Andersson", "given": "Annika", "initials": "A"}, {"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Vunk", "given": "Helian", "initials": "H"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ilag", "given": "Leopold L", "initials": "LL"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "Clin. Chim. Acta", "issn": "1873-3492", "volume": "494", "issue": null, "pages": "79-93", "issn-l": "0009-8981"}, "abstract": "Detailed knowledge of protein changes in cerebrospinal fluid (CSF) across healthy and diseased individuals would provide a better understanding of the onset and progression of neurodegenerative disorders. In this study, we selected 20 brain-enriched proteins previously identified in CSF by antibody suspension bead arrays (SBA) to be potentially biomarkers for Alzheimer's disease (AD) and verified these using an orthogonal approach. We examined the same set of 94 CSF samples from patients affected by AD (including preclinical and prodromal), mild cognitive impairment (MCI), non-AD dementia and healthy individuals, which had previously been analyzed by SBA. Twenty-eight parallel reaction monitoring (PRM) assays were developed and 13 of them could be validated for protein quantification. Antibody profiles were verified by PRM. For seven proteins, the antibody profiles were highly correlated with the PRM results (r > 0.7) and GAP43, VCAM1 and PSAP were identified as potential markers of preclinical AD. In conclusion, we demonstrate the usefulness of targeted mass spectrometry as a tool for the orthogonal verification of antibody profiling data, suggesting that these complementary methods can be successfully applied for comprehensive exploration of CSF protein levels in neurodegenerative disorders.", "doi": "10.1016/j.cca.2019.03.243", "pmid": "30858094", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0009-8981(19)30348-1"}], "notes": [], "created": "2020-01-08T10:40:27.440Z", "modified": "2021-07-08T13:44:33.634Z"}, {"entity": "publication", "iuid": "6ab4121934ba49068e285057df24bd62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ab4121934ba49068e285057df24bd62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ab4121934ba49068e285057df24bd62"}}, "title": "SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.", "authors": [{"family": "Hu", "given": "Francis Jingxin", "initials": "FJ"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-04-08", "journal": {"volume": "47", "issn": "1362-4962", "issue": "6", "pages": "e34", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Mutagenesis libraries are essential for combinatorial protein engineering. Despite improvements in gene synthesis and directed mutagenesis, current methodologies still have limitations regarding the synthesis of complete antibody single-chain variable fragment (scFv) genes and simultaneous diversification of all six CDRs. Here, we describe the generation of mutagenesis libraries for antibody affinity maturation using a cell-free solid-phase technique for annealing of single-strand mutagenic oligonucleotides. The procedure consists of PCR-based incorporation of uracil into a wild-type template, bead-based capture, elution of single-strand DNA, and in vitro uracil excision enzyme based degradation of the template DNA. Our approach enabled rapid (8 hours) mutagenesis and automated cloning of 50 position-specific alanine mutants for mapping of a scFv antibody paratope. We further exemplify our method by generating affinity maturation libraries with diversity introduced in critical, nonessential, or all CDR positions randomly. Assessment with Illumina deep sequencing showed less than 1% wild-type in two libraries and the ability to diversify all CDR positions simultaneously. Selections of the libraries with bacterial display and deep sequencing evaluation of the selection output showed that diversity introduced in non-essential positions allowed for a more effective enrichment of improved binders compared to the other two diversification strategies.", "doi": "10.1093/nar/gkz050", "pmid": "30715449", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5304719"}, {"db": "pmc", "key": "PMC6451119"}], "notes": [], "created": "2019-12-02T16:50:56.362Z", "modified": "2024-01-16T13:48:44.498Z"}, {"entity": "publication", "iuid": "b80d77eea7d44b3da4c34cce978d12ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b80d77eea7d44b3da4c34cce978d12ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b80d77eea7d44b3da4c34cce978d12ea"}}, "title": "A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.", "authors": [{"family": "Wang", "given": "Dongxue", "initials": "D", "orcid": "0000-0002-4402-0690", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e916e3dc0e146eca88aff76d9af2dd7.json"}}, {"family": "Eraslan", "given": "Basak", "initials": "B"}, {"family": "Wieland", "given": "Thomas", "initials": "T"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hopf", "given": "Thomas", "initials": "T"}, {"family": "Zolg", "given": "Daniel Paul", "initials": "DP"}, {"family": "Zecha", "given": "Jana", "initials": "J"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Li", "given": "Li-Hua", "initials": "LH"}, {"family": "Meng", "given": "Chen", "initials": "C"}, {"family": "Frejno", "given": "Martin", "initials": "M", "orcid": "0000-0002-6651-1773", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5acc7237f9b4987bb4f819f8a3e8bb8.json"}}, {"family": "Schmidt", "given": "Tobias", "initials": "T"}, {"family": "Schnatbaum", "given": "Karsten", "initials": "K"}, {"family": "Wilhelm", "given": "Mathias", "initials": "M"}, {"family": "Ponten", "given": "Frederik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gagneur", "given": "Julien", "initials": "J", "orcid": "0000-0002-8924-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dcbe1ca0ed4f18ad1e928862e873f5.json"}}, {"family": "Hahne", "given": "Hannes", "initials": "H", "orcid": "0000-0003-3601-0051", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a519deb0cc49019c31e57aa45c7ad3.json"}}, {"family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "researcher": {"href": "https://publications.scilifelab.se/researcher/33488ede76b34566903fea22c400aa3e.json"}}], "type": "journal article", "published": "2019-02-18", "journal": {"volume": "15", "issn": "1744-4292", "issue": "2", "pages": "e8503", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.", "doi": "10.15252/msb.20188503", "pmid": "30777892", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6379049"}], "notes": [], "created": "2020-01-08T16:47:13.410Z", "modified": "2021-07-08T13:44:33.541Z"}, {"entity": "publication", "iuid": "ff283a0beebc45f2932247fe9c082748", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff283a0beebc45f2932247fe9c082748.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff283a0beebc45f2932247fe9c082748"}}, "title": "Individual and stable autoantibody repertoires in healthy individuals.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Sallinen", "given": "Riitta", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "clinical trial", "published": "2019-02-00", "journal": {"title": "Autoimmunity", "issn": "1607-842X", "volume": "52", "issue": "1", "pages": "1-11", "issn-l": "0891-6934"}, "abstract": "In the era towards precision medicine, we here present the individual specific autoantibody signatures of 193 healthy individuals. The self-reactive IgG signatures are stable over time in a way that each individual profile is recognized in longitudinal sampling. The IgG autoantibody reactivity towards an antigen array comprising 335 protein fragments, representing 204 human proteins with potential relevance to autoimmune disorders, was measured in longitudinal plasma samples from 193 healthy individuals. This analysis resulted in unique autoantibody barcodes for each individual that were maintained over one year's time. The reactivity profiles, or signatures, are person specific in regards to the number of reactivities and antigen specificity. Two independent data sets were consistent in that each healthy individual displayed reactivity towards 0-16 antigens, with a median of six. Subsequently, four selected individuals were profiled on in-house produced high-density protein arrays containing 23,000 protein fragments representing 14,000 unique protein coding genes. Based on a unique, broad and deep longitudinal profiling of autoantibody reactivities, our results demonstrate a unique autoreactive profile in each analyzed healthy individual. The need and interest for broad-ranged and high-resolution molecular profiling of healthy individuals is rising. We have here generated and assessed an initial perspective on the global distribution of the self-reactive IgG repertoire in healthy individuals, by investigating 193 well-characterized healthy individuals. Highlights A unique longitudinal profiling of autoantibody repertoires in healthy individuals Autoantibody profiles are highly individual and stable over time All individuals display IgG binding to human protein fragments The specificity of disease associated autoantigens needs to be thoroughly characterized The identification of a small set of highly reactive autoantigens Importance of stringent antigen and sample specific cut-offs for defining reactivity.", "doi": "10.1080/08916934.2019.1581774", "pmid": "30835561", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-03-15T14:31:46.423Z", "modified": "2021-07-08T13:44:33.785Z"}, {"entity": "publication", "iuid": "18e29d752735475b84a271e4be906d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18e29d752735475b84a271e4be906d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18e29d752735475b84a271e4be906d40"}}, "title": "Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders.", "authors": [{"family": "Hu", "given": "Francis Jingxin", "initials": "FJ"}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "S\u00e4ll", "given": "Anna", "initials": "A"}, {"family": "Borrebaeck", "given": "Carl", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2018-10-25", "journal": {"volume": "45", "issn": "1876-4347", "issue": null, "pages": "80-88", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Surface display couples genotype with a surface exposed phenotype and thereby allows screening of gene-encoded protein libraries for desired characteristics. Of the various display systems available, phage display is by far the most popular, mainly thanks to its ability to harbour large size libraries. Here, we describe the first use of a Gram-positive bacterial host for display of a library of human antibody genes which, when combined with phage display, provides ease of use for screening, sorting and ranking by flow cytometry. We demonstrate the utility of this method by identifying low nanomolar affinity scFv fragments towards human epidermal growth factor receptor 2 (HER2). The ranking and performance of the scFv isolated by flow sorting in surface-immobilised form was retained when expressed as soluble scFv and analysed by biolayer interferometry, as well as after expression as full-length antibodies in mammalian cells. We also demonstrate the possibility of using Gram-positive bacterial display to directly improve the affinity of the identified binders via an affinity maturation step using random mutagenesis and flow sorting. This combined approach has the potential for a more complete scan of the antibody repertoire and for affinity maturation of human antibody formats.", "doi": "10.1016/j.nbt.2017.07.011", "pmid": "28778816", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(17)30212-1"}], "notes": [], "created": "2017-10-25T06:01:24.113Z", "modified": "2025-10-17T13:05:08.346Z"}, {"entity": "publication", "iuid": "d794f36d72b34629b910abcbdfae6a78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d794f36d72b34629b910abcbdfae6a78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d794f36d72b34629b910abcbdfae6a78"}}, "title": "Enhanced validation of antibodies for research applications.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "Linderb\u00e4ck", "given": "Klas", "initials": "K"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23dc2e614784017b08cb2d8f6b60ded.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2018-10-08", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "4130", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.", "doi": "10.1038/s41467-018-06642-y", "pmid": "30297845", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06642-y"}, {"db": "pmc", "key": "PMC6175901"}], "notes": [], "created": "2018-10-31T19:45:59.871Z", "modified": "2024-01-16T13:48:45.378Z"}, {"entity": "publication", "iuid": "56eeca5c99ad4f519428e5c2b73e2b3c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56eeca5c99ad4f519428e5c2b73e2b3c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56eeca5c99ad4f519428e5c2b73e2b3c"}}, "title": "A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.", "authors": [{"family": "Dusart", "given": "Philip", "initials": "P", "orcid": "0000-0003-2747-3214", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dffee863552446eb498f96e04a0fe4d.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Perisic", "given": "Ljubica", "initials": "L"}, {"family": "Civelek", "given": "Mete", "initials": "M", "orcid": "0000-0002-8141-0284", "researcher": {"href": "https://publications.scilifelab.se/researcher/647c7636e87f43ec960627d299d4cc2b.json"}}, {"family": "Struck", "given": "Eike", "initials": "E"}, {"family": "Hedin", "given": "Ulf", "initials": "U", "orcid": "0000-0001-9212-3945", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a6ec281f5d4f1a8f317dedf0404cdd.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Renn\u00e9", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4594-5975", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc8b1c2969a74aa8bdc4a8ca8bee335a.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Butler", "given": "Lynn M", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}], "type": "journal article", "published": "2018-10-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "8", "issue": "1", "pages": "14668"}, "abstract": "The intermediate filament protein nestin is expressed during embryonic development, but considered largely restricted to areas of regeneration in the adult. Here, we perform a body-wide transcriptome and protein-profiling analysis to reveal that nestin is constitutively, and highly-selectively, expressed in adult human endothelial cells (EC), independent of proliferative status. Correspondingly, we demonstrate that it is not a marker for tumour EC in multiple malignancy types. Imaging of EC from different vascular beds reveals nestin subcellular distribution is shear-modulated. siRNA inhibition of nestin increases EC proliferation, and nestin expression is reduced in atherosclerotic plaque neovessels. eQTL analysis reveals an association between SNPs linked to cardiovascular disease and reduced aortic EC nestin mRNA expression. Our study challenges the dogma that nestin is a marker of proliferation, and provides insight into its regulation and function in EC. Furthermore, our systems-based approach can be applied to investigate body-wide expression profiles of any candidate protein.", "doi": "10.1038/s41598-018-32859-4", "pmid": "30279450", "labels": {"Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6168570"}, {"db": "pii", "key": "10.1038/s41598-018-32859-4"}], "notes": [], "created": "2018-10-31T21:32:11.479Z", "modified": "2023-06-19T13:09:54.659Z"}, {"entity": "publication", "iuid": "50e6a1add56143eaafa43557ad8e0879", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50e6a1add56143eaafa43557ad8e0879.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50e6a1add56143eaafa43557ad8e0879"}}, "title": "Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.", "authors": [{"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Sullivan", "given": "Devin", "initials": "D"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Al-Khalili", "given": "Cristina", "initials": "C"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2018-04-13", "journal": {"volume": "9", "issn": "1949-2553", "issue": "28", "pages": "19730-19744", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing their surrounding vasculature network. Transformed cancer cells are known to exhibit phenotypic alterations, enabling continuous proliferation despite a limited oxygen supply. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O", "doi": "10.18632/oncotarget.24808", "pmid": "29731978", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "24808"}, {"db": "pmc", "key": "PMC5929421"}, {"db": "GEO", "description": "Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia", "key": "GSE109367"}], "notes": [], "created": "2018-10-31T19:45:26.772Z", "modified": "2024-01-16T13:48:46.535Z"}, {"entity": "publication", "iuid": "36bcd1b2be37481c97f831354e5d5beb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36bcd1b2be37481c97f831354e5d5beb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36bcd1b2be37481c97f831354e5d5beb"}}, "title": "An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Wu", "given": "Hao", "initials": "H"}, {"family": "Bjornson", "given": "Elias", "initials": "E"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Hakkarainen", "given": "Antti", "initials": "A"}, {"family": "R\u00e4s\u00e4nen", "given": "Sari M", "initials": "SM"}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Mancina", "given": "Rosellina M", "initials": "RM"}, {"family": "Bergentall", "given": "Mattias", "initials": "M"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "S\u00f6derlund", "given": "Sanni", "initials": "S"}, {"family": "Matikainen", "given": "Niina", "initials": "N"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO"}, {"family": "Adiels", "given": "Martin", "initials": "M"}, {"family": "Piening", "given": "Brian D", "initials": "BD"}, {"family": "Gran\u00e9r", "given": "Marit", "initials": "M"}, {"family": "Lundbom", "given": "Nina", "initials": "N"}, {"family": "Williams", "given": "Kevin J", "initials": "KJ"}, {"family": "Romeo", "given": "Stefano", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Perkins", "given": "Rosie", "initials": "R"}, {"family": "Marschall", "given": "Hanns-Ulrich", "initials": "HU"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Taskinen", "given": "Marja-Riitta", "initials": "MR"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2018-03-06", "journal": {"title": "Cell Metab.", "issn": "1932-7420", "issn-l": "1550-4131", "volume": "27", "issue": "3", "pages": "559-571.e5"}, "abstract": "A carbohydrate-restricted diet is a widely recommended intervention for non-alcoholic fatty liver disease (NAFLD), but a systematic perspective on the multiple benefits of this diet is lacking. Here, we performed a short-term intervention with an isocaloric low-carbohydrate diet with increased protein content in obese subjects with NAFLD and characterized the resulting alterations in metabolism and the gut microbiota using a multi-omics approach. We observed rapid and dramatic reductions of liver fat and other cardiometabolic risk factors paralleled by (1) marked decreases in hepatic de novo lipogenesis; (2) large increases in serum \u03b2-hydroxybutyrate concentrations, reflecting increased mitochondrial \u03b2-oxidation; and (3) rapid increases in folate-producing Streptococcus and serum folate concentrations. Liver transcriptomic analysis on biopsy samples from a second cohort revealed downregulation of the fatty acid synthesis pathway and upregulation of folate-mediated one-carbon metabolism and fatty acid oxidation pathways. Our results highlight the potential of exploring diet-microbiota interactions for treating NAFLD.", "doi": "10.1016/j.cmet.2018.01.005", "pmid": "29456073", "labels": {"Clinical Biomarkers": "Service", "PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pii", "key": "S1550-4131(18)30054-8"}, {"db": "pmc", "key": "PMC6706084"}, {"db": "mid", "key": "NIHMS1038351"}, {"db": "ClinicalTrials.gov", "key": "NCT02558530"}], "notes": [], "created": "2020-01-23T15:57:18.639Z", "modified": "2023-04-14T13:56:06.275Z"}, {"entity": "publication", "iuid": "6d6d2546a79e49f9bd07debf8066d5be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6d2546a79e49f9bd07debf8066d5be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6d2546a79e49f9bd07debf8066d5be"}}, "title": "In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.", "authors": [{"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "31", "issn": "1530-0285", "issue": "2", "title": "Mod. Pathol.", "pages": "253-263", "issn-l": "0893-3952"}, "abstract": "Antibodies are important tools in anatomical pathology and research, but the quality of in situ protein detection by immunohistochemistry greatly depends on the choice of antibodies and the abundance of the targeted proteins. Many antibodies used in scientific research do not meet requirements for specificity and sensitivity. Accordingly, methods that improve antibody performance and produce quantitative data can greatly advance both scientific investigations and clinical diagnostics based on protein expression and in situ localization. We demonstrate here protocols for antibody labeling that allow specific protein detection in tissues via bright-field in situ proximity ligation assays, where each protein molecule must be recognized by two antibodies. We further demonstrate that single polyclonal antibodies or purified serum preparations can be used for these dual recognition assays. The requirement for protein recognition by pairs of antibody conjugates can significantly improve specificity of protein detection over single-binder assays.", "doi": "10.1038/modpathol.2017.102", "pmid": "28937142", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "modpathol2017102"}], "notes": [], "created": "2017-11-03T07:29:13.291Z", "modified": "2023-04-14T13:56:07.652Z"}, {"entity": "publication", "iuid": "9a66e1ee51af4d9dacf0840a88138663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c76df55999a74ebfaada13e0cc775de8.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a62a58b12f4f4c87ebe4135826c91a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/17058abc202c4da794e35722c1f234df.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6352", "title": "Science", "pages": "eaan2507", "issn-l": "0036-8075"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2017-11-03T16:19:27.334Z", "modified": "2024-01-16T13:48:47.600Z"}, {"entity": "publication", "iuid": "216ae64b6c9f43328ad351f4c4320330", "links": {"self": {"href": "https://publications.scilifelab.se/publication/216ae64b6c9f43328ad351f4c4320330.json"}, "display": {"href": "https://publications.scilifelab.se/publication/216ae64b6c9f43328ad351f4c4320330"}}, "title": "Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis.", "authors": [{"family": "Zandian", "given": "A", "initials": "A"}, {"family": "Wing\u00e5rd", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "H", "initials": "H"}, {"family": "Sj\u00f6stedt", "given": "E", "initials": "E"}, {"family": "Johansson", "given": "D X", "initials": "DX"}, {"family": "Just", "given": "D", "initials": "D"}, {"family": "Hellstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "J M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "A", "initials": "A"}, {"family": "Norbeck", "given": "O", "initials": "O"}, {"family": "Owe-Larsson", "given": "B", "initials": "B"}, {"family": "Nilsson", "given": "P", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Persson", "given": "M A A", "initials": "MAA"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "7", "issn": "2158-3188", "issue": "7", "pages": "e1177", "title": "Transl Psychiatry", "issn-l": "2158-3188"}, "abstract": "Immunological and inflammatory reactions have been suggested to have a role in the development of schizophrenia, a hypothesis that has recently been supported by genetic data. The aim of our study was to perform an unbiased search for autoantibodies in patients with a first psychotic episode, and to explore the association between any seroreactivity and the development of a Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV) disorder characterized by chronic or relapsing psychotic symptoms. We collected plasma samples from 53 patients when they were treated for their first-episode psychosis, and 41 non-psychotic controls, after which the patients were followed for a mean duration of 7 years. Thirty patients were diagnosed with schizophrenia, delusional disorder, schizoaffective disorder, bipolar disorder or a long-term unspecified nonorganic psychosis during follow-up, whereas 23 patients achieved complete remission. At the end of follow-up, plasma samples were analyzed for IgG reactivity to 2304 fragments of human proteins using a multiplexed affinity proteomic technique. Eight patient samples showed autoreactivity to the N-terminal fragment of the PAGE (P antigen) protein family (PAGE2B/PAGE2/PAGE5), whereas no such autoreactivity was seen among the controls. PAGE autoreactivity was associated with a significantly increased risk of being diagnosed with schizophrenia during follow-up (odds ratio 6.7, relative risk 4.6). An immunohistochemistry analysis using antisera raised against the N-terminal fragment stained an unknown extracellular target in human cortical brain tissue. Our findings suggest that autoreactivity to the N-terminal portion of the PAGE protein family is associated with schizophrenia in a subset of patients with first-episode psychosis.", "doi": "10.1038/tp.2017.160", "pmid": "28742074", "labels": {"Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "tp2017160"}, {"db": "pmc", "key": "PMC5538130"}], "notes": [], "created": "2017-11-02T11:35:53.436Z", "modified": "2021-07-08T13:44:33.083Z"}, {"entity": "publication", "iuid": "feb578c0af8f44d999e4cdc360c28358", "links": {"self": {"href": "https://publications.scilifelab.se/publication/feb578c0af8f44d999e4cdc360c28358.json"}, "display": {"href": "https://publications.scilifelab.se/publication/feb578c0af8f44d999e4cdc360c28358"}}, "title": "Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Nyaiesh", "given": "Etienne-Nicholas", "initials": "EN"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2017-06-00", "journal": {"volume": "10", "issn": "1936-5233", "issue": "3", "pages": "385-395", "title": "Transl Oncol", "issn-l": null}, "abstract": "Blood-based proteomic profiling may aid and expand our understanding of diseases and their different phenotypes. The aim of the presented study was to profile serum samples from patients with malignant melanoma using affinity proteomic assays to describe proteins in the blood stream that are associated to stage or recurrence of melanoma.\n\nMultiplexed protein analysis was conducted using antibody suspension bead arrays. A total of 232 antibodies against 132 proteins were selected from (i) a screening with 4595 antibodies and 32 serum samples from melanoma patients and controls, (ii) antibodies used for immunohistochemistry, (iii) protein targets previously related with melanoma. The analysis was performed with 149 serum samples from patients with malignant melanoma. Antibody selectivity was then assessed by Western blot, immunocapture mass spectrometry, and epitope mapping. Lastly, indicative antibodies were applied for IHC analysis of melanoma tissues.\n\nSerum levels of regucalcin (RGN) and syntaxin 7 (STX7) were found to be lower in patients with both recurring tumors and a high Breslow's thickness (T-stage 3/4) compared to low thickness (T-stage 1/2) without disease recurrence. Serum levels of methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) were instead elevated in sera of T3/4 patients with recurrence. The analysis of tissue sections with S100A6 and MTHFD1L showed positive staining in a majority of patients with melanoma, and S100A6 was significantly associated to T-stage.\n\nOur findings provide a starting point to further study RGN, STX7, MTHFD1L and S100A6 in serum to elucidate their involvement in melanoma progression and to assess a possible contribution to support clinical indications.", "doi": "10.1016/j.tranon.2017.03.002", "pmid": "28433799", "labels": {"Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1936-5233(17)30031-1"}, {"db": "pmc", "key": "PMC5403766"}], "notes": [], "created": "2017-08-30T14:34:48.682Z", "modified": "2021-07-08T13:44:33.779Z"}, {"entity": "publication", "iuid": "9ffdf7a669174f9b940bb01c93fab8a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9"}}, "title": "A subcellular map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b0ca6c2a8f64be89222a6029885b08c.json"}}, {"family": "Wiking", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-6368-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69baef540a14859a7b4fd966c3b9245.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc22f13eb21a4c75a6e7cad7686bcc8a.json"}}, {"family": "Geladaki", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-0530-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/28081295132343c5bfc4b1e9bcfb8201.json"}}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Alm", "given": "Tove", "initials": "T", "orcid": "0000-0002-2643-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0b5ee89148475581faf42ea53d61bd.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L", "orcid": "0000-0002-8116-882X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1092280955d44d1f99258f4f812fb6c7.json"}}, {"family": "Breckels", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-8918-7171", "researcher": {"href": "https://publications.scilifelab.se/researcher/3efbca65f39d4f7aa8df049a39e0c8a9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Fall", "given": "Jenny", "initials": "J"}, {"family": "Gatto", "given": "Laurent", "initials": "L", "orcid": "0000-0002-1520-2268", "researcher": {"href": "https://publications.scilifelab.se/researcher/242f5219a40547439c0cc4b07e26e71d.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications.scilifelab.se/researcher/80019f26676347d5b6c4124d63eeaf86.json"}}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Mulvey", "given": "Claire M", "initials": "CM", "orcid": "0000-0002-2989-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc08b919bd8a423f8a6df8b880979045.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a96138841741f9acff4a50100c2a25.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Winsnes", "given": "Casper", "initials": "C", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a64c707c8b54b6bbd31dae6485a1392.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2017-05-26", "journal": {"volume": "356", "issn": "1095-9203", "issue": "6340", "pages": null, "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.", "doi": "10.1126/science.aal3321", "pmid": "28495876", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aal3321"}], "notes": [], "created": "2017-10-31T15:27:28.787Z", "modified": "2024-01-16T13:48:47.941Z"}, {"entity": "publication", "iuid": "914e667e695641e7827adaf9b0dcf69b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/914e667e695641e7827adaf9b0dcf69b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/914e667e695641e7827adaf9b0dcf69b"}}, "title": "Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.", "authors": [{"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Henriksen", "given": "Tora Ida", "initials": "TI"}, {"family": "Scheele", "given": "Camilla", "initials": "C"}, {"family": "Broholm", "given": "Christa", "initials": "C"}, {"family": "Pedersen", "given": "Maria", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pedersen", "given": "Bente Klarlund", "initials": "BK"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "9", "issn": "1756-994X", "issue": "1", "pages": "47", "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": "Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity.\n\nWe generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription. This setup enabled us to identify intrinsic properties, originating from muscle precursor cells and retained in the corresponding myocytes. Bioinformatic and statistical methods, including differential expression analysis, gene-set analysis, and metabolic network analysis, were used to characterize the different myocytes.\n\nWe found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional signatures. T2D and obesity were independently associated with dysregulated myogenesis, down-regulated muscle function, and up-regulation of inflammation and extracellular matrix components. Metabolic network analysis identified that in T2D but not obesity a specific metabolite subnetwork involved in sphingolipid metabolism was transcriptionally regulated.\n\nOur findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D.", "doi": "10.1186/s13073-017-0432-2", "pmid": "28545587", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13073-017-0432-2"}, {"db": "pmc", "key": "PMC5444103"}], "notes": [], "created": "2017-11-03T15:53:40.517Z", "modified": "2024-01-16T13:48:47.954Z"}, {"entity": "publication", "iuid": "f45ab5374259462a85a914ce26350231", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f45ab5374259462a85a914ce26350231.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f45ab5374259462a85a914ce26350231"}}, "title": "FZD10-G\u03b113 signalling axis points to a role of FZD10 in CNS angiogenesis.", "authors": [{"family": "Hot", "given": "Belma", "initials": "B"}, {"family": "Valnohova", "given": "Jana", "initials": "J"}, {"family": "Arthofer", "given": "Elisa", "initials": "E"}, {"family": "Simon", "given": "Katharina", "initials": "K"}, {"family": "Shin", "given": "Jaekyung", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Kostenis", "given": "Evi", "initials": "E"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2017-04-00", "journal": {"title": "Cell. Signal.", "issn": "1873-3913", "volume": "32", "issue": null, "pages": "93-103", "issn-l": "0898-6568"}, "abstract": "Among the 10 Frizzled (FZD) isoforms belonging to the Class F of G protein-coupled receptors (GPCRs), FZD10 remains the most enigmatic. FZD10 shows homology to FZD4 and FZD9 and was previously implicated in both \u03b2-catenin-dependent and -independent signalling. In normal tissue, FZD10 levels are generally very low; however, its upregulation in synovial carcinoma has attracted some attention for therapy. Our findings identify FZD10 as a receptor interacting with and signalling through the heterotrimeric G protein G\u03b113 but not G\u03b112, G\u03b1i1, G\u03b1oA, G\u03b1s, or G\u03b1q. Stimulation with the FZD agonist WNT induced the dissociation of the G\u03b113 protein from FZD10, and led to global G\u03b112/13-dependent cell changes assessed by dynamic mass redistribution measurements. Furthermore, we show that FZD10 mediates G\u03b112/13 activation-dependent induction of YAP/TAZ transcriptional activity. In addition, we show a distinct expression of FZD10 in embryonic CNS endothelial cells at E11.5-E14.5. Given the well-known importance of G\u03b113 signalling for the development of the vascular system, the selective expression of FZD10 in brain vascular endothelial cells points at a potential role of FZD10-G\u03b113 signalling in CNS angiogenesis.", "doi": "10.1016/j.cellsig.2017.01.023", "pmid": "28126591", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0898-6568(17)30029-3"}], "notes": [], "created": "2017-10-30T14:58:32.429Z", "modified": "2021-07-08T13:44:33.744Z"}, {"entity": "publication", "iuid": "442e355248544b87a31a6f4208cade10", "links": {"self": {"href": "https://publications.scilifelab.se/publication/442e355248544b87a31a6f4208cade10.json"}, "display": {"href": "https://publications.scilifelab.se/publication/442e355248544b87a31a6f4208cade10"}}, "title": "Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy.", "authors": [{"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}], "type": "journal article", "published": "2017-03-03", "journal": {"volume": "16", "issn": "1535-3907", "issue": "3", "pages": "1300-1314", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2.2 million 12-mer peptides with a six amino acid lateral shift. On the basis of the IgG reactivities found on these whole-proteome peptide microarrays, a set of 23 samples was then studied on a targeted array with 174\u202f000 12-mer peptides of single amino acid lateral shift. Finally, verification of IgG reactivities was conducted with a larger sample set (n = 448) using the bead-based peptide microarrays. The presented workflow employed three different peptide microarray formats to discover and resolve the epitopes of human autoantibodies and revealed two potentially new autoantigens: MAP3K7 in multiple sclerosis and NRXN1 in narcolepsy. The presented strategy provides insights into antibody repertoire reactivity at a peptide level and may accelerate the discovery and validation of autoantigens in human diseases.", "doi": "10.1021/acs.jproteome.6b00916", "pmid": "28121444", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-02T11:40:32.221Z", "modified": "2021-07-08T13:44:33.196Z"}, {"entity": "publication", "iuid": "74fcedf830fe4da28feaf59862e5d126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74fcedf830fe4da28feaf59862e5d126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74fcedf830fe4da28feaf59862e5d126"}}, "title": "A novel RNA sequencing data analysis method for cell line authentication.", "authors": [{"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Raso", "given": "Cinzia", "initials": "C"}, {"family": "Kennedy", "given": "Susan", "initials": "S"}, {"family": "Rauch", "given": "Nora", "initials": "N"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Kolch", "given": "Walter", "initials": "W"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications.scilifelab.se/researcher/cff94d8d749248d38f5da13c1f636c9d.json"}}], "type": "journal article", "published": "2017-02-13", "journal": {"volume": "12", "issn": "1932-6203", "issue": "2", "pages": "e0171435", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.", "doi": "10.1371/journal.pone.0171435", "pmid": "28192450", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-35145"}, {"db": "pmc", "key": "PMC5305277"}], "notes": [], "created": "2017-11-03T16:20:58.076Z", "modified": "2021-07-08T13:44:33.358Z"}, {"entity": "publication", "iuid": "8e9f2942aae54865a9b27b0869aeffb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e9f2942aae54865a9b27b0869aeffb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e9f2942aae54865a9b27b0869aeffb0"}}, "title": "The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "158", "issn": "1945-7170", "issue": "2", "pages": "239-251", "title": "Endocrinology", "issn-l": "0013-7227"}, "abstract": "The adrenal gland is a composite endocrine organ with vital functions that include the synthesis and release of glucocorticoids and catecholamines. To define the molecular landscape that underlies the specific functions of the adrenal gland, we combined a genome-wide transcriptomics approach using messenger RNA sequencing of human tissues with immunohistochemistry-based protein profiling on tissue microarrays. Approximately two-thirds of all putative protein coding genes were expressed in the adrenal gland, and the analysis identified 253 genes with an elevated pattern of expression in the adrenal gland, with only 37 genes showing a markedly greater expression level (more than fivefold) in the adrenal gland compared with 31 other normal human tissue types analyzed. The analyses allowed for an assessment of the relative expression levels for well-known proteins involved in adrenal gland function but also identified previously poorly characterized proteins in the adrenal cortex, such as the FERM (4.1 protein, ezrin, radixin, moesin) domain containing 5 and the nephroblastoma overexpressed (NOV) protein homolog. We have provided a global analysis of the adrenal gland transcriptome and proteome, with a comprehensive list of genes with elevated expression in the adrenal gland and spatial information with examples of protein expression patterns for corresponding proteins. These genes and proteins constitute important starting points for an improved understanding of the normal function and pathophysiology of the adrenal glands.", "doi": "10.1210/en.2016-1758", "pmid": "27901589", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:56:06.552Z", "modified": "2024-01-16T13:48:48.500Z"}, {"entity": "publication", "iuid": "6eeb153d4072463db806a9bd79c398d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6eeb153d4072463db806a9bd79c398d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6eeb153d4072463db806a9bd79c398d5"}}, "title": "Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.", "authors": [{"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Bakker", "given": "Joanne", "initials": "J"}, {"family": "Girach", "given": "Fatima", "initials": "F"}, {"family": "Hellysaz", "given": "Arash", "initials": "A"}, {"family": "Tomer", "given": "Raju", "initials": "R"}, {"family": "Alp\u00e1r", "given": "Al\u00e1n", "initials": "A"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Clotman", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}, {"family": "Keimpema", "given": "Erik", "initials": "E"}, {"family": "Hsueh", "given": "Brian", "initials": "B"}, {"family": "Crow", "given": "Ailey K", "initials": "AK"}, {"family": "Martens", "given": "Henrik", "initials": "H"}, {"family": "Schwindling", "given": "Christian", "initials": "C"}, {"family": "Calvigioni", "given": "Daniela", "initials": "D"}, {"family": "Bains", "given": "Jaideep S", "initials": "JS"}, {"family": "M\u00e1t\u00e9", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Szab\u00f3", "given": "G\u00e1bor", "initials": "G"}, {"family": "Yanagawa", "given": "Yuchio", "initials": "Y"}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD"}, {"family": "Rendeiro", "given": "Andre", "initials": "A", "orcid": "0000-0001-9362-5373", "researcher": {"href": "https://publications.scilifelab.se/researcher/e714399288874d1097d0d8c13123f756.json"}}, {"family": "Farlik", "given": "Matthias", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wulff", "given": "Peer", "initials": "P"}, {"family": "Bock", "given": "Christoph", "initials": "C", "orcid": "0000-0001-6091-3088", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab95ee1c8284fa7bf2e5a2ee987c835.json"}}, {"family": "Broberger", "given": "Christian", "initials": "C"}, {"family": "Deisseroth", "given": "Karl", "initials": "K"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Horvath", "given": "Tamas L", "initials": "TL"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "20", "issn": "1546-1726", "issue": "2", "pages": "176-188", "title": "Nat. Neurosci.", "issn-l": "1097-6256"}, "abstract": "The hypothalamus contains the highest diversity of neurons in the brain. Many of these neurons can co-release neurotransmitters and neuropeptides in a use-dependent manner. Investigators have hitherto relied on candidate protein-based tools to correlate behavioral, endocrine and gender traits with hypothalamic neuron identity. Here we map neuronal identities in the hypothalamus by single-cell RNA sequencing. We distinguished 62 neuronal subtypes producing glutamatergic, dopaminergic or GABAergic markers for synaptic neurotransmission and harboring the ability to engage in task-dependent neurotransmitter switching. We identified dopamine neurons that uniquely coexpress the Onecut3 and Nmur2 genes, and placed these in the periventricular nucleus with many synaptic afferents arising from neuromedin S+ neurons of the suprachiasmatic nucleus. These neuroendocrine dopamine cells may contribute to the dopaminergic inhibition of prolactin secretion diurnally, as their neuromedin S+ inputs originate from neurons expressing Per2 and Per3 and their tyrosine hydroxylase phosphorylation is regulated in a circadian fashion. Overall, our catalog of neuronal subclasses provides new understanding of hypothalamic organization and function.", "doi": "10.1038/nn.4462", "pmid": "27991900", "labels": {"Fluorescence Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nn.4462"}], "notes": [], "created": "2017-05-03T12:58:52.200Z", "modified": "2021-07-08T13:44:33.346Z"}, {"entity": "publication", "iuid": "3d0cc871ee8644d1b9ecf349a1eb0965", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d0cc871ee8644d1b9ecf349a1eb0965.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d0cc871ee8644d1b9ecf349a1eb0965"}}, "title": "Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.", "authors": [{"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Henjes", "given": "Frauke", "initials": "F"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Magnusson", "given": "Patrik", "initials": "P"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2017-01-06", "journal": {"volume": "16", "issn": "1535-3907", "issue": "1", "pages": "204-216", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3833 human protein fragments. Starting from planar protein arrays with 3786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens was corroborated for their reactivity in a set of 550 samples using suspension bead arrays. The antigens prostein (SLC45A3), TATA-box binding protein (TBP), and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) showed higher reactivity in PCA patients with late disease compared with early disease. Because of its prostate tissue specificity, we focused on prostein and continued with mapping epitopes of the 66-mer protein fragment using patient samples. Using bead-based assays and 15-mer peptides, a minimal peptide epitope was identified and refined by alanine scanning to the KPxAPFP. Further sequence alignment of this motif revealed homology to transmembrane protein 79 (TMEM79) and TGF-beta-induced factor 2 (TGIF2), thus providing a reasoning for cross-reactivity found in females. A comprehensive workflow to discover and validate IgG reactivity against prostein and homologous targets in human serum and plasma was applied. This study provides useful information when searching for novel biomarkers or drug targets that are guided by the reactivity of the immune system against autoantigens.", "doi": "10.1021/acs.jproteome.6b00620", "pmid": "27700103", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:14.584Z", "modified": "2021-07-08T13:44:33.168Z"}, {"entity": "publication", "iuid": "90e126a31ae94eb29dcf7d80571f9573", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90e126a31ae94eb29dcf7d80571f9573.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90e126a31ae94eb29dcf7d80571f9573"}}, "title": "Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.", "authors": [{"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L"}, {"family": "Poser", "given": "Ina", "initials": "I"}, {"family": "Hyman", "given": "Anthony", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2017-01-06", "journal": {"volume": "16", "issn": "1535-3907", "issue": "1", "pages": "147-155", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence (IF) applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP-tagged target proteins at endogenous levels. Furthermore, we assessed batch-to-batch effects for 35 target proteins, showing that both the on- and off-target binding patterns vary significantly between antibody batches and that the proposed strategy serves as a reliable procedure for ensuring reproducibility upon production of new antibody batches. In summary, we present a systematic scheme for antibody validation in IF applications using endogenous expression of tagged proteins. This is an important step toward a reproducible approach for context- and application-specific antibody validation and improved reliability of antibody-based experiments and research data.", "doi": "10.1021/acs.jproteome.6b00821", "pmid": "27723985", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:09.252Z", "modified": "2021-07-08T13:44:33.422Z"}, {"entity": "publication", "iuid": "d696eb5a55e8441fa0660644f896cd63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d696eb5a55e8441fa0660644f896cd63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d696eb5a55e8441fa0660644f896cd63"}}, "title": "A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma.", "authors": [{"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Niinivirta", "given": "Marjut", "initials": "M"}, {"family": "Laird", "given": "Alexander", "initials": "A"}, {"family": "Ljungqvist", "given": "Oscar", "initials": "O"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Khan", "given": "Naila", "initials": "N"}, {"family": "Patil", "given": "Tushar", "initials": "T"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Harrison", "given": "David J", "initials": "DJ"}, {"family": "Ullenhag", "given": "Gustav J", "initials": "GJ"}, {"family": "Stewart", "given": "Grant D", "initials": "GD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-01-04", "journal": {"title": "BMC Cancer", "issn": "1471-2407", "volume": "17", "issue": "1", "pages": "9", "issn-l": "1471-2407"}, "abstract": "There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC).\n\nHuman Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers. Two independent RCC cohorts (n = 181; n = 114) were analyzed to further establish the sensitivity of CUBN as RCC-specific marker and to explore if the fraction of RCCs lacking CUBN expression could predict differences in patient survival.\n\nCUBN was identified as highly RCC-specific protein with 58% of all primary RCCs staining positive for CUBN using immunohistochemistry. In venous tumor thrombi and metastatic lesions, the frequency of CUBN expression was increasingly lost. Clear cell RCC (ccRCC) patients with CUBN positive tumors had a significantly better prognosis compared to patients with CUBN negative tumors, independent of T-stage, Fuhrman grade and nodal status (HR 0.382, CI 0.203-0.719, P = 0.003).\n\nCUBN expression is highly specific to RCC and loss of the protein is significantly and independently associated with poor prognosis. CUBN expression in ccRCC provides a promising positive prognostic indicator for patients with ccRCC. The high specificity of CUBN expression in RCC also suggests a role as a new diagnostic marker in clinical cancer differential diagnostics to confirm or rule out RCC.", "doi": "10.1186/s12885-016-3030-6", "pmid": "28052770", "labels": {"Tissue Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-016-3030-6"}, {"db": "pmc", "key": "PMC5215231"}], "notes": [], "created": "2017-11-05T12:38:11.316Z", "modified": "2021-07-08T13:44:33.674Z"}, {"entity": "publication", "iuid": "bb9d97d33bd445a488b6c9a31e179703", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb9d97d33bd445a488b6c9a31e179703.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb9d97d33bd445a488b6c9a31e179703"}}, "title": "Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury.", "authors": [{"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Bachmann", "given": "Julie", "initials": "J"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Yimer", "given": "Getnet", "initials": "G"}, {"family": "Aklillu", "given": "Eleni", "initials": "E"}, {"family": "Makonnen", "given": "Eyasu", "initials": "E"}, {"family": "Aderaye", "given": "Getachew", "initials": "G"}, {"family": "Roach", "given": "James", "initials": "J"}, {"family": "Fier", "given": "Ian", "initials": "I"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "G\u00f6pfert", "given": "Jens", "initials": "J"}, {"family": "Perazzo", "given": "Hugo", "initials": "H"}, {"family": "Poynard", "given": "Thierry", "initials": "T"}, {"family": "Stephens", "given": "Camilla", "initials": "C"}, {"family": "Andrade", "given": "Ra\u00fal J", "initials": "RJ"}, {"family": "Lucena", "given": "M Isabel", "initials": "MI"}, {"family": "Arber", "given": "Nadir", "initials": "N"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Watkins", "given": "Paul B", "initials": "PB"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "37", "issn": "1478-3231", "issue": "1", "pages": "132-140", "title": "Liver Int.", "issn-l": "1478-3223"}, "abstract": "The occurrence of drug-induced liver injury (DILI) is a major issue in all phases of drug development. To identify novel biomarker candidates associated with DILI, we utilised an affinity proteomics strategy, where antibody suspension bead arrays were applied to profile plasma and serum samples from human DILI cases and controls.\n\nAn initial screening was performed using 4594 randomly selected antibodies, representing 3450 human proteins. Resulting candidate proteins together with proposed DILI biomarker candidates generated a DILI array of 251 proteins for subsequent target analysis and verifications. In total, 1196 samples from 241 individuals across four independent cohorts were profiled: healthy volunteers receiving acetaminophen, patients with human immunodeficiency virus and/or tuberculosis receiving treatment, DILI cases originating from a wide spectrum of drugs, and healthy volunteers receiving heparins.\n\nWe observed elevated levels of cadherin 5, type 2 (CDH5) and fatty acid-binding protein 1 (FABP1) in DILI cases. In the two longitudinal cohorts, CDH5 was elevated already at baseline. FABP1 was elevated after treatment initiation and seemed to respond more rapidly than alanine aminotransferase (ALT). The elevations were verified in the DILI cases treated with various drugs. In the heparin cohort, CDH5 was stable over time whereas FABP1 was elevated.\n\nThese results suggest that CDH5 may have value as a susceptibility marker for DILI. FABP1 was identified as a biomarker candidate with superior characteristics regarding tissue distribution and kinetics compared to ALT but likely with limited predictive value for the development of severe DILI. Further studies are needed to determine the clinical utility of the proposed markers.", "doi": "10.1111/liv.13174", "pmid": "27224670", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5215406"}], "notes": [], "created": "2017-05-03T12:59:07.167Z", "modified": "2021-07-08T13:44:33.558Z"}, {"entity": "publication", "iuid": "aaaf64893fe54c5196aaf8f4943829e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aaaf64893fe54c5196aaf8f4943829e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aaaf64893fe54c5196aaf8f4943829e6"}}, "title": "PDGFB, a new candidate plasma biomarker for venous thromboembolism: results from the VEREMA affinity proteomics study.", "authors": [{"family": "Bruzelius", "given": "Maria", "initials": "M"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ", "orcid": "0000-0003-4122-1945", "researcher": {"href": "https://publications.scilifelab.se/researcher/adccb07f0a744e648516bd7b672d70be.json"}}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG", "orcid": "0000-0001-8808-7128", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ca6e46c2f1486199d08bc9f9b702be.json"}}, {"family": "Sanchez-Rivera", "given": "Laura", "initials": "L"}, {"family": "Gyorgy", "given": "Beata", "initials": "B"}, {"family": "Souto", "given": "Juan Carlos", "initials": "JC"}, {"family": "Fr\u00e5nberg", "given": "Mattias", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ", "orcid": "0000-0001-8506-3585", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac5060a3b37466dae002d4ad8f4d0ac.json"}}, {"family": "Holmstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Hamsten", "given": "Anders", "initials": "A", "orcid": "0000-0002-0618-0538", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb944b0f90b64afc8162f15874069946.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Silveira", "given": "Angela", "initials": "A", "orcid": "0000-0003-2063-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd1197769804dd48b9de86f11340ef2.json"}}, {"family": "Soria", "given": "Jose Manuel", "initials": "JM"}, {"family": "Smadja", "given": "David M", "initials": "DM", "orcid": "0000-0001-7731-9202", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc861e04da204cc9a00a047a026c8b7a.json"}}, {"family": "Butler", "given": "Lynn M", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Morange", "given": "Pierre-Emmanuel", "initials": "PE", "orcid": "0000-0002-9065-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a85b080902c04dacb81456efa67374db.json"}}, {"family": "Tr\u00e9gou\u00ebt", "given": "David-Alexandre", "initials": "DA", "orcid": "0000-0001-9084-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb3fe1a732b41d79a4a165a64c322d1.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}], "type": "clinical trial", "published": "2016-12-08", "journal": {"volume": "128", "issn": "1528-0020", "issue": "23", "pages": "e59-e66", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "There is a clear clinical need for high-specificity plasma biomarkers for predicting risk of venous thromboembolism (VTE), but thus far, such markers have remained elusive. Utilizing affinity reagents from the Human Protein Atlas project and multiplexed immuoassays, we extensively analyzed plasma samples from 2 individual studies to identify candidate protein markers associated with VTE risk. We screened plasma samples from 88 VTE cases and 85 matched controls, collected as part of the Swedish \"Venous Thromboembolism Biomarker Study,\" using suspension bead arrays composed of 755 antibodies targeting 408 candidate proteins. We identified significant associations between VTE occurrence and plasma levels of human immunodeficiency virus type I enhancer binding protein 1 (HIVEP1), von Willebrand factor (VWF), glutathione peroxidase 3 (GPX3), and platelet-derived growth factor \u03b2 (PDGFB). For replication, we profiled plasma samples of 580 cases and 589 controls from the French FARIVE study. These results confirmed the association of VWF and PDGFB with VTE after correction for multiple testing, whereas only weak trends were observed for HIVEP1 and GPX3. Although plasma levels of VWF and PDGFB correlated modestly (\u03c1 \u223c 0.30) with each other, they were independently associated with VTE risk in a joint model in FARIVE (VWF P < .001; PDGFB P = .002). PDGF\u0392 was verified as the target of the capture antibody by immunocapture mass spectrometry and sandwich enzyme-linked immunosorbent assay. In conclusion, we demonstrate that high-throughput affinity plasma proteomic profiling is a valuable research strategy to identify potential candidate biomarkers for thrombosis-related disorders, and our study suggests a novel association of PDGFB plasma levels with VTE.", "doi": "10.1182/blood-2016-05-711846", "pmid": "27742707", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)33937-9"}], "notes": [], "created": "2017-05-03T12:59:07.466Z", "modified": "2023-06-19T13:11:23.382Z"}, {"entity": "publication", "iuid": "7362064a1f044c14a2e50a26392e171a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7362064a1f044c14a2e50a26392e171a"}}, "title": "CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer's disease.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J"}, {"family": "Just", "given": "David", "initials": "D"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Nellg\u00e5rd", "given": "Bengt", "initials": "B"}, {"family": "Zetterberg", "given": "Henrik", "initials": "H"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "10", "issn": "1862-8354", "issue": "12", "pages": "1242-1253", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "This study is part of a larger effort aiming to expand the knowledge of brain-enriched proteins in human cerebrospinal fluid (CSF) and to provide novel insight into the relation between such proteins and different neurodegenerative diseases.\n\nHere 280 brain-enriched proteins in CSF from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are profiled. In total, 441 human samples of ventricular CSF collected post mortem and lumbar CSF collected ante mortem are analyzed using 376 antibodies in a suspension bead array setup, utilizing a direct labelling approach.\n\nAmong several proteins displaying differentiated profiles between sample groups, we focus here on two synaptic proteins, neuromodulin (GAP43) and neurogranin (NRGN). They are both found at elevated levels in CSF from AD patients in two independent cohorts, providing disease-associated profiles in addition to verifying and strengthening previously observed patterns. Increased levels are also observed for patients for whom the AD diagnosis was not established at the time of sampling.\n\nThese findings indicate that analyzing the brain-enriched proteins in CSF is of particular interest to increase the understanding of the CSF proteome and its relation to neurodegenerative disorders. In addition, this study lends support to the notion that measurements of these synaptic proteins could potentially be of great relevance in future diagnostic tests for AD.", "doi": "10.1002/prca.201500150", "pmid": "27604409", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5157753"}], "notes": [], "created": "2017-05-03T12:59:05.983Z", "modified": "2021-07-08T13:44:33.352Z"}, {"entity": "publication", "iuid": "508c656babda482a96344a438394dbd5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/508c656babda482a96344a438394dbd5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/508c656babda482a96344a438394dbd5"}}, "title": "ANLN is a prognostic biomarker independent of Ki-67 and essential for cell cycle progression in primary breast cancer.", "authors": [{"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L"}, {"family": "Pont\u00e9n", "given": "Victor", "initials": "V"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2016-11-18", "journal": {"volume": "16", "issn": "1471-2407", "issue": "1", "pages": "904", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Anillin (ANLN), an actin-binding protein required for cytokinesis, has recently been presented as part of a prognostic marker panel in breast cancer. The objective of the current study was to further explore the prognostic and functional value of ANLN as a single biomarker in breast cancer.\n\nImmunohistochemical assessment of ANLN protein expression was performed in two well characterized breast cancer cohorts (n = 484) with long-term clinical follow-up data and the results were further validated at the mRNA level in a publicly available transcriptomics dataset. The functional relevance of ANLN was investigated in two breast cancer cell lines using RNA interference.\n\nHigh nuclear fraction of ANLN in breast tumor cells was significantly associated with large tumor size, high histological grade, high proliferation rate, hormone receptor negative tumors and poor prognosis in both examined cohorts. Multivariable analysis showed that the association between ANLN and survival was significantly independent of age in cohort I and significantly independent of proliferation, as assessed by Ki-67 expression in tumor cells, age, tumor size, ER and PR status, HER2 status and nodal status in cohort II. Analysis of ANLN mRNA expression confirmed that high expression of ANLN was significantly correlated to poor overall survival in breast cancer patients. Consistent with the role of ANLN during cytokinesis, transient knock-down of ANLN protein expression in breast cancer cell lines resulted in an increase of senescent cells and an accumulation of cells in the G2/M phase of the cell cycle with altered cell morphology including large, poly-nucleated cells. Moreover, ANLN siRNA knockdown also resulted in decreased expression of cyclins D1, A2 and B1.\n\nANLN expression in breast cancer cells plays an important role during cell division and a high fraction of nuclear ANLN expression in tumor cells is correlated to poor prognosis in breast cancer patients, independent of Ki-67, tumor size, hormone receptor status, HER2 status, nodal status and age.", "doi": "10.1186/s12885-016-2923-8", "pmid": "27863473", "labels": {"Tissue Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-016-2923-8"}, {"db": "pmc", "key": "PMC5116155"}], "notes": [], "created": "2017-05-03T12:59:20.815Z", "modified": "2021-07-08T13:44:33.234Z"}, {"entity": "publication", "iuid": "07c67e69fc3948739042d9185b0062de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07c67e69fc3948739042d9185b0062de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07c67e69fc3948739042d9185b0062de"}}, "title": "Gene-specific correlation of RNA and protein levels in human cells and tissues.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "comparative study", "published": "2016-10-20", "journal": {"volume": "12", "issn": "1744-4292", "issue": "10", "pages": "883", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.", "doi": "10.15252/msb.20167144", "pmid": "27951527", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5081484"}], "notes": [], "created": "2017-05-03T12:58:57.561Z", "modified": "2021-07-05T16:33:38.545Z"}, {"entity": "publication", "iuid": "489f13ae6632480998792a7befd4e27b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/489f13ae6632480998792a7befd4e27b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/489f13ae6632480998792a7befd4e27b"}}, "title": "A proposal for validation of antibodies.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bandrowski", "given": "Anita", "initials": "A"}, {"family": "Carr", "given": "Steven", "initials": "S"}, {"family": "Edwards", "given": "Aled", "initials": "A"}, {"family": "Ellenberg", "given": "Jan", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Rimm", "given": "David L", "initials": "DL"}, {"family": "Rodriguez", "given": "Henry", "initials": "H"}, {"family": "Hiltke", "given": "Tara", "initials": "T"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "Yamamoto", "given": "Tadashi", "initials": "T"}], "type": "journal article", "published": "2016-10-00", "journal": {"volume": "13", "issn": "1548-7105", "issue": "10", "pages": "823-827", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/nmeth.3995", "pmid": "27595404", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nmeth.3995"}], "notes": [], "created": "2017-05-03T12:59:09.549Z", "modified": "2021-07-08T13:36:19.874Z"}, {"entity": "publication", "iuid": "8adfdd7e088343359c7eb7999e56de49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8adfdd7e088343359c7eb7999e56de49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8adfdd7e088343359c7eb7999e56de49"}}, "title": "Analysis of Body-wide Unfractionated Tissue Data to Identify a Core Human Endothelial Transcriptome.", "authors": [{"family": "Butler", "given": "Lynn Marie", "initials": "LM"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn Mikael", "initials": "BM"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Renn\u00e9", "given": "Thomas", "initials": "T"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2016-09-28", "journal": {"volume": "3", "issn": "2405-4712", "issue": "3", "pages": "287-301.e3", "title": "Cell Syst", "issn-l": null}, "abstract": "Endothelial cells line blood vessels and regulate hemostasis, inflammation, and blood pressure. Proteins critical for these specialized functions tend to be predominantly expressed in endothelial cells across vascular beds. Here, we present a systems approach to identify a panel of human endothelial-enriched genes using global, body-wide transcriptomics data from 124 tissue samples from 32 organs. We identified known and unknown endothelial-enriched gene transcripts and used antibody-based profiling to confirm expression across vascular beds. The majority of identified transcripts could be detected in cultured endothelial cells from various vascular beds, and we observed maintenance of relative expression in early passage cells. In summary, we describe a widely applicable method to determine cell-type-specific transcriptome profiles in a whole-organism context, based on differential abundance across tissues. We identify potential vascular drug targets or endothelial biomarkers and highlight candidates for functional studies to increase understanding of the endothelium in health and disease.", "doi": "10.1016/j.cels.2016.08.001", "pmid": "27641958", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2405-4712(16)30256-3"}], "notes": [], "created": "2017-05-03T12:59:17.628Z", "modified": "2021-07-08T13:44:33.401Z"}, {"entity": "publication", "iuid": "fa3ef484e6d748b4966432d39d1173e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa3ef484e6d748b4966432d39d1173e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa3ef484e6d748b4966432d39d1173e0"}}, "title": "Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Mattsson", "given": "Cecilia", "initials": "C"}, {"family": "Andersson", "given": "Eni", "initials": "E"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-09-25", "journal": {"volume": "33", "issn": "1876-4347", "issue": "5 Pt A", "pages": "582-592", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "High-density protein microarrays of recombinant human protein fragments, representing 12,412 unique Ensembl Gene IDs, have here been produced and explored. These protein microarrays were used to analyse antibody off-target interactions, as well as for profiling the human autoantibody repertoire in plasma against the antigens represented by the protein fragments. Affinity-purified polyclonal antibodies produced within the Human Protein Atlas (HPA) were analysed on microarrays of three different sizes, ranging from 384 antigens to 21,120 antigens, for evaluation of the antibody validation criteria in the HPA. Plasma samples from secondary progressive multiple sclerosis patients were also screened in order to explore the feasibility of these arrays for broad-scale profiling of autoantibody reactivity. Furthermore, analysis on these near proteome-wide microarrays was complemented with analysis on HuProt\u2122 Human Proteome protein microarrays. The HPA recombinant protein microarray with 21,120 antigens and the HuProt\u2122 Human Proteome protein microarray are currently the largest protein microarray platforms available to date. The results on these arrays show that the Human Protein Atlas antibodies have few off-target interactions if the antibody validation criteria are kept stringent and demonstrate that the HPA-produced high-density recombinant protein fragment microarrays allow for a high-throughput analysis of plasma for identification of possible autoantibody targets in the context of various autoimmune conditions.", "doi": "10.1016/j.nbt.2015.09.002", "pmid": "26417875", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(15)00154-5"}], "notes": [], "created": "2017-05-02T12:58:25.314Z", "modified": "2021-07-08T13:44:33.755Z"}, {"entity": "publication", "iuid": "cec0e6d64af84e8a85d94a5a36393b4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cec0e6d64af84e8a85d94a5a36393b4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cec0e6d64af84e8a85d94a5a36393b4b"}}, "title": "Autoantibody targets in vaccine-associated narcolepsy.", "authors": [{"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Arnheim-Dahlstr\u00f6m", "given": "Lisen", "initials": "L"}, {"family": "Hallb\u00f6\u00f6k", "given": "Tove", "initials": "T"}, {"family": "Darin", "given": "Niklas", "initials": "N"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Partinen", "given": "Markku", "initials": "M"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "49", "issn": "1607-842X", "issue": "6", "pages": "421-433", "title": "Autoimmunity", "issn-l": "0891-6934"}, "abstract": "Narcolepsy is a chronic sleep disorder with a yet unknown cause, but the specific loss of hypocretin-producing neurons together with a strong human leukocyte antigen (HLA) association has led to the hypothesis that autoimmune mechanisms might be involved. Here, we describe an extensive effort to profile autoimmunity repertoires in serum with the aim to find disease-related autoantigens. Initially, 57 serum samples from vaccine-associated and sporadic narcolepsy patients and controls were screened for IgG reactivity towards 10 846 fragments of human proteins using planar microarrays. The discovered differential reactivities were verified on suspension bead arrays in the same sample collection followed by further investigation of 14 antigens in 176 independent samples, including 57 narcolepsy patients. Among these 14 antigens, methyltransferase-like 22 (METTL22) and 5'-nucleotidase cytosolic IA (NT5C1A) were recognized at a higher frequency in narcolepsy patients of both sample sets. Upon sequence analysis of the 14 proteins, polymerase family, member 3 (PARP3), acyl-CoA-binding domain containing 7 (ARID4B), glutaminase 2 (GLS2) and cyclin-dependent kinase-like 1 (CDKL1) were found to contain amino acid sequences with homology to proteins found in the H1N1 vaccine. These findings could become useful elements of further clinical assays that aim towards a better phenotypic understanding of narcolepsy and its triggers.", "doi": "10.1080/08916934.2016.1183655", "pmid": "27206786", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:15.201Z", "modified": "2021-07-08T13:44:33.640Z"}, {"entity": "publication", "iuid": "2e7aaf67a1334b1fad955fe8439da928", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e7aaf67a1334b1fad955fe8439da928.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e7aaf67a1334b1fad955fe8439da928"}}, "title": "Profiling cancer testis antigens in non-small-cell lung cancer.", "authors": [{"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Horie", "given": "Masafumi", "initials": "M"}, {"family": "Mattsson", "given": "Johanna Sofia Margareta", "initials": "JSM"}, {"family": "La Fleur", "given": "Linnea", "initials": "L"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Madjar", "given": "Katrin", "initials": "K"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "St\u00e5hle", "given": "Elisabeth", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Saito", "given": "Akira", "initials": "A"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2016-07-07", "journal": {"volume": "1", "issn": "2379-3708", "issue": "10", "pages": "e86837", "title": "JCI Insight", "issn-l": "2379-3708"}, "abstract": "Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small-cell lung cancer (NSCLC), we compared RNAseq data from 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the Caner Testis Database (CTdatabase), 96 were confirmed in NSCLC. To obtain an unbiased CTA profile of NSCLC, we applied stringent criteria on our RNAseq data set and defined 90 genes as CTAs, of which 55 genes were not annotated in the CTdatabase, thus representing potential new CTAs. Cluster analysis revealed that CTA expression is histology dependent and concurrent expression is common. IHC confirmed tissue-specific protein expression of selected new CTAs (TKTL1, TGIF2LX, VCX, and CXORF67). Furthermore, methylation was identified as a regulatory mechanism of CTA expression based on independent data from The Cancer Genome Atlas. The proposed prognostic impact of CTAs in lung cancer was not confirmed, neither in our RNAseq cohort nor in an independent meta-analysis of 1,117 NSCLC cases. In summary, we defined a set of 90 reliable CTAs, including information on protein expression, methylation, and survival association. The detailed RNAseq catalog can guide biomarker studies and efforts to identify targets for immunotherapeutic strategies.", "doi": "10.1172/jci.insight.86837", "pmid": "27699219", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "86837"}, {"db": "pmc", "key": "PMC5033889"}], "notes": [], "created": "2017-05-08T07:56:19.862Z", "modified": "2024-01-16T13:48:49.815Z"}, {"entity": "publication", "iuid": "dd6d859f676b4de796fcf2fd433aa840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd6d859f676b4de796fcf2fd433aa840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd6d859f676b4de796fcf2fd433aa840"}}, "title": "Elevated levels of FN1 and CCL2 in bronchoalveolar lavage fluid from sarcoidosis patients.", "authors": [{"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Wiklundh", "given": "Emil", "initials": "E"}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Eklund", "given": "Anders", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "H\u00e4ggmark-M\u00e5nberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-06-04", "journal": {"volume": "17", "issn": "1465-993X", "issue": "1", "pages": "69", "title": "Respir. Res.", "issn-l": "1465-9921"}, "abstract": "Sarcoidosis is a granulomatous systemic inflammatory disease in which more than 90\u00a0% of all patients develop pulmonary manifestations. Several gene associations have previously been described, but established and clinically useful biomarkers are still absent. This study aimed to find proteins in bronchoalveolar lavage (BAL) fluid that can be associated with the disease.\n\nWe developed and performed profiling of 94 selected proteins in BAL fluid and serum samples obtained from newly diagnosed and non-treated patients with sarcoidosis. Using multiplexed immunoassays, a total of 317 BAL and 217 serum samples were analyzed, including asthmatic patients and healthy individuals as controls.\n\nOur analyses revealed increased levels of eight proteins in sarcoidosis patients compared to controls. Out of these, fibronectin (FN1) and C-C motif chemokine 2 (CCL2) revealed the strongest associations. In addition, cadherin 5 (CDH5) was found to correlate positively with lymphocyte cell numbers in BAL fluid.\n\nApplying a high throughput proteomics screening technique, we found proteins of potential clinical relevance in the context of sarcoidosis.", "doi": "10.1186/s12931-016-0381-0", "pmid": "27259755", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12931-016-0381-0"}, {"db": "pmc", "key": "PMC4893268"}], "notes": [], "created": "2017-05-03T12:59:07.765Z", "modified": "2021-07-08T13:44:33.690Z"}, {"entity": "publication", "iuid": "5da8c8b6ed79477ba89c81ae7013ac7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5da8c8b6ed79477ba89c81ae7013ac7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5da8c8b6ed79477ba89c81ae7013ac7f"}}, "title": "Transcriptomics resources of human tissues and\u00a0organs.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2016-04-04", "journal": {"volume": "12", "issn": "1744-4292", "issue": "4", "pages": "862", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome-wide transcriptome analyses of different tissues. Gene expression measurements from these independent datasets, generated using samples from fresh frozen surgical specimens and postmortem tissues, are consistent. Overall, the different genome-wide analyses support a distribution in which many proteins are found in all tissues and relatively few in a tissue-restricted manner. Moreover, we discuss the applications of publicly available omics data for building genome-scale metabolic models, used for analyzing cell and tissue functions both in physiological and in disease contexts.", "doi": "10.15252/msb.20155865", "pmid": "27044256", "labels": {"Systems Biology": "Technology development", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4848759"}], "notes": [], "created": "2017-05-03T12:58:59.635Z", "modified": "2021-07-08T13:44:33.307Z"}, {"entity": "publication", "iuid": "51d03343148f40518927bc37a26e37cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51d03343148f40518927bc37a26e37cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51d03343148f40518927bc37a26e37cd"}}, "title": "Multiplexed protein profiling by sequential affinity capture.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Birgersson", "given": "Elin", "initials": "E"}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "16", "issn": "1615-9861", "issue": "8", "pages": "1251-1256", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off-target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi-automated sequential capture assay. This novel bead-based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read-out by a secondary capture bead array. We demonstrate in a proof-of-concept setting that target detection via two sequential affinity interactions reduced off-target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA-based signal amplification, and demonstrate the applicability of the dual capture bead-based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond.", "doi": "10.1002/pmic.201500398", "pmid": "26935855", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC5071697"}], "notes": [], "created": "2017-05-03T12:59:05.678Z", "modified": "2021-07-08T13:44:33.244Z"}, {"entity": "publication", "iuid": "1fc2070f62c74b61866aa02ca06f973e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fc2070f62c74b61866aa02ca06f973e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fc2070f62c74b61866aa02ca06f973e"}}, "title": "Anoctamin 2 identified as an autoimmune target in multiple sclerosis.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Zandian", "given": "Arash", "initials": "A"}, {"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bredenberg", "given": "Johan", "initials": "J"}, {"family": "Lima Bomfim", "given": "Izaura", "initials": "I"}, {"family": "Holmgren", "given": "Erik", "initials": "E"}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H"}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO"}, {"family": "Abdelmagid", "given": "Nada", "initials": "N"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Waterboer", "given": "Tim", "initials": "T"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2016-02-23", "journal": {"volume": "113", "issn": "1091-6490", "issue": "8", "pages": "2188-2193", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Multiple sclerosis (MS) is the most common chronic inflammatory disease of the central nervous system and also is regarded as an autoimmune condition. However, the antigenic targets of the autoimmune response in MS have not yet been deciphered. In an effort to mine the autoantibody repertoire within MS, we profiled 2,169 plasma samples from MS cases and population-based controls using bead arrays built with 384 human protein fragments selected from an initial screening with 11,520 antigens. Our data revealed prominently increased autoantibody reactivity against the chloride-channel protein anoctamin 2 (ANO2) in MS cases compared with controls. This finding was corroborated in independent assays with alternative protein constructs and by epitope mapping with peptides covering the identified region of ANO2. Additionally, we found a strong interaction between the presence of ANO2 autoantibodies and the HLA complex MS-associated DRB1*15 allele, reinforcing a potential role for ANO2 autoreactivity in MS etiopathogenesis. Furthermore, immunofluorescence analysis in human MS brain tissue showed ANO2 expression as small cellular aggregates near and inside MS lesions. Thus this study represents one of the largest efforts to characterize the autoantibody repertoire within MS. The findings presented here demonstrate that an ANO2 autoimmune subphenotype may exist in MS and lay the groundwork for further studies focusing on the pathogenic role of ANO2 autoantibodies in MS.", "doi": "10.1073/pnas.1518553113", "pmid": "26862169", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1518553113"}, {"db": "pmc", "key": "PMC4776531"}], "notes": [], "created": "2017-05-03T12:59:10.751Z", "modified": "2021-07-08T13:44:33.077Z"}, {"entity": "publication", "iuid": "d852a0e2b7b34fdd8fe46a5d3b682ca7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d852a0e2b7b34fdd8fe46a5d3b682ca7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d852a0e2b7b34fdd8fe46a5d3b682ca7"}}, "title": "The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Habuka", "given": "Masato", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Yamamoto", "given": "Tadashi", "initials": "T"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2015-12-22", "journal": {"volume": "10", "issn": "1932-6203", "issue": "12", "pages": "e0145301", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To understand functions and diseases of urinary bladder, it is important to define its molecular constituents and their roles in urinary bladder biology. Here, we performed genome-wide deep RNA sequencing analysis of human urinary bladder samples and identified genes up-regulated in the urinary bladder by comparing the transcriptome data to those of all other major human tissue types. 90 protein-coding genes were elevated in the urinary bladder, either with enhanced expression uniquely in the urinary bladder or elevated expression together with at least one other tissue (group enriched). We further examined the localization of these proteins by immunohistochemistry and tissue microarrays and 20 of these 90 proteins were localized to the whole urothelium with a majority not yet described in the context of the urinary bladder. Four additional proteins were found specifically in the umbrella cells (Uroplakin 1a, 2, 3a, and 3b), and three in the intermediate/basal cells (KRT17, PCP4L1 and ATP1A4). 61 of the 90 elevated genes have not been previously described in the context of urinary bladder and the corresponding proteins are interesting targets for more in-depth studies. In summary, an integrated omics approach using transcriptomics and antibody-based profiling has been used to define a comprehensive list of proteins elevated in the urinary bladder.", "doi": "10.1371/journal.pone.0145301", "pmid": "26694548", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-11078"}, {"db": "pmc", "key": "PMC4687928"}], "notes": [], "created": "2017-05-02T12:57:10.743Z", "modified": "2021-07-08T13:44:33.679Z"}, {"entity": "publication", "iuid": "eb22b31c5fbe4e418ad14cfd63c28a51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb22b31c5fbe4e418ad14cfd63c28a51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb22b31c5fbe4e418ad14cfd63c28a51"}}, "title": "High levels of WNT-5A in human glioma correlate with increased presence of tumor-associated microglia/monocytes.", "authors": [{"family": "Dijksterhuis", "given": "Jacomijn P", "initials": "JP"}, {"family": "Arthofer", "given": "Elisa", "initials": "E"}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD"}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Frederik", "initials": "F"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schulte", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2015-12-10", "journal": {"title": "Exp. Cell Res.", "issn": "1090-2422", "volume": "339", "issue": "2", "pages": "280-288", "issn-l": "0014-4827"}, "abstract": "Malignant gliomas are among the most severe types of cancer, and the most common primary brain tumors. Treatment options are limited and the prognosis is poor. WNT-5A, a member of the WNT family of lipoglycoproteins, plays a role in oncogenesis and tumor progression in various cancers, whereas the role of WNT-5A in glioma remains obscure. Based on the role of WNT-5A as an oncogene, its potential to regulate microglia cells and the glioma-promoting capacities of microglia cells, we hypothesize that WNT-5A has a role in regulation of immune functions in glioma. We investigated WNT-5A expression by in silico analysis of the cancer genome atlas (TCGA) transcript profiling of human glioblastoma samples and immunohistochemistry experiments of human glioma tissue microarrays (TMA). Our results reveal higher WNT-5A protein levels and mRNA expression in a subgroup of gliomas (WNT-5A(high)) compared to non-malignant control brain tissue. Furthermore, we show a significant correlation between WNT-5A in the tumor and presence of major histocompatibility complex Class II-positive microglia/monocytes. Our data pinpoint a positive correlation between WNT-5A and a proinflammatory signature in glioma. We identify increased presence of microglia/monocytes as an important aspect in the inflammatory transformation suggesting a novel role for WNT-5A in human glioma.", "doi": "10.1016/j.yexcr.2015.10.022", "pmid": "26511503", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0014-4827(15)30133-6"}], "notes": [], "created": "2017-11-05T12:57:27.403Z", "modified": "2021-07-08T13:44:33.711Z"}, {"entity": "publication", "iuid": "042bd68daa014d59b178e63954eac1ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/042bd68daa014d59b178e63954eac1ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/042bd68daa014d59b178e63954eac1ad"}}, "title": "Immunocapture strategies in translational proteomics.", "authors": [{"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2015-11-11", "journal": {"volume": "13", "issn": "1744-8387", "issue": "1", "pages": "83-98", "title": "Expert Rev Proteomics", "issn-l": "1478-9450"}, "abstract": "Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.", "doi": "10.1586/14789450.2016.1111141", "pmid": "26558424", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4732419"}], "notes": [], "created": "2017-05-02T12:56:45.584Z", "modified": "2021-07-08T13:44:32.996Z"}, {"entity": "publication", "iuid": "599626457fda4ba3b2d8135ec113c389", "links": {"self": {"href": "https://publications.scilifelab.se/publication/599626457fda4ba3b2d8135ec113c389.json"}, "display": {"href": "https://publications.scilifelab.se/publication/599626457fda4ba3b2d8135ec113c389"}}, "title": "The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Olovsson", "given": "Matts", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Oskarsson", "given": "Linda", "initials": "L"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Tolf", "given": "Anna", "initials": "A"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "19", "issn": "1557-8100", "issue": "11", "pages": "659-668", "title": "OMICS", "issn-l": "1536-2310"}, "abstract": "The human uterus includes the complex endometrial mucosa, the endometrium that undergoes dynamic, hormone-dependent alterations throughout the life of fertile females. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to analyze gene expression patterns in the normal endometrium. Human endometrial tissues from five women were used for deep sequencing (RNA-Seq). The mRNA and protein expression data from the endometrium were compared to 31 (RNA) and 44 (protein) other normal tissue types, to identify genes with elevated expression in the endometrium and to localize the expression of corresponding proteins at a cellular resolution. Based on the expression levels of transcripts, we could classify all putative human protein coding genes into categories defined by expression patterns and found altogether 101 genes that showed an elevated pattern of expression in the endometrium, with only four genes showing more than five-fold higher expression levels in the endometrium compared to other tissues. In conclusion, our analysis based on transcriptomics and antibody-based protein profiling reports here comprehensive lists of genes with elevated expression levels in the endometrium, providing important starting points for a better molecular understanding of human reproductive biology and disease.", "doi": "10.1089/omi.2015.0115", "pmid": "26488136", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:59:02.026Z", "modified": "2021-07-08T13:44:33.285Z"}, {"entity": "publication", "iuid": "c4b1ba70725c46388e85498a2f5b63c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4b1ba70725c46388e85498a2f5b63c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4b1ba70725c46388e85498a2f5b63c0"}}, "title": "Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.", "authors": [{"family": "Huang", "given": "Mingtao", "initials": "M"}, {"family": "Bai", "given": "Yunpeng", "initials": "Y"}, {"family": "Sjostrom", "given": "Staffan L", "initials": "SL"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Liu", "given": "Zihe", "initials": "Z"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Joensson", "given": "Haakan N", "initials": "HN"}, {"family": "Andersson-Svahn", "given": "Helene", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2015-08-25", "journal": {"volume": "112", "issn": "1091-6490", "issue": "34", "pages": "E4689-E4696", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "There is an increasing demand for biotech-based production of recombinant proteins for use as pharmaceuticals in the food and feed industry and in industrial applications. Yeast Saccharomyces cerevisiae is among preferred cell factories for recombinant protein production, and there is increasing interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV mutagenesis. Several screening and sorting rounds resulted in the selection of eight yeast clones with significantly improved secretion of recombinant \u03b1-amylase. Efficient secretion was genetically stable in the selected clones. We performed whole-genome sequencing of the eight clones and identified 330 mutations in total. Gene ontology analysis of mutated genes revealed many biological processes, including some that have not been identified before in the context of protein secretion. Mutated genes identified in this study can be potentially used for reverse metabolic engineering, with the objective to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could broadly facilitate design of novel cell factories.", "doi": "10.1073/pnas.1506460112", "pmid": "26261321", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1506460112"}, {"db": "pmc", "key": "PMC4553813"}], "notes": [], "created": "2017-05-02T12:57:19.915Z", "modified": "2021-07-08T13:44:33.607Z"}, {"entity": "publication", "iuid": "9d58f3908ade4e4f9c9db7643ece3ee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d58f3908ade4e4f9c9db7643ece3ee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d58f3908ade4e4f9c9db7643ece3ee7"}}, "title": "Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.", "authors": [{"family": "Yu", "given": "Nancy Yiu-Lin", "initials": "NY", "orcid": "0000-0001-8321-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7b0ebe0de64edca6546aff2292c376.json"}}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Kawaji", "given": "Hideya", "initials": "H"}, {"family": "Carninci", "given": "Piero", "initials": "P"}, {"family": "Forrest", "given": "Alistair R R", "initials": "AR"}, {"family": "Fantom Consortium", "given": "", "initials": ""}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}], "type": "evaluation study", "published": "2015-08-18", "journal": {"volume": "43", "issn": "1362-4962", "issue": "14", "pages": "6787-6798", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.", "doi": "10.1093/nar/gkv608", "pmid": "26117540", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gkv608"}, {"db": "pmc", "key": "PMC4538815"}], "notes": [], "created": "2017-05-02T12:59:00.235Z", "modified": "2021-07-08T13:44:33.475Z"}, {"entity": "publication", "iuid": "a17590f906c24e878725bc0543917772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a17590f906c24e878725bc0543917772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a17590f906c24e878725bc0543917772"}}, "title": "Heat differentiated complement factor profiling.", "authors": [{"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Skattum", "given": "Lillemor", "initials": "L"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "von D\u00f6beln", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Neiman", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2015-08-03", "journal": {"volume": "126", "issn": "1876-7737", "issue": null, "pages": "155-162", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Complement components and their cascade of reactions are important defense mechanisms within both innate and adaptive immunity. Many complement deficient patients still remain undiagnosed because of a lack of high throughput screening tools. Aiming towards neonatal proteome screening for immunodeficiencies, we used a multiplex profiling approach with antibody bead arrays to measure 9 complement proteins in serum and dried blood spots. Several complement components have been described as heat sensitive, thus their heat-dependent detectability was investigated. Using sera from 16 patients with complement deficiencies and 23 controls, we confirmed that the proteins C1q, C2, C3, C6, C9 and factor H were positively affected by heating, thus the identification of deficient patients was improved when preheating samples. Measurements of C7, C8 and factor I were negatively affected by heating and non-heated samples should be used in analysis of these components. In addition, a proof of concept study demonstrated the feasibility of labeling eluates from dried blood spots to perform a subsequent correct classification of C2-deficiencies. Our study demonstrates the potential of using multiplexed single binder assays for screening of complement components that open possibilities to expand such analysis to other forms of deficiencies.", "doi": "10.1016/j.jprot.2015.05.027", "pmid": "26047714", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1874-3919(15)30029-4"}], "notes": [], "created": "2017-05-02T12:56:42.050Z", "modified": "2021-07-08T13:44:33.492Z"}, {"entity": "publication", "iuid": "a9ab16991ce84822a4ab77925fc8528c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9ab16991ce84822a4ab77925fc8528c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9ab16991ce84822a4ab77925fc8528c"}}, "title": "Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.", "authors": [{"family": "O'Hurley", "given": "Gillian", "initials": "G"}, {"family": "Busch", "given": "Christer", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Tolf", "given": "Anna", "initials": "A"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-08-03", "journal": {"volume": "10", "issn": "1932-6203", "issue": "8", "pages": "e0133449", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To better understand prostate function and disease, it is important to define and explore the molecular constituents that signify the prostate gland. The aim of this study was to define the prostate specific transcriptome and proteome, in comparison to 26 other human tissues. Deep sequencing of mRNA (RNA-seq) and immunohistochemistry-based protein profiling were combined to identify prostate specific gene expression patterns and to explore tissue biomarkers for potential clinical use in prostate cancer diagnostics. We identified 203 genes with elevated expression in the prostate, 22 of which showed more than five-fold higher expression levels compared to all other tissue types. In addition to previously well-known proteins we identified two poorly characterized proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. In conclusion, we have applied a genome-wide analysis to identify the prostate specific proteome using transcriptomics and antibody-based protein profiling to identify genes with elevated expression in the prostate. Our data provides a starting point for further functional studies to explore the molecular repertoire of normal and diseased prostate including potential prostate cancer markers such as TMEM79 and ACOXL.", "doi": "10.1371/journal.pone.0133449", "pmid": "26237329", "labels": {"NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "Spatial Proteomics": null, "Affinity Proteomics Stockholm": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-13741"}, {"db": "pmc", "key": "PMC4523174"}], "notes": [], "created": "2017-05-02T12:57:06.092Z", "modified": "2021-07-08T13:44:33.508Z"}, {"entity": "publication", "iuid": "c43f0bab915c4d528cd487794cf3c8d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c43f0bab915c4d528cd487794cf3c8d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c43f0bab915c4d528cd487794cf3c8d2"}}, "title": "The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Linn\u00e9", "given": "Jerker", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}, {"family": "Lindholm", "given": "Malene", "initials": "M"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Choi", "given": "Howard", "initials": "H"}, {"family": "Liem", "given": "David A", "initials": "DA"}, {"family": "Ping", "given": "Peipei", "initials": "P"}, {"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2015-06-25", "journal": {"volume": "16", "issn": "1471-2164", "issue": null, "pages": "475", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level.\n\nOur study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction.\n\nOur results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.", "doi": "10.1186/s12864-015-1686-y", "pmid": "26109061", "labels": {"Tissue Profiling": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-015-1686-y"}, {"db": "pmc", "key": "PMC4479346"}, {"db": "GEO", "key": "GSE58387"}, {"db": "GEO", "key": "GSE58608"}], "notes": [], "created": "2017-05-02T12:57:51.478Z", "modified": "2021-07-08T13:44:33.602Z"}, {"entity": "publication", "iuid": "b019e78a23ef453e9060d6188198a6c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b019e78a23ef453e9060d6188198a6c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b019e78a23ef453e9060d6188198a6c2"}}, "title": "Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2015-06-15", "journal": {"volume": "10", "issn": "1932-6203", "issue": "6", "pages": "e0130028", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The mammalian brain is a complex organ composed of many specialized cells, harboring sets of both common, widely distributed, as well as specialized and discretely localized proteins. Here we focus on the human brain, utilizing transcriptomics and public available Human Protein Atlas (HPA) data to analyze brain-enriched (frontal cortex) polyadenylated messenger RNA and long non-coding RNA and generate a genome-wide draft of global and cellular expression patterns of the brain. Based on transcriptomics analysis of altogether 27 tissues, we have estimated that approximately 3% (n=571) of all protein coding genes and 13% (n=87) of the long non-coding genes expressed in the human brain are enriched, having at least five times higher expression levels in brain as compared to any of the other analyzed peripheral tissues. Based on gene ontology analysis and detailed annotation using antibody-based tissue micro array analysis of the corresponding proteins, we found the majority of brain-enriched protein coding genes to be expressed in astrocytes, oligodendrocytes or in neurons with molecular properties linked to synaptic transmission and brain development. Detailed analysis of the transcripts and the genetic landscape of brain-enriched coding and non-coding genes revealed brain-enriched splice variants. Several clusters of neighboring brain-enriched genes were also identified, suggesting regulation of gene expression on the chromatin level. This multi-angle approach uncovered the brain-enriched transcriptome and linked genes to cell types and functions, providing novel insights into the molecular foundation of this highly specialized organ.", "doi": "10.1371/journal.pone.0130028", "pmid": "26076492", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-09576"}, {"db": "pmc", "key": "PMC4468152"}, {"db": "ArrayExpress", "description": "sequences", "key": "E-MTAB-1733"}], "notes": [], "created": "2017-05-02T12:58:34.528Z", "modified": "2021-07-08T13:44:33.530Z"}, {"entity": "publication", "iuid": "fafdd20822164209a31bc80ea150967e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fafdd20822164209a31bc80ea150967e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fafdd20822164209a31bc80ea150967e"}}, "title": "Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma.", "authors": [{"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Huvila", "given": "Jutta", "initials": "J"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Talve", "given": "Lauri", "initials": "L"}, {"family": "Carp\u00e9n", "given": "Olli", "initials": "O"}, {"family": "Salvesen", "given": "Helga B", "initials": "HB"}, {"family": "Krakstad", "given": "Camilla", "initials": "C"}, {"family": "Gr\u00e9nman", "given": "Seija", "initials": "S"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Ljungqvist", "given": "Oscar", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Auranen", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2015-06-00", "journal": {"volume": "137", "issn": "1095-6859", "issue": "3", "pages": "529-537", "title": "Gynecol. Oncol.", "issn-l": "0090-8258"}, "abstract": "For endometrial carcinoma, prognostic stratification methods do not satisfactorily identify patients with adverse outcome. Currently, histology, tumor grade and stage are used to tailoring surgical treatment and to determine the need for adjuvant treatment. Low-risk patients are not considered to require adjuvant therapy or staging lymphadenectomy. For patients with intermediate or high risk, some guidelines recommend tailoring adjuvant treatment according to additional negative prognostic factors. Our objective was to evaluate the biomarker potential of the ASRGL1 protein in endometrial carcinoma.\n\nUsing The Human Protein Atlas (www.proteinatlas.org), the l-asparaginase (ASRGL1) protein was identified as an endometrial carcinoma biomarker candidate. ASRGL1 expression was immunohistochemically evaluated with an extensively validated antibody on two independent endometrial carcinoma cohorts (n=229 and n=286) arranged as tissue microarrays. Staining results were correlated with clinical features.\n\nReduced expression of ASRGL1, defined as <75% positively stained tumor cells, was significantly associated with poor prognosis and reduced disease-specific survival in endometrioid endometrial adenocarcinoma (EEA). In multivariate analysis the hazard ratios for disease-specific survival were 3.55 (95% CI=1.10-11.43; p=0.003) and 3.23 (95% CI=1.53-6.81; p=0.002) in the two cohorts, respectively. Of the 48 cases with Grade 3 Stage I tumor all disease-related deaths were associated with low ASRGL1 expression.\n\nLoss of ASRGL1 in EEA is a powerful biomarker for poor prognosis and retained ASRGL1 has a positive impact on survival. ASRGL1 immunohistochemistry has potential to become an additional tool for prognostication in cases where tailoring adjuvant treatment according to additional prognostic factors besides grade and stage is recommended.", "doi": "10.1016/j.ygyno.2015.03.055", "pmid": "25858696", "labels": {"Tissue Profiling": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0090-8258(15)00783-0"}], "notes": [], "created": "2017-11-05T13:01:35.585Z", "modified": "2021-07-08T13:44:33.761Z"}, {"entity": "publication", "iuid": "9b379261e5574a0cbfc364715c570bfc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b379261e5574a0cbfc364715c570bfc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b379261e5574a0cbfc364715c570bfc"}}, "title": "Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "63", "issn": "1551-5044", "issue": "2", "pages": "129-141", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "To increase our understanding of skin, it is important to define the molecular constituents of the cell types and epidermal layers that signify normal skin. We have combined a genome-wide transcriptomics analysis, using deep sequencing of mRNA from skin biopsies, with immunohistochemistry-based protein profiling to characterize the landscape of gene and protein expression in normal human skin. The transcriptomics and protein expression data of skin were compared to 26 (RNA) and 44 (protein) other normal tissue types. All 20,050 putative protein-coding genes were classified into categories based on patterns of expression. We found that 417 genes showed elevated expression in skin, with 106 genes expressed at least five-fold higher than that in other tissues. The 106 genes categorized as skin enriched encoded for well-known proteins involved in epidermal differentiation and proteins with unknown functions and expression patterns in skin, including the C1orf68 protein, which showed the highest relative enrichment in skin. In conclusion, we have applied a genome-wide analysis to identify the human skin-specific proteome and map the precise localization of the corresponding proteins in different compartments of the skin, to facilitate further functional studies to explore the molecular repertoire of normal skin and to identify biomarkers related to various skin diseases.", "doi": "10.1369/0022155414562646", "pmid": "25411189", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "0022155414562646"}, {"db": "pmc", "key": "PMC4305515"}], "notes": [], "created": "2017-05-02T12:56:54.324Z", "modified": "2021-07-08T13:44:33.465Z"}, {"entity": "publication", "iuid": "3777a5cd8954424fb426f5163d4d01bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3777a5cd8954424fb426f5163d4d01bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3777a5cd8954424fb426f5163d4d01bf"}}, "title": "Proteomics. Tissue-based map of the human proteome.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Olsson", "given": "IngMarie", "initials": "I"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Alm", "given": "Tove", "initials": "T"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Persson", "given": "Lukas", "initials": "L"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-01-23", "journal": {"volume": "347", "issn": "1095-9203", "issue": "6220", "pages": "1260419", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.", "doi": "10.1126/science.1260419", "pmid": "25613900", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "347/6220/1260419"}], "notes": [], "created": "2017-05-02T12:58:49.180Z", "modified": "2023-11-21T16:24:57.712Z"}, {"entity": "publication", "iuid": "5babb8d9418f48e1aad7bca526c93fd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5babb8d9418f48e1aad7bca526c93fd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5babb8d9418f48e1aad7bca526c93fd3"}}, "title": "A secretagogin locus of the mammalian hypothalamus controls stress hormone release.", "authors": [{"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Alp\u00e1r", "given": "Al\u00e1n", "initials": "A"}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Calas", "given": "Andr\u00e9", "initials": "A"}, {"family": "Landry", "given": "Marc", "initials": "M"}, {"family": "Fuszard", "given": "Matthew", "initials": "M"}, {"family": "Shirran", "given": "Sally L", "initials": "SL"}, {"family": "Schnell", "given": "Robert", "initials": "R"}, {"family": "Dobolyi", "given": "\u00c1rp\u00e1d", "initials": "\u00c1"}, {"family": "Ol\u00e1h", "given": "M\u00e1rk", "initials": "M"}, {"family": "Spence", "given": "Lauren", "initials": "L"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Martens", "given": "Henrik", "initials": "H"}, {"family": "Palkovits", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Sitte", "given": "Harald H", "initials": "HH"}, {"family": "Botting", "given": "Catherine H", "initials": "CH"}, {"family": "Wagner", "given": "Ludwig", "initials": "L"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}], "type": "journal article", "published": "2015-01-02", "journal": {"volume": "34", "issn": "1460-2075", "issue": "1", "pages": "36-54", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "A hierarchical hormonal cascade along the hypothalamic-pituitary-adrenal axis orchestrates bodily responses to stress. Although corticotropin-releasing hormone (CRH), produced by parvocellular neurons of the hypothalamic paraventricular nucleus (PVN) and released into the portal circulation at the median eminence, is known to prime downstream hormone release, the molecular mechanism regulating phasic CRH release remains poorly understood. Here, we find a cohort of parvocellular cells interspersed with magnocellular PVN neurons expressing secretagogin. Single-cell transcriptome analysis combined with protein interactome profiling identifies secretagogin neurons as a distinct CRH-releasing neuron population reliant on secretagogin's Ca(2+) sensor properties and protein interactions with the vesicular traffic and exocytosis release machineries to liberate this key hypothalamic releasing hormone. Pharmacological tools combined with RNA interference demonstrate that secretagogin's loss of function occludes adrenocorticotropic hormone release from the pituitary and lowers peripheral corticosterone levels in response to acute stress. Cumulatively, these data define a novel secretagogin neuronal locus and molecular axis underpinning stress responsiveness.", "doi": "10.15252/embj.201488977", "pmid": "25430741", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "embj.201488977"}, {"db": "pmc", "key": "PMC4291479"}], "notes": [], "created": "2017-05-04T14:55:19.558Z", "modified": "2021-07-08T13:44:33.302Z"}, {"entity": "publication", "iuid": "8eb8153ee920494d99bb060da3ba565a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8eb8153ee920494d99bb060da3ba565a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8eb8153ee920494d99bb060da3ba565a"}}, "title": "The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.", "authors": [{"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Wanders", "given": "Alkwin", "initials": "A"}, {"family": "Cedernaes", "given": "Jonathan", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-01-00", "journal": {"volume": "50", "issn": "1435-5922", "issue": "1", "pages": "46-57", "title": "J. Gastroenterol.", "issn-l": "0944-1174"}, "abstract": "The gastrointestinal tract (GIT) is subdivided into different anatomical organs with many shared functions and characteristics, but also distinct differences. We have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to describe the gene and protein expression patterns that define the human GIT.\n\nRNA sequencing data derived from stomach, duodenum, jejunum/ileum and colon specimens were compared to gene expression levels in 23 other normal human tissues analysed with the same method. Protein profiling based on immunohistochemistry and tissue microarrays was used to sub-localize the corresponding proteins with GIT-specific expression into sub-cellular compartments and cell types.\n\nApproximately 75% of all human protein-coding genes were expressed in at least one of the GIT tissues. Only 51 genes showed enriched expression in either one of the GIT tissues and an additional 83 genes were enriched in two or more GIT tissues. The list of GIT-enriched genes with validated protein expression patterns included various well-known but also previously uncharacterised or poorly studied genes. For instance, the colon-enriched expression of NXPE family member 1 (NXPE1) was established, while NLR family, pyrin domain-containing 6 (NLRP6) expression was primarily found in the human small intestine.\n\nWe have applied a genome-wide analysis based on transcriptomics and antibody-based protein profiling to identify genes that are expressed in a specific manner within the human GIT. These genes and proteins constitute important starting points for an improved understanding of the normal function and the different states of disease associated with the GIT.", "doi": "10.1007/s00535-014-0958-7", "pmid": "24789573", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:08.698Z", "modified": "2021-07-08T13:44:33.417Z"}, {"entity": "publication", "iuid": "bbad5325f0ff401b8c54f97df23d3c7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbad5325f0ff401b8c54f97df23d3c7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbad5325f0ff401b8c54f97df23d3c7f"}}, "title": "The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Hellwig", "given": "Birte", "initials": "B"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2014-12-00", "journal": {"volume": "28", "issn": "1530-6860", "issue": "12", "pages": "5184-5196", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "The combined action of multiple cell types is essential for the physiological function of the lung, and increased awareness of the molecular constituents characterizing each cell type is likely to advance the understanding of lung biology and disease. In the current study, we used genome-wide RNA sequencing of normal lung parenchyma and 26 additional tissue types, combined with antibody-based protein profiling, to localize the expression to specific cell types. Altogether, 221 genes were found to be elevated in the lung compared with their expression in other analyzed tissues. Among the gene products were several well-known markers, but also several proteins previously not described in the context of the lung. To link the lung-specific molecular repertoire to human disease, survival associations of pneumocyte-specific genes were assessed by using transcriptomics data from 7 non-small-cell lung cancer (NSCLC) cohorts. Transcript levels of 10 genes (SFTPB, SFTPC, SFTPD, SLC34A2, LAMP3, CACNA2D2, AGER, EMP2, NKX2-1, and NAPSA) were significantly associated with survival in the adenocarcinoma subgroup, thus qualifying as promising biomarker candidates. In summary, based on an integrated omics approach, we identified genes with elevated expression in lung and localized corresponding protein expression to different cell types. As biomarker candidates, these proteins may represent intriguing starting points for further exploration in health and disease.", "doi": "10.1096/fj.14-254862", "pmid": "25169055", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "fj.14-254862"}], "notes": [], "created": "2017-05-04T14:56:05.381Z", "modified": "2021-07-08T13:44:33.564Z"}, {"entity": "publication", "iuid": "25565c8cb6d2410bbf72e122aebc4349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25565c8cb6d2410bbf72e122aebc4349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25565c8cb6d2410bbf72e122aebc4349"}}, "title": "Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2014-11-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "11", "pages": "5106-5119", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "White adipose tissue (WAT) has a major role in the progression of obesity. Here, we combined data from RNA-Seq and antibody-based immunohistochemistry to describe the normal physiology of human WAT obtained from three female subjects and explored WAT-specific genes by comparing WAT to 26 other major human tissues. Using the protein evidence in WAT, we validated the content of a genome-scale metabolic model for adipocytes. We employed this high-quality model for the analysis of subcutaneous adipose tissue (SAT) gene expression data obtained from subjects included in the Swedish Obese Subjects Sib Pair study to reveal molecular differences between lean and obese individuals. We integrated SAT gene expression and plasma metabolomics data, investigated the contribution of the metabolic differences in the mitochondria of SAT to the occurrence of obesity, and eventually identified cytosolic branched-chain amino acid (BCAA) transaminase 1 as a potential target that can be used for drug development. We observed decreased glutaminolysis and alterations in the BCAAs metabolism in SAT of obese subjects compared to lean subjects. We also provided mechanistic explanations for the changes in the plasma level of BCAAs, glutamate, pyruvate, and \u03b1-ketoglutarate in obese subjects. Finally, we validated a subset of our model-based predictions in 20 SAT samples obtained from 10 lean and 10 obese male and female subjects.", "doi": "10.1021/pr500586e", "pmid": "25219818", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:07.093Z", "modified": "2021-07-08T13:44:33.100Z"}, {"entity": "publication", "iuid": "d25e8eeba2b9401a99f09ce2238e2a9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d25e8eeba2b9401a99f09ce2238e2a9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d25e8eeba2b9401a99f09ce2238e2a9f"}}, "title": "Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.", "authors": [{"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Amor", "given": "Sandra", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2014-11-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "11", "pages": "4607-4619", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.", "doi": "10.1021/pr500609e", "pmid": "25231264", "labels": {"Fluorescence Tissue Profiling": null, "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:19.857Z", "modified": "2021-07-08T13:44:33.645Z"}, {"entity": "publication", "iuid": "9b8a235e5dbf47648b747e04e2210661", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b8a235e5dbf47648b747e04e2210661.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b8a235e5dbf47648b747e04e2210661"}}, "title": "Defining the human gallbladder proteome by transcriptomics and affinity proteomics.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "21-22", "pages": "2498-2507", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics.", "doi": "10.1002/pmic.201400201", "pmid": "25175928", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:10.318Z", "modified": "2021-07-08T13:44:33.470Z"}, {"entity": "publication", "iuid": "41358535cb1f4aa1afc24a14e5bbd90b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41358535cb1f4aa1afc24a14e5bbd90b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41358535cb1f4aa1afc24a14e5bbd90b"}}, "title": "Analysis of candidate genes for lineage-specific expression changes in humans and primates.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M"}, {"family": "Davierwala", "given": "Armaity", "initials": "A"}, {"family": "Fu", "given": "Ning", "initials": "N"}, {"family": "Hegde", "given": "Geeta", "initials": "G"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "P\u00e4\u00e4bo", "given": "Svante", "initials": "S"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-08-01", "journal": {"volume": "13", "issn": "1535-3907", "issue": "8", "pages": "3596-3606", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "RUNX2, a gene involved in skeletal development, has previously been shown to be potentially affected by positive selection during recent human evolution. Here we have used antibody-based proteomics to characterize potential differences in expression patterns of RUNX2 interacting partners during primate evolution. Tissue microarrays consisting of a large set of normal tissues from human and macaque were used for protein profiling of 50 RUNX2 partners with immunohistochemistry. Eleven proteins (AR, CREBBP, EP300, FGF2, HDAC3, JUN, PRKD3, RUNX1, SATB2, TCF3, and YAP1) showed differences in expression between humans and macaques. These proteins were further profiled in tissues from chimpanzee, gorilla, and orangutan, and the corresponding genes were analyzed with regard to genomic features. Moreover, protein expression data were compared with previously obtained RNA sequencing data from six different organs. One gene (TCF3) showed significant expression differences between human and macaque at both the protein and RNA level, with higher expression in a subset of germ cells in human testis compared with macaque. In conclusion, normal tissues from macaque and human showed differences in expression of some RUNX2 partners that could be mapped to various defined cell types. The applied strategy appears advantageous to characterize the consequences of altered genes selected during evolution.", "doi": "10.1021/pr500045f", "pmid": "24911366", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:07.393Z", "modified": "2021-07-08T13:44:33.185Z"}, {"entity": "publication", "iuid": "7667c1109ce844e994cca622ff027fa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7667c1109ce844e994cca622ff027fa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7667c1109ce844e994cca622ff027fa5"}}, "title": "Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mikus", "given": "Maria", "initials": "M"}, {"family": "Mohsenchian", "given": "Atefeh", "initials": "A"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gajewska", "given": "Beata", "initials": "B"}, {"family": "Bara\u0144czyk-Ku\u017ama", "given": "Anna", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ku\u017ama-Kozakiewicz", "given": "Magdalena", "initials": "M"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "1", "issn": "2328-9503", "issue": "8", "pages": "544-553", "title": "Ann Clin Transl Neurol", "issn-l": "2328-9503"}, "abstract": "Amyotrophic lateral sclerosis (ALS) is the most common adult motor neuron disease leading to muscular paralysis and death within 3-5 years from onset. Currently, there are no reliable and sensitive markers able to substantially shorten the diagnosis delay. The objective of the study was to analyze a large number of proteins in plasma from patients with various clinical phenotypes of ALS in search for novel proteins or protein profiles that could serve as potential indicators of disease.\r\n\r\nAffinity proteomics in the form of antibody suspension bead arrays were applied to profile plasma samples from 367 ALS patients and 101 controls. The plasma protein content was directly labeled and protein profiles obtained using 352 antibodies from the Human Protein Atlas targeting 278 proteins. A focused bead array was then built to further profile eight selected protein targets in all available samples.\r\n\r\nDisease-associated significant differences were observed and replicated for profiles from antibodies targeting the proteins: neurofilament medium polypeptide (NEFM), solute carrier family 25 (SLC25A20), and regulator of G-protein signaling 18 (RGS18).\r\n\r\nUpon further validation in several independent cohorts with inclusion of a broad range of other neurological disorders as controls, the alterations of these three protein profiles in plasma could potentially provide new molecular markers of disease that contribute to the quest of understanding ALS pathology.", "doi": "10.1002/acn3.83", "pmid": "25356426", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC4184557"}], "notes": [], "created": "2017-05-04T14:55:39.286Z", "modified": "2021-07-08T13:44:33.363Z"}, {"entity": "publication", "iuid": "abbffa2b72424f4ea317a691b4554caa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abbffa2b72424f4ea317a691b4554caa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abbffa2b72424f4ea317a691b4554caa"}}, "title": "Peroxiredoxin-1 protects estrogen receptor \u03b1 from oxidative stress-induced suppression and is a protein biomarker of favorable prognosis in breast cancer.", "authors": [{"family": "O'Leary", "given": "Patrick C", "initials": "PC"}, {"family": "Terrile", "given": "Marta", "initials": "M"}, {"family": "Bajor", "given": "Malgorzata", "initials": "M"}, {"family": "Gaj", "given": "Pawel", "initials": "P"}, {"family": "Hennessy", "given": "Bryan T", "initials": "BT"}, {"family": "Mills", "given": "Gordon B", "initials": "GB"}, {"family": "Zagozdzon", "given": "Agnieszka", "initials": "A"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Connor", "given": "Kate", "initials": "K"}, {"family": "Li", "given": "Jane", "initials": "J"}, {"family": "Gonzalez-Angulo", "given": "Ana Maria", "initials": "AM"}, {"family": "Sun", "given": "Han-Dong", "initials": "HD"}, {"family": "Pu", "given": "Jian-Xin", "initials": "JX"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Nowis", "given": "Dominika A", "initials": "DA"}, {"family": "Crown", "given": "John P", "initials": "JP"}, {"family": "Zagozdzon", "given": "Radoslaw", "initials": "R"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}], "type": "journal article", "published": "2014-07-10", "journal": {"volume": "16", "issn": "1465-542X", "issue": "4", "pages": "R79", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "Peroxiredoxin-1 (PRDX1) is a multifunctional protein, acting as a hydrogen peroxide (H2O2) scavenger, molecular chaperone and immune modulator. Although differential PRDX1 expression has been described in many tumors, the potential role of PRDX1 in breast cancer remains highly ambiguous. Using a comprehensive antibody-based proteomics approach, we interrogated PRDX1 protein as a putative biomarker in estrogen receptor (ER)-positive breast cancer.\n\nAn anti-PRDX1 antibody was validated in breast cancer cell lines using immunoblotting, immunohistochemistry and reverse phase protein array (RPPA) technology. PRDX1 protein expression was evaluated in two independent breast cancer cohorts, represented on a screening RPPA (n = 712) and a validation tissue microarray (n = 498). In vitro assays were performed exploring the functional contribution of PRDX1, with oxidative stress conditions mimicked via treatment with H2O2, peroxynitrite, or adenanthin, a PRDX1/2 inhibitor.\n\nIn ER-positive cases, high PRDX1 protein expression is a biomarker of improved prognosis across both cohorts. In the validation cohort, high PRDX1 expression was an independent predictor of improved relapse-free survival (hazard ratio (HR) = 0.62, 95% confidence interval (CI) = 0.40 to 0.96, P = 0.032), breast cancer-specific survival (HR = 0.44, 95% CI = 0.24 to 0.79, P = 0.006) and overall survival (HR = 0.61, 95% CI = 0.44 to 0.85, P = 0.004). RPPA screening of cancer signaling proteins showed that ER\u03b1 protein was upregulated in PRDX1 high tumors. Exogenous H2O2 treatment decreased ER\u03b1 protein levels in ER-positive cells. PRDX1 knockdown further sensitized cells to H2O2- and peroxynitrite-mediated effects, whilst PRDX1 overexpression protected against this response. Inhibition of PRDX1/2 antioxidant activity with adenanthin dramatically reduced ER\u03b1 levels in breast cancer cells.\n\nPRDX1 is shown to be an independent predictor of improved outcomes in ER-positive breast cancer. Through its antioxidant function, PRDX1 may prevent oxidative stress-mediated ER\u03b1 loss, thereby potentially contributing to maintenance of an ER-positive phenotype in mammary tumors. These results for the first time imply a close connection between biological activity of PRDX1 and regulation of estrogen-mediated signaling in breast cancer.", "doi": "10.1186/bcr3691", "pmid": "25011585", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "bcr3691"}, {"db": "pmc", "key": "PMC4226972"}], "notes": [], "created": "2017-05-04T14:56:03.723Z", "modified": "2021-07-08T13:44:33.519Z"}, {"entity": "publication", "iuid": "1f7684007f4544b08926f588ccbd5296", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f7684007f4544b08926f588ccbd5296.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f7684007f4544b08926f588ccbd5296"}}, "title": "The human liver-specific proteome defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-07-00", "journal": {"volume": "28", "issn": "1530-6860", "issue": "7", "pages": "2901-2914", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "Human liver physiology and the genetic etiology of the liver diseases can potentially be elucidated through the identification of proteins with enriched expression in the liver. Here, we combined data from RNA sequencing (RNA-Seq) and antibody-based immunohistochemistry across all major human tissues to explore the human liver proteome with enriched expression, as well as the cell type-enriched expression in hepatocyte and bile duct cells. We identified in total 477 protein-coding genes with elevated expression in the liver: 179 genes have higher expression as compared to all the other analyzed tissues; 164 genes have elevated transcript levels in the liver shared with at least one other tissue type; and an additional 134 genes have a mild level of increased expression in the liver. We identified the precise localization of these proteins through antibody-based protein profiling and the subcellular localization of these proteins through immunofluorescent-based profiling. We also identified the biological processes and metabolic functions associated with these proteins, investigated their contribution in the occurrence of liver diseases, and identified potential targets for their treatment. Our study demonstrates the use of RNA-Seq and antibody-based immunohistochemistry for characterizing the human liver proteome, as well as the use of tissue-specific proteins in identification of novel drug targets and discovery of biomarkers.-Kampf, C., Mardinoglu, A., Fagerberg, L., Hallstr\u00f6m, B. M., Edlund, K., Lundberg, E., Pont\u00e9n, F., Nielsen, J., Uhlen, M. The human liver-specific proteome defined by transcriptomics and antibody-based profiling.", "doi": "10.1096/fj.14-250555", "pmid": "24648543", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "fj.14-250555"}], "notes": [], "created": "2017-05-04T14:55:15.921Z", "modified": "2021-07-08T13:44:33.071Z"}, {"entity": "publication", "iuid": "c2f170156b274272b4560b2dc5dc14b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2f170156b274272b4560b2dc5dc14b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2f170156b274272b4560b2dc5dc14b1"}}, "title": "Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Chaouch", "given": "Amina", "initials": "A"}, {"family": "Lochm\u00fcller", "given": "Hanns", "initials": "H"}, {"family": "Politano", "given": "Luisa", "initials": "L"}, {"family": "Bertini", "given": "Enrico", "initials": "E"}, {"family": "Spitali", "given": "Pietro", "initials": "P"}, {"family": "Hiller", "given": "Monika", "initials": "M"}, {"family": "Niks", "given": "Eric H", "initials": "EH"}, {"family": "Gualandi", "given": "Francesca", "initials": "F"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Bushby", "given": "Kate", "initials": "K"}, {"family": "Aartsma-Rus", "given": "Annemieke", "initials": "A"}, {"family": "Schwartz", "given": "Elena", "initials": "E"}, {"family": "Le Priol", "given": "Yannick", "initials": "Y"}, {"family": "Straub", "given": "Volker", "initials": "V"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Cirak", "given": "Sebahattin", "initials": "S"}, {"family": "'t Hoen", "given": "Peter A C", "initials": "PAC"}, {"family": "Muntoni", "given": "Francesco", "initials": "F"}, {"family": "Ferlini", "given": "Alessandra", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}], "type": "journal article", "published": "2014-07-00", "journal": {"volume": "6", "issn": "1757-4684", "issue": "7", "pages": "918-936", "title": "EMBO Mol Med", "issn-l": "1757-4676"}, "abstract": "Despite the recent progress in the broad-scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA). Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies.", "doi": "10.15252/emmm.201303724", "pmid": "24920607", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "emmm.201303724"}, {"db": "pmc", "key": "PMC4119355"}], "notes": [], "created": "2017-05-04T14:55:39.591Z", "modified": "2021-07-08T13:44:33.596Z"}, {"entity": "publication", "iuid": "3653dadad4754b7a8e2865919a0685d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3653dadad4754b7a8e2865919a0685d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3653dadad4754b7a8e2865919a0685d7"}}, "title": "Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Bostr\u00f6m", "given": "Tove", "initials": "T"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Zeiler", "given": "Marlis", "initials": "M"}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "6", "pages": "1611-1624", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The combination of immuno-based methods and mass spectrometry detection has great potential in the field of quantitative proteomics. Here, we describe a new method (immuno-SILAC) for the absolute quantification of proteins in complex samples based on polyclonal antibodies and stable isotope-labeled recombinant protein fragments to allow affinity enrichment prior to mass spectrometry analysis and accurate quantification. We took advantage of the antibody resources publicly available from the Human Protein Atlas project covering more than 80% of all human protein-coding genes. Epitope mapping revealed that a majority of the polyclonal antibodies recognized multiple linear epitopes, and based on these results, a semi-automated method was developed for peptide enrichment using polyclonal antibodies immobilized on protein A-coated magnetic beads. A protocol based on the simultaneous multiplex capture of more than 40 protein targets showed that approximately half of the antibodies enriched at least one functional peptide detected in the subsequent mass spectrometry analysis. The approach was further developed to also generate quantitative data via the addition of heavy isotope-labeled recombinant protein fragment standards prior to trypsin digestion. Here, we show that we were able to use small amounts of antibodies (50 ng per target) in this manner for efficient multiplex analysis of quantitative levels of proteins in a human HeLa cell lysate. The results suggest that polyclonal antibodies generated via immunization of recombinant protein fragments could be used for the enrichment of target peptides to allow for rapid mass spectrometry analysis taking advantage of a substantial reduction in sample complexity. The possibility of building up a proteome-wide resource for immuno-SILAC assays based on publicly available antibody resources is discussed.", "doi": "10.1074/mcp.M113.034140", "pmid": "24722731", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M113.034140"}, {"db": "pmc", "key": "PMC4047479"}], "notes": [], "created": "2017-05-04T14:55:17.123Z", "modified": "2021-07-08T13:44:33.140Z"}, {"entity": "publication", "iuid": "6435089b8b354ebf812b692036692fab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6435089b8b354ebf812b692036692fab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6435089b8b354ebf812b692036692fab"}}, "title": "Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.", "authors": [{"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Axn\u00e4s", "given": "Barbara Bis\u0142awska", "initials": "BB"}, {"family": "Stengele", "given": "Klaus-Peter", "initials": "K"}, {"family": "B\u00fchler", "given": "Jochen", "initials": "J"}, {"family": "Albert", "given": "Thomas J", "initials": "TJ"}, {"family": "Richmond", "given": "Todd A", "initials": "TA"}, {"family": "Hu", "given": "Francis Jingxin", "initials": "FJ"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "6", "pages": "1585-1597", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Antibodies are of importance for the field of proteomics, both as reagents for imaging cells, tissues, and organs and as capturing agents for affinity enrichment in mass-spectrometry-based techniques. It is important to gain basic insights regarding the binding sites (epitopes) of antibodies and potential cross-reactivity to nontarget proteins. Knowledge about an antibody's linear epitopes is also useful in, for instance, developing assays involving the capture of peptides obtained from trypsin cleavage of samples prior to mass spectrometry analysis. Here, we describe, for the first time, the design and use of peptide arrays covering all human proteins for the analysis of antibody specificity, based on parallel in situ photolithic synthesis of a total of 2.1 million overlapping peptides. This has allowed analysis of on- and off-target binding of both monoclonal and polyclonal antibodies, complemented with precise mapping of epitopes based on full amino acid substitution scans. The analysis suggests that linear epitopes are relatively short, confined to five to seven residues, resulting in apparent off-target binding to peptides corresponding to a large number of unrelated human proteins. However, subsequent analysis using recombinant proteins suggests that these linear epitopes have a strict conformational component, thus giving us new insights regarding how antibodies bind to their antigens.", "doi": "10.1074/mcp.M113.033308", "pmid": "24705123", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "M113.033308"}, {"db": "pmc", "key": "PMC4047477"}], "notes": [], "created": "2017-05-04T14:55:39.895Z", "modified": "2021-07-08T13:44:33.318Z"}, {"entity": "publication", "iuid": "78c3ad5a0d7e42e5a6a81a16e47c965f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78c3ad5a0d7e42e5a6a81a16e47c965f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78c3ad5a0d7e42e5a6a81a16e47c965f"}}, "title": "The human testis-specific proteome defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Djureinovic", "given": "D", "initials": "D"}, {"family": "Fagerberg", "given": "L", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "B", "initials": "B"}, {"family": "Danielsson", "given": "A", "initials": "A"}, {"family": "Lindskog", "given": "C", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "F", "initials": "F"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "20", "issn": "1460-2407", "issue": "6", "pages": "476-488", "title": "Mol. Hum. Reprod.", "issn-l": "1360-9947"}, "abstract": "The testis' function is to produce haploid germ cells necessary for reproduction. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to characterize the molecular components of the testis. Deep sequencing (RNA-Seq) of normal human testicular tissue from seven individuals was performed and compared with 26 other normal human tissue types. All 20 050 putative human genes were classified into categories based on expression patterns. The analysis shows that testis is the tissue with the most tissue-specific genes by far. More than 1000 genes show a testis-enriched expression pattern in testis when compared with all other analyzed tissues. Highly testis enriched genes were further characterized with respect to protein localization within the testis, such as spermatogonia, spermatocytes, spermatids, sperm, Sertoli cells and Leydig cells. Here we present an immunohistochemistry-based analysis, showing the localization of corresponding proteins in different cell types and various stages of spermatogenesis, for 62 genes expressed at >50-fold higher levels in testis when compared with other tissues. A large fraction of these genes were unexpectedly expressed in early stages of spermatogenesis. In conclusion, we have applied a genome-wide analysis to identify the human testis-specific proteome using transcriptomics and antibody-based protein profiling, providing lists of genes expressed in a tissue-enriched manner in the testis. The majority of these genes and proteins were previously poorly characterised in terms of localization and function, and our list provides an important starting point to increase our molecular understanding of human reproductive biology and disease.", "doi": "10.1093/molehr/gau018", "pmid": "24598113", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gau018"}], "notes": [], "created": "2017-05-04T14:56:08.213Z", "modified": "2021-07-08T13:44:33.374Z"}, {"entity": "publication", "iuid": "0b1cdeccb7ce4053b281d23616c5542d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b1cdeccb7ce4053b281d23616c5542d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b1cdeccb7ce4053b281d23616c5542d"}}, "title": "The role of SATB2 as a diagnostic marker for tumors of colorectal origin: Results of a pathology-based clinical prospective study.", "authors": [{"family": "Dragomir", "given": "Anca", "initials": "A"}, {"family": "de Wit", "given": "Meike", "initials": "M"}, {"family": "Johansson", "given": "Christine", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-05-00", "journal": {"volume": "141", "issn": "1943-7722", "issue": "5", "pages": "630-638", "title": "Am. J. Clin. Pathol.", "issn-l": "0002-9173"}, "abstract": "Immunohistochemistry is an important extension to clinical information and morphology, and prevails as an invaluable tool for establishing a correct cancer diagnosis in clinical diagnostic pathology. The applicability of immunohistochemistry is limited by the availability of validated cell- and cancer-type specific antibodies, rendering an unmet need to discover, test, and validate novel markers. The SATB2 protein is selectively expressed in glandular cells from the lower gastrointestinal tract and expression is retained in a large majority of primary and metastatic colorectal cancers.\n\nWe analyzed the expression of SATB2 in all clinical cases (n = 840), in which immunohistochemistry for detection of CK20 was deemed necessary for a final diagnosis.\n\nSATB2 showed a high sensitivity (93%) and specificity (77%) to determine a cancer of colorectal origin and in combination with CK7 and CK20, the specificity increased to 100%.\n\nWe conclude that SATB2 provides a new and advantageous supplement for clinical differential diagnostics.", "doi": "10.1309/AJCPWW2URZ9JKQJU", "pmid": "24713733", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "141/5/630"}], "notes": [], "created": "2017-05-04T14:56:03.201Z", "modified": "2021-07-08T13:44:33.008Z"}, {"entity": "publication", "iuid": "17bfb81127154e4d930e93dd1461bbbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17bfb81127154e4d930e93dd1461bbbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17bfb81127154e4d930e93dd1461bbbf"}}, "title": "RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-04-04", "journal": {"volume": "13", "issn": "1535-3907", "issue": "4", "pages": "2019-2027", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "An important part of the Human Proteome Project is to characterize the protein complement of the genome with antibody-based profiling. Within the framework of this effort, a new version 12 of the Human Protein Atlas ( www.proteinatlas.org ) has been launched, including transcriptomics data for 27 tissues and 44 cell lines to complement the protein expression data from antibody-based profiling. Besides the extensive addition of transcriptomics data, the Human Protein Atlas now contains antibody-based protein profiles for 82% of the 20\u2009329 putative protein-coding genes. The comprehensive data resulting from RNA-seq analysis and antibody-based profiling performed within the Human Protein Atlas as well as information from UniProt were used to generate evidence summary scores for each of the 20\u2009329 genes, of which 94% now have experimental evidence at least at transcript level. The evidence scores for all individual genes are displayed with regards to both RNA- and antibody-based protein profiles, including chromosome-centric visualizations. An analysis of the human chromosome 19 shows that \u223c43% of the genes are expressed at the transcript level in all 27 tissues analyzed, suggesting a \"house-keeping\" function, while 12% of the genes show a more tissue-specific pattern with enriched expression in one of the analyzed tissues only.", "doi": "10.1021/pr401156g", "pmid": "24579871", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:16.817Z", "modified": "2021-07-08T13:44:33.044Z"}, {"entity": "publication", "iuid": "f368c76367db4f02886060683e16b0dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f368c76367db4f02886060683e16b0dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f368c76367db4f02886060683e16b0dc"}}, "title": "Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.", "authors": [{"family": "Bachmann", "given": "Julie", "initials": "J"}, {"family": "Burt\u00e9", "given": "Florence", "initials": "F"}, {"family": "Pramana", "given": "Setia", "initials": "S"}, {"family": "Conte", "given": "Ianina", "initials": "I"}, {"family": "Brown", "given": "Biobele J", "initials": "BJ"}, {"family": "Orimadegun", "given": "Adebola E", "initials": "AE"}, {"family": "Ajetunmobi", "given": "Wasiu A", "initials": "WA"}, {"family": "Afolabi", "given": "Nathaniel K", "initials": "NK"}, {"family": "Akinkunmi", "given": "Francis", "initials": "F"}, {"family": "Omokhodion", "given": "Samuel", "initials": "S"}, {"family": "Akinbami", "given": "Felix O", "initials": "FO"}, {"family": "Shokunbi", "given": "Wuraola A", "initials": "WA"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Sodeinde", "given": "Olugbemiro", "initials": "O"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}, {"family": "Fernandez-Reyes", "given": "Delmiro", "initials": "D"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2014-04-00", "journal": {"volume": "10", "issn": "1553-7374", "issue": "4", "pages": "e1004038", "title": "PLoS Pathog.", "issn-l": "1553-7366"}, "abstract": "Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.", "doi": "10.1371/journal.ppat.1004038", "pmid": "24743550", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PPATHOGENS-D-13-01973"}, {"db": "pmc", "key": "PMC3990714"}], "notes": [], "created": "2017-05-04T14:55:40.729Z", "modified": "2021-07-08T13:44:33.732Z"}, {"entity": "publication", "iuid": "c513eea994a04816b2264dd96388abfe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c513eea994a04816b2264dd96388abfe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c513eea994a04816b2264dd96388abfe"}}, "title": "Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury.", "authors": [{"family": "Zhang", "given": "Ming-Dong", "initials": "MD"}, {"family": "Tortoriello", "given": "Giuseppe", "initials": "G"}, {"family": "Hsueh", "given": "Brian", "initials": "B"}, {"family": "Tomer", "given": "Raju", "initials": "R"}, {"family": "Ye", "given": "Li", "initials": "L"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Borgius", "given": "Lotta", "initials": "L"}, {"family": "Grant", "given": "Gunnar", "initials": "G"}, {"family": "Kiehn", "given": "Ole", "initials": "O"}, {"family": "Watanabe", "given": "Masahiko", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Deisseroth", "given": "Karl", "initials": "K"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "H\u00f6kfelt", "given": "Tomas G M", "initials": "TG"}], "type": "journal article", "published": "2014-03-25", "journal": {"volume": "111", "issn": "1091-6490", "issue": "12", "pages": "E1149-E1158", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Neuronal calcium (Ca(2+))-binding proteins 1 and 2 (NECAB1/2) are members of the phylogenetically conserved EF-hand Ca(2+)-binding protein superfamily. To date, NECABs have been explored only to a limited extent and, so far, not at all at the spinal level. Here, we describe the distribution, phenotype, and nerve injury-induced regulation of NECAB1/NECAB2 in mouse dorsal root ganglia (DRGs) and spinal cord. In DRGs, NECAB1/2 are expressed in around 70% of mainly small- and medium-sized neurons. Many colocalize with calcitonin gene-related peptide and isolectin B4, and thus represent nociceptors. NECAB1/2 neurons are much more abundant in DRGs than the Ca(2+)-binding proteins (parvalbumin, calbindin, calretinin, and secretagogin) studied to date. In the spinal cord, the NECAB1/2 distribution is mainly complementary. NECAB1 labels interneurons and a plexus of processes in superficial layers of the dorsal horn, commissural neurons in the intermediate area, and motor neurons in the ventral horn. Using CLARITY, a novel, bilaterally connected neuronal system with dendrites that embrace the dorsal columns like palisades is observed. NECAB2 is present in cell bodies and presynaptic boutons across the spinal cord. In the dorsal horn, most NECAB1/2 neurons are glutamatergic. Both NECAB1/2 are transported into dorsal roots and peripheral nerves. Peripheral nerve injury reduces NECAB2, but not NECAB1, expression in DRG neurons. Our study identifies NECAB1/2 as abundant Ca(2+)-binding proteins in pain-related DRG neurons and a variety of spinal systems, providing molecular markers for known and unknown neuron populations of mechanosensory and pain circuits in the spinal cord.", "doi": "10.1073/pnas.1402318111", "pmid": "24616509", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1402318111"}, {"db": "pmc", "key": "PMC3970515"}], "notes": [], "created": "2017-05-04T14:55:20.159Z", "modified": "2021-07-08T13:44:33.613Z"}, {"entity": "publication", "iuid": "d5deec6089364dd88b311d8ae8be6954", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5deec6089364dd88b311d8ae8be6954.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5deec6089364dd88b311d8ae8be6954"}}, "title": "Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling.", "authors": [{"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2014-03-19", "journal": {"volume": "10", "issn": "1744-4292", "issue": null, "pages": "721", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Genome-scale metabolic models (GEMs) have proven useful as scaffolds for the integration of omics data for understanding the genotype-phenotype relationship in a mechanistic manner. Here, we evaluated the presence/absence of proteins encoded by 15,841 genes in 27 hepatocellular carcinoma (HCC) patients using immunohistochemistry. We used this information to reconstruct personalized GEMs for six HCC patients based on the proteomics data, HMR 2.0, and a task-driven model reconstruction algorithm (tINIT). The personalized GEMs were employed to identify anticancer drugs using the concept of antimetabolites; i.e., drugs that are structural analogs to metabolites. The toxicity of each antimetabolite was predicted by assessing the in silico functionality of 83 healthy cell type-specific GEMs, which were also reconstructed with the tINIT algorithm. We predicted 101 antimetabolites that could be effective in preventing tumor growth in all HCC patients, and 46 antimetabolites which were specific to individual patients. Twenty-two of the 101 predicted antimetabolites have already been used in different cancer treatment strategies, while the remaining antimetabolites represent new potential drugs. Finally, one of the identified targets was validated experimentally, and it was confirmed to attenuate growth of the HepG2 cell line.", "doi": "10.1002/msb.145122", "pmid": "24646661", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pmc", "key": "PMC4017677"}], "notes": [], "created": "2017-05-04T14:56:08.814Z", "modified": "2021-07-08T13:44:33.663Z"}, {"entity": "publication", "iuid": "339c9ba893c04cf19331effac10c05e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/339c9ba893c04cf19331effac10c05e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/339c9ba893c04cf19331effac10c05e7"}}, "title": "A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.", "authors": [{"family": "Alm", "given": "Tove", "initials": "T"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-03-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "3", "pages": "1669-1676", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Antibodies are crucial for the study of human proteins and have been defined as one of the three pillars in the human chromosome-centric Human Proteome Project (C-HPP). In this article the chromosome-centric structure has been used to analyze the availability of antibodies as judged by the presence within the portal Antibodypedia, a database designed to allow comparisons and scoring of publicly available antibodies toward human protein targets. This public database displays antibody data from more than one million antibodies toward human protein targets. A summary of the content in this knowledge resource reveals that there exist more than 10 antibodies to over 70% of all the putative human genes, evenly distributed over the 24 human chromosomes. The analysis also shows that at present, less than 10% of the putative human protein-coding genes (n = 1882) predicted from the genome sequence lack antibodies, suggesting that focused efforts from the antibody-based and mass spectrometry-based proteomic communities should be encouraged to pursue the analysis of these missing proteins. We show that Antibodypedia may be used to track the development of available and validated antibodies to the individual chromosomes, and thus the database is an attractive tool to identify proteins with no or few antibodies yet generated.", "doi": "10.1021/pr4011525", "pmid": "24533432", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:16.221Z", "modified": "2021-07-08T13:44:33.129Z"}, {"entity": "publication", "iuid": "fbcceacdc948469eb9a2de32a539d258", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbcceacdc948469eb9a2de32a539d258.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbcceacdc948469eb9a2de32a539d258"}}, "title": "Molecular- and organelle-based predictive paradigm underlying recovery by left ventricular assist device support.", "authors": [{"family": "Liem", "given": "David A", "initials": "DA"}, {"family": "Nsair", "given": "Ali", "initials": "A"}, {"family": "Setty", "given": "Shaun P", "initials": "SP"}, {"family": "Cadeiras", "given": "Martin", "initials": "M"}, {"family": "Wang", "given": "Ding", "initials": "D"}, {"family": "Maclellan", "given": "Robb", "initials": "R"}, {"family": "Lotz", "given": "Chris", "initials": "C"}, {"family": "Lin", "given": "Amanda J", "initials": "AJ"}, {"family": "Tabaraki", "given": "Jason", "initials": "J"}, {"family": "Li", "given": "Hua", "initials": "H"}, {"family": "Ge", "given": "Junbo", "initials": "J"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Larson", "given": "Erik", "initials": "E"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Weiss", "given": "James N", "initials": "JN"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ping", "given": "Peipei", "initials": "P"}, {"family": "Deng", "given": "Mario C", "initials": "MC"}], "type": "journal article", "published": "2014-03-01", "journal": {"volume": "7", "issn": "1941-3297", "issue": "2", "pages": "359-366", "title": "Circ Heart Fail", "issn-l": "1941-3289"}, "abstract": null, "doi": "10.1161/CIRCHEARTFAILURE.113.000250", "pmid": "24643888", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "CIRCHEARTFAILURE.113.000250"}, {"db": "pmc", "key": "PMC4397259"}, {"db": "mid", "key": "NIHMS557965"}], "notes": [], "created": "2017-05-04T14:55:15.619Z", "modified": "2021-07-08T13:44:33.773Z"}, {"entity": "publication", "iuid": "c0034e9a600646e7ae016f0897affcba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0034e9a600646e7ae016f0897affcba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0034e9a600646e7ae016f0897affcba"}}, "title": "Antibody performance in western blot applications is context-dependent.", "authors": [{"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Agaton", "given": "Charlotta", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Bj\u00f6rling", "given": "Erik", "initials": "E"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Persson", "given": "Anja", "initials": "A"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wern\u00e9rus", "given": "Henrik", "initials": "H"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ottosson Takanen", "given": "Jenny", "initials": "J"}, {"family": "Hober", "given": "Sophia", "initials": "S"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "9", "issn": "1860-7314", "issue": "3", "pages": "435-445", "title": "Biotechnol J", "issn-l": "1860-6768"}, "abstract": "An important concern for the use of antibodies in various applications, such as western blot (WB) or immunohistochemistry (IHC), is specificity. This calls for systematic validations using well-designed conditions. Here, we have analyzed 13\u2009000 antibodies using western blot with lysates from human cell lines, tissues, and plasma. Standardized stratification showed that 45% of the antibodies yielded supportive staining, and the rest either no staining (12%) or protein bands of wrong size (43%). A comparative study of WB and IHC showed that the performance of antibodies is application-specific, although a correlation between no WB staining and weak IHC staining could be seen. To investigate the influence of protein abundance on the apparent specificity of the antibody, new WB analyses were performed for 1369 genes that gave unsupportive WBs in the initial screening using cell lysates with overexpressed full-length proteins. Then, more than 82% of the antibodies yielded a specific band corresponding to the full-length protein. Hence, the vast majority of the antibodies (90%) used in this study specifically recognize the target protein when present at sufficiently high levels. This demonstrates the context- and application-dependence of antibody validation and emphasizes that caution is needed when annotating binding reagents as specific or cross-reactive. WB is one of the most commonly used methods for validation of antibodies. Our data implicate that solely using one platform for antibody validation might give misleading information and therefore at least one additional method should be used to verify the achieved data.", "doi": "10.1002/biot.201300341", "pmid": "24403002", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:15.317Z", "modified": "2021-07-08T13:44:33.580Z"}, {"entity": "publication", "iuid": "ef02a7c09ee04259ad9d5d188407e72e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef02a7c09ee04259ad9d5d188407e72e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef02a7c09ee04259ad9d5d188407e72e"}}, "title": "Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis", "authors": [{"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "O\u2019Hurley", "given": "Gillian", "initials": "G"}, {"family": "Branca", "given": "Rui", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal-article", "published": "2014-03-00", "journal": {"volume": "2", "issn": "2212-9626", "issue": null, "pages": "14-24", "title": "Translational Proteomics", "issn-l": null}, "abstract": null, "doi": "10.1016/j.trprot.2013.12.001", "pmid": null, "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:41.613Z", "modified": "2021-07-08T12:12:51.627Z"}, {"entity": "publication", "iuid": "25fee1b507254b40b328c5dd1a7f3ce2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25fee1b507254b40b328c5dd1a7f3ce2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25fee1b507254b40b328c5dd1a7f3ce2"}}, "title": "Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Habuka", "given": "Masato", "initials": "M"}, {"family": "Tahmasebpoor", "given": "Simin", "initials": "S"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Olsson", "given": "IngMarie", "initials": "I"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-02-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "2", "pages": "397-406", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to \u223c80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.", "doi": "10.1074/mcp.M113.035600", "pmid": "24309898", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Autoimmunity and Serology Profiling": "Technology development", "Spatial Proteomics": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "M113.035600"}, {"db": "pmc", "key": "PMC3916642"}], "notes": [], "created": "2017-05-04T14:55:17.424Z", "modified": "2021-07-08T13:44:33.111Z"}, {"entity": "publication", "iuid": "54e26e482cb24dc7af06502b2d69948a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e26e482cb24dc7af06502b2d69948a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e26e482cb24dc7af06502b2d69948a"}}, "title": "Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "comparative study", "published": "2014-01-15", "journal": {"volume": "5", "issn": "2041-1723", "issue": null, "pages": "3083", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Several liver disorders result from perturbations in the metabolism of hepatocytes, and their underlying mechanisms can be outlined through the use of genome-scale metabolic models (GEMs). Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an extensive description of lipid metabolism. We build iHepatocytes2322 using Human Metabolic Reaction 2.0 database and proteomics data in Human Protein Atlas, which experimentally validates the incorporated reactions. The reconstruction process enables improved annotation of the proteomics data using the network centric view of iHepatocytes2322. We then use iHepatocytes2322 to analyse transcriptomics data obtained from patients with non-alcoholic fatty liver disease. We show that blood concentrations of chondroitin and heparan sulphates are suitable for diagnosing non-alcoholic steatohepatitis and for the staging of non-alcoholic fatty liver disease. Furthermore, we observe serine deficiency in patients with NASH and identify PSPH, SHMT1 and BCAT1 as potential therapeutic targets for the treatment of non-alcoholic steatohepatitis.", "doi": "10.1038/ncomms4083", "pmid": "24419221", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "ncomms4083"}], "notes": [], "created": "2017-05-04T14:56:09.113Z", "modified": "2021-07-08T13:44:33.268Z"}, {"entity": "publication", "iuid": "4ac0bfc8e0b94f23abd7acdc37be06f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ac0bfc8e0b94f23abd7acdc37be06f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ac0bfc8e0b94f23abd7acdc37be06f3"}}, "title": "A systematic analysis of commonly used antibodies in cancer diagnostics.", "authors": [{"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Maindad", "given": "Vikas", "initials": "V"}, {"family": "Bharambe", "given": "Bhavana M", "initials": "BM"}, {"family": "Khan", "given": "Wasif Ali Z A", "initials": "WA"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Elebro", "given": "Jacob", "initials": "J"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Hellberg", "given": "Dan", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-01-00", "journal": {"volume": "64", "issn": "1365-2559", "issue": "2", "pages": "293-305", "title": "Histopathology", "issn-l": "0309-0167"}, "abstract": "Immunohistochemistry plays a pivotal role in cancer differential diagnostics. To identify the primary tumour from a metastasis specimen remains a significant challenge, despite the availability of an increasing number of antibodies. The aim of the present study was to provide evidence-based data on the diagnostic power of antibodies used frequently for clinical differential diagnostics.\n\nA tissue microarray cohort comprising 940 tumour samples, of which 502 were metastatic lesions, representing tumours from 18 different organs and four non-localized cancer types, was analysed using immunohistochemistry with 27 well-established antibodies used in clinical differential diagnostics. Few antibodies, e.g. prostate-specific antigen and thyroglobulin, showed a cancer type-related sensitivity and specificity of more than 95%. A majority of the antibodies showed a low degree of sensitivity and specificity for defined cancer types. Combinations of antibodies provided limited added value for differential diagnostics of cancer types.\n\nThe results from analysing 27 diagnostic antibodies on consecutive sections of 940 defined tumours provide a unique repository of data that can empower a more optimal use of clinical immunohistochemistry. Our results highlight the benefit of immunohistochemistry and the unmet need for novel markers to improve differential diagnostics of cancer.", "doi": "10.1111/his.12255", "pmid": "24330150", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:58.649Z", "modified": "2021-07-08T13:44:33.223Z"}, {"entity": "publication", "iuid": "e2c12498a4ee40849faac3f32a0dfe51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2c12498a4ee40849faac3f32a0dfe51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2c12498a4ee40849faac3f32a0dfe51"}}, "title": "Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.", "authors": [{"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "M"}, {"family": "Tybring", "given": "Gunnel", "initials": "G"}, {"family": "Divers", "given": "Mark", "initials": "M"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "clinical trial", "published": "2013-12-16", "journal": {"volume": "95", "issn": "1876-7737", "issue": null, "pages": "46-54", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Several biobanking initiatives have emerged to create extensive collections of specimen for biomedical studies and various analytical platforms. An affinity proteomic analysis with antibody suspension bead arrays was conducted to investigate the influence of the pre-analytical time and temperature conditions on blood derived samples. Serum and EDTA plasma prepared from 16 individuals was centrifuged and aliquots were kept either at 4\u00b0C or in ambient temperature for 1h and up to 36h prior to first storage. Multiplexed protein profiles of post-centrifugation delay were generated in 384 biotinylated samples using 373 antibodies that targeted 343 unique proteins. Very few profiles were observed as significantly altered by the studied temperature and time intervals. Single binder and sandwich assays revealed decreasing levels of caldesmon 1 (CALD1) related to EDTA standard tubes and prolonged post-centrifugation delay of 36h. Indications from changes in CALD1 levels require further confirmation in independent material, but the current data suggests that samples should preferentially be frozen during the day of collection when to be profiled with antibody arrays selected for this study.\r\n\r\nAffinity-based profiling of serum and plasma by microarray assays can provide unique opportunities for the discovery of biomarkers. It is though often not known how differences in sample handling after collection influence the downstream analysis. By profiling three types of blood preparations for alterations in protein profiles with respect to time and temperature post centrifugation, we addressed an important component in the analysis and of such specimen. We believe that this analysis adds valuable information to be considered when biobanking blood derived samples. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.", "doi": "10.1016/j.jprot.2013.04.020", "pmid": "23631827", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1874-3919(13)00209-1"}], "notes": [], "created": "2017-05-04T14:55:37.485Z", "modified": "2021-07-08T13:44:33.695Z"}, {"entity": "publication", "iuid": "87e3d2bb0d5442fe9c4911cc26f86f2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e3d2bb0d5442fe9c4911cc26f86f2f"}}, "title": "Selectivity analysis of single binder assays used in plasma protein profiling.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "23-24", "pages": "3406-3410", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The increasing availability of antibodies toward human proteins enables broad explorations of the proteomic landscape in cells, tissues, and body fluids. This includes assays with antibody suspension bead arrays that generate protein profiles of plasma samples by flow cytometer analysis. However, antibody selectivity is context dependent so it is necessary to corroborate on-target detection over off-target binding. To address this, we describe a concept to directly verify interactions from antibody-coupled beads by analysis of their eluates by Western blots and MS. We demonstrate selective antibody binding in complex samples with antibodies toward a set of chosen proteins with different abundance in plasma and serum, and illustrate the need to adjust sample and bead concentrations accordingly. The presented approach will serve as an important tool for resolving differential protein profiles from antibody arrays within plasma biomarker discoveries.", "doi": "10.1002/pmic.201300030", "pmid": "24151238", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4265267"}], "notes": [], "created": "2017-05-04T14:55:38.987Z", "modified": "2021-07-08T13:44:33.385Z"}, {"entity": "publication", "iuid": "946ff156ff6d4f3da475a7dd36b2ec55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/946ff156ff6d4f3da475a7dd36b2ec55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/946ff156ff6d4f3da475a7dd36b2ec55"}}, "title": "Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.", "authors": [{"family": "Anfelt", "given": "Josefine", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2013-12-00", "journal": {"volume": "79", "issn": "1098-5336", "issue": "23", "pages": "7419-7427", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host.", "doi": "10.1128/AEM.02694-13", "pmid": "24056459", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "AEM.02694-13"}, {"db": "pmc", "key": "PMC3837751"}], "notes": [], "created": "2017-05-04T14:57:48.179Z", "modified": "2021-07-08T13:44:33.438Z"}, {"entity": "publication", "iuid": "f867fad229be45769f13368f45cf3d6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f867fad229be45769f13368f45cf3d6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f867fad229be45769f13368f45cf3d6a"}}, "title": "FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.", "authors": [{"family": "Gardberg", "given": "Maria", "initials": "M"}, {"family": "Kaipio", "given": "Katja", "initials": "K"}, {"family": "Lehtinen", "given": "Laura", "initials": "L"}, {"family": "Mikkonen", "given": "Piia", "initials": "P"}, {"family": "Heuser", "given": "Vanina D", "initials": "VD"}, {"family": "Talvinen", "given": "Kati", "initials": "K"}, {"family": "Iljin", "given": "Kristiina", "initials": "K"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gr\u00e9nman", "given": "Reidar", "initials": "R"}, {"family": "Koivisto", "given": "Mari", "initials": "M"}, {"family": "Carp\u00e9n", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2013-09-26", "journal": {"volume": "8", "issn": "1932-6203", "issue": "9", "pages": "e74923", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Cancer cells can obtain their ability to invade and metastasise by undergoing epithelial-to-mesenchymal transition (EMT). Exploiting this mechanism of cellular plasticity, malignant cells can remodel their actin cytoskeleton and down-regulate proteins needed for cell-cell contacts. The mechanisms of cytoskeletal reorganisation resulting in mesenchymal morphology and increased invasive potential are poorly understood. Actin nucleating formins have been implicated as key players in EMT. Here, we analysed which formins are altered in squamous cell carcinoma related EMT. FHOD1, a poorly studied formin, appeared to be markedly upregulated upon EMT. In human tissues FHOD1 was primarily expressed in mesenchymal cells, with little expression in epithelia. However, specimens from oral squamous cell cancers demonstrated consistent FHOD1 upregulation in mesenchymally transformed cells at the invasive edge. This upregulation was confirmed in an oral squamous carcinoma model, where FHOD1 expression was markedly increased upon EMT in a PI3K signalling dependent manner. In the EMT cells FHOD1 contributed to the spindle-shaped morphology and mesenchymal F-actin organization. Furthermore, functional assays demonstrated that FHOD1 contributes to cell migration and invasion. Finally, FHOD1 depletion reduced the ability of EMT cancer cells to form invadopodia and to degrade extracellular matrix. Our results indicate that FHOD1 participates in cytoskeletal changes in EMT. In addition, we show that FHOD1 upregulation occurs during cancer cell EMT in vivo, which indicates that FHOD1 may contribute to tumour progression.", "doi": "10.1371/journal.pone.0074923", "pmid": "24086398", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-15073"}, {"db": "pmc", "key": "PMC3784416"}], "notes": [], "created": "2017-05-04T14:56:02.087Z", "modified": "2021-07-08T13:44:33.750Z"}, {"entity": "publication", "iuid": "0d26cf1338444ca88be5a65923130cb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d26cf1338444ca88be5a65923130cb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d26cf1338444ca88be5a65923130cb5"}}, "title": "Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2013-09-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "9", "pages": "2657-2672", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing \u223c38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.", "doi": "10.1074/mcp.M112.026757", "pmid": "23732997", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "M112.026757"}, {"db": "pmc", "key": "PMC3769337"}], "notes": [], "created": "2017-05-04T14:55:38.084Z", "modified": "2021-07-08T13:44:33.014Z"}, {"entity": "publication", "iuid": "135f821176884e3480bb7c2a8062b568", "links": {"self": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568.json"}, "display": {"href": "https://publications.scilifelab.se/publication/135f821176884e3480bb7c2a8062b568"}}, "title": "Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Bystr\u00f6m", "given": "Sanna", "initials": "S"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Qundos", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2013-08-00", "journal": {"volume": "13", "issn": "1615-9861", "issue": "15", "pages": "2256-2267", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.", "doi": "10.1002/pmic.201200580", "pmid": "23696371", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:38.686Z", "modified": "2021-07-08T13:44:33.026Z"}, {"entity": "publication", "iuid": "b866fb216f3d4d56ae6d8df86a91b97d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b866fb216f3d4d56ae6d8df86a91b97d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b866fb216f3d4d56ae6d8df86a91b97d"}}, "title": "CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer.", "authors": [{"family": "Cepeda", "given": "Diana", "initials": "D"}, {"family": "Ng", "given": "Hwee-Fang", "initials": "HF"}, {"family": "Sharifi", "given": "Hamid Reza", "initials": "HR"}, {"family": "Mahmoudi", "given": "Salah", "initials": "S"}, {"family": "Cerrato", "given": "Vanessa Soto", "initials": "VS"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "Nilsson", "given": "Hel\u00e9n", "initials": "H"}, {"family": "Malyukova", "given": "Alena", "initials": "A"}, {"family": "Rantala", "given": "Juha", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Vi\u00f1als", "given": "Francesc", "initials": "F"}, {"family": "Bhaskaran", "given": "Nimesh", "initials": "N"}, {"family": "Zakaria", "given": "Siti Mariam", "initials": "SM"}, {"family": "Rahmanto", "given": "Aldwin Suryo", "initials": "AS"}, {"family": "Grotegut", "given": "Stefan", "initials": "S"}, {"family": "Nielsen", "given": "Michael Lund", "initials": "ML"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Sun", "given": "Dahui", "initials": "D"}, {"family": "Lerner", "given": "Mikael", "initials": "M"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Widschwendter", "given": "Martin", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wohlschlegel", "given": "James", "initials": "J"}, {"family": "Grand\u00e9r", "given": "Dan", "initials": "D"}, {"family": "Spruck", "given": "Charles", "initials": "C"}, {"family": "Larsson", "given": "Lars-Gunnar", "initials": "LG"}, {"family": "Sangfelt", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2013-07-00", "journal": {"volume": "5", "issn": "1757-4684", "issue": "7", "pages": "1067-1086", "title": "EMBO Mol Med", "issn-l": "1757-4676"}, "abstract": "SCF (Skp1/Cul1/F-box) ubiquitin ligases act as master regulators of cellular homeostasis by targeting key proteins for ubiquitylation. Here, we identified a hitherto uncharacterized F-box protein, FBXO28 that controls MYC-dependent transcription by non-proteolytic ubiquitylation. SCF(FBXO28) activity and stability are regulated during the cell cycle by CDK1/2-mediated phosphorylation of FBXO28, which is required for its efficient ubiquitylation of MYC and downsteam enhancement of the MYC pathway. Depletion of FBXO28 or overexpression of an F-box mutant unable to support MYC ubiquitylation results in an impairment of MYC-driven transcription, transformation and tumourigenesis. Finally, in human breast cancer, high FBXO28 expression and phosphorylation are strong and independent predictors of poor outcome. In conclusion, our data suggest that SCF(FBXO28) plays an important role in transmitting CDK activity to MYC function during the cell cycle, emphasizing the CDK-FBXO28-MYC axis as a potential molecular drug target in MYC-driven cancers, including breast cancer.", "doi": "10.1002/emmm.201202341", "pmid": "23776131", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pmc", "key": "PMC3721474"}], "notes": [], "created": "2017-05-04T14:55:57.444Z", "modified": "2021-07-08T13:44:33.547Z"}, {"entity": "publication", "iuid": "46fcccfe99494658bf5552e1a28e8a73", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46fcccfe99494658bf5552e1a28e8a73.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46fcccfe99494658bf5552e1a28e8a73"}}, "title": "Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Olsson", "given": "Ingmarie", "initials": "I"}, {"family": "Rydberg", "given": "Urban", "initials": "U"}, {"family": "Hudson", "given": "Paul", "initials": "P"}, {"family": "Ottosson Takanen", "given": "Jenny", "initials": "J"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2013-06-07", "journal": {"volume": "12", "issn": "1535-3907", "issue": "6", "pages": "2439-2448", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas ( www.proteinatlas.org ).", "doi": "10.1021/pr300924j", "pmid": "23276153", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:13.479Z", "modified": "2021-07-08T13:44:33.207Z"}, {"entity": "publication", "iuid": "38deb04ab67148e9bfa7ba2cd6bbf4eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38deb04ab67148e9bfa7ba2cd6bbf4eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38deb04ab67148e9bfa7ba2cd6bbf4eb"}}, "title": "Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.", "authors": [{"family": "Geiger", "given": "Tamar", "initials": "T"}, {"family": "Velic", "given": "Ana", "initials": "A"}, {"family": "Macek", "given": "Boris", "initials": "B"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Nagaraj", "given": "Nagarjuna", "initials": "N"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Cox", "given": "Juergen", "initials": "J"}, {"family": "Mann", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2013-06-00", "journal": {"volume": "12", "issn": "1535-9484", "issue": "6", "pages": "1709-1722", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Identifying the building blocks of mammalian tissues is a precondition for understanding their function. In particular, global and quantitative analysis of the proteome of mammalian tissues would point to tissue-specific mechanisms and place the function of each protein in a whole-organism perspective. We performed proteomic analyses of 28 mouse tissues using high-resolution mass spectrometry and used a mix of mouse tissues labeled via stable isotope labeling with amino acids in cell culture as a \"spike-in\" internal standard for accurate protein quantification across these tissues. We identified a total of 7,349 proteins and quantified 6,974 of them. Bioinformatic data analysis showed that physiologically related tissues clustered together and that highly expressed proteins represented the characteristic tissue functions. Tissue specialization was reflected prominently in the proteomic profiles and is apparent already in their hundred most abundant proteins. The proportion of strictly tissue-specific proteins appeared to be small. However, even proteins with household functions, such as those in ribosomes and spliceosomes, can have dramatic expression differences among tissues. We describe a computational framework with which to correlate proteome profiles with physiological functions of the tissue. Our data will be useful to the broad scientific community as an initial atlas of protein expression of a mammalian species.", "doi": "10.1074/mcp.M112.024919", "pmid": "23436904", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M112.024919"}, {"db": "pmc", "key": "PMC3675825"}], "notes": [], "created": "2017-05-04T14:55:14.094Z", "modified": "2021-07-08T13:44:33.162Z"}, {"entity": "publication", "iuid": "1dae3a5e0d3f4edfaa37026908d2f20f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dae3a5e0d3f4edfaa37026908d2f20f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dae3a5e0d3f4edfaa37026908d2f20f"}}, "title": "A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.", "authors": [{"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Agnarsd\u00f3ttir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2013-05-17", "journal": {"volume": "8", "issn": "1932-6203", "issue": "5", "pages": "e62070", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Immunohistochemistry is a routine practice in clinical cancer diagnostics and also an established technology for tissue-based research regarding biomarker discovery efforts. Tedious manual assessment of immunohistochemically stained tissue needs to be fully automated to take full advantage of the potential for high throughput analyses enabled by tissue microarrays and digital pathology. Such automated tools also need to be reproducible for different experimental conditions and biomarker targets. In this study we present a novel supervised melanoma specific pattern recognition approach that is fully automated and quantitative.\n\nMelanoma samples were immunostained for the melanocyte specific target, Melan-A. Images representing immunostained melanoma tissue were then digitally processed to segment regions of interest, highlighting Melan-A positive and negative areas. Color deconvolution was applied to each region of interest to separate the channel containing the immunohistochemistry signal from the hematoxylin counterstaining channel. A support vector machine melanoma classification model was learned from a discovery melanoma patient cohort (n = 264) and subsequently validated on an independent cohort of melanoma patient tissue sample images (n = 157).\n\nHere we propose a novel method that takes advantage of utilizing an immuhistochemical marker highlighting melanocytes to fully automate the learning of a general melanoma cell classification model. The presented method can be applied on any protein of interest and thus provides a tool for quantification of immunohistochemistry-based protein expression in melanoma.", "doi": "10.1371/journal.pone.0062070", "pmid": "23690928", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-33946"}, {"db": "pmc", "key": "PMC3656869"}], "notes": [], "created": "2017-05-04T14:55:15.014Z", "modified": "2021-07-08T13:44:33.066Z"}, {"entity": "publication", "iuid": "168f78a27d1e42f1ace305c0f5399d47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/168f78a27d1e42f1ace305c0f5399d47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/168f78a27d1e42f1ace305c0f5399d47"}}, "title": "Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.", "authors": [{"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "O'Hurley", "given": "Gillian", "initials": "G"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Gad", "given": "Annica K B", "initials": "AK"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2013-04-23", "journal": {"volume": "110", "issn": "1091-6490", "issue": "17", "pages": "6853-6858", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The transformation of normal cells to malignant, metastatic tumor cells is a multistep process caused by the sequential acquirement of genetic changes. To identify these changes, we compared the transcriptomes and levels and distribution of proteins in a four-stage cell model of isogenically matched normal, immortalized, transformed, and metastatic human cells, using deep transcriptome sequencing and immunofluorescence microscopy. The data show that \u223c6% (n = 1,357) of the human protein-coding genes are differentially expressed across the stages in the model. Interestingly, the majority of these genes are down-regulated, linking malignant transformation to dedifferentiation. The up-regulated genes are mainly components that control cellular proliferation, whereas the down-regulated genes consist of proteins exposed on or secreted from the cell surface. As many of the identified gene products control basic cellular functions that are defective in cancers, the data provide candidates for follow-up studies to investigate their functional roles in tumor formation. When we further compared the expression levels of four of the identified proteins in clinical cancer cohorts, similar differences were observed between benign and cancer cells, as in the cell model. This shows that this comprehensive demonstration of the molecular changes underlying malignant transformation is a relevant model to study the process of tumor formation.", "doi": "10.1073/pnas.1216436110", "pmid": "23569271", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1216436110"}, {"db": "pmc", "key": "PMC3637701"}], "notes": [], "created": "2017-05-04T14:55:14.694Z", "modified": "2021-07-08T13:44:33.038Z"}, {"entity": "publication", "iuid": "588bcc002c0247a2b0dd46872c4c105b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588bcc002c0247a2b0dd46872c4c105b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588bcc002c0247a2b0dd46872c4c105b"}}, "title": "Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer.", "authors": [{"family": "O Leary", "given": "Patrick C", "initials": "PC"}, {"family": "Penny", "given": "Sarah A", "initials": "SA"}, {"family": "Dolan", "given": "Roisin T", "initials": "RT"}, {"family": "Kelly", "given": "Catherine M", "initials": "CM"}, {"family": "Madden", "given": "Stephen F", "initials": "SF"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "McCann", "given": "Amanda H", "initials": "AH"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zagozdzon", "given": "Radoslaw", "initials": "R"}, {"family": "Duffy", "given": "Michael J", "initials": "MJ"}, {"family": "Kell", "given": "Malcolm R", "initials": "MR"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}], "type": "journal article", "published": "2013-04-02", "journal": {"volume": "13", "issn": "1471-2407", "issue": null, "pages": "175", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Although omic-based discovery approaches can provide powerful tools for biomarker identification, several reservations have been raised regarding the clinical applicability of gene expression studies, such as their prohibitive cost. However, the limited availability of antibodies is a key barrier to the development of a lower cost alternative, namely a discrete collection of immunohistochemistry (IHC)-based biomarkers. The aim of this study was to use a systematic approach to generate and screen affinity-purified, mono-specific antibodies targeting progression-related biomarkers, with a view towards developing a clinically applicable IHC-based prognostic biomarker panel for breast cancer.\n\nWe examined both in-house and publicly available breast cancer DNA microarray datasets relating to invasion and metastasis, thus identifying a cohort of candidate progression-associated biomarkers. Of these, 18 antibodies were released for extended analysis. Validated antibodies were screened against a tissue microarray (TMA) constructed from a cohort of consecutive breast cancer cases (n\u2009=\u2009512) to test the immunohistochemical surrogate signature.\n\nAntibody screening revealed 3 candidate prognostic markers: the cell cycle regulator, Anillin (ANLN); the mitogen-activated protein kinase, PDZ-Binding Kinase (PBK); and the estrogen response gene, PDZ-Domain Containing 1 (PDZK1). Increased expression of ANLN and PBK was associated with poor prognosis, whilst increased expression of PDZK1 was associated with good prognosis. A 3-marker signature comprised of high PBK, high ANLN and low PDZK1 expression was associated with decreased recurrence-free survival (p\u2009<\u20090.001) and breast cancer-specific survival (BCSS) (p\u2009<\u20090.001). This novel signature was associated with high tumour grade (p\u2009<\u20090.001), positive nodal status (p\u2009=\u20090.029), ER-negativity (p\u2009=\u20090.006), Her2-positivity (p\u2009=\u20090.036) and high Ki67 status (p\u2009<\u20090.001). However, multivariate Cox regression demonstrated that the signature was not a significant predictor of BCSS (HR\u2009=\u20096.38; 95% CI\u2009=\u20090.79-51.26, p\u2009=\u20090.082).\n\nWe have developed a comprehensive biomarker pathway that extends from discovery through to validation on a TMA platform. This proof-of-concept study has resulted in the identification of a novel 3-protein prognostic panel. Additional biochemical markers, interrogated using this high-throughput platform, may further augment the prognostic accuracy of this panel to a point that may allow implementation into routine clinical practice.", "doi": "10.1186/1471-2407-13-175", "pmid": "23547718", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1471-2407-13-175"}, {"db": "pmc", "key": "PMC3668187"}], "notes": [], "created": "2017-05-04T14:55:55.320Z", "modified": "2021-07-08T13:44:33.279Z"}, {"entity": "publication", "iuid": "d3a818a1f7574d1886530d913b06ad00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3a818a1f7574d1886530d913b06ad00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3a818a1f7574d1886530d913b06ad00"}}, "title": "Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Singan", "given": "Vasanth R", "initials": "VR"}, {"family": "Murphy", "given": "Robert F", "initials": "RF"}, {"family": "Pepperkok", "given": "Rainer", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Simpson", "given": "Jeremy C", "initials": "JC"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2013-04-00", "journal": {"volume": "10", "issn": "1548-7105", "issue": "4", "pages": "315-323", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Imaging techniques such as immunofluorescence (IF) and the expression of fluorescent protein (FP) fusions are widely used to investigate the subcellular distribution of proteins. Here we report a systematic analysis of >500 human proteins comparing the localizations obtained in live versus fixed cells using FPs and IF, respectively. We identify systematic discrepancies between IF and FPs as well as between FP tagging at the N and C termini. The analysis shows that for 80% of the proteins, IF and FPs yield the same subcellular distribution, and the locations of 250 previously unlocalized proteins were determined by the overlap between the two methods. Approximately 60% of proteins localize to multiple organelles for both methods, indicating a complex subcellular protein organization. These results show that both IF and FP tagging are reliable techniques and demonstrate the usefulness of an integrative approach for a complete investigation of the subcellular human proteome.", "doi": "10.1038/nmeth.2377", "pmid": "23435261", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "nmeth.2377"}], "notes": [], "created": "2017-05-04T14:55:14.395Z", "modified": "2021-07-08T13:44:33.657Z"}, {"entity": "publication", "iuid": "e700dbb99ef54d5d8b85d15655ee5e50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e700dbb99ef54d5d8b85d15655ee5e50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e700dbb99ef54d5d8b85d15655ee5e50"}}, "title": "Integration of clinical data with a genome-scale metabolic model of the human adipocyte.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Jacobson", "given": "Peter", "initials": "P"}, {"family": "Walley", "given": "Andrew J", "initials": "AJ"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Carlsson", "given": "Lena M", "initials": "LM"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2013-03-21", "journal": {"volume": "9", "issn": "1744-4292", "issue": null, "pages": "649", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "We evaluated the presence/absence of proteins encoded by 14\u2009077 genes in adipocytes obtained from different tissue samples using immunohistochemistry. By combining this with previously published adipocyte-specific proteome data, we identified proteins associated with 7340 genes in human adipocytes. This information was used to reconstruct a comprehensive and functional genome-scale metabolic model of adipocyte metabolism. The resulting metabolic model, iAdipocytes1809, enables mechanistic insights into adipocyte metabolism on a genome-wide level, and can serve as a scaffold for integration of omics data to understand the genotype-phenotype relationship in obese subjects. By integrating human transcriptome and fluxome data, we found an increase in the metabolic activity around androsterone, ganglioside GM2 and degradation products of heparan sulfate and keratan sulfate, and a decrease in mitochondrial metabolic activities in obese subjects compared with lean subjects. Our study hereby shows a path to identify new therapeutic targets for treating obesity through combination of high throughput patient data and metabolic modeling.", "doi": "10.1038/msb.2013.5", "pmid": "23511207", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "msb20135"}, {"db": "pmc", "key": "PMC3619940"}], "notes": [], "created": "2017-05-04T14:56:01.784Z", "modified": "2021-07-08T13:44:33.705Z"}, {"entity": "publication", "iuid": "97551f87fce64e9ea072d060659c720c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97551f87fce64e9ea072d060659c720c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97551f87fce64e9ea072d060659c720c"}}, "title": "A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.", "authors": [{"family": "Liu", "given": "Suli", "initials": "S"}, {"family": "Im", "given": "Hogune", "initials": "H"}, {"family": "Bairoch", "given": "Amos", "initials": "A"}, {"family": "Cristofanilli", "given": "Massimo", "initials": "M"}, {"family": "Chen", "given": "Rui", "initials": "R"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Dalton", "given": "Stephen", "initials": "S"}, {"family": "Fenyo", "given": "David", "initials": "D"}, {"family": "Fanayan", "given": "Susan", "initials": "S"}, {"family": "Gates", "given": "Chris", "initials": "C"}, {"family": "Gaudet", "given": "Pascale", "initials": "P"}, {"family": "Hincapie", "given": "Marina", "initials": "M"}, {"family": "Hanash", "given": "Samir", "initials": "S"}, {"family": "Kim", "given": "Hoguen", "initials": "H"}, {"family": "Jeong", "given": "Seul-Ki", "initials": "SK"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Mias", "given": "George", "initials": "G"}, {"family": "Menon", "given": "Rajasree", "initials": "R"}, {"family": "Mu", "given": "Zhaomei", "initials": "Z"}, {"family": "Nice", "given": "Edouard", "initials": "E"}, {"family": "Paik", "given": "Young-Ki", "initials": "YK"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Wells", "given": "Lance", "initials": "L"}, {"family": "Wu", "given": "Shiaw-Lin", "initials": "SL"}, {"family": "Yan", "given": "Fangfei", "initials": "F"}, {"family": "Zhang", "given": "Fan", "initials": "F"}, {"family": "Zhang", "given": "Yue", "initials": "Y"}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS"}, {"family": "Beavis", "given": "Ronald C", "initials": "RC"}, {"family": "Hancock", "given": "William S", "initials": "WS"}], "type": "journal article", "published": "2013-01-04", "journal": {"volume": "12", "issn": "1535-3907", "issue": "1", "pages": "45-57", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 \"missing\" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of \"missing\" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.", "doi": "10.1021/pr300985j", "pmid": "23259914", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pmc", "key": "PMC4142220"}, {"db": "mid", "key": "NIHMS431316"}], "notes": [], "created": "2017-05-04T14:55:13.784Z", "modified": "2021-07-08T13:44:33.454Z"}, {"entity": "publication", "iuid": "a897a3ab2afe4d01bcf41c0404b265d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a897a3ab2afe4d01bcf41c0404b265d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a897a3ab2afe4d01bcf41c0404b265d0"}}, "title": "RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.", "authors": [{"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2013-01-04", "journal": {"volume": "12", "issn": "1535-3907", "issue": "1", "pages": "299-307", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "One of the major challenges of a chromosome-centric proteome project is to explore in a systematic manner the potential proteins identified from the chromosomal genome sequence, but not yet characterized on a protein level. Here, we describe the use of RNA deep sequencing to screen human cell lines for RNA profiles and to use this information to select cell lines suitable for characterization of the corresponding gene product. In this manner, the subcellular localization of proteins can be analyzed systematically using antibody-based confocal microscopy. We demonstrate the usefulness of selecting cell lines with high expression levels of RNA transcripts to increase the likelihood of high quality immunofluorescence staining and subsequent successful subcellular localization of the corresponding protein. The results show a path to combine transcriptomics with affinity proteomics to characterize the proteins in a gene- or chromosome-centric manner.", "doi": "10.1021/pr3009308", "pmid": "23227862", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:13.177Z", "modified": "2021-07-08T13:44:33.502Z"}, {"entity": "publication", "iuid": "504f7661fda94a749fe7d389d0bb14fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/504f7661fda94a749fe7d389d0bb14fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/504f7661fda94a749fe7d389d0bb14fe"}}, "title": "High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays.", "authors": [{"family": "Buus", "given": "S\u00f8ren", "initials": "S"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schafer-Nielsen", "given": "Claus", "initials": "C"}], "type": "journal article", "published": "2012-12-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "12", "pages": "1790-1800", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high-resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against linear epitopes of the human proteome and obtained very detailed descriptions of the involved specificities. The epitopes identified ranged from 4 to 12 amino acids in size. In general, the antibodies were of exquisite specificity, frequently disallowing even single conservative substitutions. In several cases, multiple distinct epitopes could be identified for the same target protein, suggesting an efficient approach to the generation of paired antibodies. Two alternative epitope mapping approaches identified similar, although not necessarily identical, epitopes. These results show that ultrahigh-density peptide microarrays can be used for linear epitope mapping. With an upper theoretical limit of 2,000,000 individual peptides per array, these peptide microarrays may even be used for a systematic validation of antibodies at the proteomic level.", "doi": "10.1074/mcp.M112.020800", "pmid": "22984286", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pii", "key": "M112.020800"}, {"db": "pmc", "key": "PMC3518105"}], "notes": [], "created": "2017-05-04T14:55:36.590Z", "modified": "2021-07-08T13:44:33.228Z"}, {"entity": "publication", "iuid": "e34eea78ce26495ba3984e5271abacd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e34eea78ce26495ba3984e5271abacd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e34eea78ce26495ba3984e5271abacd9"}}, "title": "Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas.", "authors": [{"family": "Li", "given": "Jieyue", "initials": "J"}, {"family": "Newberg", "given": "Justin Y", "initials": "JY"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Murphy", "given": "Robert F", "initials": "RF"}], "type": "journal article", "published": "2012-11-30", "journal": {"volume": "7", "issn": "1932-6203", "issue": "11", "pages": "e50514", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training classifiers to recognize the annotated patterns. By ranking proteins according to the confidence of the classifier, we generated a list of proteins that were strong candidates for reexamination. In parallel, we applied hierarchical clustering to group proteins and identified proteins whose annotations were inconsistent with the remainder of the proteins in their cluster. These proteins were reexamined by the original annotators, and a significant fraction had their annotations changed. The results demonstrate that automated approaches can provide an important complement to visual annotation.", "doi": "10.1371/journal.pone.0050514", "pmid": "23226299", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "PONE-D-12-11801"}, {"db": "pmc", "key": "PMC3511558"}], "notes": [], "created": "2017-05-04T14:55:12.577Z", "modified": "2021-07-08T13:44:33.700Z"}, {"entity": "publication", "iuid": "18a47010d25b47b2bb656d6e7d31ffa9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18a47010d25b47b2bb656d6e7d31ffa9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18a47010d25b47b2bb656d6e7d31ffa9"}}, "title": "Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.", "authors": [{"family": "Akan", "given": "Pelin", "initials": "P"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Costea", "given": "Paul Igor", "initials": "PI"}, {"family": "Hedberg", "given": "Lilia", "initials": "L"}, {"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2012-11-18", "journal": {"volume": "4", "issn": "1756-994X", "issue": "11", "pages": "86", "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": "We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.", "doi": "10.1186/gm387", "pmid": "23158748", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "gm387"}, {"db": "pmc", "key": "PMC3580420"}], "notes": [], "created": "2017-05-04T14:55:10.176Z", "modified": "2021-07-08T13:44:33.049Z"}, {"entity": "publication", "iuid": "0dc2a140d296454ea162ebc52988e560", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dc2a140d296454ea162ebc52988e560.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dc2a140d296454ea162ebc52988e560"}}, "title": "A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Papini", "given": "Marta", "initials": "M"}, {"family": "Pornputtapong", "given": "Natapol", "initials": "N"}, {"family": "Scalcinati", "given": "Gionata", "initials": "G"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "comparative study", "published": "2012-11-01", "journal": {"volume": "40", "issn": "1362-4962", "issue": "20", "pages": "10084-10097", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation\u22650.99) and high consistency between the two platforms for analysis of gene expression levels (correlation\u22650.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data.", "doi": "10.1093/nar/gks804", "pmid": "22965124", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "gks804"}, {"db": "pmc", "key": "PMC3488244"}, {"db": "GDB", "key": "SRR453566"}, {"db": "GDB", "key": "SRR453567"}, {"db": "GDB", "key": "SRR453568"}, {"db": "GDB", "key": "SRR453569"}, {"db": "GDB", "key": "SRR453570"}, {"db": "GDB", "key": "SRR453571"}, {"db": "GDB", "key": "SRR453578"}, {"db": "GDB", "key": "SRS307298"}, {"db": "GEO", "key": "GSE37599"}, {"db": "SRA", "description": "Yeast RNA-seq", "key": "SRP012047"}], "notes": [], "created": "2017-05-04T14:56:19.115Z", "modified": "2021-07-08T13:44:33.019Z"}, {"entity": "publication", "iuid": "3d17bf49ee824c219202eacebf916ef0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d17bf49ee824c219202eacebf916ef0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d17bf49ee824c219202eacebf916ef0"}}, "title": "Secretagogin is expressed in sensory CGRP neurons and in spinal cord of mouse and complements other calcium-binding proteins, with a note on rat and human.", "authors": [{"family": "Shi", "given": "Tie-Jun Sten", "initials": "TJ"}, {"family": "Xiang", "given": "Qiong", "initials": "Q"}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD"}, {"family": "Tortoriello", "given": "Giuseppe", "initials": "G"}, {"family": "Hammarberg", "given": "Henrik", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Wagner", "given": "Ludwig", "initials": "L"}, {"family": "Josephson", "given": "Anna", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2012-10-29", "journal": {"volume": "8", "issn": "1744-8069", "issue": null, "pages": "80", "title": "Mol Pain", "issn-l": "1744-8069"}, "abstract": "Secretagogin (Scgn), a member of the EF-hand calcium-binding protein (CaBP) superfamily, has recently been found in subsets of developing and adult neurons. Here, we have analyzed the expression of Scgn in dorsal root ganglia (DRGs) and trigeminal ganglia (TGs), and in spinal cord of mouse at the mRNA and protein levels, and in comparison to the well-known CaBPs, calbindin D-28k, parvalbumin and calretinin. Rat DRGs, TGs and spinal cord, as well as human DRGs and spinal cord were used to reveal phylogenetic variations.\n\nWe found Scgn mRNA expressed in mouse and human DRGs and in mouse ventral spinal cord. Our immunohistochemical data showed a complementary distribution of Scgn and the three CaBPs in mouse DRG neurons and spinal cord. Scgn was expressed in ~7% of all mouse DRG neuron profiles, mainly small ones and almost exclusively co-localized with calcitonin gene-related peptide (CGRP). This co-localization was also seen in human, but not in rat DRGs. Scgn could be detected in the mouse sciatic nerve and accumulated proximal to its constriction. In mouse spinal cord, Scgn-positive neuronal cell bodies and fibers were found in gray matter, especially in the dorsal horn, with particularly high concentrations of fibers in the superficial laminae, as well as in cell bodies in inner lamina II and in some other laminae. A dense Scgn-positive fiber network and some small cell bodies were also found in the superficial dorsal horn of humans. In the ventral horn, a small number of neurons were Scgn-positive in mouse but not rat, confirming mRNA distribution. Both in mouse and rat, a subset of TG neurons contained Scgn. Dorsal rhizotomy strongly reduced Scgn fiber staining in the dorsal horn. Peripheral axotomy did not clearly affect Scgn expression in DRGs, dorsal horn or ventral horn neurons in mouse.\n\nScgn is a CaBP expressed in a subpopulation of nociceptive DRG neurons and their processes in the dorsal horn of mouse, human and rat, the former two co-expressing CGRP, as well as in dorsal horn neurons in all three species. Functional implications of these findings include the cellular refinement of sensory information, in particular during the processing of pain.", "doi": "10.1186/1744-8069-8-80", "pmid": "23102406", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1744-8069-8-80"}, {"db": "pmc", "key": "PMC3560279"}], "notes": [], "created": "2017-05-04T14:55:18.337Z", "modified": "2021-07-08T13:44:33.173Z"}, {"entity": "publication", "iuid": "36aa2c1a1e004c4581aec22ec50609dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36aa2c1a1e004c4581aec22ec50609dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36aa2c1a1e004c4581aec22ec50609dd"}}, "title": "Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.", "authors": [{"family": "Papini", "given": "Marta", "initials": "M"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2012-10-09", "journal": {"volume": "11", "issn": "1475-2859", "issue": null, "pages": "136", "title": "Microb. Cell Fact.", "issn-l": "1475-2859"}, "abstract": "Scheffersomyces stipitis is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as Saccharomyces cerevisiae, the onset of fermentation in S. stipitis is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations.\n\nStarting from the analysis of physiological data, we confirmed through 13C-based flux analysis the fully respiratory metabolism of S. stipitis when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for S. cerevisiae under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through in silico transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways.\n\nThe work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for S. stipitis under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for S. cerevisiae under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, in silico analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of S. stiptis is investigated in details and is compared to S. cerevisiae. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of S. stipitis as cell factory.", "doi": "10.1186/1475-2859-11-136", "pmid": "23043429", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1475-2859-11-136"}, {"db": "pmc", "key": "PMC3528450"}], "notes": [], "created": "2017-05-04T14:56:17.576Z", "modified": "2021-07-08T13:44:33.145Z"}, {"entity": "publication", "iuid": "c022dd2b61674f24a4e4235c9a1634c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c022dd2b61674f24a4e4235c9a1634c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c022dd2b61674f24a4e4235c9a1634c1"}}, "title": "Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.", "authors": [{"family": "Bock", "given": "Thomas", "initials": "T"}, {"family": "Moest", "given": "Hansjoerg", "initials": "H"}, {"family": "Omasits", "given": "Ulrich", "initials": "U"}, {"family": "Dolski", "given": "Silvia", "initials": "S"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Frei", "given": "Andreas", "initials": "A"}, {"family": "Hofmann", "given": "Andreas", "initials": "A"}, {"family": "Bausch-Fluck", "given": "Damaris", "initials": "D"}, {"family": "Jacobs", "given": "Andrea", "initials": "A"}, {"family": "Krayenbuehl", "given": "Niklaus", "initials": "N"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R"}, {"family": "Frei", "given": "Karl", "initials": "K"}, {"family": "Wollscheid", "given": "Bernd", "initials": "B"}], "type": "journal article", "published": "2012-10-05", "journal": {"volume": "11", "issn": "1535-3907", "issue": "10", "pages": "4885-4893", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Glioblastoma is the most common primary brain tumor in adults with low average survival time after diagnosis. In order to improve glioblastoma treatment, new drug-accessible targets need to be identified. Cell surface glycoproteins are prime drug targets due to their accessibility at the surface of cancer cells. To overcome the limited availability of suitable antibodies for cell surface protein detection, we performed a comprehensive mass spectrometric investigation of the glioblastoma surfaceome. Our combined cell surface capturing analysis of primary ex vivo glioblastoma cell lines in combination with established glioblastoma cell lines revealed 633 N-glycoproteins, which vastly extends the known data of surfaceome drug targets at subcellular resolution. We provide direct evidence of common glioblastoma cell surface glycoproteins and an approximate estimate of their abundances, information that could not be derived from genomic and/or transcriptomic glioblastoma studies. Apart from our pharmaceutically valuable repertoire of already and potentially drug-accessible cell surface glycoproteins, we built a mass-spectrometry-based toolbox enabling directed, sensitive, and repetitive glycoprotein measurements for clinical follow-up studies. The included Skyline Glioblastoma SRM assay library provides an elevated starting point for parallel testing of the abundance level of the detected glioblastoma surfaceome members in future drug perturbation experiments.", "doi": "10.1021/pr300360a", "pmid": "22909291", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:10.473Z", "modified": "2021-07-08T13:44:33.585Z"}, {"entity": "publication", "iuid": "951aea7e94e94e769ea8d79a783a125a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/951aea7e94e94e769ea8d79a783a125a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/951aea7e94e94e769ea8d79a783a125a"}}, "title": "Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes.", "authors": [{"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2012-10-04", "journal": {"volume": "2", "issn": "2045-2322", "issue": null, "pages": "706", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "As antibody-based diagnosis and therapy grow at an increased pace, there is a need for methods which rapidly and accurately determine antibody-antigen interactions. Here, we report a method for the multiplex determination of antibody epitopes using bacterial cell-surface display. A protein-fragment library with 10(7) cell clones, covering 60 clinically-relevant protein targets, was created and characterized with massively parallel sequencing. Using this multi-target fragment library we determined simultaneously epitopes of commercial monoclonal and polyclonal antibodies targeting PSMA, EGFR, and VEGF. Off-target binding was observed for one of the antibodies, which demonstrates the methods ability to reveal cross-reactivity. We exemplify the detection of structural epitopes by mapping the therapeutic antibody Avastin. Based on our findings we suggest this method to be suitable for mapping linear and structural epitopes of monoclonal and polyclonal antibodies in a multiplex fashion and could find applicability in serum profiling as well as other protein-protein interaction studies.", "doi": "10.1038/srep00706", "pmid": "23050090", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3463815"}], "notes": [], "created": "2017-05-04T14:57:46.018Z", "modified": "2021-07-08T13:44:33.449Z"}, {"entity": "publication", "iuid": "5af2b1cc2957448da246fde20468dff6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5af2b1cc2957448da246fde20468dff6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5af2b1cc2957448da246fde20468dff6"}}, "title": "A tool to facilitate clinical biomarker studies--a tissue dictionary based on the Human Protein Atlas.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2012-09-12", "journal": {"volume": "10", "issn": "1741-7015", "issue": null, "pages": "103", "title": "BMC Med", "issn-l": "1741-7015"}, "abstract": "The complexity of tissue and the alterations that distinguish normal from cancer remain a challenge for translating results from tumor biological studies into clinical medicine. This has generated an unmet need to exploit the findings from studies based on cell lines and model organisms to develop, validate and clinically apply novel diagnostic, prognostic and treatment predictive markers. As one step to meet this challenge, the Human Protein Atlas project has been set up to produce antibodies towards human protein targets corresponding to all human protein coding genes and to map protein expression in normal human tissues, cancer and cells. Here, we present a dictionary based on microscopy images created as an amendment to the Human Protein Atlas. The aim of the dictionary is to facilitate the interpretation and use of the image-based data available in the Human Protein Atlas, but also to serve as a tool for training and understanding tissue histology, pathology and cell biology. The dictionary contains three main parts, normal tissues, cancer tissues and cells, and is based on high-resolution images at different magnifications of full tissue sections stained with H & E. The cell atlas is centered on immunofluorescence and confocal microscopy images, using different color channels to highlight the organelle structure of a cell. Here, we explain how this dictionary can be used as a tool to aid clinicians and scientists in understanding the use of tissue histology and cancer pathology in diagnostics and biomarker studies.", "doi": "10.1186/1741-7015-10-103", "pmid": "22971420", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1741-7015-10-103"}, {"db": "pmc", "key": "PMC3523031"}], "notes": [], "created": "2017-05-04T14:55:09.873Z", "modified": "2021-07-08T13:44:33.290Z"}, {"entity": "publication", "iuid": "1c65428b58d9411b8a95e81e4cab18b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c65428b58d9411b8a95e81e4cab18b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c65428b58d9411b8a95e81e4cab18b5"}}, "title": "Validation of affinity reagents using antigen microarrays.", "authors": [{"family": "Sj\u00f6berg", "given": "Ronald", "initials": "R", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Sundberg", "given": "M\u00e5rten", "initials": "M"}, {"family": "Gundberg", "given": "Anna", "initials": "A"}, {"family": "Sivertsson", "given": "Asa", "initials": "A"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "555-563", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.", "doi": "10.1016/j.nbt.2011.11.009", "pmid": "22134247", "labels": {"Autoimmunity and Serology Profiling": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00257-3"}], "notes": [], "created": "2017-05-04T14:55:37.189Z", "modified": "2021-07-08T13:44:33.060Z"}, {"entity": "publication", "iuid": "5baa7889c10943b3a05a955706c46c32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5baa7889c10943b3a05a955706c46c32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5baa7889c10943b3a05a955706c46c32"}}, "title": "Classification of protein profiles from antibody microarrays using heat and detergent treatment.", "authors": [{"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Drobin", "given": "Kimi", "initials": "K"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2012-06-15", "journal": {"volume": "29", "issn": "1876-4347", "issue": "5", "pages": "564-570", "title": "N Biotechnol", "issn-l": "1871-6784"}, "abstract": "Antibody microarrays offer new opportunities for exploring the proteome and to identify biomarker candidates in human serum and plasma. Here, we have investigated the effect of heat and detergents on an antibody-based suspension bead array (SBA) assay using polyclonal antibodies and biotinylated plasma samples. With protein profiles from more than 2300 antibodies generated in 384-plex antibody SBAs, three major classes of heat and detergent susceptibility could be described. The results show that washing of the beads with SDS (rather than Tween) after target binding lowered intensity levels of basically all profiles and that about 50% of the profiles appeared to be lowered to a similar extent by heating of the sample. About 33% of the profiles appeared to be insensitive to heat treatment while another 17% showed a positive influence of heat to yield elevated profiles. The results suggest that the classification of antibodies is driven by the molecular properties of the antibody-antigen interaction and can generally not be predicted based on protein class or Western blot data. The experimental scheme presented here can be used to systematically categorize antibodies and thereby combine antibodies with similar properties into targeted arrays for analysis of plasma and serum.", "doi": "10.1016/j.nbt.2011.10.005", "pmid": "22023822", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1871-6784(11)00225-1"}], "notes": [], "created": "2017-05-04T14:55:36.890Z", "modified": "2021-07-08T13:44:33.296Z"}, {"entity": "publication", "iuid": "32ee13d08d2f4563bbbdb19dff26644c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32ee13d08d2f4563bbbdb19dff26644c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32ee13d08d2f4563bbbdb19dff26644c"}}, "title": "Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Neumann", "given": "Beate", "initials": "B"}, {"family": "Jonasson", "given": "Kalle", "initials": "K"}, {"family": "Pepperkok", "given": "Rainer", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2012-04-03", "journal": {"volume": "75", "issn": "1876-7737", "issue": "7", "pages": "2236-2251", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "We have developed a platform for validation of antibody binding and protein subcellular localization data obtained from immunofluorescence using siRNA technology combined with automated confocal microscopy and image analysis. By combining the siRNA technology with automated sample preparation, automated imaging and quantitative image analysis, a high-throughput assay has been set-up to enable confirmation of accurate protein binding and localization in a systematic manner. Here, we describe the analysis and validation of the subcellular location of 65 human proteins, targeted by 75 antibodies and silenced by 130 siRNAs. A large fraction of (80%) the subcellular locations, including locations of several previously uncharacterized proteins, could be confirmed by the significant down-regulation of the antibody signal after the siRNA silencing. A quantitative analysis was set-up using automated image analysis to facilitate studies of targets found in more than one compartment. The results obtained using the platform demonstrate that siRNA silencing in combination with quantitative image analysis of antibody signals in different compartments of the cells is an attractive approach for ensuring accurate protein localization as well as antibody binding using immunofluorescence. With a large fraction of the human proteome still unexplored, we suggest this approach to be of great importance under the continued work of mapping the human proteome on a subcellular level.", "doi": "10.1016/j.jprot.2012.01.030", "pmid": "22361696", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(12)00070-X"}], "notes": [], "created": "2017-05-04T14:55:10.773Z", "modified": "2021-07-08T13:44:33.123Z"}, {"entity": "publication", "iuid": "5488813a095a489d96085f5df73da1f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5488813a095a489d96085f5df73da1f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5488813a095a489d96085f5df73da1f8"}}, "title": "Antibody-based protein profiling of the human chromosome 21.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "\u00c4lgen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Hamsten", "given": "Carl", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Kondo", "given": "Tadashi", "initials": "T"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.013458", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The Human Proteome Project has been proposed to create a knowledge-based resource based on a systematical mapping of all human proteins, chromosome by chromosome, in a gene-centric manner. With this background, we here describe the systematic analysis of chromosome 21 using an antibody-based approach for protein profiling using both confocal microscopy and immunohistochemistry, complemented with transcript profiling using next generation sequencing data. We also describe a new approach for protein isoform analysis using a combination of antibody-based probing and isoelectric focusing. The analysis has identified several genes on chromosome 21 with no previous evidence on the protein level, and the isoform analysis indicates that a large fraction of human proteins have multiple isoforms. A chromosome-wide matrix is presented with status for all chromosome 21 genes regarding subcellular localization, tissue distribution, and molecular characterization of the corresponding proteins. The path to generate a chromosome-specific resource, including integrated data from complementary assay platforms, such as mass spectrometry and gene tagging analysis, is discussed.", "doi": "10.1074/mcp.M111.013458", "pmid": "22042635", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M111.013458"}, {"db": "pmc", "key": "PMC3316724"}], "notes": [], "created": "2017-05-04T14:55:11.382Z", "modified": "2021-07-08T13:44:33.262Z"}, {"entity": "publication", "iuid": "7d06fc08dada4b148a9d889a8ed92d01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d06fc08dada4b148a9d889a8ed92d01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d06fc08dada4b148a9d889a8ed92d01"}}, "title": "A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.", "authors": [{"family": "Zeiler", "given": "Marlis", "initials": "M"}, {"family": "Straube", "given": "Werner L", "initials": "WL"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "O111.009613", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Mass spectrometry-based proteomics increasingly relies on relative or absolute quantification. In relative quantification, stable isotope based methods often allow mixing at early stages of sample preparation, whereas for absolute quantification this has generally required recombinant expression of full length, labeled protein standards. Here we make use of a very large library of Protein Epitope Signature Tags (PrESTs) that has been developed in the course of the Human Protein Atlas Project. These PrESTs are expressed recombinantly in E. coli and they consist of a short and unique region of the protein of interest as well as purification and solubility tags. We first quantify a highly purified, stable isotope labeling of amino acids in cell culture (SILAC)-labeled version of the solubility tag and use it determine the precise amount of each PrEST by its SILAC ratios. The PrESTs are then spiked into cell lysates and the SILAC ratios of PrEST peptides to peptides from endogenous target proteins yield their cellular quantities. The procedure can readily be multiplexed, as we demonstrate by simultaneously determining the copy number of 40 proteins in HeLa cells. Among the proteins analyzed, the cytoskeletal protein vimentin was found to be most abundant with 20 million copies per cell, while the transcription factor and oncogene FOS only had 6000 copies. Direct quantification of the absolute amount of single proteins is possible via a SILAC experiment in which labeled cell lysate is mixed both with the heavy labeled solubility tag and with the corresponding PrEST. The SILAC-PrEST combination allows accurate and streamlined quantification of the absolute or relative amount of proteins of interest in a wide variety of applications.", "doi": "10.1074/mcp.O111.009613", "pmid": "21964433", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "O111.009613"}, {"db": "pmc", "key": "PMC3316735"}], "notes": [], "created": "2017-05-04T14:55:12.279Z", "modified": "2021-07-08T13:44:33.380Z"}, {"entity": "publication", "iuid": "a19edf0632554037ad7018099f0fc4c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a19edf0632554037ad7018099f0fc4c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a19edf0632554037ad7018099f0fc4c1"}}, "title": "Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.", "authors": [{"family": "Ahmad", "given": "Yasmeen", "initials": "Y"}, {"family": "Boisvert", "given": "Francois-Michel", "initials": "FM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lamond", "given": "Angus I", "initials": "AI"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.013680", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "In higher eukaryotes many genes encode protein isoforms whose properties and biological roles are often poorly characterized. Here we describe systematic approaches for detection of either distinct isoforms, or separate pools of the same isoform, with differential biological properties. Using information from ion intensities we have estimated protein abundance levels and using rates of change in stable isotope labeling with amino acids in cell culture isotope ratios we measured turnover rates and subcellular distribution for the HeLa cell proteome. Protein isoforms were detected using three data analysis strategies that evaluate differences between stable isotope labeling with amino acids in cell culture isotope ratios for specific groups of peptides within the total set of peptides assigned to a protein. The candidate approach compares stable isotope labeling with amino acids in cell culture isotope ratios for predicted isoform-specific peptides, with ratio values for peptides shared by all the isoforms. The rule of thirds approach compares the mean isotope ratio values for all peptides in each of three equal segments along the linear length of the protein, assessing differences between segment values. The three in a row approach compares mean isotope ratio values for each sequential group of three adjacent peptides, assessing differences with the mean value for all peptides assigned to the protein. Protein isoforms were also detected and their properties evaluated by fractionating cell extracts on one-dimensional SDS-PAGE prior to trypsin digestion and MS analysis and independently evaluating isotope ratio values for the same peptides isolated from different gel slices. The effect of protein phosphorylation on turnover rates was analyzed by comparing mean turnover values calculated for all peptides assigned to a protein, either including, or excluding, values for cognate phosphopeptides. Collectively, these experimental and analytical approaches provide a framework for expanding the functional annotation of the genome.", "doi": "10.1074/mcp.M111.013680", "pmid": "22002106", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "M111.013680"}, {"db": "pmc", "key": "PMC3316725"}], "notes": [], "created": "2017-05-04T14:55:11.982Z", "modified": "2021-07-08T13:44:33.497Z"}, {"entity": "publication", "iuid": "c76cc56dd91f4a708ab21d5a78761a7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c76cc56dd91f4a708ab21d5a78761a7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c76cc56dd91f4a708ab21d5a78761a7b"}}, "title": "Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.", "authors": [{"family": "Larance", "given": "Mark", "initials": "M"}, {"family": "Kirkwood", "given": "Kathryn J", "initials": "KJ"}, {"family": "Xirodimas", "given": "Dimitris P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lamond", "given": "Angus I", "initials": "AI"}], "type": "journal article", "published": "2012-03-00", "journal": {"volume": "11", "issn": "1535-9484", "issue": "3", "pages": "M111.014407", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "The NEDD8-Cullin E3 ligase pathway plays an important role in protein homeostasis, in particular the degradation of cell cycle regulators and transcriptional control networks. To characterize NEDD8-cullin target proteins, we performed a quantitative proteomic analysis of cells treated with MLN4924, a small molecule inhibitor of the NEDD8 conjugation pathway. MRFAP1 and its interaction partner, MORF4L1, were among the most up-regulated proteins after NEDD8 inhibition in multiple human cell lines. We show that MRFAP1 has a fast turnover rate in the absence of MLN4924 and is degraded via the ubiquitin-proteasome system. The increased abundance of MRFAP1 after MLN4924 treatment results from a decreased rate of degradation. Characterization of the binding partners of both MRFAP1 and MORF4L1 revealed a complex protein-protein interaction network. MRFAP1 bound to a number of E3 ubiquitin ligases, including CUL4B, but not to components of the NuA4 complex, including MRGBP, which bound to MORF4L1. These data indicate that MRFAP1 may regulate the ability of MORF4L1 to interact with chromatin-modifying enzymes by binding to MORF4L1 in a mutually exclusive manner with MRGBP. Analysis of MRFAP1 expression in human tissues by immunostaining with a MRFAP1-specific antibody revealed that it was detectable in only a small number of tissues, in particular testis and brain. Strikingly, analysis of the seminiferous tubules of the testis showed the highest nuclear staining in the spermatogonia and much weaker staining in the spermatocytes and spermatids. MRGBP was inversely correlated with MRFAP1 expression in these cell types, consistent with an exchange of MORF4L1 interaction partners as cells progress through meiosis in the testis. These data highlight an important new arm of the NEDD8-cullin pathway.", "doi": "10.1074/mcp.M111.014407", "pmid": "22038470", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1535-9476(20)30503-X"}, {"db": "pmc", "key": "PMC3316733"}], "notes": [], "created": "2017-05-04T14:55:11.687Z", "modified": "2021-07-08T13:44:33.624Z"}, {"entity": "publication", "iuid": "51f66210bc9f4fdc8ad849038b7e87cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51f66210bc9f4fdc8ad849038b7e87cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51f66210bc9f4fdc8ad849038b7e87cc"}}, "title": "High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Zendehrokh", "given": "Nooreldin", "initials": "N"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gaber", "given": "Alexander", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Smaragdi", "given": "Kristina", "initials": "K"}, {"family": "Frantz", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Johnson", "given": "Louis B", "initials": "LB"}, {"family": "P\u00e5hlman", "given": "Sven", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2011-12-00", "journal": {"volume": "5", "issn": "1862-8354", "issue": "11-12", "pages": "624-635", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis.\n\nOne polyclonal antibody and four monoclonal anti-RBM3 antibodies were generated and epitope mapped using two different methods. Bacterial display revealed five distinct epitopes for the polyclonal antibody, while the four mouse monoclonal antibodies were found to bind to three of the five epitopes. A peptide suspension bead array assay confirmed the five epitopes of the polyclonal antibody, while only one of the monoclonal antibodies could be mapped using this approach. Antibody specificity was confirmed by Western blotting and immunohistochemistry, including siRNA-mediated knock-down. Two of the antibodies (polyclonal and monoclonal) were subsequently used to analyze RBM3 expression in tumor samples from two independent colorectal cancer cohorts, one consecutive cohort (n=270) and one prospectively collected cohort of patients with cancer of the sigmoid colon (n=305). RBM3-expression was detected, with high correlation between both antibodies (R=0.81, p<0.001).\n\nIn both cohorts, tumors with high nuclear RBM3 staining had significantly prolonged the overall survival. This was also confirmed in multivariate analysis, adjusted for established prognostic factors.\n\nThese data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.", "doi": "10.1002/prca.201100020", "pmid": "21956899", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:48.538Z", "modified": "2021-07-08T13:44:33.250Z"}, {"entity": "publication", "iuid": "c2e9c06ba1ef4c7882ff2869b01abad4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2e9c06ba1ef4c7882ff2869b01abad4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2e9c06ba1ef4c7882ff2869b01abad4"}}, "title": "Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model.", "authors": [{"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Holmes", "given": "Chris C", "initials": "CC"}, {"family": "Barrett", "given": "Amy", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2011-11-17", "journal": {"volume": "9", "issn": "1477-5956", "issue": null, "pages": "73", "title": "Proteome Sci", "issn-l": "1477-5956"}, "abstract": "The advent of affinity-based proteomics technologies for global protein profiling provides the prospect of finding new molecular biomarkers for common, multifactorial disorders. The molecular phenotypes obtained from studies on such platforms are driven by multiple sources, including genetic, environmental, and experimental components. In characterizing the contribution of different sources of variation to the measured phenotypes, the aim is to facilitate the design and interpretation of future biomedical studies employing exploratory and multiplexed technologies. Thus, biometrical genetic modelling of twin or other family data can be used to decompose the variation underlying a phenotype into biological and experimental components.\n\nUsing antibody suspension bead arrays and antibodies from the Human Protein Atlas, we study unfractionated serum from a longitudinal study on 154 twins. In this study, we provide a detailed description of how the variation in a molecular phenotype in terms of protein profile can be decomposed into familial i.e. genetic and common environmental; individual environmental, short-term biological and experimental components. The results show that across 69 antibodies analyzed in the study, the median proportion of the total variation explained by familial sources is 12% (IQR 1-22%), and the median proportion of the total variation attributable to experimental sources is 63% (IQR 53-72%).\n\nThe variability analysis of antibody arrays highlights the importance to consider variability components and their relative contributions when designing and evaluating studies for biomarker discoveries with exploratory, high-throughput and multiplexed methods.", "doi": "10.1186/1477-5956-9-73", "pmid": "22093360", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1477-5956-9-73"}, {"db": "pmc", "key": "PMC3247853"}], "notes": [], "created": "2017-10-30T10:37:06.896Z", "modified": "2021-07-08T13:44:33.591Z"}, {"entity": "publication", "iuid": "46874109988f4ab68218f77bac6175fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46874109988f4ab68218f77bac6175fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46874109988f4ab68218f77bac6175fb"}}, "title": "Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Hedberg", "given": "Jesper J", "initials": "JJ"}, {"family": "D\u00f6nnes", "given": "Pierre R", "initials": "PR"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Hanschke", "given": "Stephan", "initials": "S"}, {"family": "Schindler", "given": "Ralf", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2011-11-04", "journal": {"volume": "10", "issn": "1535-3907", "issue": "11", "pages": "4925-4934", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "There is a need for reliable and sensitive biomarkers for renal impairments to detect early signs of kidney toxicity and to monitor progression of disease. Here, antibody suspension bead arrays were applied to profile plasma samples from patients with four types of kidney disorders: glomerulonephritis, diabetic nephropathy, obstructive uropathy, and analgesic abuse. In total, 200 clinical renal-associated cases and control plasma samples from different cohorts were profiled. Parallel plasma protein profiles were obtained using biotinylated and nonfractionated samples and a selected set of 94 proteins targeted by 129 antigen-purified polyclonal antibodies. Out of the analyzed target proteins, human fibulin-1 was detected at significantly higher levels in the glomerulonephritis patient group compared to the controls and with elevated levels in patient samples for all other renal disorders investigated. Two polyclonal antibodies and one monoclonal antibody directed toward separate, nonoverlapping epitopes showed the same trend in the discovery cohorts. A technical verification using Western blot analysis of selected patient plasma confirmed the trends toward higher abundance of the target protein in disease samples. Furthermore, a verification study was carried out in the context of glomerulonephritis using an independent case and control cohort, and this confirmed the results from the discovery cohort, suggesting that plasma levels of fibulin-1 could serve as a potential indicator to monitor kidney malfunction or kidney damage.", "doi": "10.1021/pr200286c", "pmid": "21888404", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:36:18.646Z", "modified": "2021-07-08T13:44:33.201Z"}, {"entity": "publication", "iuid": "d9fa2ac7e63d4b53a6e2ab95554a276a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9fa2ac7e63d4b53a6e2ab95554a276a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9fa2ac7e63d4b53a6e2ab95554a276a"}}, "title": "Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.", "authors": [{"family": "Lindfors", "given": "Charlotte", "initials": "C"}, {"family": "Nilsson", "given": "Ida A K", "initials": "IA"}, {"family": "Garcia-Roves", "given": "Pablo M", "initials": "PM"}, {"family": "Zuberi", "given": "Aamir R", "initials": "AR"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Donahue", "given": "Leah Rae", "initials": "LR"}, {"family": "Roopenian", "given": "Derry C", "initials": "DC"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Davisson", "given": "Muriel T", "initials": "MT"}, {"family": "H\u00f6kfelt", "given": "Tomas G M", "initials": "TG"}, {"family": "Schalling", "given": "Martin", "initials": "M"}, {"family": "Johansen", "given": "Jeanette E", "initials": "JE"}], "type": "journal article", "published": "2011-11-01", "journal": {"volume": "108", "issn": "1091-6490", "issue": "44", "pages": "18108-18113", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The anorectic anx/anx mouse exhibits disturbed feeding behavior and aberrances, including neurodegeneration, in peptidergic neurons in the appetite regulating hypothalamic arcuate nucleus. Poor feeding in infants, as well as neurodegeneration, are common phenotypes in human disorders caused by dysfunction of the mitochondrial oxidative phosphorylation system (OXPHOS). We therefore hypothesized that the anorexia and degenerative phenotypes in the anx/anx mouse could be related to defects in the OXPHOS. In this study, we found reduced efficiency of hypothalamic OXPHOS complex I assembly and activity in the anx/anx mouse. We also recorded signs of increased oxidative stress in anx/anx hypothalamus, possibly as an effect of the decreased hypothalamic levels of fully assembled complex I, that were demonstrated by native Western blots. Furthermore, the Ndufaf1 gene, encoding a complex I assembly factor, was genetically mapped to the anx interval and found to be down-regulated in anx/anx mice. These results suggest that the anorexia and hypothalamic neurodegeneration of the anx/anx mouse are associated with dysfunction of mitochondrial complex I.", "doi": "10.1073/pnas.1114863108", "pmid": "22025706", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1114863108"}, {"db": "pmc", "key": "PMC3207677"}], "notes": [], "created": "2017-05-04T14:55:18.035Z", "modified": "2021-07-08T13:44:33.684Z"}, {"entity": "publication", "iuid": "f1401f1407364e189b734a9b3e1582c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0"}}, "title": "Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6berg", "given": "Anna", "initials": "A"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Johansson", "given": "Christine", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2011-11-00", "journal": {"volume": "20", "issn": "1469-896X", "issue": "11", "pages": "1824-1835", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.", "doi": "10.1002/pro.716", "pmid": "21898641", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Spatial Proteomics": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC3267947"}], "notes": [], "created": "2017-05-04T14:55:09.271Z", "modified": "2021-07-08T13:44:33.721Z"}, {"entity": "publication", "iuid": "bd893df429b04bdaa7b14f91038c1707", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd893df429b04bdaa7b14f91038c1707.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd893df429b04bdaa7b14f91038c1707"}}, "title": "High RBM3 expression in prostate cancer independently predicts a reduced risk of biochemical recurrence and disease progression.", "authors": [{"family": "Jonsson", "given": "Liv", "initials": "L"}, {"family": "Gaber", "given": "Alexander", "initials": "A"}, {"family": "Ulmert", "given": "David", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-09-28", "journal": {"volume": "6", "issn": "1746-1596", "issue": null, "pages": "91", "title": "Diagn Pathol", "issn-l": "1746-1596"}, "abstract": "High expression of the RNA-binding protein RBM3 has previously been found to be associated with good prognosis in breast cancer, ovarian cancer, malignant melanoma and colorectal cancer. The aim of this study was to examine the prognostic impact of immunohistochemical RBM3 expression in prostate cancer.\n\nImmunohistochemical RBM3 expression was examined in a tissue microarray with malignant and benign prostatic specimens from 88 patients treated with radical prostatectomy for localized disease. While rarely expressed in benign prostate gland epithelium, RBM3 was found to be up-regulated in prostate intraepithelial neoplasia and present in various fractions and intensities in invasive prostate cancer. High nuclear RBM3 expression was significantly associated with a prolonged time to biochemical recurrence (BCR) (HR 0.56, 95% CI: 0.34-0.93, p = 0.024) and clinical progression (HR 0.09, 95% CI: 0.01-0.71, p = 0.021). These associations remained significant in multivariate analysis, adjusted for preoperative PSA level in blood, pathological Gleason score and presence or absence of extracapsular extension, seminal vesicle invasion and positive surgical margin (HR 0.41, 95% CI: 0.19-0.89, p = 0.024 for BCR and HR 0.06, 95% CI: 0.01-0.50, p = 0.009 for clinical progression).\n\nOur results demonstrate that high nuclear expression of RBM3 in prostate cancer is associated with a prolonged time to disease progression and, thus, a potential biomarker of favourable prognosis. The value of RBM3 for prognostication, treatment stratification and follow-up of prostate cancer patients should be further validated in larger studies.", "doi": "10.1186/1746-1596-6-91", "pmid": "21955582", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1746-1596-6-91"}, {"db": "pmc", "key": "PMC3195697"}], "notes": [], "created": "2017-05-04T14:55:46.742Z", "modified": "2021-07-08T13:44:33.574Z"}, {"entity": "publication", "iuid": "cbad22e00c3f4d66847be8d00ab25dc7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbad22e00c3f4d66847be8d00ab25dc7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbad22e00c3f4d66847be8d00ab25dc7"}}, "title": "Large-scale protein profiling in human cell lines using antibody-based proteomics.", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "El-Obeid", "given": "Adila", "initials": "A"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Nilsson", "given": "Kenneth", "initials": "K"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Asplund", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2011-09-02", "journal": {"volume": "10", "issn": "1535-3907", "issue": "9", "pages": "4066-4075", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Human cancer cell lines grown in vitro are frequently used to decipher basic cell biological phenomena and to also specifically study different forms of cancer. Here we present the first large-scale study of protein expression patterns in cell lines using an antibody-based proteomics approach. We analyzed the expression pattern of 5436 proteins in 45 different cell lines using hierarchical clustering, principal component analysis, and two-group comparisons for the identification of differentially expressed proteins. Our results show that immunohistochemically determined protein profiles can categorize cell lines into groups that overall reflect the tumor tissue of origin and that hematological cell lines appear to retain their protein profiles to a higher degree than cell lines established from solid tumors. The two-group comparisons reveal well-characterized proteins as well as previously unstudied proteins that could be of potential interest for further investigations. Moreover, multiple myeloma cells and cells of myeloid origin were found to share a protein profile, relative to the protein profile of lymphoid leukemia and lymphoma cells, possibly reflecting their common dependency of bone marrow microenvironment. This work also provides an extensive list of antibodies, for which high-resolution images as well as validation data are available on the Human Protein Atlas ( www.proteinatlas.org ), that are of potential use in cell line studies.", "doi": "10.1021/pr200259v", "pmid": "21726073", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:47.937Z", "modified": "2021-07-08T13:44:33.629Z"}, {"entity": "publication", "iuid": "24d391bebc0340e9b9fb89683845c7d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24d391bebc0340e9b9fb89683845c7d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24d391bebc0340e9b9fb89683845c7d2"}}, "title": "Mapping the subcellular protein distribution in three human cell lines.", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Jonasson", "given": "Kalle", "initials": "K"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Abergh", "given": "Annica", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2011-08-05", "journal": {"volume": "10", "issn": "1535-3907", "issue": "8", "pages": "3766-3777", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The subcellular locations of proteins are closely related to their function and constitute an essential aspect for understanding the complex machinery of living cells. A systematic effort has been initiated to map the protein distribution in three functionally different cell lines with the aim to provide a subcellular localization index for at least one representative protein from all human protein-encoding genes. Here, we present the results of more than 3500 proteins mapped to 16 subcellular compartments. The results indicate a ubiquitous protein expression with a majority of the proteins found in all three cell lines and a large portion localized to two or more compartments. The inter-relationships between the subcellular compartments are visualized in a protein-compartment network based on all detected proteins. Hierarchical clustering was performed to determine how closely related the organelles are in terms of protein constituents and compare the proteins detected in each cell type. Our results show distinct organelle proteomes, well conserved across the cell types, and demonstrate that biochemically similar organelles are grouped together.", "doi": "10.1021/pr200379a", "pmid": "21675716", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:08.969Z", "modified": "2021-07-08T13:44:33.089Z"}, {"entity": "publication", "iuid": "f52e06e45f5441fd85c12a288c5606c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f52e06e45f5441fd85c12a288c5606c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f52e06e45f5441fd85c12a288c5606c4"}}, "title": "RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.", "authors": [{"family": "Ehl\u00e9n", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Br\u00e4ndstedt", "given": "Jenny", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "4", "issn": "1936-5233", "issue": "4", "pages": "212-221", "title": "Transl Oncol", "issn-l": null}, "abstract": "The RNA-binding motif protein 3 (RBM3) was initially discovered as a putative cancer biomarker based on its differential expression in various cancer forms in the Human Protein Atlas (HPA). We previously reported an association between high expression of RBM3 and prolonged survival in breast and epithelial ovarian cancer (EOC). Because the function of RBM3 has not been fully elucidated, the aim of this study was to use gene set enrichment analysis to identify the underlying biologic processes associated with RBM3 expression in a previously analyzed EOC cohort (cohort 1, n = 267). This revealed an association between RBM3 expression and several cellular processes involved in the maintenance of DNA integrity. RBM3-regulated genes were subsequently screened in the HPA to select for putative prognostic markers, and candidate proteins were analyzed in the ovarian cancer cell line A2780, whereby an up-regulation of Chk1, Chk2, and MCM3 was demonstrated in siRBM3-treated cells compared to controls. The prognostic value of these markers was assessed at the messenger RNA level in cohort 1 and the protein level in an independent EOC cohort (cohort 2, n = 154). High expression levels of Chk1, Chk2, and MCM3 were associated with a significantly shorter survival in both cohorts, and phosphorylated Chk2 was an adverse prognostic marker in cohort 2. These results uncover a putative role for RBM3 in DNA damage response, which might, in part, explain its cisplatin-sensitizing properties and good prognostic value in EOC. Furthermore, it is demonstrated that Chk1, Chk2, and MCM3 are poor prognostic markers in EOC.", "doi": "10.1593/tlo.11106", "pmid": "21804916", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pmc", "key": "PMC3140008"}], "notes": [], "created": "2017-05-04T14:55:49.446Z", "modified": "2021-06-22T12:17:19.596Z"}, {"entity": "publication", "iuid": "884ba280b10244048de9dd250b7257b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/884ba280b10244048de9dd250b7257b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/884ba280b10244048de9dd250b7257b9"}}, "title": "Low RBM3 protein expression correlates with tumour progression and poor prognosis in malignant melanoma: an analysis of 215 cases from the Malm\u00f6 Diet and Cancer Study.", "authors": [{"family": "Jonsson", "given": "Liv", "initials": "L"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Manjer", "given": "Jonas", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-07-21", "journal": {"volume": "9", "issn": "1479-5876", "issue": null, "pages": "114", "title": "J Transl Med", "issn-l": "1479-5876"}, "abstract": "We have previously reported that expression of the RNA- and DNA-binding protein RBM3 is associated with a good prognosis in breast cancer and ovarian cancer. In this study, the prognostic value of immunohistochemical RBM3 expression was assessed in incident cases of malignant melanoma from a prospective population-based cohort study.\n\nUntil Dec 31st 2008, 264 incident cases of primary invasive melanoma had been registered in the Malm\u00f6 Diet and Cancer Study. Histopathological and clinical information was obtained for available cases and tissue microarrays (TMAs) constructed from 226 (85.6%) suitable paraffin-embedded tumours and 31 metastases. RBM3 expression was analysed by immunohistochemistry on the TMAs and a subset of full-face sections. Chi-square and Mann-Whitney U tests were used for comparison of RBM3 expression and relevant clinicopathological characteristics. Kaplan Meier analysis and Cox proportional hazards modelling were used to assess the relationship between RBM3 and recurrence free survival (RFS) and overall survival (OS).\n\nRBM3 could be assessed in 215/226 (95.1%) of primary tumours and all metastases. Longitudinal analysis revealed that 16/31 (51.6%) of metastases lacked RBM3 expression, in contrast to the primary tumours in which RBM3 was absent in 3/215 (1.4%) cases and strongly expressed in 120/215 (55.8%) cases. Strong nuclear RBM3 expression in the primary tumour was significantly associated with favourable clinicopathological parameters; i.e. non-ulcerated tumours, lower depth of invasion, lower Clark level, less advanced clinical stage, low mitotic activity and non-nodular histological type, and a prolonged RFS (RR = 0.50; 95% CI = 0.27-0.91) and OS (RR = 0.36, 95%CI = 0.20-0.64). Multivariate analysis demonstrated that the beneficial prognostic value of RBM3 remained significant for OS (RR = 0.33; 95%CI = 0.18-0.61).\n\nIn line with previous in vitro data, we here show that RBM3 is down-regulated in metastatic melanoma and high nuclear RBM3 expression in the primary tumour is an independent marker of a prolonged OS. The potential utility of RBM3 in treatment stratification of patients with melanoma should be pursued in future studies.", "doi": "10.1186/1479-5876-9-114", "pmid": "21777469", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1479-5876-9-114"}, {"db": "pmc", "key": "PMC3156749"}], "notes": [], "created": "2017-05-04T14:55:48.238Z", "modified": "2021-07-08T13:44:33.391Z"}, {"entity": "publication", "iuid": "5303e6e8eb5743bb819fab14cfeb67b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5303e6e8eb5743bb819fab14cfeb67b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5303e6e8eb5743bb819fab14cfeb67b2"}}, "title": "SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.", "authors": [{"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "de Wit", "given": "Meike", "initials": "M"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Johnson", "given": "Louis B", "initials": "LB"}, {"family": "McGee", "given": "Sharon F", "initials": "SF"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Naicker", "given": "Kirsha", "initials": "K"}, {"family": "Klinger", "given": "Rut", "initials": "R"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Kilpinen", "given": "Sami", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Belt", "given": "Eric", "initials": "E"}, {"family": "Goos", "given": "Jeroen", "initials": "J"}, {"family": "Meijer", "given": "Gerrit", "initials": "G"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2011-07-00", "journal": {"volume": "35", "issn": "1532-0979", "issue": "7", "pages": "937-948", "title": "Am. J. Surg. Pathol.", "issn-l": "0147-5185"}, "abstract": "The special AT-rich sequence-binding protein 2 (SATB2), a nuclear matrix-associated transcription factor and epigenetic regulator, was identified as a tissue type-specific protein when screening protein expression patterns in human normal and cancer tissues using an antibody-based proteomics approach. In this respect, the SATB2 protein shows a selective pattern of expression and, within cells of epithelial lineages, SATB2 expression is restricted to glandular cells lining the lower gastrointestinal tract. The expression of SATB2 protein is primarily preserved in cancer cells of colorectal origin, indicating that SATB2 could function as a clinically useful diagnostic marker to distinguish colorectal cancer (CRC) from other types of cancer. The aim of this study was to further explore and validate the specific expression pattern of SATB2 as a clinical biomarker and to compare SATB2 with the well-known cytokeratin 20 (CK20). Immunohistochemistry was used to analyze the extent of SATB2 expression in tissue microarrays with tumors from 9 independent cohorts of patients with primary and metastatic CRCs (n=1882). Our results show that SATB2 is a sensitive and highly specific marker for CRC with distinct positivity in 85% of all CRCs, and that SATB2 and/or CK20 was positive in 97% of CRCs. In conclusion, the specific expression of SATB2 in a large majority of CRCs suggests that SATB2 can be used as an important complementary tool for the differential diagnosis of carcinoma of unknown primary origin.", "doi": "10.1097/PAS.0b013e31821c3dae", "pmid": "21677534", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "00000478-201107000-00001"}], "notes": [], "created": "2017-05-04T14:55:08.363Z", "modified": "2021-07-08T13:44:33.256Z"}, {"entity": "publication", "iuid": "686f536c265a43c5be5d03c143d4c835", "links": {"self": {"href": "https://publications.scilifelab.se/publication/686f536c265a43c5be5d03c143d4c835.json"}, "display": {"href": "https://publications.scilifelab.se/publication/686f536c265a43c5be5d03c143d4c835"}}, "title": "Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.", "authors": [{"family": "Jakobsen", "given": "Lis", "initials": "L"}, {"family": "Vanselow", "given": "Katja", "initials": "K"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Toyoda", "given": "Yusuke", "initials": "Y"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Poser", "given": "Ina", "initials": "I"}, {"family": "Falkenby", "given": "Lasse G", "initials": "LG"}, {"family": "Bennetzen", "given": "Martin", "initials": "M"}, {"family": "Westendorf", "given": "Jens", "initials": "J"}, {"family": "Nigg", "given": "Erich A", "initials": "EA"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hyman", "given": "Anthony A", "initials": "AA"}, {"family": "Andersen", "given": "Jens S", "initials": "JS"}], "type": "journal article", "published": "2011-04-20", "journal": {"volume": "30", "issn": "1460-2075", "issue": "8", "pages": "1520-1535", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "Centrosomes in animal cells are dynamic organelles with a proteinaceous matrix of pericentriolar material assembled around a pair of centrioles. They organize the microtubule cytoskeleton and the mitotic spindle apparatus. Mature centrioles are essential for biogenesis of primary cilia that mediate key signalling events. Despite recent advances, the molecular basis for the plethora of processes coordinated by centrosomes is not fully understood. We have combined protein identification and localization, using PCP-SILAC mass spectrometry, BAC transgeneOmics, and antibodies to define the constituents of human centrosomes. From a background of non-specific proteins, we distinguished 126 known and 40 candidate centrosomal proteins, of which 22 were confirmed as novel components. An antibody screen covering 4000 genes revealed an additional 113 candidates. We illustrate the power of our methods by identifying a novel set of five proteins preferentially associated with mother or daughter centrioles, comprising genes implicated in cell polarity. Pulsed labelling demonstrates a remarkable variation in the stability of centrosomal protein complexes. These spatiotemporal proteomics data provide leads to the further functional characterization of centrosomal proteins.", "doi": "10.1038/emboj.2011.63", "pmid": "21399614", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "emboj201163"}, {"db": "pmc", "key": "PMC3102290"}], "notes": [], "created": "2017-05-04T14:55:08.671Z", "modified": "2021-07-08T13:44:33.329Z"}, {"entity": "publication", "iuid": "afa95f4100dc4c0da07afa5c8d24a1b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afa95f4100dc4c0da07afa5c8d24a1b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afa95f4100dc4c0da07afa5c8d24a1b6"}}, "title": "Systematic antibody and antigen-based proteomic profiling with microarrays.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "11", "issn": "1744-8352", "issue": "2", "pages": "219-234", "title": "Expert Rev. Mol. Diagn.", "issn-l": "1473-7159"}, "abstract": "Current approaches within affinity-based proteomics are driven both by the accessibility and availability of antigens and capture reagents, and by suitable multiplexed technologies onto which these are implemented. By combining planar microarrays and other multiparallel systems with sets of reagents, possibilities to discover new and unpredicted protein-disease associations, either via directed hypothesis-driven or via undirected hypothesis-generating target selection, can be created. In the following stages, the discoveries made during these screening phases have to be verified for potential clinical relevance based on both technical and biological aspects. The use of affinity tools throughout discovery and verification has the potential to streamline the introduction of new markers, as transition into clinically required assay formats appears straightforward. In this article, we summarize some of the current building blocks within array- and affinity-based proteomic profiling with a focus on body fluids, by giving a perspective on how current and upcoming developments in this bioscience could enable a path of pursuit for biomarker discovery.", "doi": "10.1586/erm.10.110", "pmid": "21405972", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.977Z", "modified": "2021-07-08T13:44:33.525Z"}, {"entity": "publication", "iuid": "2554eb3b0bec43aebf752978fa30a3c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2554eb3b0bec43aebf752978fa30a3c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2554eb3b0bec43aebf752978fa30a3c1"}}, "title": "Tumor-specific HMG-CoA reductase expression in primary premenopausal breast cancer predicts response to tamoxifen.", "authors": [{"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Laursen", "given": "Henriette", "initials": "H"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Borgquist", "given": "Signe", "initials": "S"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Millikan", "given": "Robert C", "initials": "RC"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-01-31", "journal": {"volume": "13", "issn": "1465-542X", "issue": "1", "pages": "R12", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "We previously reported an association between tumor-specific 3-hydroxy-3-methylglutharyl-coenzyme A reductase (HMG-CoAR) expression and a good prognosis in breast cancer. Here, the predictive value of HMG-CoAR expression in relation to tamoxifen response was examined.\n\nHMG-CoAR protein and RNA expression was analyzed in a cell line model of tamoxifen resistance using western blotting and PCR. HMG-CoAR mRNA expression was examined in 155 tamoxifen-treated breast tumors obtained from a previously published gene expression study (Cohort I). HMG-CoAR protein expression was examined in 422 stage II premenopausal breast cancer patients, who had previously participated in a randomized control trial comparing 2 years of tamoxifen with no systemic adjuvant treatment (Cohort II). Kaplan-Meier analysis and Cox proportional hazards modeling were used to estimate the risk of recurrence-free survival (RFS) and the effect of HMG-CoAR expression on tamoxifen response.\n\nHMG-CoAR protein and RNA expression were decreased in tamoxifen-resistant MCF7-LCC9 cells compared with their tamoxifen-sensitive parental cell line. HMG-CoAR mRNA expression was decreased in tumors that recurred following tamoxifen treatment (P < 0.001) and was an independent predictor of RFS in Cohort I (hazard ratio = 0.63, P = 0.009). In Cohort II, adjuvant tamoxifen increased RFS in HMG-CoAR-positive tumors (P = 0.008). Multivariate Cox regression analysis demonstrated that HMG-CoAR was an independent predictor of improved RFS in Cohort II (hazard ratio = 0.67, P = 0.010), and subset analysis revealed that this was maintained in estrogen receptor (ER)-positive patients (hazard ratio = 0.65, P = 0.029). Multivariate interaction analysis demonstrated a difference in tamoxifen efficacy relative to HMG-CoAR expression (P = 0.05). Analysis of tamoxifen response revealed that patients with ER-positive/HMG-CoAR tumors had a significant response to tamoxifen (P = 0.010) as well as patients with ER-positive or HMG-CoAR-positive tumors (P = 0.035). Stratification according to ER and HMG-CoAR status demonstrated that ER-positive/HMG-CoAR-positive tumors had an improved RFS compared with ER-positive/HMG-CoAR-negative tumors in the treatment arm (P = 0.033); this effect was lost in the control arm (P = 0.138), however, suggesting that HMG-CoAR predicts tamoxifen response.\n\nHMG-CoAR expression is a predictor of response to tamoxifen in both ER-positive and ER-negative disease. Premenopausal patients with tumors that express ER or HMG-CoAR respond to adjuvant tamoxifen.", "doi": "10.1186/bcr2820", "pmid": "21281480", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "bcr2820"}, {"db": "pmc", "key": "PMC3109580"}], "notes": [], "created": "2017-05-04T14:55:45.527Z", "modified": "2021-07-08T13:44:33.095Z"}, {"entity": "publication", "iuid": "8976e73062c743639011aea31322f5c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8976e73062c743639011aea31322f5c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8976e73062c743639011aea31322f5c4"}}, "title": "Defining the transcriptome and proteome in three functionally different human cell lines.", "authors": [{"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Matic", "given": "Ivan", "initials": "I"}, {"family": "Geiger", "given": "Tamar", "initials": "T"}, {"family": "Cox", "given": "Juergen", "initials": "J"}, {"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2010-12-21", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "issn-l": "1744-4292", "volume": "6", "issue": null, "pages": "450"}, "abstract": "An essential question in human biology is how cells and tissues differ in gene and protein expression and how these differences delineate specific biological function. Here, we have performed a global analysis of both mRNA and protein levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based mass spectrometry analysis and antibody-based confocal microscopy. The study was performed in three functionally different human cell lines and based on the global analysis, we estimated the fractions of mRNA and protein that are cell specific or expressed at similar/different levels in the cell lines. A highly ubiquitous RNA expression was found with >60% of the gene products detected in all cells. The changes of mRNA and protein levels in the cell lines using SILAC and RNA ratios show high correlations, even though the genome-wide dynamic range is substantially higher for the proteins as compared with the transcripts. Large general differences in abundance for proteins from various functional classes are observed and, in general, the cell-type specific proteins are low abundant and highly enriched for cell-surface proteins. Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins.", "doi": "10.1038/msb.2010.106", "pmid": "21179022", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "msb2010106"}, {"db": "pmc", "key": "PMC3018165"}, {"db": "BioProject", "description": "Deep sequencing of the transcriptome of three human cell lines for the Human Protein Atlas", "key": "PRJNA79633"}, {"db": "SRA", "description": "Deep sequencing of the transcriptome of three human cell lines for the Human Protein Atlas (short read raw data)", "key": "SRP002338"}], "notes": [], "created": "2017-05-04T14:55:07.459Z", "modified": "2023-04-27T09:48:59.529Z"}, {"entity": "publication", "iuid": "bbc4aa27752846dea221f0b103fdcdbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbc4aa27752846dea221f0b103fdcdbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbc4aa27752846dea221f0b103fdcdbf"}}, "title": "Analysis of transcript and protein overlap in a human osteosarcoma cell line.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-12-02", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "684", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).\r\n\r\nA large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.\r\n\r\nThis suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.", "doi": "10.1186/1471-2164-11-684", "pmid": "21126332", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-684"}, {"db": "pmc", "key": "PMC3014981"}, {"db": "BioProject", "description": "RNA-seq of human osteosarcoma cell line U2-OS", "key": "PRJNA79747"}, {"db": "SRA", "description": "RNA-seq of human osteosarcoma cell line U2-OS", "key": "SRP003405"}], "notes": [], "created": "2017-05-04T14:55:06.554Z", "modified": "2021-07-08T13:44:33.569Z"}, {"entity": "publication", "iuid": "78b877d735664093a8a37345d69d87c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78b877d735664093a8a37345d69d87c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78b877d735664093a8a37345d69d87c7"}}, "title": "SOX10 expression in superficial spreading and nodular malignant melanomas.", "authors": [{"family": "Agnarsd\u00f3ttir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Sooman", "given": "Linda", "initials": "L"}, {"family": "Bolander", "given": "Asa", "initials": "A"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Gallagher", "given": "William", "initials": "W"}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hedstrand", "given": "H\u00e5kan", "initials": "H"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "20", "issn": "1473-5636", "issue": "6", "pages": "468-478", "title": "Melanoma Res.", "issn-l": "0960-8931"}, "abstract": "SOX10 is a transcription factor expressed in nerve cells and melanocytes. The aim of this study was to investigate the protein expression pattern of SOX10 in malignant melanoma tumors and to analyze whether the results correlated with clinical parameters and the proliferation marker Ki-67. Furthermore, proliferation and migration were analyzed in three different cell lines employing SOX10 small interfering RNA-mediated silencing. Expression patterns were determined in 106 primary tumors and 39 metastases in addition to 16 normal skin samples and six benign nevi employing immunohistochemistry and tissue microarrays. The immunohistochemical staining was evaluated manually and with an automated algorithm. SOX10 was strongly expressed in the benign tissues, but for the malignant tumors superficial spreading melanomas stained stronger than nodular malignant melanomas (P=0.008). The staining intensity was also inversely correlated with T-stage (Spearman's \u03c1=-0.261, P=0.008). Overall survival and time to recurrence were significantly correlated with SOX10 intensity, but not in multivariate analysis including T-stage. With the automated algorithm there was an inverse correlation between the SOX10 staining intensity and the proliferation marker, Ki-67 (\u03c1=-0.173, P=0.02) and a significant difference in the intensity signal between the benign tissues, the primary tumors and the metastases where the metastases stained the weakest (P\u22640.001). SOX10 downregulation resulted in variable effects on proliferation and migration rates in the melanoma cell lines. In conclusion, the SOX10 intensity level differed depending on the tissue studied and SOX10 might have a role in survival. No conclusion regarding the role of SOX10 for in-vitro proliferation and migration could be drawn.", "doi": "10.1097/CMR.0b013e3283403ccd", "pmid": "20890226", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:44.709Z", "modified": "2021-07-08T13:44:33.369Z"}, {"entity": "publication", "iuid": "fb446ca4d0534cbfab21de4404938c49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb446ca4d0534cbfab21de4404938c49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb446ca4d0534cbfab21de4404938c49"}}, "title": "Towards a knowledge-based Human Protein Atlas.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Jonasson", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Wernerus", "given": "Henrik", "initials": "H"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "letter", "published": "2010-12-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "28", "issue": "12", "pages": "1248-1250"}, "abstract": null, "doi": "10.1038/nbt1210-1248", "pmid": "21139605", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "nbt1210-1248"}], "notes": [], "created": "2017-05-04T14:55:07.757Z", "modified": "2021-07-08T13:44:33.767Z"}, {"entity": "publication", "iuid": "64c09e829c5b4b38acb0651cdc56bed7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64c09e829c5b4b38acb0651cdc56bed7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64c09e829c5b4b38acb0651cdc56bed7"}}, "title": "Creation of an antibody-based subcellular protein atlas.", "authors": [{"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2010-11-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "22", "pages": "3984-3996", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "An important part for understanding the complex machinery of living cells is to know the spatial distribution of proteins all the way from organ to organelle levels. An equally important part of proteomics is to map the subcellular distribution of all human proteins. Here, we discuss methodologies for systematic subcellular profiling with emphasis on the antibody-based approach performed as a part of the Human Protein Atlas project. The considerations made when creating the subcellular protein atlas and critical parameters of this approach are discussed.", "doi": "10.1002/pmic.201000125", "pmid": "20648481", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:08.056Z", "modified": "2021-07-08T13:44:33.324Z"}, {"entity": "publication", "iuid": "9972459d788b4187a2c11c60c744ce88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9972459d788b4187a2c11c60c744ce88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9972459d788b4187a2c11c60c744ce88"}}, "title": "Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Langen", "given": "Hanno", "initials": "H"}, {"family": "Becker", "given": "Charlotte", "initials": "C"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "evaluation studies", "published": "2010-11-00", "journal": {"volume": "9", "issn": "1535-9484", "issue": "11", "pages": "2497-2507", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format.", "doi": "10.1074/mcp.M110.001560", "pmid": "20682762", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "M110.001560"}, {"db": "pmc", "key": "PMC2984230"}], "notes": [], "created": "2017-05-04T14:55:29.167Z", "modified": "2021-07-08T13:44:33.459Z"}, {"entity": "publication", "iuid": "48f20361419045e3bacde5fd8576433b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48f20361419045e3bacde5fd8576433b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48f20361419045e3bacde5fd8576433b"}}, "title": "Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer.", "authors": [{"family": "Ehl\u00e9n", "given": "Asa", "initials": "A"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M"}, {"family": "Jeffrey", "given": "Ian B", "initials": "IB"}, {"family": "Manjer", "given": "Jonas", "initials": "J"}, {"family": "Br\u00e4ndstedt", "given": "Jenny", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2010-08-20", "journal": {"volume": "8", "issn": "1479-5876", "issue": null, "pages": "78", "title": "J Transl Med", "issn-l": "1479-5876"}, "abstract": "We recently demonstrated that increased expression of the RNA-binding protein RBM3 is associated with a favourable prognosis in breast cancer. The aim of this study was to examine the prognostic value of RBM3 mRNA and protein expression in epithelial ovarian cancer (EOC) and the cisplatin response upon RBM3 depletion in a cisplatin-sensitive ovarian cancer cell line.\n\nRBM3 mRNA expression was analysed in tumors from a cohort of 267 EOC cases (Cohort I) and RBM3 protein expression was analysed using immunohistochemistry (IHC) in an independent cohort of 154 prospectively collected EOC cases (Cohort II). Kaplan Meier analysis and Cox proportional hazards modelling were applied to assess the relationship between RBM3 and recurrence free survival (RFS) and overall survival (OS). Immunoblotting and IHC were used to examine the expression of RBM3 in a cisplatin-resistant ovarian cancer cell line A2780-Cp70 and its cisplatin-responsive parental cell line A2780. The impact of RBM3 on cisplatin response in EOC was assessed using siRNA-mediated silencing of RBM3 in A2780 cells followed by cell viability assay and cell cycle analysis.\n\nIncreased RBM3 mRNA expression was associated with a prolonged RFS (HR = 0.64, 95% CI = 0.47-0.86, p = 0.003) and OS (HR = 0.64, 95% CI = 0.44-0.95, p = 0.024) in Cohort I. Multivariate analysis confirmed that RBM3 mRNA expression was an independent predictor of a prolonged RFS, (HR = 0.61, 95% CI = 0.44-0.84, p = 0.003) and OS (HR = 0.62, 95% CI = 0.41-0.95; p = 0.028) in Cohort I. In Cohort II, RBM3 protein expression was associated with a prolonged OS (HR = 0.53, 95% CI = 0.35-0.79, p = 0.002) confirmed by multivariate analysis (HR = 0.61, 95% CI = 0.40-0.92, p = 0.017). RBM3 mRNA and protein expression levels were significantly higher in the cisplatin sensitive A2780 cell line compared to the cisplatin resistant A2780-Cp70 derivative. siRNA-mediated silencing of RBM3 expression in the A2780 cells resulted in a decreased sensitivity to cisplatin as demonstrated by increased cell viability and reduced proportion of cells arrested in the G2/M-phase.\n\nThese data demonstrate that RBM3 expression is associated with cisplatin sensitivity in vitro and with a good prognosis in EOC. Taken together these findings suggest that RBM3 may be a useful prognostic and treatment predictive marker in EOC.", "doi": "10.1186/1479-5876-8-78", "pmid": "20727170", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1479-5876-8-78"}, {"db": "pmc", "key": "PMC2936876"}], "notes": [], "created": "2017-05-04T14:55:44.411Z", "modified": "2021-07-08T13:44:33.212Z"}, {"entity": "publication", "iuid": "bca7359920d249f580926e20f55a251d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bca7359920d249f580926e20f55a251d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bca7359920d249f580926e20f55a251d"}}, "title": "Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Engkvist", "given": "Margareta", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "9", "issn": "1944-7930", "issue": "49", "pages": "565-578", "title": "Discov Med", "issn-l": "1539-6509"}, "abstract": "Abnormal glucose tolerance and deviant blood glucose levels are late stage clinical parameters that signify diabetes mellitus. To be able to diagnose the disease at an earlier stage and develop new tools for beta cell imaging, new molecular markers are needed. In the present study, five proteins highly expressed in pancreatic islets with no expression in the surrounding exocrine glandular cells of pancreas, and one protein with the opposite expression pattern, were identified by searches in the Human Protein Atlas (www.proteinatlas.org). The proteins were analyzed immunohistochemically on a specially designed tissue microarray, containing isolated human islets and pancreatic tissues with different characteristics, and compared to the expression of previously known markers of endocrine and exocrine pancreatic cells. Of the five novel endocrine markers, tetraspanin-7 was identified as a membrane-bound protein with exclusive positivity in islet cells. Also beta-2-microglobulin and ubiquitin carboxyl-terminal hydrolase isozyme L1 were expressed in a majority of islet cells, whereas sad1/unc-84 domain-containing protein 1 and beta-1,3-glucuronyltransferase 1 were positive in a smaller subset of islet cells. The potential exocrine marker galectin-2 was expressed in both exocrine acinary cells and pancreatic ductal cells, with no or low positivity in islet cells. In conclusion, antibody-based proteomics and specially designed tissue microarrays enable identification and exploration of novel proteins with differential expression in pancreatic islets. Here we describe 5 candidate proteins for further investigation of their physiological role and potential involvement in the pathogenesis of diabetes. One of these proteins, tetraspanin-7, is expressed on the cell membrane and could thus be a potential candidate for future development of tracers for beta cell imaging.", "doi": null, "pmid": "20587347", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:43.077Z", "modified": "2025-12-01T07:53:07.307Z"}, {"entity": "publication", "iuid": "90e28024d1b044f989e50b6052ceca1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90e28024d1b044f989e50b6052ceca1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90e28024d1b044f989e50b6052ceca1a"}}, "title": "A single fixation protocol for proteome-wide immunofluorescence localization studies.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2010-04-18", "journal": {"volume": "73", "issn": "1876-7737", "issue": "6", "pages": "1067-1078", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Immunofluorescence microscopy is a valuable tool for analyzing protein expression and localization at a subcellular level thus providing information regarding protein function, interaction partners and its role in cellular processes. When performing sample fixation, parameters such as difference in accessibility of proteins present in various cellular compartments as well as the chemical composition of the protein to be studied, needs to be taken into account. However, in systematic and proteome-wide efforts, a need exists for standard fixation protocol(s) that works well for the majority of all proteins independent of subcellular localization. Here, we report on a study with the goal to find a standardized protocol based on the analysis of 18 human proteins localized in 11 different organelles and subcellular structures. Six fixation protocols were tested based on either dehydration by alcohols (methanol, ethanol or iso-propanol) or cross-linking by paraformaldehyde followed by detergent permeabilization (Triton X-100 or saponin) in three human cell lines. Our results show that cross-linking is essential for proteome-wide localization studies and that cross-linking using paraformaldehyde followed by Triton X-100 permeabilization successfully can be used as a single fixation protocol for systematic studies.", "doi": "10.1016/j.jprot.2009.10.012", "pmid": "19896565", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(09)00310-8"}], "notes": [], "created": "2017-05-04T14:55:07.153Z", "modified": "2021-07-08T13:44:33.428Z"}, {"entity": "publication", "iuid": "429804ab762c412ca8c87002ab2edf17", "links": {"self": {"href": "https://publications.scilifelab.se/publication/429804ab762c412ca8c87002ab2edf17.json"}, "display": {"href": "https://publications.scilifelab.se/publication/429804ab762c412ca8c87002ab2edf17"}}, "title": "Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer.", "authors": [{"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Br\u00e4ndstedt", "given": "Jenny", "initials": "J"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Foley", "given": "Michael", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "O'Herlihy", "given": "Colm", "initials": "C"}, {"family": "Jirstrom", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2010-04-01", "journal": {"volume": "10", "issn": "1471-2407", "issue": null, "pages": "125", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Our group previously reported that tumour-specific expression of the rate-limiting enzyme in the mevalonate pathway, 3-hydroxy-3-methylglutharyl-coenzyme A reductase (HMG-CoAR) is associated with more favourable tumour parameters and a good prognosis in breast cancer. In the present study, the prognostic value of HMG-CoAR expression was examined in tumours from a cohort of patients with primary epithelial ovarian cancer.\n\nHMG-CoAR expression was assessed using immunohistochemistry (IHC) on tissue microarrays (TMA) consisting of 76 ovarian cancer cases, analysed using automated algorithms to develop a quantitative scoring model. Kaplan Meier analysis and Cox proportional hazards modelling were used to estimate the risk of recurrence free survival (RFS).\n\nSeventy-two tumours were suitable for analysis. Cytoplasmic HMG-CoAR expression was present in 65% (n = 46) of tumours. No relationship was seen between HMG-CoAR and age, histological subtype, grade, disease stage, estrogen receptor or Ki-67 status. Patients with tumours expressing HMG-CoAR had a significantly prolonged RFS (p = 0.012). Multivariate Cox regression analysis revealed that HMG-CoAR expression was an independent predictor of improved RFS (RR = 0.49, 95% CI (0.25-0.93); p = 0.03) when adjusted for established prognostic factors such as residual disease, tumour stage and grade.\n\nHMG-CoAR expression is an independent predictor of prolonged RFS in primary ovarian cancer. As HMG-CoAR inhibitors, also known as statins, have demonstrated anti-neoplastic effects in vitro, further studies are required to evaluate HMG-CoAR expression as a surrogate marker of response to statin treatment, especially in conjunction with current chemotherapeutic regimens.", "doi": "10.1186/1471-2407-10-125", "pmid": "20359358", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1471-2407-10-125"}, {"db": "pmc", "key": "PMC3087316"}], "notes": [], "created": "2017-05-04T14:55:42.475Z", "modified": "2021-07-08T13:44:33.190Z"}, {"entity": "publication", "iuid": "56cce9107c664ed28106aea7b9231404", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56cce9107c664ed28106aea7b9231404.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56cce9107c664ed28106aea7b9231404"}}, "title": "Molecular profiling using tissue microarrays as a tool to identify predictive biomarkers in laryngeal cancer treated with radiotherapy.", "authors": [{"family": "Holgersson", "given": "Georg", "initials": "G"}, {"family": "Ekman", "given": "Simon", "initials": "S", "orcid": "0000-0002-8343-6226", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fcb2b2956a84f43a7b485573f445ff2.json"}}, {"family": "Reizenstein", "given": "Johan", "initials": "J"}, {"family": "Bergqvist", "given": "Michael", "initials": "M", "orcid": "0009-0003-5716-3716", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d33e374d0642479a80683a989f095a.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "Mattias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "Jonnalagadda", "given": "Pallavi", "initials": "P"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "Linder", "given": "Arne", "initials": "A"}, {"family": "Blomquist", "given": "Erik", "initials": "E"}, {"family": "Liljeholm", "given": "Martin", "initials": "M"}, {"family": "L\u00f6d\u00e9n", "given": "Britta", "initials": "B"}, {"family": "Hellstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Bergstr\u00f6m", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2010-02-26", "journal": {"volume": "7", "issn": "1790-6245", "issue": "1", "pages": "1-7", "title": "Cancer Genomics Proteomics", "issn-l": "1109-6535"}, "abstract": "To explore the usefulness of the expression of five potential cancer biomarkers in predicting outcome in patients with laryngeal cancer.\n\nIn the present study, the Swedish National Cancer Registry databases were used to identify patients with laryngeal cancer diagnosed during the years 1978-2004 in the Uppsala-Orebro region and treated with radiotherapy. The expression of Ki-67, MutS homolog 2, (MSH2), p53, B-cell CLL/lymphoma 2 (Bcl-2) and cyclin D1 in the cancer cells was assessed immunohistochemically using tissue microarrays (TMAs) and its predicitve value on survival and relapse was analyzed using Cox regression models.\n\nA total of 39 patients were included in the present study. Nuclear MSH2 staining was statistically significantly correlated to Ki-67 expression (p=0.022). However, univariate and multivariate Cox analyses showed no statistically significant association between the expression of the investigated biomarkers and overall survival or relapse.\n\nThe present exploratory study does not show any significant predictive value of the biomarkers examined with respect to survival or relapse. However, with larger patient cohorts, we believe that protein profiling using TMAs and immunohistochemistry is a feasible strategy for prognostic and predictive biomarker screening in laryngeal cancer.", "doi": null, "pmid": "20181625", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "7/1/1"}], "notes": [], "created": "2017-05-04T14:55:42.778Z", "modified": "2025-11-17T09:52:58.446Z"}, {"entity": "publication", "iuid": "948787308e4448c8b8ce4ef0438881e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2"}}, "title": "Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "3", "pages": "532-540", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead array. The intensity levels were used to define protein profiles and no significant differences between serum and plasma were observed for 79% of the 174 antibodies (targeting 156 proteins). By excluding 36 antibodies giving rise to differential intensity levels, cluster analysis revealed donor-specific rather than preparation-dependent grouping. With a cohort from a clinically relevant medical condition, the metabolic syndrome, the influence of the sample type on a multiplexed biomarker discovery approach was further investigated. Independent comparisons of protein profiles in serum and plasma revealed an antibody targeting ADAMTSL-4, a protein that would qualify to be studied further in association with the condition. In general, the preparation type had an impact on the results of the applied antibody suspension bead array, and while the technical variability was equal, plasma offered a greater biological variability and allowed to give rise to more discoveries than serum.", "doi": "10.1002/pmic.200900657", "pmid": "19953555", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.681Z", "modified": "2021-07-08T13:44:33.443Z"}, {"entity": "publication", "iuid": "9e8e6184e92141b8947d4bd5b6f3c8df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e8e6184e92141b8947d4bd5b6f3c8df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e8e6184e92141b8947d4bd5b6f3c8df"}}, "title": "Tissue-Specific Protein Expression in Human Cells, Tissues and Organs", "authors": [{"family": "Marcus", "given": "Gry", "initials": "G"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Pont\u00e9n", "given": "F", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal-article", "published": "2010-00-00", "journal": {"title": "JPB", "issn": "0974-276X", "issn-l": "0974-276X", "volume": "03", "issue": "10", "pages": null}, "abstract": "An important part of understanding human biology is the study of tissue-speci fi c expression both at the gene and protein level. In this study, the analysis of tissue speci fi c protein expression was performed based on tissue micro array data available on the public Human Protein Atlas database (www.proteinatlas.org). An analysis of human proteins, corresponding to approximately one third of the protein-encoding genes, was carried out in 65 human tissues and cell types. The spatial distribution and relative abundance of 6,678 human proteins, were analyzed in different cell populations from various organs and tissues in the human body using unsupervised methods, such as hierarchical clustering and principal component analysis, as well as with supervised methods (Breiman, 2001). Well-known markers, such as neuromodulin for the central nervous system, keratin 20 for gastrointestinal tract and CD45 for hematopoietic cells, were identi fi ed as tissue-speci fi c. Proteins expressed in a tissue-speci fi c manner were identi fi ed for cells in all of the investigated tissues, including the central nervous system, hematopoietic system, squamous epithelium, mesenchymal cells and cells from the gastrointestinal tract. Several proteins not yet associated with tissue-speci fi city were identi fi ed, providing starting points for further studies to explore tissue-speci fi c functions. This includes proteins with no known function, such as ZNF509 expressed in CNS and C1orf201 expressed in the gastro-intestinal tract. In general, the majority of the gene products are expressed in a ubiquitous manner and few proteins are detected exclusively in cells from a particular tissue class, as exempli fi ed by less than 1% of the analyzed proteins found only in the brain.", "doi": "10.4172/jpb.1000153", "pmid": null, "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:44.151Z", "modified": "2021-06-22T12:11:12.782Z"}]}