{"entity": "researcher", "timestamp": "2026-07-14T01:37:42.957Z", "family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31"}}, "publications": [{"entity": "publication", "iuid": "b523e0bb42a74513b082b7459e71438f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b523e0bb42a74513b082b7459e71438f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b523e0bb42a74513b082b7459e71438f"}}, "title": "Image based subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing.", "authors": [{"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "H Le", "given": "Trang", "initials": "T"}, {"family": "Asp", "given": "Elin", "initials": "E"}, {"family": "Kalman", "given": "Adelinn", "initials": "A"}, {"family": "Kaimal", "given": "Jayasankar Mohanakrishnan", "initials": "JM"}, {"family": "Njenda", "given": "Duncan", "initials": "D", "orcid": "0000-0001-8276-9726", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14c27f4d60549da9949c97ed66a15b5.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e276634741d45249c7cec0b46a7d9f4.json"}}, {"family": "Axelsson", "given": "Hanna", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "Marabita", "given": "Francesco", "initials": "F", "orcid": "0000-0001-6180-0106", "researcher": {"href": "https://publications.scilifelab.se/researcher/05a6497e6561419f86f3227618e536fa.json"}}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2359-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a0f932253042239c1d38ea00ca0018.json"}}, {"family": "Sepulveda", "given": "Carolina Oses", "initials": "CO", "orcid": "0000-0001-8194-1168", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9dd54ba67d4f10a5ba6d0b4ede67bc.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Vernersson", "given": "Caroline", "initials": "C"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-5501-466X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0461a910ec4b4faa8668bb4044e76f61.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "journal article", "published": "2025-08-16", "journal": {"title": "Biomed Pharmacother", "issn": "1950-6007", "volume": "191", "pages": "118447", "issn-l": null}, "abstract": "The COVID-19 pandemic has resulted in millions of deaths and affected socioeconomic structure worldwide and the search for new antivirals and treatments are still ongoing. In the search for new drug targets and to increase our understanding of the disease, we applied large-scale immunofluorescence profiling to explore host cell response to SARS-CoV-2 infection. Among the 602 host proteins studied in this host response profiling, changes in abundance and subcellular localization were observed for 97 proteins, with 45 proteins showing increased abundance and 10 reduced abundance. 20 proteins displayed changed localization upon infection and an additional 22 proteins displayed altered abundance and localization, together contributing to diverse reshuffling of the host cell protein landscape during infection. We then selected existing and approved small-molecule drugs (n = 123) against our identified host response proteins and identified one compound - elesclomol, that significantly reduced antiviral activity. Our study introduces a novel, targeted and systematic approach based on host protein profiling, to identify new targets for drug repurposing. The dataset of > 100,000 immunofluorescence images from this study are published as a resource available for further studies. AUTHOR SUMMARY: In this study we have evaluated a new approach for identifying drugs that could be used as antiviral drugs, in this case demonstrated for SARS CoV-2. By mining the literature for reported interactions between SARS CoV-2 viral components and host cell proteins, we identified a few hundred host proteins suggested to interact with the virus upon infection. To explore these viral-host interaction proteins further, we developed an image based assay using immunofluorescence and confocal microscopy to visualize the host proteins within infected and non infected cells. This was possible due to the proteome wide collection of antibodies generated within the Human Protein Atlas project, with the aim to systematically map the human proteome in cells and across tissues. The host proteins that altered their location or abundance level upon infection were regarded as putative targets for drug repurposing and we subsequently tested 123 drugs that were targeting a subset of these host proteins. Applying these drugs on two different cell types infected with SARS-CoV-2, revealed a non toxic antiviral effect for one compound that can be explored further as a treatment regimen for SARS-CoV-2 infection. The approach is novel since it combines a targeted approach for drug repurposing screening, giving insight into mechanism of action from start. As such it has the potential to accelerate drug repurposing or identification of targets for new drugs.", "doi": "10.1016/j.biopha.2025.118447", "pmid": "40819539", "labels": {"Spatial Proteomics": "Collaborative", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0753-3322(25)00641-9"}], "notes": [], "created": "2025-08-19T14:16:21.879Z", "modified": "2025-10-17T13:04:26.503Z"}, {"entity": "publication", "iuid": "43ff9ae2ee304005b3b75d388520674e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43ff9ae2ee304005b3b75d388520674e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43ff9ae2ee304005b3b75d388520674e"}}, "title": "From Recruitment to Retirement: Research Infrastructure Staff Views on the Diversification of Scientific Career Paths at Universities in Sweden in 2024.", "authors": [{"family": "Schroeder", "given": "Kristen", "initials": "K", "orcid": "0000-0002-6271-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/79f3c1b13a9844be86fdce0b7f425fb3.json"}}, {"family": "Fern\u00e1ndez-Rodr\u00edguez", "given": "Julia", "initials": "J"}, {"family": "Jenmalm-Jensen", "given": "Annika", "initials": "A"}, {"family": "Lundgren-Gawell", "given": "Josefin", "initials": "J"}, {"family": "Sandin", "given": "Sara", "initials": "S"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}], "type": "journal article", "published": "2025-07-04", "journal": {"title": "F1000Res", "issn": "2046-1402", "issn-l": "2046-1402", "volume": "14", "issue": null, "pages": "652"}, "abstract": "There is an ongoing need to develop diverse career paths that support the vital contributions of staff scientists, research engineers, scientific officers, and other knowledge professionals in scientific discovery. Research infrastructures and core facilities have a particular need to support sustainable and diverse careers, as they either employ - if being a legal entity - or daily manage research professionals in a broad variety of roles to enable resources, services, and innovation.\r\n\r\nIn 2019, a survey of the facility staff at SciLifeLab, a large national research infrastructure in Sweden, led to a recommendation for universities to develop career paths for their staff scientists. Five years later, we have conducted a survey and workshop to determine current views of infrastructure staff on career path diversity in Sweden.\r\n\r\nOur results indicate there is a strong need for clarity and communication about planning and implementation of career path structures at Swedish universities, as well as opportunities to foster excellence in infrastructure staff. While the workshop participants ranked Sweden as a stable and attractive place to work and reported continuous development of their technical and service skills, the lack of recognition of this expertise presents a barrier to a sustainable career.\r\n\r\nWe conclude that there is a need to continue advocating for increased clarity and diversity in career paths for staff scientists in Sweden, and raise the views presented by infrastructure staff on the challenges and opportunities unique to their roles.", "doi": "10.12688/f1000research.164794.1", "pmid": "40904623", "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12402762"}], "notes": [], "created": "2025-11-05T14:09:53.317Z", "modified": "2025-11-05T14:10:39.124Z"}, {"entity": "publication", "iuid": "92139d604e30428c85b0f16ddccb99c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92139d604e30428c85b0f16ddccb99c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92139d604e30428c85b0f16ddccb99c8"}}, "title": "Spatial profiling of the mouse colonic immune landscape associated with colitis and sex.", "authors": [{"family": "Holm", "given": "Matilda", "initials": "M"}, {"family": "Stepanauskait\u0117", "given": "Lina", "initials": "L", "orcid": "0000-0003-4173-6009", "researcher": {"href": "https://publications.scilifelab.se/researcher/429f33fed9a44ff4b70ff88d5af917d9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2024-11-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "7", "issue": "1", "pages": "1595"}, "abstract": "Inflammatory intestinal conditions are a major disease burden. Numerous factors shape the distribution of immune cells in the colon, but a spatial characterization of the homeostatic and inflamed colonic immune microenvironment is lacking. Here, we use the COMET platform for multiplex immunofluorescence to profile the infiltration of nine immune cell populations in mice of both sexes (N = 16) with full spatial context, including in regions of squamous metaplasia. Unsupervised clustering, neighborhood analysis, and manual quantification along the proximal-distal axis characterized the colonic immune landscape, quantified cell-cell interactions, and revealed sex differences. The distal colon was the most affected region during colitis, which was pronounced in males, who exhibited a sex-dependent increase of B cells and reduction of M2-like macrophages. Regions of squamous metaplasia exhibited strong infiltration of numerous immune cell populations, especially in males. Females exhibited more helper T cells and neutrophils at homeostasis and increased M2-like macrophage infiltration in the mid-colon upon colitis. Sex differences were corroborated by plasma cytokine profiles. Our results provide a foundation for future studies of inflammatory intestinal conditions.", "doi": "10.1038/s42003-024-07276-1", "pmid": "39613949", "labels": {"Affinity Proteomics Stockholm": "Service", "Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11606951"}, {"db": "pii", "key": "10.1038/s42003-024-07276-1"}], "notes": [], "created": "2024-12-04T20:14:13.972Z", "modified": "2025-02-17T09:58:33.843Z"}, {"entity": "publication", "iuid": "8d950590445341e6a83dd636c0171874", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d950590445341e6a83dd636c0171874.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d950590445341e6a83dd636c0171874"}}, "title": "Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels.", "authors": [{"family": "Deen", "given": "Ashik Jawahar", "initials": "AJ", "orcid": "0000-0002-8200-6849", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c59fa0cba5d4da0819bbf41998f33e0.json"}}, {"family": "Thorsson", "given": "Johan", "initials": "J"}, {"family": "O'Roberts", "given": "Eleanor M", "initials": "EM", "orcid": "0000-0002-5375-459X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5472fa88ba584d54952d2f1581ebd48a.json"}}, {"family": "Panshikar", "given": "Pranauti", "initials": "P", "orcid": "0009-0003-6239-6952", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5a7aeb9efec4840bb1d761a2e3597f4.json"}}, {"family": "Ullman", "given": "Tony", "initials": "T", "orcid": "0009-0001-4865-5925", "researcher": {"href": "https://publications.scilifelab.se/researcher/d167706b90c84b01a987132f301a247a.json"}}, {"family": "Krantz", "given": "David", "initials": "D"}, {"family": "Oses", "given": "Carolina", "initials": "C"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "journal article", "published": "2024-08-31", "journal": {"title": "J. Histochem. Cytochem.", "issn": "1551-5044", "issn-l": "0022-1554", "volume": "72", "issue": "8-9", "pages": "517-544"}, "abstract": "Multiplexed immunofluorescence (IF) can be achieved using different commercially available platforms, often making use of conjugated antibodies detected in iterative cycles. A growing portfolio of pre-conjugated antibodies is offered by the providers, as well as the possibility for in-house conjugation. For many conjugation methods and kits, there are limitations in which antibodies can be used, and conjugation results are sometimes irreproducible. The conjugation process can limit or slow down the progress of studies requiring conjugation of essential markers needed for a given project. Here, we demonstrate a protocol combining manual indirect immunofluorescence (IF) of primary antibodies, followed by antibody elution and staining with multiplexed panels of commercially pre-conjugated antibodies on the PhenoCycler platform. We present detailed protocols for applying the workflow on fresh frozen and formalin fixed paraffin embedded tissue sections. We also provide a ready to use workflow for coregistration of the images and demonstrate this for two examples.", "doi": "10.1369/00221554241274856", "pmid": "39215640", "labels": {"BioImage Informatics": "Service", "Spatial Proteomics": "Technology development", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11421402"}], "notes": [], "created": "2024-11-13T09:53:21.828Z", "modified": "2025-01-22T09:31:34.703Z"}, {"entity": "publication", "iuid": "6f4356e732354312b7588bdbfa0e5509", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f4356e732354312b7588bdbfa0e5509.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f4356e732354312b7588bdbfa0e5509"}}, "title": "N-terminal proteoforms may engage in different protein complexes.", "authors": [{"family": "Bogaert", "given": "Annelies", "initials": "A", "orcid": "0000-0002-4467-4299", "researcher": {"href": "https://publications.scilifelab.se/researcher/7715a192853b4e6bb3394b4eb5886750.json"}}, {"family": "Fijalkowska", "given": "Daria", "initials": "D"}, {"family": "Staes", "given": "An", "initials": "A"}, {"family": "Van de Steene", "given": "Tessa", "initials": "T"}, {"family": "Vuylsteke", "given": "Marnik", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Eyckerman", "given": "Sven", "initials": "S", "orcid": "0000-0001-7525-0096", "researcher": {"href": "https://publications.scilifelab.se/researcher/beccd762faa845839a3020863dcc40cd.json"}}, {"family": "Spirohn", "given": "Kerstin", "initials": "K"}, {"family": "Hao", "given": "Tong", "initials": "T"}, {"family": "Calderwood", "given": "Michael A", "initials": "MA"}, {"family": "Gevaert", "given": "Kris", "initials": "K", "orcid": "0000-0002-4237-0283", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0bd930cc50842a19f3fa7e619b405b4.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "6", "issue": "8", "issn-l": "2575-1077"}, "abstract": "Alternative translation initiation and alternative splicing may give rise to N-terminal proteoforms, proteins that differ at their N-terminus compared with their canonical counterparts. Such proteoforms can have altered localizations, stabilities, and functions. Although proteoforms generated from splice variants can be engaged in different protein complexes, it remained to be studied to what extent this applies to N-terminal proteoforms. To address this, we mapped the interactomes of several pairs of N-terminal proteoforms and their canonical counterparts. First, we generated a catalogue of N-terminal proteoforms found in the HEK293T cellular cytosol from which 22 pairs were selected for interactome profiling. In addition, we provide evidence for the expression of several N-terminal proteoforms, identified in our catalogue, across different human tissues, as well as tissue-specific expression, highlighting their biological relevance. Protein-protein interaction profiling revealed that the overlap of the interactomes for both proteoforms is generally high, showing their functional relation. We also showed that N-terminal proteoforms can be engaged in new interactions and/or lose several interactions compared with their canonical counterparts, thus further expanding the functional diversity of proteomes.", "doi": "10.26508/lsa.202301972", "pmid": "37316325", "labels": {"Spatial Proteomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6/8/e202301972"}, {"db": "pmc", "key": "PMC10267514"}], "notes": [], "created": "2023-06-16T07:42:19.726Z", "modified": "2023-06-16T07:42:41.209Z"}, {"entity": "publication", "iuid": "e7e14d0e1a974aa58d35f2718a82b256", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7e14d0e1a974aa58d35f2718a82b256.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7e14d0e1a974aa58d35f2718a82b256"}}, "title": "Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing", "authors": [{"family": "Kaimal", "given": "Jayasankar Mohanakrishnan", "initials": "JM"}, {"family": "Tampere", "given": "Marianna", "initials": "M", "orcid": "0000-0001-5744-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c6c86cb20394d17abebb40db23407c8.json"}}, {"family": "Le", "given": "Trang H", "initials": "TH"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-0273-9306", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8832ebbddc449a49c67c8a9e05a99d8.json"}}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Axelsson", "given": "Hanna", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0003-3390-8456", "researcher": {"href": "https://publications.scilifelab.se/researcher/adaa82c5ab804bfcb80a04539c23e1d9.json"}}, {"family": "Marabita", "given": "Francesco", "initials": "F", "orcid": "0000-0001-6180-0106", "researcher": {"href": "https://publications.scilifelab.se/researcher/05a6497e6561419f86f3227618e536fa.json"}}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2359-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a0f932253042239c1d38ea00ca0018.json"}}, {"family": "Njenda", "given": "Duncan", "initials": "D", "orcid": "0000-0001-8276-9726", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14c27f4d60549da9949c97ed66a15b5.json"}}, {"family": "Sepulveda", "given": "Carolina Oses", "initials": "CO", "orcid": "0000-0001-8194-1168", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9dd54ba67d4f10a5ba6d0b4ede67bc.json"}}, {"family": "Oyuang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e276634741d45249c7cec0b46a7d9f4.json"}}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B", "orcid": "0000-0001-8658-5967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4645bc97a8024c548111802101b83571.json"}}, {"family": "Vernersson", "given": "Caroline", "initials": "C"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-5501-466X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0461a910ec4b4faa8668bb4044e76f61.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "posted-content", "published": "2022-03-29", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.03.29.482838", "pmid": null, "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2022-06-15T20:30:04.837Z", "modified": "2025-12-18T20:00:54.993Z"}, {"entity": "publication", "iuid": "ccd54446c7604b2d944e433c3fc245ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ccd54446c7604b2d944e433c3fc245ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ccd54446c7604b2d944e433c3fc245ab"}}, "title": "Subcellular proteomics.", "authors": [{"family": "Christopher", "given": "Josie A", "initials": "JA"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Martin", "given": "Claire E", "initials": "CE", "orcid": "0000-0001-8346-414X", "researcher": {"href": "https://publications.scilifelab.se/researcher/283b9e3574454cd6892ab5bc964f7353.json"}}, {"family": "Morgenstern", "given": "Marcel", "initials": "M", "orcid": "0000-0001-6880-4839", "researcher": {"href": "https://publications.scilifelab.se/researcher/8da72791863f463cad99442103d83338.json"}}, {"family": "Pan", "given": "Yanbo", "initials": "Y", "orcid": "0000-0001-9442-7782", "researcher": {"href": "https://publications.scilifelab.se/researcher/00403ea0d7bd4218a6b9ba507fa2fa26.json"}}, {"family": "Betsinger", "given": "Cora N", "initials": "CN", "orcid": "0000-0001-9263-3873", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fe36ad250546f7af5422c53e1aff77.json"}}, {"family": "Rattray", "given": "David G", "initials": "DG", "orcid": "0000-0002-2444-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/090cec60bc574c29809b7124d80b6170.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc22f13eb21a4c75a6e7cad7686bcc8a.json"}}, {"family": "Gingras", "given": "Anne-Claude", "initials": "A", "orcid": "0000-0002-6090-4437", "researcher": {"href": "https://publications.scilifelab.se/researcher/21315bcb23a144069b3568d7afd0b00b.json"}}, {"family": "Warscheid", "given": "Bettina", "initials": "B", "orcid": "0000-0001-5096-1975", "researcher": {"href": "https://publications.scilifelab.se/researcher/24f95112121a4e0c88c746703712017c.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Cristea", "given": "Ileana M", "initials": "IM"}, {"family": "Foster", "given": "Leonard J", "initials": "LJ", "orcid": "0000-0001-8551-4817", "researcher": {"href": "https://publications.scilifelab.se/researcher/84bc1af03ee243ca91c3f230ce711154.json"}}, {"family": "Emili", "given": "Andrew", "initials": "A", "orcid": "0000-0001-8995-246X", "researcher": {"href": "https://publications.scilifelab.se/researcher/337c75cec31e4051b979e7217d823999.json"}}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS", "orcid": "0000-0003-0594-6543", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b4e7e18a88455199308070d6da7ea3.json"}}], "type": "journal article", "published": "2021-04-29", "journal": {"title": "Nat Rev Methods Primers", "issn": "2662-8449", "issn-l": null, "volume": "1", "issue": "1", "pages": null}, "abstract": "The eukaryotic cell is compartmentalized into subcellular niches, including membrane-bound and membrane-less organelles. Proteins localize to these niches to fulfil their function, enabling discreet biological processes to occur in synchrony. Dynamic movement of proteins between niches is essential for cellular processes such as signalling, growth, proliferation, motility and programmed cell death, and mutations causing aberrant protein localization are associated with a wide range of diseases. Determining the location of proteins in different cell states and cell types and how proteins relocalize following perturbation is important for understanding their functions, related cellular processes and pathologies associated with their mislocalization. In this Primer, we cover the major spatial proteomics methods for determining the location, distribution and abundance of proteins within subcellular structures. These technologies include fluorescent imaging, protein proximity labelling, organelle purification and cell-wide biochemical fractionation. We describe their workflows, data outputs and applications in exploring different cell biological scenarios, and discuss their main limitations. Finally, we describe emerging technologies and identify areas that require technological innovation to allow better characterization of the spatial proteome.", "doi": "10.1038/s43586-021-00029-y", "pmid": "34549195", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8451152"}, {"db": "mid", "key": "NIHMS1715590"}], "notes": [], "created": "2021-05-04T13:33:02.777Z", "modified": "2023-06-19T11:25:03.018Z"}, {"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": "10d32e326ad143b48c7352913a9537b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10d32e326ad143b48c7352913a9537b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10d32e326ad143b48c7352913a9537b3"}}, "title": "A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface.", "authors": [{"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Kugel", "given": "Laura", "initials": "L"}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Xu", "given": "Hao", "initials": "H"}, {"family": "Aslan", "given": "Joseph E", "initials": "JE"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "J. Histochem. Cytochem.", "issn": "1551-5044", "issn-l": "0022-1554", "volume": "68", "issue": "7", "pages": "473-489"}, "abstract": "Imaging is a powerful approach for studying protein expression and has the advantage over other methodologies in providing spatial information in situ at single cell level. Using immunofluorescence and confocal microscopy, detailed information of subcellular distribution of proteins can be obtained. While adherent cells of different tissue origin are relatively easy to prepare for imaging applications, non-adherent cells from hematopoietic origin, present a challenge due to their poor attachment to surfaces and subsequent loss of a substantial fraction of the cells. Still, these cell types represent an important part of the human proteome and express genes that are not expressed in adherent cell types. In the era of cell mapping efforts, overcoming the challenge with suspension cells for imaging applications would enable systematic profiling of hematopoietic cells. In this work, we successfully established an immunofluorescence protocol for preparation of suspension cell lines, peripheral blood mononucleated cells (PBMC) and human platelets on an adherent surface. The protocol is based on a multi-well plate format with automated sample preparation, allowing for robust high throughput imaging applications. In combination with confocal microscopy, the protocol enables systematic exploration of protein localization to all major subcellular structures.", "doi": "10.1369/0022155420935403", "pmid": "32564662", "labels": {"Spatial Proteomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC7350080"}], "notes": [], "created": "2020-01-07T15:30:10.784Z", "modified": "2021-12-09T13:58:56.335Z"}, {"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": "cf7bf4bafff647f7ab3501fe1e844770", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf7bf4bafff647f7ab3501fe1e844770.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf7bf4bafff647f7ab3501fe1e844770"}}, "title": "TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells.", "authors": [{"family": "Joshi", "given": "Rubin Narayan", "initials": "RN"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lehmann", "given": "Robert", "initials": "R"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Schmidt", "given": "Angelika", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2019-11-26", "journal": {"volume": "10", "issn": "1664-3224", "issue": null, "pages": "2708", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "We have curated an in-depth subcellular proteomic map of primary human CD4+ T cells, divided into cytosolic, nuclear and membrane fractions generated by an optimized fractionation and HiRIEF-LC-MS/MS workflow for limited amounts of primary cells. The subcellular proteome of T cells was mapped under steady state conditions, as well as upon 15 min and 1 h of T cell receptor (TCR) stimulation, respectively. We quantified the subcellular distribution of 6,572 proteins and identified a subset of 237 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization, respectively. We further provide the data in an easy-to-use web platform to facilitate re-use, as the data can be relevant for basic research as well as for clinical exploitation of T cells as therapeutic targets.", "doi": "10.3389/fimmu.2019.02708", "pmid": "31849937", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6902019"}], "notes": [], "created": "2019-12-03T08:36:31.738Z", "modified": "2021-07-08T11:26:52.822Z"}, {"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": "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": "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": "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": "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": "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": "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": "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": "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": "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"}]}