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"Yang", "given": "Hong", "initials": "H", "orcid": "0009-0002-0414-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52bdf7cbd1745e3a4578f17322c83f1.json"}}, {"family": "Ye\u015filkaya", "given": "Umit Haluk", "initials": "UH"}, {"family": "Yuan", "given": "Meng", "initials": "M", "orcid": "0000-0002-9248-3294", "researcher": {"href": "https://publications.scilifelab.se/researcher/befeb12cfba142eb9dadf81497d6c419.json"}}, {"family": "Zeybel", "given": "Mujdat", "initials": "M", "orcid": "0000-0001-5440-4623", "researcher": {"href": "https://publications.scilifelab.se/researcher/0559b83985134a0a9283ea39601a95a7.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.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": "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": "72c0bcbc6ed645e4a14dd4aa365fac7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72c0bcbc6ed645e4a14dd4aa365fac7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72c0bcbc6ed645e4a14dd4aa365fac7e"}}, "title": "Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.", "authors": [{"family": "Kvedaraite", "given": "Egle", "initials": "E", "orcid": "0000-0001-5308-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/78502177bad3453a8d3ed96d4ad334ac.json"}}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Mouratidou", "given": "Natalia", "initials": "N"}, {"family": "D\u00fcking", "given": "Tim", "initials": "T", "orcid": "0000-0002-4347-7648", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acbe8ae50d94479a37dda5f37336422.json"}}, {"family": "Padhi", "given": "Avinash", "initials": "A"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Xagoraris", "given": "Ioanna", "initials": "I"}, {"family": "Kokkinou", "given": "Efthymia", "initials": "E"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Hartwig", "given": "Olga", "initials": "O", "orcid": "0000-0001-5016-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a50cebd9533432e80d2fd284c9137eb.json"}}, {"family": "Santos", "given": "Telma E", "initials": "TE"}, {"family": "Soini", "given": "Tea", "initials": "T"}, {"family": "Van Acker", "given": "Aline", "initials": "A"}, {"family": "Rahkonen", "given": "Nelly", "initials": "N"}, {"family": "Flodstr\u00f6m Tullberg", "given": "Malin", "initials": "M", "orcid": "0000-0003-2685-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6d04afbe8141c2b9297854de64dab8.json"}}, {"family": "Ringqvist", "given": "Emma", "initials": "E"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Lindforss", "given": "Ulrik", "initials": "U"}, {"family": "Nordenvall", "given": "Caroline", "initials": "C"}, {"family": "Stamper", "given": "Christopher T", "initials": "CT"}, {"family": "Unnersj\u00f6-Jess", "given": "David", "initials": "D", "orcid": "0000-0002-4162-0973", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d475fc7a52a46e4abe984191c5b5b5f.json"}}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Nadisauskaite", "given": "Ruta", "initials": "R"}, {"family": "Jansson", "given": "Jessica", "initials": "J"}, {"family": "Vandamme", "given": "Niels", "initials": "N"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Grundeken", "given": "Marijke Elise", "initials": "ME", "orcid": "0000-0001-6915-0339", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64d9493eccd419d8c8908dea19602df.json"}}, {"family": "Rolandsdotter", "given": "Helena", "initials": "H"}, {"family": "Rassidakis", "given": "George", "initials": "G"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Idestr\u00f6m", "given": "Maja", "initials": "M"}, {"family": "Eulitz", "given": "Stefan", "initials": "S"}, {"family": "Arnell", "given": "Henrik", "initials": "H"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI", "orcid": "0000-0002-0629-2126", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1a0d663491c4665a32a612e423dff1b.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}], "type": "journal article", "published": "2024-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1752", "issn-l": "2041-1723"}, "abstract": "Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA+CD142-/low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA+CD142-/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures have a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.", "doi": "10.1038/s41467-024-46076-3", "pmid": "38409190", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10897309"}, {"db": "pii", "key": "10.1038/s41467-024-46076-3"}], "notes": [], "created": "2024-03-14T11:08:33.238Z", "modified": "2024-10-31T10:36:41.256Z"}, {"entity": "publication", "iuid": "9322d91734fa4ade8db29e7f933c0ac0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9322d91734fa4ade8db29e7f933c0ac0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9322d91734fa4ade8db29e7f933c0ac0"}}, "title": "The Karolinska KI/K COVID-19 Immune Atlas: An open resource for immunological research and educational purposes.", "authors": [{"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG", "orcid": "0000-0003-0908-7387", "researcher": {"href": "https://publications.scilifelab.se/researcher/54d696167bca4a389807143f84baeafe.json"}}, {"family": "Ask", "given": "Eivind Heggernes", "initials": "EH", "orcid": "0000-0001-8655-1433", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4a3a0f566a342db89c54b87a50d5e5b.json"}}, {"family": "Cornillet", "given": "Martin", "initials": "M"}, {"family": "Strunz", "given": "Benedikt", "initials": "B"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Rao Muvva", "given": "Jagadeeswara", "initials": "J"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Chambers", "given": "Benedict J", "initials": "BJ", "orcid": "0000-0003-0437-8441", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bdd56cf648f4411945163135f9a7140.json"}}, {"family": "Cuapio", "given": "Angelica", "initials": "A", "orcid": "0000-0002-9451-1914", "researcher": {"href": "https://publications.scilifelab.se/researcher/8391879473274bc1b14b3f8fea7f9fc9.json"}}, {"family": "Dzidic", "given": "Majda", "initials": "M"}, {"family": "Filipovic", "given": "Iva", "initials": "I", "orcid": "0000-0002-8166-5500", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfe34a0a54954684bd1e405afd479ab3.json"}}, {"family": "Flodstr\u00f6m-Tullberg", "given": "Malin", "initials": "M"}, {"family": "Garcia", "given": "Marina", "initials": "M"}, {"family": "Gorin", "given": "Jean-Baptiste", "initials": "JB"}, {"family": "Gredmark-Russ", "given": "Sara", "initials": "S"}, {"family": "Hertwig", "given": "Laura", "initials": "L"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J"}, {"family": "Kokkinou", "given": "Efthymia", "initials": "E"}, {"family": "Kvedaraite", "given": "Egle", "initials": "E"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}, {"family": "Maucourant", "given": "Christopher", "initials": "C"}, {"family": "Norrby-Teglund", "given": "Anna", "initials": "A"}, {"family": "Palma Medina", "given": "Laura M", "initials": "LM"}, {"family": "Parrot", "given": "Tiphaine", "initials": "T"}, {"family": "Perez-Potti", "given": "Andr\u00e9", "initials": "A"}, {"family": "Ponzetta", "given": "Andrea", "initials": "A"}, {"family": "Ringqvist", "given": "Emma", "initials": "E"}, {"family": "Rivera-Ballesteros", "given": "Olga", "initials": "O"}, {"family": "Rooyackers", "given": "Olav", "initials": "O"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK"}, {"family": "Sandberg", "given": "J Tyler", "initials": "JT"}, {"family": "Sekine", "given": "Takuya", "initials": "T"}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}, {"family": "Varnaite", "given": "Renata", "initials": "R"}, {"family": "Wullimann", "given": "David", "initials": "D"}, {"family": "Karolinska KI/K COVID-19 Study Group", "given": "", "initials": ""}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "Malmberg", "given": "Karl-Johan", "initials": "KJ"}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}], "type": "journal article", "published": "2022-06-02", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "pages": "e13195", "issn-l": "0300-9475"}, "abstract": "The Karolinska KI/K COVID-19 Immune Atlas project was conceptualized in March 2020 as a part of the academic research response to the developing SARS-CoV-2 pandemic. The aim was to rapidly provide a curated dataset covering the acute immune response towards SARS-CoV-2 infection in humans, as it occurred during the first wave. The Immune Atlas was built as an open resource for broad research and educational purposes. It contains a presentation of the response evoked by different immune and inflammatory cells in defined na\u00efve patient-groups as they presented with moderate and severe COVID-19 disease. The present Resource Article describes how the Karolinska KI/K COVID-19 Immune Atlas allow scientists, students, and other interested parties to freely explore the nature of the immune response towards human SARS-CoV-2 infection in an online setting.", "doi": "10.1111/sji.13195", "pmid": "35652743", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9287045"}], "notes": [], "created": "2022-11-16T17:15:26.201Z", "modified": "2022-11-16T17:15:26.261Z"}, {"entity": "publication", "iuid": "6aff0432d2a54d15ac7fdb6ffc28707d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6aff0432d2a54d15ac7fdb6ffc28707d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6aff0432d2a54d15ac7fdb6ffc28707d"}}, "title": "Major alterations in the mononuclear phagocyte landscape associated with COVID-19 severity.", "authors": [{"family": "Kvedaraite", "given": "Egle", "initials": "E"}, {"family": "Hertwig", "given": "Laura", "initials": "L", "orcid": "0000-0002-1170-0948", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b64addfb67f4e8b898bbb1ced5f5e77.json"}}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Ponzetta", "given": "Andrea", "initials": "A", "orcid": "0000-0003-3224-802X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b06c3ab1bae404dba4ec9a1eee4f78b.json"}}, {"family": "Hed Myrberg", "given": "Ida", "initials": "I"}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Dzidic", "given": "Majda", "initials": "M"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Klingstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0001-9076-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/95c1b345ae434fb383b7fe6a1d053c80.json"}}, {"family": "Folkesson", "given": "Elin", "initials": "E"}, {"family": "Muvva", "given": "Jagadeeswara Rao", "initials": "JR"}, {"family": "Chen", "given": "Puran", "initials": "P", "orcid": "0000-0002-2890-0022", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b2580e94a2145d58db680762eec30bf.json"}}, {"family": "Gredmark-Russ", "given": "Sara", "initials": "S", "orcid": "0000-0002-2446-4323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f7958a9ee7748cf8806253a7aeef673.json"}}, {"family": "Brighenti", "given": "Susanna", "initials": "S"}, {"family": "Norrby-Teglund", "given": "Anna", "initials": "A", "orcid": "0000-0001-9372-1795", "researcher": {"href": "https://publications.scilifelab.se/researcher/25c11b43fc984bbca28fcc5bbf211d58.json"}}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "Rooyackers", "given": "Olav", "initials": "O"}, {"family": "Aleman", "given": "Soo", "initials": "S", "orcid": "0000-0003-0461-4870", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a125a916b34de985de977dd8384650.json"}}, {"family": "Str\u00e5lin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0002-8801-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6ffa1185f4142b7ab7c372c0c139df6.json"}}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "H"}, {"family": "Ginhoux", "given": "Florent", "initials": "F"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK", "orcid": "0000-0002-0967-076X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf38521350ae490099f01bda1d10be4c.json"}}, {"family": "Henter", "given": "Jan-Inge", "initials": "J"}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}, {"family": "Karolinska KI/K COVID-19 Study Group", "given": "", "initials": "", "orcid": "0000-0003-2685-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6d04afbe8141c2b9297854de64dab8.json"}}], "type": "journal article", "published": "2021-02-09", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "118", "issue": "6", "pages": "e2018587118"}, "abstract": "Dendritic cells (DCs) and monocytes are crucial mediators of innate and adaptive immune responses during viral infection, but misdirected responses by these cells may contribute to immunopathology. Here, we performed high-dimensional flow cytometry-analysis focusing on mononuclear phagocyte (MNP) lineages in SARS-CoV-2-infected patients with moderate and severe COVID-19. We provide a deep and comprehensive map of the MNP landscape in COVID-19. A redistribution of monocyte subsets toward intermediate monocytes and a general decrease in circulating DCs was observed in response to infection. Severe disease coincided with the appearance of monocytic myeloid-derived suppressor cell-like cells and a higher frequency of pre-DC2. Furthermore, phenotypic alterations in MNPs, and their late precursors, were cell-lineage-specific and associated either with the general response against SARS-CoV-2 or COVID-19 severity. This included an interferon-imprint in DC1s observed in all patients and a decreased expression of the coinhibitory molecule CD200R in pre-DCs, DC2s, and DC3 subsets of severely sick patients. Finally, unsupervised analysis revealed that the MNP profile, alone, pointed to a cluster of COVID-19 nonsurvivors. This study provides a reference for the MNP response to SARS-CoV-2 infection and unravels mononuclear phagocyte dysregulations associated with severe COVID-19.", "doi": "10.1073/pnas.2018587118", "pmid": "33479167", "labels": {"Affinity Proteomics Stockholm": "Service"}, "xrefs": [{"db": "pii", "key": "2018587118"}, {"db": "pmc", "key": "PMC8017719"}], "notes": [], "created": "2021-10-06T10:58:11.905Z", "modified": "2021-12-09T13:41:42.272Z"}]}