{"entity": "researcher", "timestamp": "2026-07-18T02:34:05.867Z", "family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "affiliations": ["Science for Life Laboratory Department of Biochemistry and Biophysics National Bioinformatics Infrastructure Sweden Stockholm University  Solna Sweden"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560"}}, "publications": [{"entity": "publication", "iuid": "626dde82bebd4d8bb7880ecc0a2237e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0"}}, "title": "Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.", "authors": [{"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boger", "given": "Mathias Franzen", "initials": "MF"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Bradley", "given": "Frideborg", "initials": "F", "orcid": "0000-0003-3006-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d51eaeb949e94bd39ab3605d495dc647.json"}}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Fowke", "given": "Keith", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "1014"}, "abstract": "The injectable contraceptive, depot medroxyprogesterone acetate (DMPA), is associated with compromised cervical mucosal barriers. High-resolution spatial transcriptomics is applied here to reveal the spatial localization of these altered molecular markers. Ectocervical tissue samples from Kenyan sex workers using DMPA, or non-hormonal contraceptives, underwent spatial transcriptomics and gene set enrichment analyses. Integrated systemic estradiol levels and bulk tissue gene expression data from a larger cohort enhanced the study's scope. Unsupervised clustering unveiled four epithelial and seven submucosal layers, showcasing spatially restricted and diverse functional epithelial responses, and a less structured submucosal spatial ordering. DMPA associated with mucosal-wide immunoglobulin gene upregulation, verified by CD20+ B-cell immunostaining, and upregulated immune markers adjacent to the basal membrane. Downregulated genes represented spatially restricted disrupted epithelial barrier integrity and submucosal extracellular matrix dysfunction. The transcriptional profile was associated with markers of estrogen regulation. Collectively, our findings reveal estrogen-modulated distinct ectocervical transcriptional profiles associated with DMPA usage. While upregulation of immunoglobulin genes occurs throughout the mucosa, activation of innate immune responses and dysregulation of barrier integrity markers are spatially restricted. These results extend previous analyses using bulk transcriptomics and provide insights into the molecular landscape influenced by DMPA, shedding light on contraceptive effects and health implications.", "doi": "10.1038/s41598-024-83775-9", "pmid": "39762272", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11704007"}, {"db": "pii", "key": "10.1038/s41598-024-83775-9"}], "notes": [], "created": "2025-01-23T12:51:23.407Z", "modified": "2025-11-19T08:36:34.197Z"}, {"entity": "publication", "iuid": "07cd66044bbe4799bb39d2ca83fa2edf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07cd66044bbe4799bb39d2ca83fa2edf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07cd66044bbe4799bb39d2ca83fa2edf"}}, "title": "High-parametric protein maps reveal the spatial organization in early-developing human lung.", "authors": [{"family": "Sariyar", "given": "Sanem", "initials": "S", "orcid": "0000-0003-0735-5595", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a057942e8804bd19530d9faf484c72f.json"}}, {"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Hansen", "given": "Jan Niklas", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications.scilifelab.se/researcher/272dfc4476064018bc7ed0235b7d3e55.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Mardamshina", "given": "Mariya", "initials": "M", "orcid": "0000-0003-0066-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff68d3499c01447b8a48d99b86bd882b.json"}}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Ballllosera Navarro", "given": "Frederic", "initials": "F"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z", "orcid": "0000-0002-4350-2524", "researcher": {"href": "https://publications.scilifelab.se/researcher/f89be535ddfa4c6ab46201fb383f4a2b.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b9ccd9ae84cdfbcb663591f39a77b.json"}}], "type": "journal article", "published": "2024-10-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "9381"}, "abstract": "The respiratory system, including the lungs, is essential for terrestrial life. While recent research has advanced our understanding of lung development, much still relies on animal models and transcriptome analyses. In this study conducted within the Human Developmental Cell Atlas (HDCA) initiative, we describe the protein-level spatiotemporal organization of the lung during the first trimester of human gestation. Using high-parametric tissue imaging with a 30-plex antibody panel, we analyzed human lung samples from 6 to 13 post-conception weeks, generating data from over 2 million cells across five developmental timepoints. We present a resource detailing spatially resolved cell type composition of the developing human lung, including proliferative states, immune cell patterns, spatial arrangement traits, and their temporal evolution. This represents an extensive single-cell resolved protein-level examination of the developing human lung and provides a valuable resource for further research into the developmental roots of human respiratory health and disease.", "doi": "10.1038/s41467-024-53752-x", "pmid": "39477961", "labels": {"BioImage Informatics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11525936"}, {"db": "pii", "key": "10.1038/s41467-024-53752-x"}], "notes": [], "created": "2024-11-13T10:04:30.594Z", "modified": "2025-12-19T07:56:09.718Z"}, {"entity": "publication", "iuid": "c4b84ce2a57f40308f42f57e75b10952", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4b84ce2a57f40308f42f57e75b10952.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4b84ce2a57f40308f42f57e75b10952"}}, "title": "Vaginal candida infection is associated with host molecular signatures of neutrophil activation in the adjacent ectocervical mucosa in Kenyan sex workers", "authors": [{"family": "Hasselrot", "given": "Tyra", "initials": "T", "orcid": "0009-0002-5951-5618", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b6969d7b33f4b1286c9dbea2fbaf79e.json"}}, {"family": "Boger", "given": "Mathias Franz\u00e9n", "initials": "MF"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "\u00c5hlberg", "given": "Alexandra", "initials": "A"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Fowke", "given": "Keith R", "initials": "KR"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal-article", "published": "2024-02-00", "journal": {"title": "American J Rep Immunol", "issn": "1046-7408", "issn-l": null, "volume": "91", "issue": "2", "pages": "e13814"}, "abstract": "Overgrowth of candida species in the human vaginal mucosa causes inflammation, which could render the mucosal barrier more susceptible to HIV infection. Here, we investigated whether this condition also affects the ectocervical mucosa, a potential site of HIV entry, in women at high risk of HIV infection.\n\nRetrospective medical data and ectocervical tissue samples were obtained from a cohort of Kenyan sex workers. Among 108 women, seven had signs of vaginal candida infection by wet smear microscopy and/or the presence of characteristic discharge. Women lacking these two criteria served as controls. Host transcriptomic profiling and quantitative in situ image analysis of epithelial barrier markers and CD4+ cell distribution were performed.\n\nThe candida group had 162 differentially expressed genes out of 15 435 genes as compared with the control group. Among these 162 genes, 147 were upregulated and 15 were downregulated. Gene expression pathway analysis indicated associations with an upregulated inflammatory response, defined primarily by markers of neutrophil activation. Transcription factor analysis revealed upregulation of pathways related to RELA/REL/NFKB1, JUN and STAT1 in the candida group. In situ image analysis of ectocervical tissue samples showed no differences between groups in terms of epithelial height, expression of epithelial junction proteins (E-cadherin, claudin-1, zonula occludens 1, and desmoglein-1), or epithelial CD4+ cell distribution.\n\nVaginal candida infection was associated with inflammation and neutrophil infiltration, but not with severe epithelial disruption or CD4+ cell infiltration, in the ectocervical mucosa.", "doi": "10.1111/aji.13814", "pmid": "40600913", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "BioImage Informatics": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11717577"}], "notes": [], "created": "2024-10-31T10:37:29.647Z", "modified": "2025-12-04T19:33:29.727Z"}, {"entity": "publication", "iuid": "f9d5f8d15fc7400e9233f987f8a71a33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9d5f8d15fc7400e9233f987f8a71a33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9d5f8d15fc7400e9233f987f8a71a33"}}, "title": "Multimodal Single-Cell Sequencing of B Cells in Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Arvidsson", "given": "Gustav", "initials": "G", "orcid": "0000-0001-7396-1820", "researcher": {"href": "https://publications.scilifelab.se/researcher/29beb4f9dd8b460382eab4f916fc1072.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Johansson", "given": "Alina", "initials": "A"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "issn-l": "2326-5191", "volume": "76", "issue": "2", "pages": "255-267"}, "abstract": "B cells are important in the pathogenesis of primary Sj\u00f6gren's syndrome (pSS). Patients positive for Sj\u00f6gren's syndrome antigen A/Sj\u00f6gren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression, and B cell receptor usage in pSS subgroups stratified for SSA/SSB antibodies.\r\n\r\nOver 230,000 B cells were isolated from peripheral blood of patients with pSS (n = 6 SSA-, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls and processed for single-cell RNA sequencing (scRNA-seq) and single-cell variable, diversity, and joining (VDJ) gene sequencing (scVDJ-seq).\r\n\r\nWe show that SSA/SSB+ patients present the highest and lowest proportion of na\u00efve and memory B cells, respectively, and the highest up-regulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared with other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification of patients with pSS and identified novel parameters that correlated to disease manifestations and antibody status.\r\n\r\nWe describe heterogeneity and molecular characteristics in B cells from patients with pSS, providing clues to intrinsic differences in B cells that affect the phenotype and outcome and allowing stratification of patients with pSS at improved resolution.", "doi": "10.1002/art.42683", "pmid": "37610265", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-09-20T16:42:27.105Z", "modified": "2024-11-05T18:21:35.829Z"}, {"entity": "publication", "iuid": "e32fd724b739422db6fef1905f9b5493", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e32fd724b739422db6fef1905f9b5493.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e32fd724b739422db6fef1905f9b5493"}}, "title": "Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.", "authors": [{"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Liu", "given": "Yang", "initials": "Y"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z"}, {"family": "Lee", "given": "Hower", "initials": "H"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Kallner", "given": "Helena Kopp", "initials": "HK"}, {"family": "\u00c5kesson", "given": "Elisabet", "initials": "E"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "26", "issue": "5", "pages": "891-901"}, "abstract": "The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.", "doi": "10.1038/s41593-023-01312-9", "pmid": "37095395", "labels": {"BioImage Informatics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10166856"}, {"db": "pii", "key": "10.1038/s41593-023-01312-9"}], "notes": [], "created": "2023-05-31T11:06:10.725Z", "modified": "2025-10-17T13:02:17.029Z"}, {"entity": "publication", "iuid": "c92cbd6e5d684872a9bd87af735238d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c92cbd6e5d684872a9bd87af735238d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c92cbd6e5d684872a9bd87af735238d8"}}, "title": "Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows", "authors": [{"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Kuemmerle", "given": "Louis B", "initials": "LB", "orcid": "0000-0002-9193-1243", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d339771ed9a4559ad56a63e9e4e9e80.json"}}, {"family": "Helgadottir", "given": "Saga", "initials": "S", "orcid": "0000-0001-8070-147X", "researcher": {"href": "https://publications.scilifelab.se/researcher/98648914489b45dca447d2425a460c99.json"}}, {"family": "Matsson-Langseth", "given": "Christoffer", "initials": "C", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Tismeyer", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-0492-1523", "researcher": {"href": "https://publications.scilifelab.se/researcher/73fa7867433147ef927fdd0768e45387.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Rehman", "given": "Habib", "initials": "H", "orcid": "0000-0002-8671-982X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dff0d9994c0f4237a5afbcd66d706dbf.json"}}, {"family": "Tiklova", "given": "Katarina", "initials": "K", "orcid": "0000-0002-9529-4552", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bbad41b8ed42268b71014ce111d247.json"}}, {"family": "Andersson", "given": "Axel", "initials": "A", "orcid": "0000-0002-4714-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027f6b47684ff4be205e2d547c5f8a.json"}}, {"family": "Chatzinikolaou", "given": "Maria", "initials": "M", "orcid": "0000-0002-3539-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fa3519e517549bc854f19983e649074.json"}}, {"family": "Theis", "given": "Fabian J", "initials": "FJ", "orcid": "0000-0002-2419-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/15139e290953411590201d9bb402da1f.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Ishaque", "given": "Naveed", "initials": "N", "orcid": "0000-0002-8426-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38be333e07614a13bf8c559e7935381a.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "posted-content", "published": "2023-02-14", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.02.13.528102", "pmid": null, "labels": {"In Situ Sequencing": "Technology development"}, "xrefs": [], "notes": [], "created": "2023-05-31T11:12:14.703Z", "modified": "2025-12-18T19:55:14.931Z"}, {"entity": "publication", "iuid": "544b98439adf410680a670acbe0660a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/544b98439adf410680a670acbe0660a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/544b98439adf410680a670acbe0660a5"}}, "title": "A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Avenel", "given": "Christophe", "initials": "C"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Vicari", "given": "Marco", "initials": "M", "orcid": "0000-0002-3042-6278", "researcher": {"href": "https://publications.scilifelab.se/researcher/6348d0901b3e44cd80bde25cecd0205b.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Abalo", "given": "Xesus", "initials": "X", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Andrusivov\u00e1", "given": "\u017daneta", "initials": "\u017d"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Asp", "given": "Michaela", "initials": "M"}, {"family": "Li", "given": "Xiaofei", "initials": "X"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Sariyar", "given": "Sanem", "initials": "S"}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Firsova", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "issn-l": null, "volume": "25", "issue": "2", "pages": "351-365"}, "abstract": "The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.", "doi": "10.1038/s41556-022-01064-x", "pmid": "36646791", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9928586"}, {"db": "pii", "key": "10.1038/s41556-022-01064-x"}], "notes": [], "created": "2023-03-06T13:47:35.567Z", "modified": "2025-10-17T13:02:17.126Z"}, {"entity": "publication", "iuid": "601f2cafa2194c0b9554d477b9dacdb2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/601f2cafa2194c0b9554d477b9dacdb2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/601f2cafa2194c0b9554d477b9dacdb2"}}, "title": "Developmental origins of cell heterogeneity in the human lung", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM", "orcid": "0000-0002-4636-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db8123d7b0f47afbb06b0559fcd79ff.json"}}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}}, {"family": "Vicari", "given": "Marco", "initials": "M", "orcid": "0000-0002-3042-6278", "researcher": {"href": "https://publications.scilifelab.se/researcher/6348d0901b3e44cd80bde25cecd0205b.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A", "orcid": "0000-0003-0838-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/af0596d61a794c188112ba7b256efac6.json"}}, {"family": "Abalo", "given": "Xesus", "initials": "X", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Andrusivov\u00e1", "given": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/9ac0b87b8e4548158ac5ea20a08f7a28.json"}}, {"family": "Firsova", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J", "orcid": "0000-0001-6948-7281", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b05fc1689e4d6c9ec0ecd513905a36.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "posted-content", "published": "2022-01-12", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2022.01.11.475631", "pmid": null, "labels": {"In Situ Sequencing": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-28T09:49:49.063Z", "modified": "2025-12-18T20:03:09.998Z"}, {"entity": "publication", "iuid": "092a2fc7f73040e68081e9553c7bcf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/092a2fc7f73040e68081e9553c7bcf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/092a2fc7f73040e68081e9553c7bcf56"}}, "title": "Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin.", "authors": [{"family": "Veerman", "given": "Rosanne E", "initials": "RE"}, {"family": "Teeuwen", "given": "Loes", "initials": "L"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "G\u00fccl\u00fcler Akpinar", "given": "G\u00f6zde", "initials": "G"}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A", "orcid": "0000-0002-9681-3342", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd34d8e107be4a87b60c8dc525277463.json"}}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4e49a93b0143db88059c4d1e9fdc59.json"}}, {"family": "Gabrielsson", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1771-1346", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d446cb52d7e4a01ad8478a9cfe22ae1.json"}}, {"family": "Eldh", "given": "Maria", "initials": "M", "orcid": "0000-0003-2173-1796", "researcher": {"href": "https://publications.scilifelab.se/researcher/61b27da9f7184beab8c9a6d358a2c4df.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "10", "issue": "9", "pages": "e12128", "issn-l": "2001-3078"}, "abstract": "Extracellular vesicles (EVs) are increasingly tested as therapeutic vehicles and biomarkers, but still EV subtypes are not fully characterised. To isolate EVs with few co-isolated entities, a combination of methods is needed. However, this is time-consuming and requires large sample volumes, often not feasible in most clinical studies or in studies where small sample volumes are available. Therefore, we compared EVs rendered by five commonly used methods based on different principles from conditioned cell medium and 250 \u03bcl or 3 ml plasma, that is, precipitation (ExoQuick ULTRA), membrane affinity (exoEasy Maxi Kit), size-exclusion chromatography (qEVoriginal), iodixanol gradient (OptiPrep), and phosphatidylserine affinity (MagCapture). EVs were characterised by electron microscopy, Nanoparticle Tracking Analysis, Bioanalyzer, flow cytometry, and LC-MS/MS. The different methods yielded samples of different morphology, particle size, and proteomic profile. For the conditioned medium, Izon 35 isolated the highest number of EV proteins followed by exoEasy, which also isolated fewer non-EV proteins. For the plasma samples, exoEasy isolated a high number of EV proteins and few non-EV proteins, while Izon 70 isolated the most EV proteins. We conclude that no method is perfect for all studies, rather, different methods are suited depending on sample type and interest in EV subtype, in addition to sample volume and budget.", "doi": "10.1002/jev2.12128", "pmid": "34322205", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "JEV212128"}, {"db": "pmc", "key": "PMC8298890"}], "notes": [], "created": "2021-09-10T08:46:39.753Z", "modified": "2024-01-16T13:48:39.263Z"}, {"entity": "publication", "iuid": "b240293236c041008c1ccbfdf6820588", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b240293236c041008c1ccbfdf6820588.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b240293236c041008c1ccbfdf6820588"}}, "title": "Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.", "authors": [{"family": "Lepzien", "given": "Rico", "initials": "R", "orcid": "0000-0001-8584-2917", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcee0bb2ad9743bdb5114d11bf8efdda.json"}}, {"family": "Liu", "given": "Sang", "initials": "S"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Nie", "given": "Mu", "initials": "M"}, {"family": "\u00d6sterberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Baharom", "given": "Faezzah", "initials": "F", "orcid": "0000-0003-4513-3600", "researcher": {"href": "https://publications.scilifelab.se/researcher/44f038206b284bbdacd90e380a1241cb.json"}}, {"family": "Pourazar", "given": "Jamshid", "initials": "J", "orcid": "0000-0003-0041-4644", "researcher": {"href": "https://publications.scilifelab.se/researcher/50b09635f4e94688b834029691f9aa15.json"}}, {"family": "Rankin", "given": "Gregory", "initials": "G", "orcid": "0000-0002-8753-830X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dcc67a128bc4d0f804079a0651782e3.json"}}, {"family": "Eklund", "given": "Anders", "initials": "A", "orcid": "0000-0002-7263-7057", "researcher": {"href": "https://publications.scilifelab.se/researcher/7581bb705798439b942a79a2687a9d5f.json"}}, {"family": "Bottai", "given": "Matteo", "initials": "M", "orcid": "0000-0002-3531-2739", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2f6ca7ec48f4296864e5da572e2fc94.json"}}, {"family": "Kullberg", "given": "Susanna", "initials": "S", "orcid": "0000-0003-2844-4773", "researcher": {"href": "https://publications.scilifelab.se/researcher/e81e4d898e1d45e9ac309575c9c03946.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-2452-7347", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c5b4f5240384d718af7db5d501c637d.json"}}, {"family": "Grunewald", "given": "Johan", "initials": "J", "orcid": "0000-0003-0473-3984", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f22badaa9634052a9ab013666fb4fda.json"}}, {"family": "Smed-S\u00f6rensen", "given": "Anna", "initials": "A", "orcid": "0000-0001-6966-7039", "researcher": {"href": "https://publications.scilifelab.se/researcher/b874ce1e1fd4455e9d681c3d3db74ed0.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Eur. Respir. J.", "issn": "1399-3003", "volume": "58", "issue": "1", "pages": "2003468", "issn-l": "0903-1936"}, "abstract": "Pulmonary sarcoidosis is an inflammatory disease characterised by granuloma formation and heterogeneous clinical outcome. Tumour necrosis factor (TNF) is a pro-inflammatory cytokine contributing to granuloma formation and high levels of TNF have been shown to associate with progressive disease. Mononuclear phagocytes (MNPs) are potent producers of TNF and highly responsive to inflammation. In sarcoidosis, alveolar macrophages have been well studied. However, MNPs also include monocytes/monocyte-derived cells and dendritic cells, which are poorly studied in sarcoidosis, despite their central role in inflammation.\n\nTo determine the role of pulmonary monocyte-derived cells and dendritic cells during sarcoidosis.\n\nWe performed in-depth phenotypic, functional and transcriptomic analysis of MNP subsets from blood and bronchoalveolar lavage (BAL) fluid from 108 sarcoidosis patients and 30 healthy controls. We followed the clinical development of patients and assessed how the repertoire and function of MNP subsets at diagnosis correlated with 2-year disease outcome.\n\nMonocytes/monocyte-derived cells were increased in blood and BAL of sarcoidosis patients compared to healthy controls. Interestingly, high frequencies of blood intermediate monocytes at time of diagnosis associated with chronic disease development. RNA sequencing analysis showed highly inflammatory MNPs in BAL of sarcoidosis patients. Furthermore, frequencies of BAL monocytes/monocyte-derived cells producing TNF without exogenous stimulation at time of diagnosis increased in patients that were followed longitudinally. In contrast to alveolar macrophages, the frequency of TNF-producing BAL monocytes/monocyte-derived cells at time of diagnosis was highest in sarcoidosis patients that developed progressive disease.\n\nOur data show that pulmonary monocytes/monocyte-derived cells are highly inflammatory and can be used as a predictor of disease outcome in sarcoidosis patients.", "doi": "10.1183/13993003.03468-2020", "pmid": "33446605", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "13993003.03468-2020"}, {"db": "pmc", "key": "PMC8295505"}], "notes": [], "created": "2021-01-26T15:22:33.589Z", "modified": "2024-01-16T13:48:39.255Z"}, {"entity": "publication", "iuid": "661c201d37c949e7a6db545f120153a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/661c201d37c949e7a6db545f120153a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/661c201d37c949e7a6db545f120153a2"}}, "title": "Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells", "authors": [{"family": "Mathew", "given": "Nimitha R", "initials": "NR"}, {"family": "Jayanthan", "given": "Jayalal K", "initials": "JK"}, {"family": "Smirnov", "given": "Ilya V", "initials": "IV"}, {"family": "Robinson", "given": "Jonathan L", "initials": "JL", "orcid": "0000-0001-8567-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/b70b6d9b64fd45e882c4108aded013d4.json"}}, {"family": "Axelsson", "given": "Hannes", "initials": "H", "orcid": "0000-0003-2365-1749", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b88c4d11c443f39121c6d93fcff1f0.json"}}, {"family": "Nakka", "given": "Sravya S", "initials": "SS"}, {"family": "Emmanouilidi", "given": "Aikaterini", "initials": "A", "orcid": "0000-0001-9431-6900", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c06a1851eea457199282fc3544563ef.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Yewdell", "given": "William T", "initials": "WT"}, {"family": "Sch\u00f6n", "given": "Karin", "initials": "K"}, {"family": "Lebrero-Fern\u00e1ndez", "given": "Cristina", "initials": "C"}, {"family": "Bernasconi", "given": "Valentina", "initials": "V"}, {"family": "Rodin", "given": "William", "initials": "W"}, {"family": "Harandi", "given": "Ali M", "initials": "AM"}, {"family": "Lycke", "given": "Nils", "initials": "N", "orcid": "0000-0003-1155-4861", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc624dbe15d24b8a90ad8d8673ffd390.json"}}, {"family": "Borcherding", "given": "Nicholas", "initials": "N"}, {"family": "Yewdell", "given": "Jonathan W", "initials": "JW"}, {"family": "Greiff", "given": "Victor", "initials": "V", "orcid": "0000-0003-2622-5032", "researcher": {"href": "https://publications.scilifelab.se/researcher/1545e9cb92db4ccc93c1b2dc398e1777.json"}}, {"family": "Bemark", "given": "Mats", "initials": "M", "orcid": "0000-0001-7416-9819", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a7ee472e2e0453b98ee9fdfc02de2b3.json"}}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}], "type": "journal-article", "published": "2021-06-00", "journal": {"title": "Cell Rep", "issn": "2211-1247", "issn-l": null, "volume": "35", "issue": "12", "pages": "109286"}, "abstract": "B cell responses are critical for antiviral immunity. However, a comprehensive picture of antigen-specific B cell differentiation, clonal proliferation, and dynamics in different organs after infection is lacking. Here, by combining single-cell RNA and B cell receptor (BCR) sequencing of antigen-specific cells in lymph nodes, spleen, and lungs after influenza infection in mice, we identify several germinal center (GC) B cell subpopulations and organ-specific differences that persist over the course of the response. We discover transcriptional differences between memory cells in lungs and lymphoid organs and organ-restricted clonal expansion. Remarkably, we find significant clonal overlap between GC-derived memory and plasma cells. By combining BCR-mutational analyses with monoclonal antibody (mAb) expression and affinity measurements, we find that memory B cells are highly diverse and can be selected from both low- and high-affinity precursors. By linking antigen recognition with transcriptional programming, clonal proliferation, and differentiation, these finding provide important advances in our understanding of antiviral immunity.", "doi": "10.1016/j.celrep.2021.109286", "pmid": "34161770", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Systems Biology": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "mid", "key": "EMS146188"}, {"db": "pmc", "key": "PMC7612943"}, {"db": "pii", "key": "S2211-1247(21)00657-4"}], "notes": [], "created": "2021-06-24T07:56:29.627Z", "modified": "2023-06-19T11:26:37.988Z"}, {"entity": "publication", "iuid": "a38ee778ff164c3f81c0f75f0c598e62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a38ee778ff164c3f81c0f75f0c598e62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a38ee778ff164c3f81c0f75f0c598e62"}}, "title": "Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.", "authors": [{"family": "Mazzurana", "given": "Luca", "initials": "L"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Wigge", "given": "Leif", "initials": "L"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Williams", "given": "Teresa C", "initials": "TC"}, {"family": "Ravindran", "given": "Avinash", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "S\u00e4fholm", "given": "Jesper", "initials": "J"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dahl\u00e9n", "given": "Sven-Erik", "initials": "SE"}, {"family": "Orre", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "H\u00f6\u00f6g", "given": "Charlotte", "initials": "C"}, {"family": "Hedin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-4921-8516", "researcher": {"href": "https://publications.scilifelab.se/researcher/d451be670f7f456ebca935690af79076.json"}}, {"family": "Szczegielniak", "given": "Sylwester", "initials": "S"}, {"family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Cell Res", "issn": "1001-0602", "issn-l": null, "volume": "31", "issue": "5", "pages": "554-568"}, "abstract": "The impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident na\u00efve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2+ and CRTH2- ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-\u03b4 rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease.", "doi": "10.1038/s41422-020-00445-x", "pmid": "33420427", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41422-020-00445-x"}, {"db": "pmc", "key": "PMC8089104"}], "notes": [], "created": "2021-01-11T12:39:39.962Z", "modified": "2024-01-16T13:48:39.843Z"}]}