{"entity": "researcher", "timestamp": "2026-08-15T07:06:21.979Z", "family": "Lycke", "given": "Nils", "initials": "N", "orcid": "0000-0003-1155-4861", "affiliations": ["Mucosal Immunobiology and Vaccine Center (MIVAC), Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden. nils.lycke@microbio.gu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/cc624dbe15d24b8a90ad8d8673ffd390.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/cc624dbe15d24b8a90ad8d8673ffd390"}}, "publications": [{"entity": "publication", "iuid": "2f54b302697c4891b3ea172032b6c3ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f54b302697c4891b3ea172032b6c3ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f54b302697c4891b3ea172032b6c3ac"}}, "title": "Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity", "authors": [{"family": "Omokanye", "given": "Ajibola", "initials": "A"}, {"family": "Ong", "given": "Li Ching", "initials": "LC"}, {"family": "Lebrero-Fernandez", "given": "Cristina", "initials": "C"}, {"family": "Bernasconi", "given": "Valentina", "initials": "V"}, {"family": "Sch\u00f6n", "given": "Karin", "initials": "K"}, {"family": "Str\u00f6mberg", "given": "Anneli", "initials": "A"}, {"family": "Bemark", "given": "Mats", "initials": "M"}, {"family": "Saelens", "given": "Xavier", "initials": "X"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Lycke", "given": "Nils", "initials": "N", "orcid": "0000-0003-1155-4861", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc624dbe15d24b8a90ad8d8673ffd390.json"}}], "type": "journal-article", "published": "2022-04-00", "journal": {"title": "Mucosal Immunol", "issn": "1933-0219", "volume": "15", "issue": "4", "pages": "717-729", "issn-l": null}, "abstract": "The fate of tissue-resident memory CD4 T cells (Trm) has been incompletely investigated. Here we show that intranasal, but not parenteral, immunization with CTA1-3M2e-DD stimulated M2e-specific Th17 Trm cells, which conferred strong protection against influenza virus infection in the lung. These cells rapidly expanded upon infection and effectively restricted virus replication as determined by CD4 T cell depletion studies. Single-cell RNAseq transcriptomic and TCR VDJ-analysis of M2e-tetramer-sorted CD4 T cells on day 3 and 8 post infection revealed complete Th17-lineage dominance (no Th1 or Tregs) with extensive functional diversity and expression of gene markers signifying mature resident Trm cells (Cd69, Nfkbid, Brd2, FosB). Unexpectedly, the same TCR clonotype hosted cells with different Th17 subcluster functions (IL-17, IL-22), regulatory and cytotoxic cells, suggesting a tissue and context-dependent differentiation of reactivated Th17 Trm cells. A gene set enrichment analysis demonstrated up-regulation of regulatory genes (Lag3, Tigit, Ctla4, Pdcd1) in M2e-specific Trm cells on day 8, indicating a tissue damage preventing function. Thus, contrary to current thinking, lung M2e-specific Th17 Trm cells are sufficient for controlling infection and for protecting against tissue injury. These findings will have strong implications for vaccine development against respiratory virus infections and influenza virus infections, in particular.", "doi": "10.1038/s41385-022-00497-9", "pmid": "35260804", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41385-022-00497-9"}, {"db": "pmc", "key": "PMC8903128"}], "notes": [], "created": "2022-04-04T19:19:42.737Z", "modified": "2023-04-26T11:54:18.956Z"}, {"entity": "publication", "iuid": "d36c2b0a3e7e445991d019d2c87c528b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d36c2b0a3e7e445991d019d2c87c528b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d36c2b0a3e7e445991d019d2c87c528b"}}, "title": "ADP-ribosylating adjuvant reveals plasticity in cDC1 cells that drive mucosal Th17 cell development and protection against influenza virus infection.", "authors": [{"family": "Arabpour", "given": "Mohammad", "initials": "M"}, {"family": "Lebrero-Fernandez", "given": "Cristina", "initials": "C"}, {"family": "Sch\u00f6n", "given": "Karin", "initials": "K"}, {"family": "Str\u00f6mberg", "given": "Anneli", "initials": "A"}, {"family": "B\u00f6rjesson", "given": "Vanja", "initials": "V"}, {"family": "Lahl", "given": "Katharina", "initials": "K"}, {"family": "Ballegeer", "given": "Marlies", "initials": "M"}, {"family": "Saelens", "given": "Xavier", "initials": "X"}, {"family": "Angeletti", "given": "Davide", "initials": "D"}, {"family": "Agace", "given": "William", "initials": "W"}, {"family": "Lycke", "given": "Nils", "initials": "N", "orcid": "0000-0003-1155-4861", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc624dbe15d24b8a90ad8d8673ffd390.json"}}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Mucosal Immunol", "issn": "1935-3456", "issn-l": "1933-0219", "volume": "15", "issue": "4", "pages": "745-761"}, "abstract": "Migratory dendritic cells expressing CD103 are the targets for mucosal vaccines. These belong to either of two lineage-restricted subsets, cDC1 or cDC2 cells, which have been linked to priming of functionally distinct CD4 T cells. However, recent studies have identified plasticity in cDC2 cells with overlapping functions with cDC1 cells, while the converse has not been reported. We genetically engineered a vaccine adjuvant platform that targeted the cholera toxin A1 (CTA1) ADP-ribosylating enzyme to CD103+ cDC1 and cDC2 cells using a single-chain antibody (scFv) to CD103. Unexpectedly, intranasal immunization with the CTA1-svFcCD103 adjuvant modified cDC1 cells to effectively prime Th17 cells, a function previously limited to cDC2 cells. In fact, cDC2 cells were dispensible, while cDC1 cells, lacking in Batf3-/- mice, were critical. Following intranasal immunizations isolated cDC1 cells from mLN exclusively promoted Rorgt+ T cells and IL-17, IL-21, and IL-22 production. Strong CD8 T cell responses through antigen cross presentation by cDC1 cells were also observed. Single-cell RNAseq analysis revealed upregulation of Th17-promoting gene signatures in sorted cDC1 cells. Gene expression in isolated cDC2 cells was largely unaffected. Our finding represents a major shift of paradigm as we have documented functional plasticity in cDC1 cells.", "doi": "10.1038/s41385-022-00510-1", "pmid": "35418673", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9259495"}, {"db": "pii", "key": "10.1038/s41385-022-00510-1"}], "notes": [], "created": "2022-12-02T12:23:18.797Z", "modified": "2023-05-15T16:36:15.231Z"}, {"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"}]}