{"entity": "researcher", "timestamp": "2026-07-15T01:09:50.805Z", "family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "affiliations": ["Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713"}}, "publications": [{"entity": "publication", "iuid": "d28325d47fdb47cda393a1e60d677055", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d28325d47fdb47cda393a1e60d677055.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d28325d47fdb47cda393a1e60d677055"}}, "title": "Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.", "authors": [{"family": "Mandolesi", "given": "Marco", "initials": "M", "orcid": "0000-0003-2927-7831", "researcher": {"href": "https://publications.scilifelab.se/researcher/29e6c31be1704c97a2853aca0833f6b0.json"}}, {"family": "Das", "given": "Hrishikesh", "initials": "H", "orcid": "0000-0001-7495-7065", "researcher": {"href": "https://publications.scilifelab.se/researcher/b150c8ccf1164aaab678a9f6c1acd97b.json"}}, {"family": "de Vries", "given": "Liset", "initials": "L", "orcid": "0000-0002-4797-086X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6b05b7eec7c4120b4bee2ff15ac8035.json"}}, {"family": "Yang", "given": "Yiqiu", "initials": "Y"}, {"family": "Kim", "given": "Changil", "initials": "C"}, {"family": "Dhinakaran", "given": "Manojj", "initials": "M", "orcid": "0000-0003-2536-8699", "researcher": {"href": "https://publications.scilifelab.se/researcher/de859a6247424dd285f56b841dc23a36.json"}}, {"family": "Castro Dopico", "given": "Xaquin", "initials": "X", "orcid": "0000-0002-9005-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1d266d61654951a684193993ca53b1.json"}}, {"family": "Fischbach", "given": "Julian", "initials": "J", "orcid": "0000-0001-9411-9181", "researcher": {"href": "https://publications.scilifelab.se/researcher/20e4fea1f9f54727b1bf3ef1cb8f81a4.json"}}, {"family": "Kim", "given": "Sungyong", "initials": "S"}, {"family": "Guryleva", "given": "Mariia V", "initials": "MV"}, {"family": "\u00c0dori", "given": "Monika", "initials": "M"}, {"family": "Chernyshev", "given": "Mark", "initials": "M", "orcid": "0000-0003-1622-9240", "researcher": {"href": "https://publications.scilifelab.se/researcher/678134399edb44afac5e7eacc8622fcb.json"}}, {"family": "St\u00e5lmarck", "given": "Aron", "initials": "A"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "McInerney", "given": "Gerald M", "initials": "GM", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-0227-5636", "researcher": {"href": "https://publications.scilifelab.se/researcher/6105f3617cdf4241bf335299ac957ee5.json"}}, {"family": "Corcoran", "given": "Martin", "initials": "M"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM", "orcid": "0000-0002-6781-0345", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b7e4327d0ac48288afd6061f149156d.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6338", "issn-l": "2041-1723"}, "abstract": "The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.", "doi": "10.1038/s41467-024-50286-0", "pmid": "39068149", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11283548"}, {"db": "pii", "key": "10.1038/s41467-024-50286-0"}], "notes": [], "created": "2024-10-14T13:07:16.627Z", "modified": "2024-11-25T10:17:09.411Z"}, {"entity": "publication", "iuid": "dceccccd7b74440b9e8f1acfe66fa9a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dceccccd7b74440b9e8f1acfe66fa9a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dceccccd7b74440b9e8f1acfe66fa9a7"}}, "title": "Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque.", "authors": [{"family": "Castro Dopico", "given": "Xaquin", "initials": "X", "orcid": "0000-0002-9005-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1d266d61654951a684193993ca53b1.json"}}, {"family": "Guryleva", "given": "Mariia", "initials": "M", "orcid": "0009-0004-6370-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e8d6837c5fa48e99698c9f465ae1412.json"}}, {"family": "Mandolesi", "given": "Marco", "initials": "M", "orcid": "0000-0003-2927-7831", "researcher": {"href": "https://publications.scilifelab.se/researcher/29e6c31be1704c97a2853aca0833f6b0.json"}}, {"family": "Corcoran", "given": "Martin", "initials": "M", "orcid": "0000-0002-2774-0936", "researcher": {"href": "https://publications.scilifelab.se/researcher/7177b777948c4efa882ffef30764e223.json"}}, {"family": "Coquet", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0002-5967-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b74959951024d6ea9712b55f115652e.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "Clin Transl Immunology", "issn": "2050-0068", "volume": "13", "issue": "5", "pages": "e1508", "issn-l": null}, "abstract": "The caecum bridges the small and large intestine and plays a front-line role in discriminating gastrointestinal antigens. Although dysregulated in acute and chronic conditions, the tissue is often overlooked immunologically.\n\nTo address this issue, we applied single-cell transcriptomic-V(D)J sequencing to FACS-isolated CD45+ caecal patch/lamina propria leukocytes from a healthy (5-year-old) female rhesus macaque ex vivo and coupled these data to VDJ deep sequencing reads from haematopoietic tissues.\n\nWe found caecal NK cells and ILC3s to co-exist with a spectrum of effector T cells partially derived from SOX4 + recent thymic emigrants. Tolerogenic V\u03b38V\u03b41-T cells, plastic CD4+ T helper cells and GZMK + EOMES + and TMIGD2 + tissue-resident memory CD8+ T cells were present and differed metabolically. An IL13 + GATA3 + Th2 subset expressing eicosanoid pathway enzymes was accompanied by IL1RL1 + GATA3 + regulatory T cells and a minor proportion of IgE+ plasma cells (PCs), illustrating tightly regulated type 2 immunity devoid of ILC2s. In terms of B lymphocyte lineages, caecal patch antigen-presenting memory B cells sat alongside germinal centre cells undergoing somatic hypermutation and differentiation into IGF1 + PCs. Prototypic gene expression signatures decreased across PC clusters, and notably, expanded IgA clonotypes could be traced in VDJ deep sequencing reads from additional compartments, including the bone marrow, supporting that these cells contribute a steady stream of systemic antibodies.\n\nThe data advance our understanding of caecal immunological function, revealing processes involved in barrier maintenance and molecular networks relevant to disease.", "doi": "10.1002/cti2.1508", "pmid": "38707998", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11063928"}, {"db": "pii", "key": "CTI21508"}], "notes": [], "created": "2024-10-14T13:07:00.500Z", "modified": "2025-02-28T14:09:49.646Z"}, {"entity": "publication", "iuid": "2f5b1a01cfc945bcbe4a0dad8b6f87a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f5b1a01cfc945bcbe4a0dad8b6f87a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f5b1a01cfc945bcbe4a0dad8b6f87a2"}}, "title": "Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.", "authors": [{"family": "Phad", "given": "Ganesh E", "initials": "GE", "orcid": "0000-0002-0047-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/a231cb66fab941df968de8f204c39782.json"}}, {"family": "Pushparaj", "given": "Pradeepa", "initials": "P"}, {"family": "Tran", "given": "Karen", "initials": "K"}, {"family": "Dubrovskaya", "given": "Viktoriya", "initials": "V", "orcid": "0000-0002-6563-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/58a673f27e224aed933a62c62bc16737.json"}}, {"family": "\u00c0dori", "given": "Monika", "initials": "M"}, {"family": "Martinez-Murillo", "given": "Paola", "initials": "P", "orcid": "0000-0003-0888-3867", "researcher": {"href": "https://publications.scilifelab.se/researcher/63aec47c762643f5b343ada040f1bcaa.json"}}, {"family": "V\u00e1zquez Bernat", "given": "N\u00e9stor", "initials": "N"}, {"family": "Singh", "given": "Suruchi", "initials": "S", "orcid": "0000-0002-4306-9345", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa3266660bdc40e09750af4f22d2ecd5.json"}}, {"family": "Dionne", "given": "Gilman", "initials": "G"}, {"family": "O'Dell", "given": "Sijy", "initials": "S"}, {"family": "Bhullar", "given": "Komal", "initials": "K"}, {"family": "Narang", "given": "Sanjana", "initials": "S"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Sundling", "given": "Christopher", "initials": "C", "orcid": "0000-0002-6138-690X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89c1e689a46b4b14adb0dc99e1c0a58c.json"}}, {"family": "Murrell", "given": "Benjamin", "initials": "B"}, {"family": "Mascola", "given": "John R", "initials": "JR"}, {"family": "Shapiro", "given": "Lawrence", "initials": "L"}, {"family": "Pancera", "given": "Marie", "initials": "M"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Corcoran", "given": "Martin", "initials": "M"}, {"family": "Wyatt", "given": "Richard T", "initials": "RT"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}}], "type": "journal article", "published": "2020-02-03", "journal": {"title": "J. Exp. Med.", "issn": "1540-9538", "volume": "217", "issue": "2", "pages": null, "issn-l": "0022-1007"}, "abstract": "Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from \u223c1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.", "doi": "10.1084/jem.20191155", "pmid": "31704807", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jem.20191155"}, {"db": "pmc", "key": "PMC7041718"}], "notes": [], "created": "2021-04-06T10:57:24.634Z", "modified": "2021-11-10T12:54:12.139Z"}]}