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Cross-tissue immune cell analysis reveals tissue-specific features in humans.

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cam.issuedOnline2022-05-13
datacite.isderivedfrom.doi10.1101/2021.04.28.441762
dc.contributor.authorDomínguez Conde, C
dc.contributor.authorXu, C
dc.contributor.authorJarvis, LB
dc.contributor.authorRainbow, DB
dc.contributor.authorWells, SB
dc.contributor.authorGomes, T
dc.contributor.authorHowlett, SK
dc.contributor.authorSuchanek, O
dc.contributor.authorPolanski, K
dc.contributor.authorKing, HW
dc.contributor.authorMamanova, L
dc.contributor.authorHuang, N
dc.contributor.authorSzabo, PA
dc.contributor.authorRichardson, L
dc.contributor.authorBolt, L
dc.contributor.authorFasouli, ES
dc.contributor.authorMahbubani, KT
dc.contributor.authorPrete, M
dc.contributor.authorTuck, L
dc.contributor.authorRichoz, N
dc.contributor.authorTuong, ZK
dc.contributor.authorCampos, L
dc.contributor.authorMousa, HS
dc.contributor.authorNeedham, EJ
dc.contributor.authorPritchard, S
dc.contributor.authorLi, T
dc.contributor.authorElmentaite, R
dc.contributor.authorPark, J
dc.contributor.authorRahmani, E
dc.contributor.authorChen, D
dc.contributor.authorMenon, DK
dc.contributor.authorBayraktar, OA
dc.contributor.authorJames, LK
dc.contributor.authorMeyer, KB
dc.contributor.authorYosef, N
dc.contributor.authorClatworthy, MR
dc.contributor.authorSims, PA
dc.contributor.authorFarber, DL
dc.contributor.authorSaeb-Parsy, K
dc.contributor.authorJones, JL
dc.contributor.authorTeichmann, SA
dc.contributor.orcidDomínguez Conde, C [0000-0002-8684-4655]
dc.contributor.orcidXu, C [0000-0002-6265-999X]
dc.contributor.orcidJarvis, LB [0000-0002-5760-0125]
dc.contributor.orcidRainbow, DB [0000-0003-4931-3289]
dc.contributor.orcidWells, SB [0000-0001-5428-0683]
dc.contributor.orcidGomes, T [0000-0003-1333-0191]
dc.contributor.orcidHowlett, SK [0000-0003-0504-4937]
dc.contributor.orcidPolanski, K [0000-0002-2586-9576]
dc.contributor.orcidKing, HW [0000-0001-5972-8926]
dc.contributor.orcidMamanova, L [0000-0003-1463-8622]
dc.contributor.orcidHuang, N [0000-0001-8849-038X]
dc.contributor.orcidSzabo, PA [0000-0003-1603-761X]
dc.contributor.orcidRichardson, L [0000-0001-9064-1271]
dc.contributor.orcidBolt, L [0000-0001-7293-0774]
dc.contributor.orcidFasouli, ES [0000-0003-1621-3396]
dc.contributor.orcidMahbubani, KT [0000-0002-1327-2334]
dc.contributor.orcidPrete, M [0000-0002-5946-821X]
dc.contributor.orcidTuck, L [0000-0002-1837-7549]
dc.contributor.orcidTuong, ZK [0000-0002-6735-6808]
dc.contributor.orcidCampos, L [0000-0003-2445-7120]
dc.contributor.orcidMousa, HS [0000-0002-8327-7114]
dc.contributor.orcidNeedham, EJ [0000-0001-7042-7462]
dc.contributor.orcidLi, T [0000-0002-8240-4476]
dc.contributor.orcidElmentaite, R [0000-0001-7366-5466]
dc.contributor.orcidPark, J [0000-0002-1687-2423]
dc.contributor.orcidChen, D [0000-0002-9710-1857]
dc.contributor.orcidMenon, DK [0000-0002-3228-9692]
dc.contributor.orcidJames, LK [0000-0002-2252-4636]
dc.contributor.orcidMeyer, KB [0000-0001-5906-1498]
dc.contributor.orcidYosef, N [0000-0001-9004-1225]
dc.contributor.orcidClatworthy, MR [0000-0002-3340-9828]
dc.contributor.orcidSims, PA [0000-0002-3921-4837]
dc.contributor.orcidFarber, DL [0000-0001-8236-9183]
dc.contributor.orcidSaeb-Parsy, K [0000-0002-0633-3696]
dc.contributor.orcidJones, JL [0000-0003-4974-1371]
dc.contributor.orcidTeichmann, SA [0000-0002-6294-6366]
dc.date.accessioned2022-06-14T01:03:02Z
dc.date.available2022-06-14T01:03:02Z
dc.date.issued2022-05-13
dc.date.updated2022-06-14T01:03:02Z
dc.description.abstractDespite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
dc.description.sponsorshipCZI NIH grant ERC grant (Thdefine)
dc.identifier.citationScience (New York, N.Y.), volume 376, issue 6594, page eabl5197
dc.identifier.doi10.17863/CAM.85466
dc.identifier.eissn1095-9203
dc.identifier.issn0036-8075
dc.identifier.other35549406
dc.identifier.otherPMC7612735
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/338057
dc.languageeng
dc.language.isoeng
dc.publisherAmerican Association for the Advancement of Science (AAAS)
dc.publisher.urlhttp://dx.doi.org/10.1126/science.abl5197
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourcenlmid: 0404511
dc.sourceessn: 1095-9203
dc.subjectB-Lymphocytes
dc.subjectCells, Cultured
dc.subjectHumans
dc.subjectMachine Learning
dc.subjectOrgan Specificity
dc.subjectSequence Analysis, RNA
dc.subjectSingle-Cell Analysis
dc.subjectT-Lymphocytes
dc.subjectTranscriptome
dc.titleCross-tissue immune cell analysis reveals tissue-specific features in humans.
dc.typeArticle
dcterms.dateAccepted2022-03-23
prism.publicationNameScience
pubs.funder-project-idWellcome Trust (105924/Z/14/Z)
pubs.funder-project-idWellcome Trust (105924/Z/14/A)
pubs.funder-project-idWellcome Trust (105924/Z/14/Z)
pubs.funder-project-idWellcome Trust (105924/Z/14/A)
pubs.funder-project-idChan Zuckerberg Initiative (via University of California) (10208)
pubs.funder-project-idWellcome Trust (211276/D/18/Z)
pubs.funder-project-idNational Institute for Health and Care Research (IS-BRC-1215-20014)
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0/
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1126/science.abl5197

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