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

C. Domínguez Conde; C. Xu; L. B. Jarvis; D. B. Rainbow; S. B. Wells; T. Gomes; S. K. Howlett; O. Suchanek; K. Polanski; H. W. King; L. Mamanova; N. Huang; P. A. Szabo; L. Richardson; L. Bolt; E. S. Fasouli; K. T. Mahbubani; M. Prete; L. Tuck; N. Richoz; Z. K. Tuong; L. Campos; H. S. Mousa; E. J. Needham; S. Pritchard; T. Li; R. Elmentaite; J. Park; E. Rahmani; D. Chen; D. K. Menon; O. A. Bayraktar; L. K. James; K. B. Meyer; N. Yosef; M. R. Clatworthy; P. A. Sims; D. L. Farber; K. Saeb-Parsy; J. L. Jones; S. A. Teichmann

doi:https://doi.org/10.1126/science.abl5197

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

C. Domínguez Conde, C. Xu, L. B. Jarvis, D. B. Rainbow, S. B. Wells, T. Gomes, S. K. Howlett, O. Suchanek, K. Polanski, H. W. King, L. Mamanova, N. Huang, P. A. Szabo, L. Richardson, L. Bolt, E. S. Fasouli, K. T. Mahbubani, M. Prete, L. Tuck, N. RichozZ. K. Tuong, L. Campos, H. S. Mousa, E. J. Needham, S. Pritchard, T. Li, R. Elmentaite, J. Park, E. Rahmani, D. Chen, D. K. Menon, O. A. Bayraktar, L. K. James, K. B. Meyer, N. Yosef, M. R. Clatworthy, P. A. Sims, D. L. Farber, K. Saeb-Parsy, J. L. Jones, S. A. Teichmann

Research output: Contribution to journal › Article › peer-review

Abstract

Despite 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.

Original language	English
Article number	eabl5197
Journal	Science
Volume	376
Issue number	6594
DOIs	https://doi.org/10.1126/science.abl5197
State	Published - 13 May 2022
Externally published	Yes

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Domínguez Conde, C., Xu, C., Jarvis, L. B., Rainbow, D. B., Wells, S. B., Gomes, T., Howlett, S. K., Suchanek, O., Polanski, K., King, H. W., Mamanova, L., Huang, N., Szabo, P. A., Richardson, L., Bolt, L., Fasouli, E. S., Mahbubani, K. T., Prete, M., Tuck, L., ... Teichmann, S. A. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376(6594), Article eabl5197. https://doi.org/10.1126/science.abl5197

@article{9b3a4cacffa642f0aad9f41f5c7065a3,

title = "Cross-tissue immune cell analysis reveals tissue-specific features in humans",

abstract = "Despite 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.",

author = "{Dom{\'i}nguez Conde}, C. and C. Xu and Jarvis, {L. B.} and Rainbow, {D. B.} and Wells, {S. B.} and T. Gomes and Howlett, {S. K.} and O. Suchanek and K. Polanski and King, {H. W.} and L. Mamanova and N. Huang and Szabo, {P. A.} and L. Richardson and L. Bolt and Fasouli, {E. S.} and Mahbubani, {K. T.} and M. Prete and L. Tuck and N. Richoz and Tuong, {Z. K.} and L. Campos and Mousa, {H. S.} and Needham, {E. J.} and S. Pritchard and T. Li and R. Elmentaite and J. Park and E. Rahmani and D. Chen and Menon, {D. K.} and Bayraktar, {O. A.} and James, {L. K.} and Meyer, {K. B.} and N. Yosef and Clatworthy, {M. R.} and Sims, {P. A.} and Farber, {D. L.} and K. Saeb-Parsy and Jones, {J. L.} and Teichmann, {S. A.}",

year = "2022",

month = may,

day = "13",

doi = "https://doi.org/10.1126/science.abl5197",

language = "الإنجليزيّة",

volume = "376",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6594",

}

Domínguez Conde, C, Xu, C, Jarvis, LB, Rainbow, DB, Wells, SB, Gomes, T, Howlett, SK, Suchanek, O, Polanski, K, King, HW, Mamanova, L, Huang, N, Szabo, PA, Richardson, L, Bolt, L, Fasouli, ES, Mahbubani, KT, Prete, M, Tuck, L, Richoz, N, Tuong, ZK, Campos, L, Mousa, HS, Needham, EJ, Pritchard, S, Li, T, Elmentaite, R, Park, J, Rahmani, E, Chen, D, Menon, DK, Bayraktar, OA, James, LK, Meyer, KB, Yosef, N, Clatworthy, MR, Sims, PA, Farber, DL, Saeb-Parsy, K, Jones, JL & Teichmann, SA 2022, 'Cross-tissue immune cell analysis reveals tissue-specific features in humans', Science, vol. 376, no. 6594, eabl5197. https://doi.org/10.1126/science.abl5197

TY - JOUR

T1 - Cross-tissue immune cell analysis reveals tissue-specific features in humans

AU - Domínguez Conde, C.

AU - Xu, C.

AU - Jarvis, L. B.

AU - Rainbow, D. B.

AU - Wells, S. B.

AU - Gomes, T.

AU - Howlett, S. K.

AU - Suchanek, O.

AU - Polanski, K.

AU - King, H. W.

AU - Mamanova, L.

AU - Huang, N.

AU - Szabo, P. A.

AU - Richardson, L.

AU - Bolt, L.

AU - Fasouli, E. S.

AU - Mahbubani, K. T.

AU - Prete, M.

AU - Tuck, L.

AU - Richoz, N.

AU - Tuong, Z. K.

AU - Campos, L.

AU - Mousa, H. S.

AU - Needham, E. J.

AU - Pritchard, S.

AU - Li, T.

AU - Elmentaite, R.

AU - Park, J.

AU - Rahmani, E.

AU - Chen, D.

AU - Menon, D. K.

AU - Bayraktar, O. A.

AU - James, L. K.

AU - Meyer, K. B.

AU - Yosef, N.

AU - Clatworthy, M. R.

AU - Sims, P. A.

AU - Farber, D. L.

AU - Saeb-Parsy, K.

AU - Jones, J. L.

AU - Teichmann, S. A.

PY - 2022/5/13

Y1 - 2022/5/13

N2 - Despite 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.

AB - Despite 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.

UR - http://www.scopus.com/inward/record.url?scp=85130632678&partnerID=8YFLogxK

U2 - https://doi.org/10.1126/science.abl5197

DO - https://doi.org/10.1126/science.abl5197

M3 - مقالة

C2 - 35549406

SN - 0036-8075

VL - 376

JO - Science

JF - Science

IS - 6594

M1 - eabl5197

ER -

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

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