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
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.
Datasets
1. Global
Metadata
donor_id
Predicted_labels_CellTypist
Majority_voting_CellTypist
Majority_voting_CellTypist_high
Manually_curated_celltype
assay_ontology_term_id
cell_type_ontology_term_id
development_stage_ontology_term_id
disease_ontology_term_id
self_reported_ethnicity_ontology_term_id
organism_ontology_term_id
sex_ontology_term_id
tissue_ontology_term_id
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
Cytotoxic T cells36883 cells Memory B cells31194 cells Helper T cells25761 cells CD16+ NK cells21495 cells Tem/Effector helper T cells21015 cells Classical monocytes18388 cells Tcm/Naive helper T cells17752 cells Tem/Effector cytotoxic T cells9749 cells Regulatory T cells9626 cells Tcm/Naive cytotoxic T cells9125 cells gamma-delta T cells6745 cells Follicular helper T cells6470 cells Type 1 helper T cells5648 cells Non-classical monocytes4178 cells Type 17 helper T cells2506 cells Double-negative thymocytes1790 cells Memory CD4+ cytotoxic T cells1470 cells Cycling T cells1131 cells Germinal center B cells581 cells Tem/Effector helper T cells PD1+555 cells Early lymphoid/T lymphoid466 cells Neutrophil-myeloid progenitor376 cells Follicular B cells328 cells Megakaryocyte precursor240 cells Double-positive thymocytes237 cells Megakaryocytes/platelets234 cells Transitional B cells213 cells Epithelial cells178 cells Monocyte precursor154 cells Endothelial cells151 cells Megakaryocyte-erythroid-mast cell progenitor136 cells Kidney-resident macrophages126 cells Immature B cells108 cells Cycling gamma-delta T cells107 cells Cycling NK cells101 cells Cycling monocytes31 cells Cytotoxic T cells59522 cells Helper T cells40087 cells Memory B cells31119 cells Tem/Effector helper T cells26763 cells Classical monocytes21719 cells CD16+ NK cells20672 cells Tcm/Naive helper T cells16484 cells Regulatory T cells11622 cells Tcm/Naive cytotoxic T cells8914 cells gamma-delta T cells7692 cells Non-classical monocytes3892 cells Type 1 helper T cells3545 cells Type 17 helper T cells2053 cells Follicular helper T cells1827 cells Tem/Effector cytotoxic T cells663 cells Immature B cells100 cells Germinal center B cells85 cells Memory B cells28915 cells Classical monocytes21847 cells Teffector/EM_CD419869 cells Alveolar macrophages17238 cells NK_CD56bright_CD16-8902 cells Tnaive/CM_CD4_activated3748 cells Nonclassical monocytes2420 cells Intermediate macrophages2236 cells Erythrophagocytic macrophages2103 cells Intestinal macrophages599 cells HsapDv:0000240158374 cells HsapDv:0000241135861 cells HsapDv:000024235527 cells NCBITaxon:9606329762 cells UBERON:000210671962 cells UBERON:000764462647 cells UBERON:000237140507 cells UBERON:000204835419 cells UBERON:000017827620 cells UBERON:000040027087 cells UBERON:000003023687 cells UBERON:000250923197 cells UBERON:000210713368 cells naive thymus-derived CD4-positive, alpha-beta T cell37613 cells CD8-positive, alpha-beta memory T cell25519 cells classical monocyte21847 cells CD16-positive, CD56-dim natural killer cell, human20591 cells effector memory CD4-positive, alpha-beta T cell19869 cells alveolar macrophage17238 cells CD4-positive helper T cell16099 cells T follicular helper cell15293 cells effector memory CD8-positive, alpha-beta T cell, terminally differentiated14612 cells CD8-positive, alpha-beta memory T cell, CD45RO-positive12674 cells regulatory T cell12143 cells gamma-delta T cell11577 cells CD16-negative, CD56-bright natural killer cell, human8902 cells naive thymus-derived CD8-positive, alpha-beta T cell7801 cells alpha-beta T cell5631 cells mucosal invariant T cell4849 cells non-classical monocyte2420 cells progenitor cell1518 cells conventional dendritic cell1503 cells group 3 innate lymphoid cell1312 cells plasmacytoid dendritic cell713 cells germinal center B cell572 cells erythroid lineage cell445 cells dendritic cell, human262 cells thoracic lymph node62647 cells jejunal epithelium27087 cells lamina propria23687 cells mesenteric lymph node23197 cells skeletal muscle tissue835 cells transverse colon262 cells sixth decade human stage158374 cells seventh decade human stage135861 cells eighth decade human stage35527 cells Analyze this study
Source data
https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3
Alias names
E-MTAB-11536, SCP1845, PMID35549406, PMC7612735
Cite this study
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. and Mamanova, L., 2022. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376(6594), p.eabl5197. https://doi.org/10.1126/science.abl5197
