Author:
Domínguez Conde C,Xu C,Jarvis LB,Gomes T,Howlett SK,Rainbow DB,Suchanek O,King HW,Mamanova L,Polanski K,Huang N,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,Menon DK,Bayraktar OA,James LK,Meyer KB,Clatworthy MR,Saeb-Parsy K,Jones JL,Teichmann SA
Abstract
AbstractDespite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. Here, we surveyed the immune compartment of 15 tissues of six deceased adult donors by single-cell RNA sequencing and paired VDJ sequencing. 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 45 finely phenotyped immune cell types and states, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. In summary, our multi-tissue 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.One Sentence SummaryWe provide an immune cell atlas, including antigen receptor repertoire profiling, across lymphoid and non-lymphoid human tissues.
Publisher
Cold Spring Harbor Laboratory