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

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. Description Immune cell diversity in the human body The human immune system is composed of many different cell types spread across the entire body, but little is currently known about the fine-grained variations in these cell types across organs. Using single-cell genomics, Domínguez Conde et al. examined the gene expression profile of more than 300,000 individual immune cells extracted from 16 different tissues in 12 deceased adult organ donors (see the Perspective by Liu and Zhang). Cell identity was assigned using CellTypist, an automated cell classification tool designed by the authors. In-depth data analysis revealed insights into how the immune system adapts to function effectively in different organ contexts. —LZ and DJ An immune cell atlas of human innate and adaptive immune cells across lymphoid, mucosal, and exocrine sites reveals tissue-specific compositions and features. INTRODUCTION Immune cells that seed peripheral tissues play a vital role in health and disease, yet most studies of human immunity focus on blood-derived cells. Immune cells adapt to local microenvironments, acquiring distinct features and functional specialization. Dissecting these molecular adaptations through the systematic assessment of cells across the human body promises to transform our understanding of the immune system at the organismal level. RATIONALE To comprehensively assess immune cell types, we collected donor-matched tissues from 12 deceased organ donors. We isolated immune cells and performed single-cell RNA sequencing and paired VDJ sequencing for T cell and B cell receptors, resulting in high-quality data for ~330,000 immune cells. To resolve cell identities, we developed CellTypist, a logistic regression–based framework using stochastic gradient descent learning. This cross-tissue annotation enabled interrogation of shared and tissue-specific expression modules and cell states within myeloid and lymphoid cell lineages. RESULTS We developed CellTypist by curating and harmonizing public datasets to assemble a comprehensive immune cell type reference database (https://www.celltypist.org). CellTypist was then applied to our data, generated across multiple tissues and individuals (https://www.tissueimmunecellatlas.org/). Altogether, we detected 101 immune populations and performed extensive cross-tissue comparisons for each subset. Although macrophages displayed prominent tissue-restricted features, some convergent features were also detected. For example, macrophages expressing erythrophagocytosis-related genes were widely found in spleen, liver, bone marrow, and lymph nodes. Heterogeneity within defined subpopulations was also observed, such as migratory dendritic cell adaptations. Within adaptive immune lineages, we identified tissue-specific distributions of memory populations. Plasma cells showed a restricted tissue distribution, whereas memory B cells were more widely distributed. Similarly, tissue-resident memory T (TRM) cells were more restricted in distribution compared with central and effector memory T cells. Notably, TRM cells harbored significant diversity, including αβ and γδ lineages, ascertained by VDJ sequencing. Assessment of clonal dynamics revealed the highest clonal expansions in TRM cells and the most frequent clonal sharing between resident and effector memory populations. CONCLUSION Here we present an immune cell atlas of myeloid and lymphoid lineages across adult human tissues. We developed CellTypist for automated immune cell annotation and performed an in-depth dissection of cell populations, identifying 101 cell types or states from more than one million cells, including previously underappreciated cell states. We also uncovered convergent phenotypes across tissues within given lineages and described tissue adaptation signatures for a number of cell types, including macrophages and resident memory T cells. Together, we have extended our understanding of how human immunity functions as an integrated, cross-tissue network, and we provide the scientific community with several key new resources. Cross-tissue atlas of human immune cells. Donor-matched tissues from 12 deceased organ donors were profiled using single-cell RNA sequencing [including single-cell VDJ sequencing (scVDJ-seq)]. Cell type annotation was achieved with CellTypist, an automated cell type annotation pipeline, followed by manual curation. In-depth analysis of transcriptional features revealed convergent and divergent gene expression programs for each cell lineage across lymphoid and nonlymphoid tissues. scVDJ-seq enabled repertoire analysis across cell subsets and tissues. scRNA-seq, single-cell RNA sequencing; TCR, T cell receptor; BCR, B cell receptor.