Single-cell RNA-seq of the human tonsil and blood lymphocytes

Tissue-selective chemotactic mechanisms direct lymphocytes to epithelial surfaces of the body to establish local immune environments, to regulate immune responses to food antigens and commensal organisms, and to protect the body from pathogens. Chemoattractants for small intestines, colon, and skin are known, but chemotropic mechanisms selective for respiratory tract and other non-intestinal mucosal tissues (NIMT) remain poorly understood. Here we leveraged diverse omics datasets to identify GPR25 as a lymphocyte receptor for CXCL17, a chemoattractant cytokine whose expression by epithelial cells of airways, upper gastrointestinal and squamous mucosae unifies the NIMT and distinguishes them from intestinal mucosae. Analyses of single cell transcriptomic data shows that GPR25 is induced on innate lymphocytes prior to emigration to the periphery, and is imprinted in secondary lymphoid tissues on activated B and T cells responding to immune challenge. GPR25 characterizes B and T tissue resident memory and regulatory T lymphocytes in NIMT and lungs in human and we show that it mediates lymphocyte homing to barrier epithelia of the the respiratory tract, stomach and biliary and genitourinary tracts in mouse models. GPR25 is also expressed by T cells in cerebrospinal fluid and CXCL17 by neurons, suggesting a link to CNS immune regulation. We reveal widespread imprinting and expression of GPR25 on regulatory T cells, suggesting a mechanistic link to population genetic evidence that GPR25 is protective in autoimmunity. Our results define a GPR25-CXCL17 chemoaffinity axis with the potential to integrate immunity and tolerance at non-intestinal mucosae and the CNS. Activated T and B cells from tonsil and total T cells from blood were isolated and enriched by FACS. Single-cell profiling was performed using the 5' 10x Genomics workflow.