Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

Abstract

T cell development and selection are coordinated in the thymus by a specialized niche of diverse stromal populations. Although much progress has been made over the years in identifying the functions of the different cell types of the thymic stromal compartment, there is no comprehensive characterization of their diversity and heterogeneity. Here we combined massively parallel single-cell RNA-sequencing, spatial mapping, chromatin profiling and gene targeting to characterize de novo the entire stromal compartment of the mouse thymus. We identified dozens of cell states, with thymic epithelial cells (TECs) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient in Pou2f3, a master regulator of tuft cells, have complete and specific depletion of mTEC IV cells, which results in increased levels of thymus-resident type-2 innate lymphoid cells. Overall, our study provides a comprehensive characterization of the thymic stroma and identifies a new tuft-like TEC population, which is critical for shaping the immune niche in the thymus.

A cell atlas of human thymic development defines T cell repertoire formation

“…After 8 PCW, developmental age was estimated from measurements of foot length and heel to knee length and compared against a standard growth chart (55). A piece of skin, or where this was not possible, chorionic villi tissue, was collected from every sample for Quantitative Fluorescence-Polymerase Chain Reaction analysis using markers for the sex chromosomes and the following autosomes: 13,15,16,18,21,22, which are the most commonly seen chromosomal abnormalities.…”

“…Seminal experiments in animal models have provided major insights into the function and cellular composition of the thymus (12,13). More recently, scRNA-seq has revealed new aspects of thymus organogenesis and new types of thymic epithelial cells (TECs) in mouse (14)(15)(16). However, the human organ matures in a mode and tempo that is unique to our species (17)(18)(19), calling for a comprehensive genome-wide study for human thymus.…”

Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells

“…TEC can be broadly categorized into cortical (c-) and medullary (m-) lineages based on their structure, anatomical location, molecular characteristics and functions (Rodewald, 2008;Vaidya et al, 2016). Studies examining TEC development and diversity have further revealed considerable heterogeneity within the mTEC compartment reflecting both maturational stages and functionally distinct mTEC subpopulations (Nishikawa et al, 2010;Metzger et al, 2013;Miragaia et al, 2018;Bornstein et al, 2018). During intrathymic selection, cTEC positively select thymocytes that express T-cell receptors (TCRs) capable of recognising peptide:MHC complexes.…”

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

“…157 158 Our analysis revealed 9 TEC subtypes (Figure 2b,c), thus providing a greater richness of 159 epithelial states than previously reported (Bornstein et al, 2018) (Supplementary Figure 3) and 160 a greater diversity than the 4 phenotypes cytometrically selected in this study (Supplementary 161 Figure 4a-b). The individual subtypes were distinguished by the expression of marker genes 162 9 Figure 2c, and SupplementaryTable 2), including some that are well established (post-AIRE 163 mTEC: Krt80, Spink5; Mature cTEC: Prss16, Cxcl12; mature mTEC: Aire, Cd52) and others that 164 have been described more recently (Tuft-like mTEC: Avil, Trpm5)(Bornstein et al, 2018; Miller 165 et al, 2018). Importantly, each TEC subtype, as defined by its single-cell transcriptome(Figure 1662b), did not segregate exclusively with a single cytometrically defined TEC population 167 (Supplementary Figure 4a,…”