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

Abstract

During thymic negative selection, medullary thymic epithelial cells (mTEC) collectively express most protein coding genes, a process termed promiscuous gene expression (PGE). Although PGE is crucial for inducing central T-cell tolerance, this process has not been established definitively as being either stochastic or coordinated. To resolve this question, we sequenced the transcriptomes of 6,894 single mTEC, including 1,795 rare cells expressing either of two tissue-restricted antigens, TSPAN8 or GP2. Transcriptional heterogeneity allowed partitioning of mTEC into 15 robustly-defined subpopulations representing distinct maturational stages and subtypes. Although 50 gene co-expression groups were robustly identified, few could be explained by chromosomal location, biological pathway, or tissue specificity. Further, GP2+ mTEC were randomly dispersed spatially within medullary islands. Thus although PGE exhibits ordered co-expression, biologically it is indeterminate. This likely enhances the presentation of diverse antigens to passing thymocytes during their medullary residency, while simultaneously maintaining mTEC identity throughout PGE.

Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla

“…In this study, we generated a comprehensive single-cell database of human thymic stromal cells with a particular focus on the epithelial compartment. This work represents a major advance beyond previous efforts, which focused mostly on mouse TECs or immune cell populations 9 , 12 , 31 , 69 – 71 . Our in-depth analysis of epithelial populations identified ionocytes as an additional subset of medullary epithelial cells and provided transcriptome information for rare subsets, including ciliated and Schwann cells that had only been described in histological analyses.…”

AIRE deficiency, from preclinical models to human APECED disease

“…Hopefully, recent advances of TEC conservation in culture will make the co-culturing of TECs with T cells possible, in order to support crosstalk between these two cell types and to enable the induction of the cellular programs that lead to their respective maturation. In addition, recent findings have revealed a substantial and unrecognized degree of TEC heterogeneity ( Bornstein et al, 2018 ; Dhalla et al, 2019 preprint). In the past, a relatively small marker set was used to define differentiated TECs, to distinguish few distinct types of TEC population.…”

“…In the past, a relatively small marker set was used to define differentiated TECs, to distinguish few distinct types of TEC population. However, the recent application of single-cell transcriptomics revealed a substantial degree of TEC heterogeneity ( Bornstein et al, 2018 ; Dhalla et al, 2019 preprint), providing us with a more precise way to identify a particular population of iPSC-derived TECs and its signaling pathways. Thus, thymic models based on iPSCs will benefit from new insights provided by single-cell transcriptomics and are expected to closely mimic the biological mechanisms that occur in vivo.…”

The prospects of single‐cell analysis in autoimmunity

“…Characterization of the healthy mouse thymus by scRNA‐seq has revealed unknown heterogeneity within the medullary thymic epithelial cell (mTEC) population, and this can aid in elucidating steady‐state processes in central tolerance development 78 . A more recent study indeed utilized scRNA‐seq to elucidate how the expression pattern of tissue‐restricted genes or antigens (TRGs or TRAs) in mTECs are not stochastically expressed but rather co‐expressed within gene modules 83 . Further work is needed to elucidate how these modules are regulated.…”