Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator

Abstract

Medullary thymic epithelial cells (mTECs) are critical for self-tolerance induction in T cells via promiscuous expression of tissue-specific antigens (TSAs), which are controlled by the transcriptional regulator, AIRE. Whereas AIRE-expressing (Aire+) mTECs undergo constant turnover in the adult thymus, mechanisms underlying differentiation of postnatal mTECs remain to be discovered. Integrative analysis of single-cell assays for transposase-accessible chromatin (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) suggested the presence of proliferating mTECs with a specific chromatin structure, which express high levels of Aire and co-stimulatory molecules, CD80 (Aire+CD80hi). Proliferating Aire+CD80hi mTECs detected using Fucci technology express a minimal number of Aire-dependent TSAs and are converted into quiescent Aire+CD80hi mTECs expressing high levels of TSAs after a transit amplification. These data provide evidence for the existence of transit-amplifying Aire+mTEC precursors during the Aire+mTEC differentiation process of the postnatal thymus.

Acute irradiation alters the heterogeneity among medullary thymic epithelial cells

“…In Aire + mTECs, cluster 1 was slightly decreased. In contrast, cluster 7, which is a transition stage from TA-mTECs to Aire + mTECs (Miyao et al, 2022), was increased. Overall, these data suggested that sublethal-dose radiation caused abundant aftereffects in Aire + mTECs and their progeny, i.e.…”

“…Recent studies using single-cell RNA sequencing analysis (scRNA-seq) revealed a high degree of TEC heterogeneity in humans and mice (Bornstein et al, 2018;Dhalla et al, 2020;Park et al, 2020;Wells et al, 2020;Miyao et al, 2022). Bornstein et al classified mTECs into four subsets (Bornstein et al, 2018).…”

“…Post-Aire mTECs are an assembly of various mimetic cells harboring signature genes expressed by extra-thymic cell types (Michelson et al, 2022). Several studies using scRNA-seq have suggested a unique mTEC cluster expressing a high level of cell cycle-related genes (Dhalla et al, 2020;Wells et al, 2020;Miyao et al, 2022). A further study demonstrated that this cluster is equivalent to transit-amplifying cells (Miyao et al, 2022), which are proliferative progenitors connecting stem cells and mature cells (Hsu et al, 2014).…”

Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity

“…6a, cluster 3, 4, and 5) and transit-amplifying mTECs (Fig. 6a, cluster 1), which are precursors of AIRE + mTECs 40,42 . We further performed flow cytometric analysis to confirm C15ORF48 protein expression by using anti-murine C15ORF48 antibody.…”

“…Recent single-cell RNA-seq analyses (scRNA-seq) revealed high heterogeneity of TECs. Thus, in addition to separation of cTECs and mTECs, mTECs are further separated based on expression of AIRE and other marker molecules [38][39][40][41] . Re-analysis of scRNA-seq data of murine TECs 40 suggested expression of murine C15orf48 in cTECs (Fig.…”