Comprehensive mapping of epigenetic events during the T-follicular helper-to-T-regulatory type-1 transdifferentiation pathway reveal a global poised state
Chronic antigenic stimulation can trigger the formation of IL-10-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that T follicular helper cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is underpinned by the progressive loss and acquision of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Through a combination of wide-ranging bulk and single-cell transcriptional and epigenetic studies, here we demonstrate that TFH cells are epigenetically poised to differentiate into TR1 cells. Specifically, we find that the TFH-to-TR1 cell transition is accompanied by a significant reduction of the open chromatin regions (OCRs) found in TFH cells. However, the OCRs shared by TR1-like and TFH cells have a remarkably similar distribution of H3K27ac-marked active enhancers. Whereas the DNA regions that overlap these active enhancers are closed and hyper-methylated in conventional T cells, they are hypo-methylated in both TFH and TR1-like cells, even in genes silent in TFH cells, such as Il10. Furthermore, these enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors (TFs) TOX-2, IRF4 and c-Maf. These data suggest that TFH cells are epigenetically poised to become TR1 cells, and that sustained TCR ligation-induced chromatin remodeling coupled to the acquisition of an alternative transcription factor expression profile are sufficient to drive their transdifferentiation into TR1 cells. Overall design: pMHCII-NP-induced Tet+, vaccination-induced TFH, and Th0 (T conventional) cells were processed for bulk ATAC-seq, ChIP-seq for H3K27Ac, H3K4me3, and H327me3, whole genome methylome, as well as single-cell scRNA-seq + scATAC-seq multiome, in order to underpin the epigenetic changes during the transdifferenation of TFH into TR1 cells induced by pMHCII-NP.