Context-dependent regulation of T follicular helper cell formation, expansion and differentiation into T-regulatory type 1 cells by multiple transcription factors
Differentiation of naïve T cell precursors into distinct T helper cell subsets, including T follicular helper (TFH) cells, is driven by the expression/repression of subset-specific transcription factors (TFs) that have well defined effects on the acquisition of alternative gene expression programs. Repetitive antigen encounters by TFH cells can trigger their differentiation into IL-10-producing Foxp3– and Foxp3+ T-regulatory type 1 (TR1) cells. Since TFH cells are epigenetically poised to differentiate into TR1 cells, we hypothesized that the cell conversion events underpinning this process are regulated at the transcriptional level. Here, we interrogate the role of 20 TFs that bind to motifs enriched in open chromatin regions along the TFH-TR1 cell axis, on the size and function of the pre-treatment TFH cell pool and the size and transcriptional make-up of the various antigen-specific TFH/TR1 cell subsets arising in vivo post repetitive antigen challenge. We find that certain TFH TFs, such as TCF-1 and TOX-2, contribute to TFH cell genesis and TFH cell function but are dispensable for antigen-specific TFH cell expansion and TR1 transdifferentiation. Eleven other TFs, including ATF-6, BATF, BCL-6, BHLHE40, BLIMP-1, ELK-4, IRF4, c-MAF, STAT-3, STAT-4 and T-BET, play distinct roles at different stages of this pathway in a context-dependent manner. Most of these TFs simultaneously promote and suppress different cell conversion events along the axis and promote the expression of subset-specific signature genes at specific cell stages while simultaneously suppressing the expression of such genes at other cell stages in the pathway. This indicates that differentiation of TFH cells into TR1 progeny is driven by a carefully orchestrated sequence of TF gene expression and silencing events that yields dynamic combinations of TFs that enable cell-to-cell transitions. The transcriptional context in which specific TFs are expressed determines their ability to either drive or suppress such transitions and promote or inhibit the expression of alternative gene expression programs at different cell states. Overall design: Single-cell RNA sequencing (scRNA-seq) was performed on T cells deficient for 11 transcription factors to investigate their roles in the TFH-to-TR1 differentiation pathway. Samples from control and TF-deficient mice were included in each sequencing run to enable accurate cell annotation across the four Tet+ subpopulations (TFH, TR1.1, Foxp3– TR1.2, and Foxp3+ TR1.2).