E proteins orchestrate dynamic transcriptional cascades to suppress ILC2 differentiation

Abstract

Differentiation of group 2 innate lymphoid cells is forcefully repressed by E protein transcription factors. This report elucidates how E proteins repress a transcriptional network important for ILC2 differentiation by up-regulating the expression of transcriptional repressors. Abstract The basic helix-loop-helix transcription factors collectively called E proteins powerfully suppress the differentiation of group2 innate lymphoid cells from bone marrow and thymic progenitors. Here we investigated the underlying molecular mechanisms using inducible gain and loss of function approaches in ILC2s and their precursors, respectively. Cross-examination of RNA sequencing and ATAC sequencing data obtained at different time points reveals a set of genes which are likely direct targets of E proteins. Consequently, a widespread down-regulation of chromatin accessibility occurs at a later time point, possibly due to the activation of transcriptional repressor genes such as Cbfa2t3 and Jdp2. The large number of genes repressed by gain of E protein function leads to the down-regulation of a transcriptional network important for ILC2 differentiation.

Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage

“…However, ET2 expression in cDC2s down-regulated STAT4 and up-regulated SMAD3 levels, respectively. This is consistent with the down-regulation of Stat4 and up-regulation of Smad3 by E proteins in T cells (33). Importantly, Stat4 transcription has been shown to be activated by ectopic expression of IRF4 but not IRF8 in Irf4 -/-Irf8 -/bone marrow progenitors (36).…”

“…We first assessed the effects of ET2 on potential E protein target genes. Since these genes in conventional dendritic cells are not known, we compared the differentially expressed genes with our gene sets found to be altered shortly after inducible ablation or addition of E proteins in T cell precursors (CD4 and CD8 double negative cells) or innate lymphoid cells (33). We found 8 out of the 34 protein coding genes in cDC1s and 29 out of 186 genes in cDC2s overlapped with a total of 2460 putative E protein-regulated genes detected in (33).…”

“…Since these genes in conventional dendritic cells are not known, we compared the differentially expressed genes with our gene sets found to be altered shortly after inducible ablation or addition of E proteins in T cell precursors (CD4 and CD8 double negative cells) or innate lymphoid cells (33). We found 8 out of the 34 protein coding genes in cDC1s and 29 out of 186 genes in cDC2s overlapped with a total of 2460 putative E protein-regulated genes detected in (33). Even with the distinct cell types included in the analysis, the intersections were deemed statistically significant using Fisher's exact test (p <0.01 for cDC1 and p < 0.0046 for cDC2), suggesting that ET2 indeed alters E protein activity in cDCs.…”