RORα is a critical checkpoint for T cell and ILC2 commitment in the embryonic thymus

Type 2 innate lymphoid cells (ILC2) contribute to immune homeostasis, protective immunity and tissue repair. Here we demonstrate that functional ILC2 cells can arise in the embryonic thymus from shared T cell precursors, preceding the emergence of CD4(+)CD8(+) (double-positive) T cells. Thymic ILC2 cells migrated to mucosal tissues, with colonization of the intestinal lamina propria. Expression of the transcription factor ROR alpha repressed T cell development while promoting ILC2 development in the thymus. From RNA-seq, assay for transposase-accessible chromatin sequencing (ATAC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) data, we propose a revised transcriptional circuit to explain the co-development of T cells and ILC2 cells from common progenitors in the thymus. When Notch signaling is present, BCL11B dampens Nfil3 and Id2 expression, permitting E protein-directed T cell commitment. However, concomitant expression of ROR alpha overrides the repression of Nfil3 and Id2 repression, allowing ID2 to repress E proteins and promote ILC2 differentiation. Thus, we demonstrate that ROR alpha expression represents a critical checkpoint at the bifurcation of the T cell and ILC2 lineages in the embryonic thymus.

Automated summary

ILC2 cells can develop in the embryonic thymus from shared T cell precursors before the emergence of double-positive T cells, and migrate to mucosal tissues. The expression of ROR alpha in the thymus promotes ILC2 development while repressing T cell development. Notch signaling, BCL11B, and ROR alpha play critical roles in the co-development of T cells and ILC2 cells in the thymus.