Id proteins suppress E2A-driven iNKT cell development prior to TCR selection [RNA-seq_new]

Id proteins have been shown to promote the differentiation of conventional aß and ?dT cells, and to suppress the expansion of invariant Natural Killer T (iNKT) cells and innate-like ?dNKT within their respective cell lineages. However, it remains to be determined whether Id proteins regulate lineage specification in developing T cells that give rise to these distinct cell fates. Here we report that in the absence of Id2 and Id3 proteins, E2A prematurely activates genes critical for the iNKT cell lineage prior to TCR expression. Lack of Id proteins also promotes a biased TCR rearrangement in favor of iNKT cell fate prior to selection at the CD4+CD8+ double positive (DP) stage. Enhanced iNKT development in Id3-deficient mice lacking ?dNKT cells suggests that Id3 regulates the lineage competition between these populations. RNA-Seq analysis establishes E2A as the transcriptional regulator of both iNKT and ?dNKT development. In the absence of pre-TCR signaling, Id2/Id3 deletion gives rise to a large population of iNKT cells and a unique innate-like DP population, despite the block in conventional aß T cell development. The transcriptional profile of these unique DP cells reflects enrichment of innate-like signature genes, including PLZF (Zbtb16) and Granzyme A (Gzma). Results from these genetic models and genome-wide analyses suggest that Id proteins suppress E2A-driven innate-like T cell programs prior to TCR selection to enforce predominance of conventional T cells. Overall design: The RNA-Seq experiment included WT DP, pTaKO DP, L-DKO DP and L-DKO pTaKO (abbreviated as LP) DP cells (where L-DKO refers to mice deficient in both Id2/Id3). Each replicate represents cells from a single mouse. One pTaKO DP (#1) sample was removed from analysis due to low quality of sequencing. All mice were B6/129 hybrids and littermates.

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Roy S, Moore AJ, Love C, Reddy A, Rajagopalan D, Dave SS, Li L, Murre C, Zhuang Y