NFIL3 and Ets1 co-regulate a cluster of genes, including Tim-3, that is associated with T cell tolerance

Abstract

Abstract Inhibitory receptor Tim-3 has critical roles in the suppression of effector T cell function. Here we demonstrate that the expression of Tim-3 is highly associated with T cell tolerance induction. TCR other than CD28 co-stimulatory signal is required for its induction. This process is accompanied with inhibition of IL-2 but upregulation of IL-10. Among the downstream pathways of TCR signaling, the calcium-calmodulin-dependent Kinase II (CaMKII) pathway is essential for Tim-3, IL-10 induction and IL-2 inhibition. CaMKII directly regulates transcription factors Ets1 and NFIL3. While NFIL3 induces Tim-3, IL-10 and suppresses IL-2 expression, Ets1 plays an opposite role for their expression. Accordingly, functional analyses suggest that NFIL3 is required, but Ets1 actually has an opposite role, in maintaining T cell tolerance/anergy. ChIP-Seq results reveal that NFIL3 and Ets1 co-localize in the loci of Tim-3, IL-2 and IL-10, suggesting a functional cooperation between NFIL3 and Ets1 in the regulation of these genes. We further identified a cluster of genes that has direct binding with both NFIL3 and Ets1. RNA-seq analysis reveals that the expression of these genes is associated with ionomycin-mediated T cell anergy induction. Collectively, our study suggests that NFIL3 and Ets1 cooperatively regulate a transcriptional network to control the expression of a cluster of genes, including Tim-3, IL-10, and IL-2, that is functionally important for T cell tolerance/anergy induction.