Dynamic transcriptional activity and chromatin remodeling of regulatory T cells after varied duration of IL-2R signaling [RNA-seq]

Regulatory T cells (Tregs) are necessary for the maintenance of immune self-tolerance and homeostasis. They have a heightened sensitivity to IL-2, which may create a therapeutic window to promote immune regulation by their selective stimulation. While IL-2 responsive genes are well characterized, yet remain unknown genetic, chromatin and metabolic programs during sustained IL-2R signaling. Longitudinal transcriptional and chromatin accessibility profiling and metabolic studies were performed on peripheral Tregs in response to long-lived mIL-2/CD25 fusion protein. We found an initially increased STAT5 dependent gene modulation enabled by enhanced chromatin accessibility, whereas a STAT5-independent genome-wide chromatin closing to inhibit transcription and cell signaling occurred later. Interestingly, IL-2-dependent genes were induced upon re-stimulation. Mitochondrial metabolism was reprogrammed to fulfill the bioenergetics demand for the burst of proliferation. We propose that a shift from euchromatin to heterochromatin represents a mechanism to restrain, but not abrogate, persistent IL-2R signaling to maintain Treg homeostasis. Overall design: Splenic murine Tregs mRNA profiles of mIL-2, mIL-2/CD25 (FP) or control PBS injected mice were generated 1.5 hr post injection by deep sequencing in quadruplicate using NextSeq 500 with a High Output Kit 150-cycle flow cell (Illumina). Reads from RNA-seq were mapped to the Mus musculus genome GRCm38 using STAR (ver.2.5.0) aligner. Raw counts were generated on Ensembl gene (GENCODE M13) with featureCounts (ver.1.5.0). Differential expressed genes in Tregs between the mIL-2 or mIL-2/CD25 and PBS injected mice were identified using DESeq2, and determined according to threshold of false discovery rate (FDR) <0.01