Transcriptome and chromatin changes as regulatory T cells expand and contract to IL-2R signaling in vivo

Abstract

Abstract Regulatory T cells are essential to maintain peripheral T cell tolerance and require IL-2R signaling for their development and homeostasis. Here, we used mouse IL-2 (mIL-2) and a fusion protein of mouse IL-2 linked to mouse CD25 (mIL-2/CD25) to induce acute, periodic, and persistent IL-2R-dependent signaling in peripheral Tregs in vivo. RNA- and ATAC-seq assessed longitudinal shifts in the transcriptome and chromatin landscape to define the molecular steps associated with IL-2R-dependent Treg activation, expansion, and subsequent contraction in vivo. Analysis of the RNA-seq data revealed that STAT5 and MYC were two critical drivers of IL-2R-dependent signaling in Tregs. Other signaling pathways were also identified that facilitate cell transcription, integration of TCR signaling, cell cycle progression, and growth. Sustained IL-2R signaling by mIL-2/CD25, but not periodic signaling by mIL-2, more effectively supported Treg expansion, oxidative phosphorylation, and development into eTregs. With respect to chromatin remodeling, IL-2R signaling initially preferentially increased accessibility to binding sites and activity of STAT5, whereas more persistent IL-2R signaling favored accessibility and activity of other transcription factors, dominantly CTCF, followed by a genome-wide less accessible chromatin. Our data favor a model whereby persistent IL-2R signaling initially supports more accessible chromatin and active transcription leading to a metabolic shift toward a more energetic type required for Treg proliferation. Subsequently, as IL-2R signaling diminishes, a shift toward less accessible chromatin occurs that facilitates contraction of the expanded Tregs to restore homeostasis. This research was supported by funding from Bristol Myers Squibb and the NIH (R01AI148675).