Hypoxia regulates Th17/Treg balance by altering chromatin accessibility and gene expression

Hypoxia plays an important role in multiple biological processes, including inflammation, and modulates the T helper 17 (Th17) and regulatory T-cell (Treg) imbalance that often contributes to inflammatory diseases. Although the transcription factor (TF) hypoxia-inducible factor 1-alpha (HIF-1α) drives gene expression changes that promote Th17 differentiation, whether hypoxia modulates chromatin openness in Th17 and Treg cells has not been well characterized. Here, we applied assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to investigate how hypoxia alters the chromatin accessibility of Th17 and Treg cells, and how this correlates with the transcriptomic consequences that impact Th17/Treg balance. Our integrated analysis led to the identification of several factors that could contribute to shifting Treg differentiation toward a Th17 phenotype. Hypoxia induced extensive gene expression changes in Treg cells, compared with Th17, including a stronger upregulation of Hif1a, and increased expression of signal transducer and activator of transcription 3 (Stat3) mRNA and protein. This crosstalk between hypoxia and STAT3 in Treg cells suggests a previously unknown potential regulatory mechanism influencing Treg cell differentiation. Furthermore, we highlight TFs protein C-ets-1 (ETS1), interferon regulatory factor 1 (IRF1), runt-related transcription factor 2 (RUNX2) and cyclic AMP-dependent transcription factor ATF-3 (ATF3), which could be relevant modulators of T helper (Th) cell differentiation in hypoxic environments, such as inflamed tissue. Our study shows that hypoxia contributes to regulating the Th17 and Treg balance by increasing accessibility of key loci that are involved in Th cell differentiation and favor a Th17 phenotype. Our results provide valuable insight into how hypoxia alters chromatin accessibility and gene expression of TFs that, in addition to HIF-1α, could modulate Treg differentiation and shift the Th17/Treg balance in hypoxic environments.