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

Hypoxia plays an important role in multiple biological processes including inflammation and impacts the Th17 and Treg imbalance that often contributes to inflammatory diseases. While the transcription factor HIF-1a 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 ATAC-seq and 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 towards a Th17 phenotype. Hypoxia induced extensive gene expression changes in Treg cells, compared to Th17, including a stronger upregulation of Hif1a, and increased expression of Stat3 mRNA and protein. This crosstalk between hypoxia and STAT3 in Treg cells suggests a novel potential regulatory mechanism influencing Treg cell differentiation. Furthermore, we highlight transcription factors ETS1, IRF1, RUNX2, and ATF3, that could be relevant modulators of Th cell differentiation in hypoxic environments such as in 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 transcription factors that, in addition to HIF-1a, could modulate Treg differentiation and shift the Th17/Treg balance in hypoxic environments.