HIF-1α integrates metabolic and immunoregulatory programs in RORγt⁺ regulatory T cells during intestinal inflammation

Regulatory T (Treg) cells expressing RORgamma-t accumulate in the intestinal mucosa, yet the signals that determine whether they remain suppressive or acquire inflammatory features are incompletely defined. We first reanalyzed human ileal single-cell data and identified Crohn's disease-enriched FOXP3+ states in which RORC, HIF1A, hypoxia-responsive, inflammatory, and metabolic programs converged. We then deleted Hif1a in RORgamma-t-expressing cells and tested acute DSS colitis, T cell transfer colitis, and azoxymethane/DSS-induced colitis-associated colorectal cancer (CAC). Hif1a-deficient mice were protected in all three settings. In lymphopenic recipients given the same pathogenic naive T cells, changing only the genotype of the cotransferred Treg population enhanced protection, linking the phenotype to regulatory-cell function in vivo. Reanalysis of mouse colonic Treg single-cell ATAC-seq nominated suppressive and mitochondrial programs for cell-intrinsic testing under conditions of low HIF-1alpha expression. Hif1a-deficient RORgamma-t Treg cells produced more IL-10 and less IL-17A and IFN-gamma, limited responder-cell proliferation, contained fewer dysfunctional mitochondria with high mitochondrial reactive oxygen species levels, favored fusion-associated transcription, and displayed greater basal and maximal oxygen consumption and reserve capacity. During CAC, HIF-1alpha loss blunted inflammatory RORgamma-t Treg accumulation and reduced tumor burden. Human trajectory and gene regulatory network analyses further predicted that HIF1A perturbation would oppose selected disease-associated branches. Together, these findings identify HIF-1alpha as a context-dependent checkpoint that connects hypoxia-responsive transcription to mitochondrial fitness and inflammatory plasticity in intestinal RORgamma-t Treg cells.