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

Regulatory T (Treg) cells expressing RORγt 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 RORγt-expressing cells and tested acute DSS colitis, T cell transfer colitis, and azoxymethane/DSS-induced colitis-associated colorectal cancer (CAC). ΔHif1a mice were protected in all three settings. In lymphopenic recipients given the same pathogenic naïve 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 during low HIF1-α expression. ΔHif1a RORγt⁺ Treg produced more IL-10 and less IL-17A and IFN-γ, limited responder-cell proliferation, contained fewer dysfunctional and mitochondrial-reactive-oxygen-species-high mitochondria, favored fusion-associated transcription, and displayed greater basal and maximal oxygen consumption and reserve capacity. During CAC, HIF-1α loss blunted inflammatory RORγt⁺ 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-1α as a context-dependent checkpoint that connects hypoxia-responsive transcription to mitochondrial fitness and inflammatory plasticity in intestinal RORγt⁺ Treg.