Enhancer-Mediated Regulation of HIF-2a by the SOCS3–JAK1–STAT3 Axis in Renal Cancer

Clear cell renal cell carcinoma (ccRCC) is characterized by frequent loss of the von Hippel–Lindau (VHL) tumor suppressor, leading to pathological accumulation of hypoxia-inducible factor 2a (HIF-2a). Although direct HIF-2a inhibitors such as Belzutifan have shown clinical efficacy, therapeutic resistance remains a major challenge. To uncover additional regulatory mechanisms governing HIF-2a activity, we performed a genome-wide CRISPR screen in VHL-deficient ccRCC cells. This revealed the TREX mRNA export complex as a positive regulator and Suppressor of Cytokine Signaling 3 (SOCS3) as the most significant negative regulator of HIF-2a. We demonstrate that SOCS3 suppresses HIF-2a expression through inhibition of the JAK1–STAT3 signaling axis. Loss of SOCS3 activates STAT3, which directly binds to enhancers upstream of the EPAS1 (HIF-2a) gene, promoting its transcription. SOCS3 overexpression or JAK1/STAT3 inhibition suppresses HIF-2a levels, impairs tumor growth, and reduces metastasis in ccRCC models. These findings define a novel SOCS3–JAK1–STAT3–HIF-2a regulatory axis and identify enhancer-mediated transcriptional control as a critical mechanism of HIF-2a regulation. Targeting this pathway offers a promising strategy to overcome resistance to current HIF-2a inhibitors and improve therapeutic outcomes in ccRCC. Overall design: ChIP-seq of STAT3 in 786-O cells, and STAT3, H3K4me1, H3K4me3, and H3K27ac in HKC8 cells, in biological duplicate with input and IgG controls. H3K27ac HiChIP in 786-O with two technical replicates pooled during analysis