AbstractDefective function of the von Hippel-Lindau (VHL) tumor suppressor ablates proteolytic regulation of hypoxia-inducible factor α subunits (HIF-1α and HIF-2α), leading to constitutive activation of hypoxia pathways in renal cell carcinoma (RCC). Here we report a comparative analysis of the functions of HIF-1α and HIF-2α in RCC and non-RCC cells. We demonstrate common patterns of HIF-α isoform transcriptional selectivity in VHL-defective RCC that show consistent and striking differences from patterns in other cell types. We also show that HIF-α isoforms display unexpected suppressive interactions in RCC cells, with enhanced expression of HIF-2α suppressing HIF-1α and vice-versa. In VHL-defective RCC cells, we demonstrate that the protumorigenic genes encoding cyclin D1, transforming growth factor alpha, and vascular endothelial growth factor respond specifically to HIF-2α and that the proapoptotic gene encoding BNip3 responds positively to HIF-1α and negatively to HIF-2α, indicating that HIF-1α and HIF-2α have contrasting properties in the biology of RCC. In keeping with this, HIF-α isoform-specific transcriptional selectivity was matched by differential effects on the growth of RCC as tumor xenografts, with HIF-1α retarding and HIF-2α enhancing tumor growth. These findings indicate that therapeutic approaches to targeting of the HIF system, at least in this setting, will need to take account of HIF isoform-specific functions. ACKNOWLEDGMENTSThis work was funded by the Wellcome Trust, Cancer Research UK, the Medical Research Council, the Urology Research Fund from Guy's Hospital, and a 6th Framework Programme at the E.U. (Euroxy Project).We thank J. Pastorek for providing the M75 antibody, K. Kranc and S. Bhattacharya for advice on retroviral work, D. Jones for help with ELISAs, and R. Peat, S. Peak, S. Johnson, and D. Watling for assistance in xenograft experiments. K.W.L. was supported by a scholarship from the Agency for Science, Technology, and Research (Singapore). R.R.R. was supported by a Rhodes scholarship.