Fig 2: HIF-2α influences the expression of MHC class I and II genes.Gene expression heatmaps for MHC class I (a), class II (b), and other antigen processing and presenting (c) genes. Rows represent row-normalised z-scores of mRNA abundance, each column represents an individual sample from WT cortex or VpR, VpRH1, and VpRH2 tumours. Source data is provided in Supplementary Data 1 and 2. d Examples of different scores for MHC class II immunohistochemical staining. All panels are the same magnification, scale bar = 100 μm. e Distribution of MHC class II staining scores in the indicated (n) number of VpR, VpRH1, and VpRH2 tumours. P values are derived from the two-sided Mann–Whitney U test without adjustments for multiple comparisons. f, g Relative HIF1A and HIF2A mRNA abundance in TCGA datasets of human chromophobe (KICH, n = 66), clear cell (KIRC, n = 533), and papillary (KIRP, n = 290) renal cell carcinomas and associated normal renal tissues (Normal_KICH n = 25, Normal_KIRC n = 72, Normal_KIRP n = 32). Box–whisker plots depict median, bounded by Q1 (25% lower quartile) and Q3 (75% upper quartile) and whiskers depict 1.5 times the Q3–Q1 interquartile range. Spearman’s correlation analyses between HIF2A mRNA abundance and mRNA abundance of two MHC class I (h, i), class II (j, k), and antigen processing/presentation (l, m) genes in ccRCC (TCGA KIRC dataset). Source data is provided in Supplementary Data 4.

Fig 3: HIF1A copy number loss and HIF2A mRNA expression levels correlate with altered immune microenvironments in human ccRCC.a Oncoprint showing the genetic alterations in HIF1A and HIF2A in human ccRCC tumours based on GISTIC. b, c Kaplan–Meier curves showing overall survival of ccRCC patients whose tumours exhibit loss of one or two copies of HIF1A (loss) or gain of a copy of HIF2A (gain) versus patients without these copy number alterations (Unaltered). P values are derived from the two-sided log-rank test. mRNA abundance (log2 transformed, normalised, RNA-seq v2 RSEM) of CD3D (d, e), CD3E (f, g), CD4 (h, i), CD8A (j, k), CD8B (l, m) in HIF1A loss and HIF2A gain ccRCC tumours compared to Unaltered tumours. P values are derived from two-sided Student’s t test. n Summary of immune deconvolution results in ccRCC (TCGA KIRC dataset) using ssGSEA with the Bindea et al. and eTME gene signatures, as well as the CIBERSORT method. Depicted are pairwise comparisons of the expression levels of each gene set between HIF2A gain (n = 65) and HIF2A diploid (Unaltered, n = 349), between HIF1A loss (n = 188) and HIF1A diploid (Unaltered, n = 220) tumours and between tumours in the top quartile (Q4) and the lowest quartile (Q1) of HIF2A expression. Columns depict the comparison between the genotypes and rows depict the gene set. Heatmap colours represent the mean differences in the z-scores. Comparisons marked with an asterisk show P values < 0.05 between each genotype, two-sided Mann–Whitney U test without multiple comparisons. Source data with z-scores and P values is provided in Supplementary Data 6.

Fig 4: ccRCC formation is strongly dependent on Hif1a and only moderately affected by Hif2a deletion.a Tumour onset in cohorts of pR, VpR, VpRH1, and VpRH2 mice. P values were calculated by two-sided log-rank Mantel–Cox test. b Number of tumours per mouse at the time of sacrifice based on μ-CT imaging (VpR n = 65, pR n = 25, VpRH1 n = 36 and VpRH2 n = 65 mice). Mean ± SEM are shown, P values were calculated by Dunn’s multiple comparisons test. c Tumour growth rates based on μ-CT imaging (VpR n = 48, pR n = 5, VpRH1 n = 7 and VpRH2 n = 56 tumours). Box–whisker plots depict median, bounded by Q1 (25% lower quartile) and Q3 (75% upper quartile) and whiskers depict 1.5 times the Q3-Q1 interquartile range. P values were calculated by two-sided Student’s t test without adjustment for multiple comparisons. d Representative immunohistochemical stainings for the indicated antibodies in samples from WT cortex, a non-tumour region of VpR cortex, VpR, VpRH1, and VpRH2 tumours. All panels are the same magnification, scale bar = 50 μm. The number of positive tumours/number of tumours examined are indicated. e Representative examples of the histological appearance of tumours assigned clear cell scores of 1, 2, or 3. Scale bars = 100 μm. f Distribution of clear cell scores between VpR (n = 10 mice, 23 tumours), VpRH1 (n = 8 mice, 14 tumours) and VpRH2 (n = 9 mice, 18 tumours) tumour cohorts. P values were calculated using the two-sided Mann–Whitney U test without adjustments for multiple comparisons.

Fig 5: HIF-2α influences the expression of MHC class I and II genes.Gene expression heatmaps for MHC class I (a), class II (b), and other antigen processing and presenting (c) genes. Rows represent row-normalised z-scores of mRNA abundance, each column represents an individual sample from WT cortex or VpR, VpRH1, and VpRH2 tumours. Source data is provided in Supplementary Data 1 and 2. d Examples of different scores for MHC class II immunohistochemical staining. All panels are the same magnification, scale bar = 100 μm. e Distribution of MHC class II staining scores in the indicated (n) number of VpR, VpRH1, and VpRH2 tumours. P values are derived from the two-sided Mann–Whitney U test without adjustments for multiple comparisons. f, g Relative HIF1A and HIF2A mRNA abundance in TCGA datasets of human chromophobe (KICH, n = 66), clear cell (KIRC, n = 533), and papillary (KIRP, n = 290) renal cell carcinomas and associated normal renal tissues (Normal_KICH n = 25, Normal_KIRC n = 72, Normal_KIRP n = 32). Box–whisker plots depict median, bounded by Q1 (25% lower quartile) and Q3 (75% upper quartile) and whiskers depict 1.5 times the Q3–Q1 interquartile range. Spearman’s correlation analyses between HIF2A mRNA abundance and mRNA abundance of two MHC class I (h, i), class II (j, k), and antigen processing/presentation (l, m) genes in ccRCC (TCGA KIRC dataset). Source data is provided in Supplementary Data 4.