Fig 2: rs4903064 resides in a renal cancer–associated regulatory element.A, ATAC-seq tracks from primary renal cancer cells at the DPF3 locus. The top track indicates SNPs in high LD with rs4903064 (r2 > 0.8). ATAC-seq was performed in cells from three individuals with different rs4903064 genotypes (TT, CT, CC). KIRC RE indicates regulatory elements defined by ATAC-seq in ccRCC TCGA samples. B, zoomed in view of (A). SNP rs4903064 resides in open chromatin and in KIRC_67261. Please note that open chromatin is only detected in cells carrying the risk allele C. C, sequences of the two alleles at rs4903064. The risk allele C creates a putative hypoxia-responsive element (HRE). D, allele-specific qPCR assay for rs4903064 indicates a shift toward the risk allele C in DNA fragments captured by ATAC experiments in tumor cells (red triangle) or tubular cells exposed to 1 mM DMOG (orange triangle) when compared to input DNA or DNA from ATAC experiments in untreated tubular cells. Cells were isolated from an individual heterozygous for rs4903064. E, allelic ratio of rs4903064 in ATAC samples from tubular cells isolated from three individuals heterozygous for the SNP performed in triplicates. Cells were exposed to 1 mM DMOG for 16 h or left untreated. Bars indicate mean values ± SD. t test, ∗∗∗∗p < 0.0001. F, allelic ratio of rs4903064 in FAIRE samples from cells of four heterozygous individuals. Cells were exposed to 1 mM DMOG for 16 h, and values were normalized to corresponding input DNA. The mean value for each individual is shown. Bars indicate mean values ± SD. ∗one sample t test, p < 0.05. G, reporter assay in HeLa cells using the pGL3 promoter vector with or without a 415 bp sequence covering the protective or the risk allele of rs4903064. Cells were treated with 1 mM DMOG for 16 h as indicated. Bars indicate mean values ± SD of one experiment performed in triplicates. H, HeLa cells were depleted for the indicated HIF-α isoforms using siRNA and transfected with the reporter plasmid including the risk allele. Cells were exposed to 1 mM DMOG for 16 h. Reporter activity was normalized to the activity of co-transfected β-galactosidase. Bars indicate mean values ± SD of one experiment performed in triplicates. I and J, DPF3 protein levels are high in HIF-positive ccRCC tumors. A total of 330 ccRCC tumors were stratified according to the immunoreactive score for HIF-1α, HIF-2α, and DPF3 staining in no, low, medium, or strong staining. Fractions of DPF3 signals are shown for each subgroup of HIF staining. Pearson χ2-test; p = 1.8 × 10−8 for HIF-1α (I) and p = 0.003 for HIF-2α (J). ATAC, Assay for Transposase-Accessible Chromatin; ccRCC, clear cell renal cell carcinoma; DMOG, dimethyloxalylglycine; DPF3, double PHD fingers 3; FAIRE, formaldehyde-assisted isolation of regulatory elements; HIF, hypoxia-inducible transcription factor; KIRC, kidney renal clear cell carcinoma; SNP, single nucleotide polymorphism.

Fig 3: Regulation of DPF3 expression and effect of DPF3 on tubular cell growth.A, relative expression levels of DPF3 in primary renal tubular cells exposed to 1 mM of DMOG for 16 h. Samples were stratified according to the rs4903064 genotype (TT = 42, CT/CC = 44). Values were normalized to expression levels of the housekeeping gene HPRT and to values from corresponding untreated cells. Each dot represents the mean value from cells of one individual. qPCR was performed in duplicates per individual. Bars indicate mean values ± SD. Student’s t test, ∗∗∗∗p < 0.0001. B, DPF3 expression levels in isolated tumor cells compared to corresponding untreated tubular cells from 8 (TT) and 14 (CT/CC) individuals, respectively. Bars indicate mean values ± SD. One sample t test, ∗p < 0.05. C, top, allelic ratios of rs4903064 in cells from heterozygous individuals exposed to DMOG 1 mM or left untreated. One sample t test, ∗∗∗ p < 0.001. Bottom, allelic ratios of rs4903064 in ccRCC cells with high (CA9+) or low (CA9−) CA9 expression as a marker for HIF-1α activity. Values are mean from technical triplicates, and each dot represents values derived from one individual. Bars indicate mean values ± SD. t test, ∗ p < 0.05. D, Western blot for DPF3 and beta actin from lysates of different clones of HKC-8 cells with or without defective DPF3. E, Western blot for DPF3 and beta actin from lysates of two different huPTC lines transfected either with nontargeting (nt) guides or guides targeting DPF3. F, proliferation assays of the clones of cells indicated in (D). Dark lines and dots indicate the mean value from the three different clones of cells, which were tested in biological triplicates. Light gray and light blue lines indicate individual values for the three different clones of cells. G, proliferation assay from cells indicated in (E). H, Western blot for DPF3 and beta actin from lysates of primary renal tubular cells (PTC) transfected either with nontargeting (nt) guides or guides targeting DPF3. Cells were harvested at day 3 after transfection. I, cyst volume of PTC 7 days after plating in a Matrigel matrix (n = 3 wells per condition, 4 quadrants per well). J, representative images of the cysts in the Matrigel matrix. Values are mean ± SD. t test, ∗p < 0.05, ∗∗p < 0.01 for F, G, and I. CA9, carbonic anhydrase 9; ccRCC, clear cell renal cell carcinoma; DMOG, dimethyloxalylglycine; DPF3, double PHD fingers 3; huPTC, human urinary primary tubular cells.

Fig 4: HIF binding to the RCC risk allele.A, HIF ChIP qPCR results for the DPF3 locus. Experiments were performed from cells isolated from 11 TT, 11 CT, and 1 CC individuals. Bars indicate mean values ± SD. Student’s t test, ∗p < 0.05, ∗∗p < 0.01. B, binding of HIF to the control locus at EGLN3 is not affected by the rs4903064 genotype. Bars indicate mean values ± SD. C, HIF ChIP-seq tracks in two different ccRCC cell lines at the rs4903064-associated enhancer (TT: RCC4 and CC: individual 40,911,432 from Yao et al.). HIF binding is only detectable in cells from a patient carrying the C allele (red, HIF-1α: 12 × C from 12 reads in total, HIF-2α 99 × C from 99 reads in total). D, same tracks as in (C) covering the EGLN3 control locus. E and F, H3K27ac ChIP-seq tracks from corresponding normal (blue) and ccRCC (red) tissue indicates increased activity of the disease-associated regulatory element at DPF3 (E, highlighted in yellow) and of the EGLN3 locus (F) in tumors. G, H3K27ac ChIP-seq tracks for two different ccRCC cell lines at the rs4903064-associated enhancer (TT: 786-O and CC: individual 40,911,432 from Yao et al.). Levels of the active enhancer mark H3K27ac are high in the individual carrying the C allele and reduced upon VHL re-expression. H, same tracks as in (G) covering the EGLN3 control locus. Note that H3K27ac levels are reduced upon VHL re-expression in both cell lines. ccRCC, clear cell renal cell carcinoma; ChIP, chromatin immunoprecipitation; DPF3, double PHD fingers 3; EGLN3, Egl-9 family hypoxia inducible factor 3; HIF, hypoxia-inducible transcription factor; KIRC, kidney renal clear cell carcinoma; SNP, single nucleotide polymorphism; VHL, von Hippel-Lindau.