Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41

Abstract

Genome-wide association studies have identified multiple renal cell carcinoma (RCC) susceptibility loci. Here, we use regional imputation and bioinformatics analysis of the 12p12.1 locus to identify the single-nucleotide polymorphism (SNP) rs7132434 as a potential functional variant. Luciferase assays demonstrate allele-specific regulatory activity and, together with data from electromobility shift assays, suggest allele-specific differences at rs7132434 for AP-1 transcription factor binding. In an analysis of The Cancer Genome Atlas data, SNPs highly correlated with rs7132434 show allele-specific differences in BHLHE41 expression (trend P value=6.3 × 10−7). Cells overexpressing BHLHE41 produce larger mouse xenograft tumours, while RNA-seq analysis reveals that constitutively increased BHLHE41 induces expression of IL-11. We conclude that the RCC risk allele at 12p12.1 maps to rs7132434, a functional variant in an enhancer that upregulates BHLHE41 expression which, in turn, induces IL-11, a member of the IL-6 cytokine family.

Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell Carcinoma

“…Motivated by the prioritization of HIF1a/HIF2a binding sites, we searched for SNPs in the RCC GWAS that overlapped asQTL peaks and HIF1a/HIF2a active sites (or sites that disrupted known HIF motifs, see Methods) and identified a total of 8 SNPs where the GWAS association was significant after Bonferroni correction: 3/8 loci were identified or connected to target genes or enhancers from asQTLs in this study: DPF3, SCARB1 , and GRAMD4; another 4/8 loci were previously linked to HIF binding and/or experimentally supported: EPAS1 (HIF2a), CCND1, BHLHE41 40 , and MYC 41 ( Figure 3b,c, Supplementary Table S14 ) and the remaining SNP was in an intron of the RBPMS gene but could not be connected to a target. In total, asQTLs were observed at all four loci previously implicated through HIF binding and highlighted three novel gene targets at four loci without previous experimental follow-up.…”

Renal cell carcinoma

“…The 2p21 locus maps to EPAS1 , a gene encoding the HIF-2α subunit 55 whereas the biological effects underlying the 11q13.3 locus seems to be attributable to changes in the regulation of CCND1 (encoding cyclin D1, which is involved in cell cycle regulation) 59 . The locus 12p11.23 probably maps to changes in BHLHE41 (encoding basic helix-loop-helix family member e41, which is thought to have a role in regulation of the circadian rhythm) 60 . The disease genes underlying the other GWAS susceptibility loci have yet to be identified.…”

Genetic and metabolic hallmarks of clear cell renal cell carcinoma

“…Interestingly, the location of this SNP (14q24) is deleted in one quarter to half of patients [30], and dysregulation of other components of BAF and PBAF complexes are common features of ccRCC. The same group also identified BHLHE41 , a gene encoding a basic helix-loop-helix protein located in the 12p12.1 susceptibility locus, from GWAS [31]. The ccRCC risk allele associated with this gene increased its expression, and the authors provided functional evidence that ectopic expression of BHLHE41 increased xenograft tumor growth.…”