Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer

Abstract

The 2q37 and 17q12-q22 loci are linked to an increased prostate cancer (PrCa) risk. No candidate gene has been localized at 2q37 and the HOXB13 variant G84E only partially explains the linkage to 17q21-q22 observed in Finland. We screened these regions by targeted DNA sequencing to search for cancer-associated variants. Altogether, four novel susceptibility alleles were identified. Two ZNF652 (17q21.3) variants, rs116890317 and rs79670217, increased the risk of both sporadic and hereditary PrCa (rs116890317: OR = 3.3-7.8, p = 0.003-3.3 × 10(-5) ; rs79670217: OR = 1.6-1.9, p = 0.002-0.009). The HDAC4 (2q37.2) variant rs73000144 (OR = 14.6, p = 0.018) and the EFCAB13 (17q21.3) variant rs118004742 (OR = 1.8, p = 0.048) were overrepresented in patients with familial PrCa. To map the variants within 2q37 and 17q11.2-q22 that may regulate PrCa-associated genes, we combined DNA sequencing results with transcriptome data obtained by RNA sequencing. This expression quantitative trait locus (eQTL) analysis identified 272 single-nucleotide polymorphisms (SNPs) possibly regulating six genes that were differentially expressed between cases and controls. In a modified approach, prefiltered PrCa-associated SNPs were exploited and interestingly, a novel eQTL targeting ZNF652 was identified. The novel variants identified in this study could be utilized for PrCa risk assessment, and they further validate the suggested role of ZNF652 as a PrCa candidate gene. The regulatory regions discovered by eQTL mapping increase our understanding of the relationship between regulation of gene expression and susceptibility to PrCa and provide a valuable starting point for future functional research.

Keywords: 17q11.2-q22; 2q37; genetic predisposition; prostate cancer risk; susceptibility loci.

Figure 1. A flowchart describing the variant characterization pipeline

The targeted re-sequencing of 2q37 and 17q11.2-q22 from 68 Finnish HPC family members produced a total of 107,479 unique sequence variants. Family-based filtering excluded 66,867 variants that did not co-segregate with affection status. Annotation enabled the selection of 24,813 variants that were located within protein-coding genes. Pathogenicity predictions were performed in silico using MutationTaster, PolyPhen-2 and PON-P. As a result, the number of candidate variants was reduced to 152. The final filtering step exploited diverse information on genes and variants as well as gene ontology and pathway data stored in several public databases. In addition, select HDAC4, ZNF652 and HOXB13 variants, which were predicted to be non-pathogenic, were included in the validation because these genes have been associated with PrCa in previous studies.

Figure 2. Cis-eQTLs targeting differentially expressed genes on chromosome 2

All statistically significant eQTLs are indicated with a track of black bars. Selected eQTLs, rs12620966 and rs983221 (targeting AGAP1) and rs1996513 and rs12712297 (targeting NDUFA10) are illustrated in more detail. DNaseI hypersensitive sites from the DNase cluster and LNCaP datasets are indicated with green and red rectangles, respectively. Blue rectangles denote TF binding sites.

Figure 3. Cis-eQTLs targeting differentially expressed genes on chromosome 17

All statistically significant eQTLs are indicated with a track of black bars. Selected eQTLs, rs11650354 (targeting TBKBP1) and rs12951323 (targeting PNPO) are illustrated in more detail. DNaseI hypersensitive sites from the DNase cluster and LNCaP datasets are indicated with green and red rectangles, respectively. Blue rectangles denote TF binding sites.