A Functional Variant at a Prostate Cancer Predisposition Locus at 8q24 Is Associated with PVT1 Expression

Abstract

Genetic mapping studies have identified multiple cancer susceptibility regions at chromosome 8q24, upstream of the MYC oncogene. MYC has been widely presumed as the regulated target gene, but definitive evidence functionally linking these cancer regions with MYC has been difficult to obtain. Here we examined candidate functional variants of a haplotype block at 8q24 encompassing the two independent risk alleles for prostate and breast cancer, rs620861 and rs13281615. We used the mapping of DNase I hypersensitive sites as a tool to prioritise regions for further functional analysis. This approach identified rs378854, which is in complete linkage disequilibrium (LD) with rs620861, as a novel functional prostate cancer-specific genetic variant. We demonstrate that the risk allele (G) of rs378854 reduces binding of the transcription factor YY1 in vitro. This factor is known to repress global transcription in prostate cancer and is a candidate tumour suppressor. Additional experiments showed that the YY1 binding site is occupied in vivo in prostate cancer, but not breast cancer cells, consistent with the observed cancer-specific effects of this single nucleotide polymorphism (SNP). Using chromatin conformation capture (3C) experiments, we found that the region surrounding rs378854 interacts with the MYC and PVT1 promoters. Moreover, expression of the PVT1 oncogene in normal prostate tissue increased with the presence of the risk allele of rs378854, while expression of MYC was not affected. In conclusion, we identified a new functional prostate cancer risk variant at the 8q24 locus, rs378854 allele G, that reduces binding of the YY1 protein and is associated with increased expression of PVT1 located 0.5 Mb downstream.

Author Summary

Genome-wide association studies have been very successful at identifying gene loci that are associated with common diseases. However for many of these it has been very difficult to elucidate the identity and function of the risk variant and how altered function predisposes to disease. A 1.2-Mb gene-poor region upstream of the MYC oncogene has been shown to contain at least 12 risk loci associated with different types of cancer. In this study, we use the analysis of chromatin conformation as a tool to identify sub-regions within this 1.2 Mb region that are involved in the control of gene expression, and we identify molecular mechanisms which may confer risk of different specific cancer types. In particular, we examine a risk locus that is associated with predisposition to prostate cancer and identify a DNA sequence variation that results in a change in the binding site for the nuclear factor YY1 as a potential causative mechanism. We show that the risk locus is able to interact with two downstream genes, MYC and PVT1, and present evidence that PVT1 is a candidate new target gene regulated by the 8q24 risk region.