A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus [RNA-Seq]

To date, single-nucleotide polymorphisms (SNPs) have been the most intensively investigated class of polymorphisms in genome wide associations studies (GWAS), however, other classes such as insertion-deletion or multiple nucleotide length polymorphism (MNLPs) may also confer disease risk. Multiple reports have shown that the 5p15.33 prostate cancer (PCa) risk region is a particularly strong expression quantitative trait locus (eQTL) for IRX4 transcripts. Here, we demonstrate using epigenome and genome editing that a biallelic (47bp/21bp) MNLP is the causal variant regulating IRX4 transcript levels. In LNCaP PCa cells (homozygous for the short allele), a single copy knock-in of the long allele potently alters the chromatin state, enabling de novo functional binding of the androgen receptor (AR) associated with increased chromatin accessibility, H3K27 acetylation, and ~3-fold upregulation of IRX4 expression. We further show that an MNLP is amongst the strongest candidate susceptibility variants at two additional PCa risk loci. We estimated that at least 5% of PCa risk loci could be explained by functional non-SNP causal variants, which may have broader implications for other cancers GWAS. More generally, our results underscore the importance of investigating other classes of inherited variation as causal mediators of human traits. Overall design: Comparative gene expression profiling analysis of RNA-seq data.

截至目前，单核苷酸多态性（single-nucleotide polymorphisms, SNPs）是全基因组关联研究（Genome-Wide Association Studies, GWAS）中研究最为深入的一类多态性。然而，插入缺失（insertion-deletion）、多核苷酸长度多态性（Multiple Nucleotide Length Polymorphisms, MNLPs）等其他类型的多态性同样可能介导疾病风险。多项研究已证实，5p15.33区域的前列腺癌（Prostate Cancer, PCa）风险位点是调控IRX4转录本的极强表达数量性状位点（expression Quantitative Trait Locus, eQTL）。本研究通过表观基因组与基因组编辑实验证明，一处双等位基因（47bp/21bp）的MNLP是调控IRX4转录水平的因果变异。在携带短等位基因纯合的LNCaP前列腺癌细胞系中，长等位基因的单拷贝敲入可显著改变染色质状态，促使雄激素受体（Androgen Receptor, AR）实现从头功能性结合，伴随染色质可及性提升、H3K27乙酰化水平升高，以及IRX4表达量约3倍上调。本研究进一步发现，在另外两处前列腺癌风险位点中，MNLP属于最强的候选易感变异之一。经估算，至少5%的前列腺癌风险位点可由功能性非SNP因果变异解释，这一结论对其他癌症的GWAS研究具有更广泛的借鉴意义。总体而言，本研究结果凸显了将其他类型遗传变异作为人类性状因果介导因子开展研究的重要性。整体实验设计：对RNA测序（RNA-seq）数据开展比较基因表达谱分析。