Systematic fine-mapping and functional studies of prostate cancer risk variants [RNA-seq]. Systematic fine-mapping and functional studies of prostate cancer risk variants [RNA-seq]

To date, genome-wide association studies (GWAS) have revealed over 200 genetic risk loci associated with prostate cancer; yet, true disease-causing variants in gene regulatory regions remain elusive. Identification of causal variants and their targets from association signals relevant to prostate cancer is complicated by high linkage disequilibrium and limited availability of functional genomics data for specific tissue/cell types. Here, we integrated statistical fine-mapping and functional annotation from prostate-specific epigenomic profiles, high resolution 3D genome features, and quantitative trait loci data to distinguish causal variants from associations and identify target genes they regulate. Our fine-mapping analysis yielded 1,892 likely causal variants, and multiscale functional annotation linked them to 406 target genes. We prioritized rs10486567, located in an enhancer, as a genome-wide top-ranked SNP and predicted HOTTIP as its target. Deletion of the rs10486567-associated enhancer in prostate cancer cells decreased their capacity for invasive migration. HOTTIP overexpression in an enhancer-KO cell line rescued defective invasive migration. Furthermore, we found that rs10486567 regulates HOTTIP through allele-specific long- range chromatin interaction. Overall design: 22Rv1 mRNA profiles of wild type (WT) and rs10486567 Knockout (KO)

截至目前，全基因组关联研究（genome-wide association studies, GWAS）已揭示超过200个与前列腺癌相关的遗传风险位点；然而，基因调控区域内真正的致病变异仍难以探明。从与前列腺癌相关的关联信号中识别致病变异及其靶基因，往往受到连锁不平衡现象普遍存在以及特定组织/细胞类型功能基因组学数据匮乏的困扰。本研究整合了基于前列腺特异性表观基因组谱、高分辨率三维基因组特征与数量性状位点数据的统计精细定位及功能注释结果，以区分关联信号中的致病变异并鉴定其调控的靶基因。本研究通过精细定位分析得到1892个潜在致病变异，并经多尺度功能注释将其与406个靶基因建立关联。我们将位于增强子区域的rs10486567列为全基因组排名最高的单核苷酸多态性（Single Nucleotide Polymorphism, SNP），并预测其靶基因为HOTTIP。在前列腺癌细胞中敲除rs10486567相关的增强子区域后，细胞的侵袭迁移能力显著下降；而在该增强子敲除的细胞系中过表达HOTTIP，则可挽救受损的侵袭迁移表型。此外，我们发现rs10486567通过等位基因特异性远程染色质相互作用调控HOTTIP的表达。整体实验设计：野生型（wild type, WT）与rs10486567敲除（Knockout, KO）的22Rv1细胞的mRNA表达谱。