Genome-wide association studies (GWAS) have identified ~20 genetic susceptibility loci for esophageal adenocarcinoma (EAC), and its precursor, Barrett’s esophagus (BE). Despite such advances, functional/causal variants and gene targets at these loci remain undefined, hindering clinical translation. A key challenge is that most causal variants map to non-coding regulatory regions such as enhancers, and typically, numerous potential candidate variants at GWAS loci require testing. We developed a systematic informatics pipeline for prioritizing candidate functional variants via integrative functional potential scores (FPS) consolidated from multi-omics annotations, and used this pipeline to identify two high-scoring variants for experimental interrogation: chr9q22.32/rs11789015 and chr19p13.11/rs10423674. Minimal candidate enhancer regions spanning these variants were evaluated using luciferase reporter assays in two EAC cell lines. One of the two variants tested (rs10423674) exhibited allele-specific enhancer activity. CRISPR-mediated deletion of the putative enhancer region in EAC cell lines correlated with reduced expression of two genes—CREB-regulated transcription coactivator 1 (CRTC1) and Cartilage oligomeric matrix protein (COMP); expression of five other genes remained unchanged (CRLF1, KLHL26, TMEM59L, UBA52, RFXANK). Expression quantitative trait locus mapping indicated that rs10423674 genotype correlated with CRTC1 and COMP expression in normal esophagus. This study represents the first experimental effort to bridge GWAS associations to biology in BE/EAC and supports the utility of FPS to guide variant prioritization. Our findings reveal a functional variant and candidate risk enhancer at chr19p13.11 and implicate CRTC1 and COMP as putative gene targets, suggesting that altered expression of these genes may underlie the BE/EAC risk association.

中文翻译：

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巴雷特食管和食管腺癌 GWAS 风险位点的优先级和功能分析

全基因组关联研究 (GWAS) 已经确定了约 20 个食管腺癌 (EAC) 及其前体 Barrett 食管 (BE) 的遗传易感位点。尽管取得了这些进展，但这些基因座的功能/因果变异和基因靶标仍未确定，阻碍了临床转化。一个关键的挑战是大多数因果变异映射到非编码调节区域，例如增强子，通常，GWAS 基因座的许多潜在候选变异需要测试。我们开发了一个系统信息学管道，用于通过从多组学注释中整合的综合功能潜力评分 (FPS) 对候选功能变体进行优先排序，并使用该管道识别两个用于实验审讯的高分变体：chr9q22.32/rs11789015 和 chr19p13.11 /rs10423674。在两个 EAC 细胞系中使用荧光素酶报告基因分析评估了跨越这些变体的最小候选增强子区域。测试的两个变体之一（rs10423674）表现出等位基因特异性增强子活性。CRISPR 介导的 EAC 细胞系中假定的增强子区域的缺失与两个基因的表达降低相关 - CREB ​​调节的转录共激活因子 1 (CRTC1) 和软骨寡聚基质蛋白 (COMP)；其他五个基因的表达保持不变（CRLF1、KLHL26、TMEM59L、UBA52、RFXANK）。表达数量性状位点作图表明rs10423674基因型与正常食管中CRTC1和COMP的表达相关。这项研究代表了第一个在 BE/EAC 中将 GWAS 关联与生物学联系起来的实验性工作，并支持使用 FPS 来指导变体优先级排序。