Genome‐wide association studies (GWAS) have identified single‐nucleotide polymorphisms (SNPs) associated with glioma risk on 20q13.33, but the biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 20q13.33 impacted the activity of an enhancer, leading to an altered expression of nearby genes. To identify candidate functional SNPs, we identified all SNPs in linkage disequilibrium with the risk‐associated SNP rs2297440 that mapped to putative enhancers. Putative enhancers containing candidate functional SNPs were tested for allele‐specific effects in luciferase enhancer activity assays against glioblastoma multiforme (GBM) cell lines. An enhancer containing SNP rs3761124 exhibited allele‐specific effects on activity. Deletion of this enhancer by CRISPR‐Cas9 editing in GBM cell lines correlated with an altered expression of multiple genes, including STMN3, RTEL1, RTEL1‐TNFRSF6B, GMEB2, and SRMS. Expression quantitative trait loci (eQTL) analyses using nondiseased brain samples, isocitrate dehydrogenase 1 (IDH1) wild‐type glioma, and neurodevelopmental tissues showed STMN3 to be a consistent significant eQTL with rs3761124. RTEL1 and GMEB2 were also significant eQTLs in the context of early CNS development and/or in IDH1 wild‐type glioma. We provide evidence that rs3761124 is a functional variant on 20q13.33 related to glioma/GBM risk that modulates the expression of STMN3 and potentially other genes across diverse cellular contexts.

中文翻译：

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20q13.33 上与神经胶质瘤风险相关的功能变异改变增强子活性并调节多个基因的表达

全基因组关联研究 (GWAS) 已经确定了与 20q13.33 上的神经胶质瘤风险相关的单核苷酸多态性 (SNP)，但这种关联背后的生物学机制尚不清楚。我们检验了这样一个假设，即 20q13.33 上的功能性 SNP 会影响增强子的活性，从而导致附近基因的表达发生改变。为了鉴定候选的功能性 SNP，我们鉴定了与风险相关的 SNP rs2297440 连锁不平衡的所有 SNP，这些 SNP 映射到推定的增强子。在针对多形性胶质母细胞瘤 (GBM) 细胞系的荧光素酶增强剂活性测定中，测试了含有候选功能性 SNP 的推定增强剂的等位基因特异性作用。含有 SNP rs3761124 的增强子对活性表现出等位基因特异性影响。STMN3、RTEL1、RTEL1-TNFRSF6B、GMEB2和SRMS。使用未患病的脑样本、异柠檬酸脱氢酶 1 ( IDH1 ) 野生型神经胶质瘤和神经发育组织进行的表达数量性状基因座 (eQTL) 分析显示， STMN3与 rs3761124 是一致的显着 eQTL。在早期 CNS 发育和/或IDH1野生型胶质瘤中， RTEL1和GMEB2也是重要的 eQTL 。我们提供的证据表明 rs3761124 是 20q13.33 上与神经胶质瘤/GBM 风险相关的功能变体，可调节STMN3和潜在其他基因在不同细胞环境中的表达。