Biancolella Michela, Fortini Barbara K, Tring Stephanie, Plummer Sarah J, Mendoza-Fandino Gustavo A, Hartiala Jaana, Hitchler Michael J, Yan Chunli, Schumacher Fredrick R, Conti David V, Edlund Christopher K, Noushmehr Houtan, Coetzee Simon G, Bresalier Robert S, Ahnen Dennis J, Barry Elizabeth L, Berman Benjamin P, Rice Judd C, Coetzee Gerhard A, Casey Graham
Department of Preventive Medicine.
Hum Mol Genet. 2014 Apr 15;23(8):2198-209. doi: 10.1093/hmg/ddt584. Epub 2013 Nov 20.
Genome-wide association studies of colorectal cancer (CRC) have identified a number of common variants associated with modest risk, including rs3802842 at chromosome 11q23.1. Several genes map to this region but rs3802842 does not map to any known transcribed or regulatory sequences. We reasoned, therefore, that rs3802842 is not the functional single-nucleotide polymorphism (SNP), but is in linkage disequilibrium (LD) with a functional SNP(s). We performed ChIP-seq for histone modifications in SW480 and HCT-116 CRC cells, and incorporated ChIP-seq and DNase I hypersensitivity data available through ENCODE within a 137-kb genomic region containing rs3802842 on 11q23.1. We identified SNP rs10891246 in LD with rs3802842 that mapped within a bidirectional promoter region of genes C11orf92 and C11orf93. Following mutagenesis to the risk allele, the promoter demonstrated lower levels of reporter gene expression. A second SNP rs7130173 was identified in LD with rs3802842 that mapped to a candidate enhancer region, which showed strong unidirectional activity in both HCT-116 and SW480 CRC cells. The risk allele of rs7130173 demonstrated reduced enhancer activity compared with the common allele, and reduced nuclear protein binding affinity in electromobility shift assays compared with the common allele suggesting differential transcription factor (TF) binding. SNPs rs10891246 and rs7130173 are on the same haplotype, and expression quantitative trait loci (eQTL) analyses of neighboring genes implicate C11orf53, C11orf92 and C11orf93 as candidate target genes. These data imply that rs10891246 and rs7130173 are functional SNPs mapping to 11q23.1 and that C11orf53, C11orf92 and C11orf93 represent novel candidate target genes involved in CRC etiology.
结直肠癌（CRC）的全基因组关联研究已经确定了一些与适度风险相关的常见变异，包括位于11号染色体q23.1区域的rs3802842。该区域有多个基因，但rs3802842并不位于任何已知的转录或调控序列上。因此，我们推断rs3802842不是功能性单核苷酸多态性（SNP），而是与一个功能性SNP处于连锁不平衡（LD）状态。我们在SW480和HCT-116结直肠癌细胞中进行了组蛋白修饰的染色质免疫沉淀测序（ChIP-seq），并将通过ENCODE获得的ChIP-seq和DNase I超敏性数据整合到11号染色体q23.1上包含rs3802842的137 kb基因组区域内。我们在与rs3802842处于LD状态的区域中鉴定出SNP rs10891246，其位于基因C11orf92和C11orf93的双向启动子区域内。将其突变为风险等位基因后，该启动子的报告基因表达水平降低。我们还鉴定出另一个与rs3802842处于LD状态的SNP rs7130173，其位于一个候选增强子区域，在HCT-116和SW480结直肠癌细胞中均表现出强烈的单向活性。与常见等位基因相比，rs7130173的风险等位基因增强子活性降低，并在电泳迁移率变动分析中显示出与常见等位基因相比核蛋白结合亲和力降低，提示转录因子（TF）结合存在差异。SNP rs10891246和rs7130173位于同一单倍型上，对相邻基因的表达数量性状位点（eQTL）分析表明C11orf53、C11orf92和C11orf93是候选靶基因。这些数据表明rs10891246和rs7130173是位于11q23.1的功能性SNP，并且C11orf53、C11orf92和C11orf93代表参与结直肠癌病因的新型候选靶基因。
