Genome-wide Associated Study Of Copy Number Variation Of Esophageal Squamous Cell Carcinoma Based Discordant Sibling Pairs

Esophageal cancer is the eighth most common cancer worldwide with vivid geographical and ethnic characteristics. In China, it ranks the fourth leading cause of cancer death. Esophageal squamous cell carcinoma (ESCC) is the dominant type of esophageal malignancy in China. In addition, the regional distribution of China is not equilibrium as well. The high incidence areas are located in the boundary of Hebei, Henan and Shanxi Provinces, which is surrounding the Taihang Mountain. Except for environmental risk factors, the heritability of ESCC was40%-93%in high incidence areas, suggesting genetic factors are considerably strong.Human genetic variations are the differences in DNA sequence within the genome of individuals in populations. Genetic variations were found associated with various human diseases including monogenic and complex disease. The field of human genetic variations has add much information about the genetic susceptibility and susceptibility genes for complex disease such as cancer. Genome-wide associated Copy number variation (CNV) study is one of the important strategies to screen the genetic variations associated with disease. CNV is an important form of gene structure variation. CNV is defined as additions or deletions in the number of copies of a particular segment of DNA (larger than1kb in length) when compared with a reference genome sequence. CNVs can cause a phenotype via several mechanisms including regulating transcription of genes by altering the dosage of an entire gene or by disrupting proximal or distant regulatory regions. CNV is also found associated with disease including cancer.Recently, genetic components underlying ESCC had been explored directly by genome-wide association studies (GWAS) in Japanese and Chinese population. Multiple common variants at seven independent loci that have moderate effects with population heterogeneity have been identified. However, the risk variants can explain only a small fraction (per-allele odds ratios1.3-1.5) of the estimated three to ten-fold familial relative risk of EC in first-degree relatives of affected individuals in high-risk areas of China. Therefore, the missing heritability of complex diseases began to be concerned in recent years. DNA structure variation such as CNV may account for some of the unexplained heritability. In this study, we conducted a GWAS of CNV based on ESCC from Yangquan area to identify CNVs associated with ESCC.We conducted a GWAS of CNV based on128discordant sibling pairs (DSPs, patient and his or her healthy sibling) from Yangquan area. Finally we identified57,774individual CNVs covering entire autosomes. After the gene-gene interaction network of238genes with frequencies more than20%constructed, we found that these genes were involved in the biological process of ESCC mainly concentrated on the Wnt, PI3K, ErbB signaling and highlighted the process of proliferation, evading apoptosis, sustained angiogenesis and DNA repairing. Among them,13q32.1was identified as a critical region. Independent sample validation demonstrated that amplification of ABCC4was significantly associated with the risk for ESCC. We also verified the enhancer activity of the variation region in ABCC4with ESCC cell specifity. Subsequently the enhancer activity can increase protein expression of ABCC4. The higher copy of ABCC4is associated with drug resistance and tumoregenesis of ESCC by altering the transport of PGE2to induce expression of EP1, EP2, EP3, phosphorylation of AKT, CREB, ERK and activation ofβ-catenin.In conclusion, we identified several significant ESCC-related CNV regions using genome-wide scan based on128DSPs from a high incidence area of Chinese Han population. The constructed network of CNVs genes further highlighted multiple ESCC-related mechanisms underlying tumorigenesis and key hub genes. The CNV of ABCC4gene at13q32.1was replicated in independent population, showing that the copy number amplification was significantly associated with the risk for ESCC. Furthermore, we demonstrated that the CNV contained an enhancer element to increase the expression of ABCC4. ABCC4might serve as a susceptible gene for ESCC via altering the PGE2-related signal pathways.