Analysis Of ESCC Genomic Alterations

Esophageal cancer is one of the most aggressive cancers.It ranks the eighth commonly diagnosed cancers and is the sixth most common cause of cancer related-death all over the world.There are two main histological subtypes of esophageal cancer:esophageal adenocarcinoma and esophageal squamous cell carcinoma.ESCC occupies 90%of esophageal cancer cases globally and about 70%of those cases are diagnosed in China.Although the level of diagnosis and treatment of ESCC has been greatly improved in the past decades,its five-year survival rate is still only 15%-25%.Therefore,it is of great significance to understand the development mechanism of ESCC and to find the effective diagnostic markers and therapeutic targets,which is of great importance to the formulation of effective treatment scheme and the improvement of the prognosis of ESCC.In recent years,with the development of sequencing technology,omics research on ESCC has been started.Several research groups,including us,performed ESCC whole-genome sequencing,revealing key genomic alterations in TP53,RBI,NOTCHI,cell cycle related genes,and signaling pathways including PI3K-AKT,WNT and RAS.Those findings helped us make certain understanding of the genome variations of ESCC.However,cancer genomic alterations are complex.In addition to the genetic variations found above,the characteristics of genomic variation in ESCC still need further excavation.This study is based on the data obtained from the genome sequencing of ESCC by our group and the research group of Professor Cui Yongping from Shanxi Medical University.The genomic variation characteristics of ESCC were analyzed from three aspects by bioinformatic method.Preliminary experimental verification of the function of related genes was performed:1.Cancer genomic alterations are closely related to its clinical characteristics.We combined the clinical features of ESCC to analyze significantly mutated genes and found genetic mutations involved in survival and lymph node metastasis status of ESCC patients.TBX20,which had not been reported in tumor,may play an important role in ESCC progression.In addition,the heavy chains encoding genes of dynein have gene mutations and gene copy number variations,and the mutation of these genes is associated with prognosis,suggesting that dynein may play a role in the progress of ESCC.We also found gene amplification related to survival and lymph node metastasis status.C11ORF24,whose detail function is unknown,was upregulated in ESCC.We further found that knocking down C11ORF24 could inhibit the proliferation,clone formation,invasion and migration of ESCC cells.This is the first report of the function of C11ORF24 in tumor,suggesting that it is a new oncogene.2.Bromodomain-containing proteins,an important class of proteins involved in epigenetic regulation,play important roles in a variety of tumors and are important targets for small molecular inhibitors.However,their roles in ESCC have rarely been reported.We found that the gene mutations and copy number variations of the Bromodomain-containing proteins encoding genes in ESCC,in which BRD9 and ATAD2,genes of the IV family,have a significant gene amplification,and it is found that this is a common feature of squamous cell carcinomas by comparing with the genetic variations in other tumors.Chang et al.have previously found that gain of BRD9 in ESCC,but detail study of function of BRD9 had not been done.The function of ATAD2 in ESCC has not yet been reported.BRD9 inhibitor I-BRD9 could inhibit the proliferation and clone formation of ESCC cells,and cause cell cycle G1/S blockade as well as induce cell apoptosis.In addition,I-BRD9 treatment could reduce the expression of cell cycle related genes CDK2 and CDK4.This is the first report of the role of I-BRD9 in ESCC inhibition.Knocking down A TAD2 affected the proliferation,clonal formation,invasion and metastasis of ESCC cells.We firstly reported the function of ATAD2 in ESCC.3.Gene variations involved in DNA damage repair pathways play important roles in the process of tumorigenesis and progression,moreover they can contribute to therapy resistance of cancers.We found four of six common DNA damage repair pathways,including the base excision repair(BER)and mismatch repair(MMR)pathways which involved in single-strand DNA break repair and Homologous recombination(HR)and non-homologous end-joining(NHEJ)pathways which contribute to DNA double-strands breaks repair.The alterations of these pathways were related to survival or lymph node metastasis status of ESCC patients.Further analysis of gene variations and gene expression,we figured out that genes in DSBs repair pathway were generally upregulated,of which RAD51B,RAD54B,MRD51A,NBN,PRKDC have amplifications and significantly high-expression in ESCC.Variations of these genes were associated with the prognosis and lymph node metastasis status of ESCC patients.These results suggested that these genes may play an important role in the development of ESCC.Our analysis preliminarily revealed the molecular basis of radiotherapy resistance of ESCC.In addition,we found that Mirin(inhibitor of the HR pathway)and NU7441(inhibitor of NHEJ pathway)can reduce cell proliferation of ESCC cells,and enhance DNA double strands breaks caused by IR treatment and promote cell apoptosis.