Explore The Origin Of Poorly And Well-differentiated Cancerous Lesions In A Patient With Gastric Adenocarcinoma Based On WGS Data

BackgroundGastric cancer(GC)is the fifth largest cancer type in the world,accounting for 7% of all cancer cases,and the third most common cause of cancer-related mortality worldwide.The burden of gastric cancer in our country is particularly serious.As the tumor and microenvironment heterogeneity is a major obstacle to successful treatment,there are blooming studies focusing on the tumor heterogeneity and evolution for better understanding of oncology.ObjectiveBy whole genome sequencing(WGS)of poorly and well-differentiated cancerous tissues in a patient with gastric adenocarcinoma,this study aims to explore the possible origins of the two cancerous lesions of this patient with different malignant degrees.We further explored mechanisms underlying the development of gastric cancer by integrating the epigenetic layers.MethodsIn this study,we collected a well-differentiated cancerous tissue(WDGA),a poorly-differentiated cancerous tissue(PDGA),and a paracancerous tissue(PCT)from a patient with gastric adenocarcinoma.To identify the mutations as well as driver genes in the gastric adenocarcinoma samples,we first detected each nucleotide for the DNA sequence by whole genome sequencing.Firstly,we mapped the single nucleotide variation(SNV)spectrum,and tested whether these newly identified SNV patterns matched the gastric cancer mutation signatures published in the database.Then,we used the db NSFP database to annotate non-synonymous mutations,to analyze the similarity and difference of the pathogenic mutations of WDGA and PDGA.Further more,an alternative approach,Oncodrive FML software was used to predict the driver genes of different genomic functional regions in gastric cancer samples.Finally,the obtained driver genes were compared with the gastric cancer driver genes reported in literatures.In order to understand the epigenetic regulatory mechanism of gastric cancer,we combined the ATAC-seq data of gastric cancer and the Cp G islands(CGIs)data to identify the potential regulatory mutations in these regions..The DNA methylation 450 K chip data of 395 gastric cancers downloaded from TCGA and the whole-genome bisulfite sequencing(WGBS)data of 4 normal gastric tissues of adults in the ENCODE project were used to compare the DNA methylation changes between gastric cancer tissues and normal gastric tissues,and explore the role of DNA methylation in gastric cancer.We also downloaded the known eukaryotic transcription factor binding sites(TFBS)from TRANSFAC database,and use MEME\MAST software to search for TFBS with the range of 40-bps upstream and downstream from the mutation site,and identify the gain and loss for each TFBS.Results1.The distribution of PDGA and WDGA mutations in each gene function region is similar,but the total number of PDGA mutations is twice that of WDGA.2.Among the genes of pathogenic mutations in PDGA(69)and the genes of pathogenic mutations in WDGA(93),only nine genes are common.3.Among the driver genes predicted by the three sets of data,only one driver gene(ZNF365)is the same between the driver genes in PDGA(32)and the driver genes in WDGA(13).Although the mutation types of ZNF365 in both lesions are Insertion and Deletion(INDEL),the mutations are located at different sites.4.Both the rs148640037 mutation of MUC6 and the rs950707828 mutation of the ITPR2 gene had increased DNA methylation levels and changes in TFBS.ConclusionAlthough the patients with WDGA and WDGA have some common background mutations in this study,it is predicted that two differently differentiated tumor foci are caused by different driver genes or different mutations of the same driver gene.The results suggest that the two tumors have different evolutionary pathways,which are likely to belong to different cancer origins,and more support the neutral theory of cancer origin and evolution.