Genomic Analysis Revealed Prognostic Signature In Hepatocellular Carcinoma Via Mining Public Of Genome Mutations Databases

Worldwide,liver cancer is the fifth most common cancer and the third most common cancer fatality rate in men.90% of primary liver cancer in China is Hepatocellular carcinoma(HCC).Patients with early stage hepatocellular carcinoma are prone to recurrence and metastasis after surgery.The 1-year recurrence rate is over 50%,and the 5-year survival rate is only 30%.Patients with advanced hepatocellular carcinoma currently is lack of effective treatment.Therefore,to find molecular markers that predict the risk of recurrence and death in patients with HCC,is particularly important for their further treatment.The molecular classification of hepatocellular carcinoma has not yet been established,and the clinical stage of liver cancer in Barcelona is the clinical method based on prognosis and treatment distribution.The tumor mutation burden(TMB)is becoming a reliable marker of immune checkpoint blockade.Some studies have also found that TMB has different prognostic value in different malignancies.There is an average of 40 genomic variants per hepatocellular carcinoma,and few of them are considered as driver mutation.Key signaling pathways that drive hepatocarcinogenesis include cell cycle control,WNT-β-catenin,epigenetic and chromatin remodeling,AKT-m TOR-MAPK,and oxidative stress.Further understanding of key molecular markers that influence hepatocellular carcinoma recurrence and death can help identify key driver genetic aberrations.With the further improvement of sequencing technology,whole genome and/or exome sequencing to explore genetic aberrations in hepatocellular carcinoma,some progress has been made,and a very complete genomic database such as TCGA(The Cancer Genome Atlas)and ICGC(International Cancer Genome Consortium).A number of articles have been published based on these public databases.PurposesThis study attempts to analyze the whole genome and/or exome sequencing data of HCC in database TCGA and ICGC and RNA sequencing data of Oriental hepatobiliary hospital samples,to study the prognostic value of TMB and genomic aberrations of key five signaling pathways,molecular markers that causes HCC recurrence and death.Methods1.Data sources: In this study,376 patients in the TCGA database was used to obtain whole exome sequencing data and gene expression data(m RNA)for HCC patients.243 patients in the schulze2015 cohort from c Bio Portal(www.cbioportal.org)was used to obtain whole exome sequencing data for HCC patients.Whole-genome sequencing data from NCC-JP 394 Japanese cohorts and LICA-FR 241 French cohorts were obtained from ICGC(dcc.icgc.org).The relationship of TMB and genetic aberrations in key signal pathway genes and prognosis in HCC patients was analyzed by survival analysis.The validation dataset was RNA-seq data of tumor and normal tissues of HCC patients from the Oriental hepatobiliary hospital.2.Sample inclusion: The study data included clinical information and follow-up information,genomic mutations,and copy number variation for patients with WES or WGS.3.TMB Value in HCC: TMB is defined as the total number of non-silent somatic mutations in the coding region.The TMB values are arranged from large to small,with the first quartile being high TMB group(TMB-H)and the rest being low TMB group (TMB-L).To analyze the relationship between TMB and age,gender,stage,cirrhosis,etiology,degree of vascular invasion and differentiation,and to explore the prognostic value of TMB.4.The value of five key pathways: To analyze the prognosis value of genetic aberrations of the five key pathway included cell cycle control,WNT-β-catenin,epigenetic and chromatin remodeling,AKT-m TOR-MAPK,and oxidative stress in HCC.Result1.In TCGA,JP,schulze2015 and FR cohorts,TMB after logarithmic transformation was correlated with age(P<0.001),meanwhile,TMB was higher in male patients(P<0.05).2.In TCGA and schulze2015 cohort,patients with HCV and HBV infection background had the highest TMB,and patients with two or more mixed etiologies had the highest proportion of TMB-H patients.At the same time,patients without cirrhosis were found to have lower TMB than those with cirrhosis(P<0.05).3.In schulze2015,TMB after logarithmic transformation was correlated with tumor size(r=0.204,P=0.002).However,there was no association between TMB and clinical stage in all four cohorts.4.Genetic aberrations in cell cycle control pathway in TCGA Asians was higher than in TCGA Caucasians and in FR French cohort.It was also found that patients with HBV and HCV backgrounds had more gene aberrations in cell cycle control pathway(P=0.005).5.In TCGA,OS and DFS of HCC patients in the high TMB group were significantly shorter than those in the low TMB group(P<0.001,P=0.088).The risk of death in HCC patients in the high TMB group was 2.156 times higher than that in the low TMB group(P<0.001).6.In TCGA,JP,and FR cohorts,it was found that the median DFS,OS of HCC patients with genetic aberrations in cell cycle control pathway were shorter than those without aberrations(P<0.05),while the risk of recurrence and death of HCC patients with genetic aberrations in cell cycle control pathway genes were higher than those without variation(P<0.05).Meanwhile,in TCGA and Oriental hepatobiliary hospital,we also found that patients with high cell cycle control gene expression level had shorter DFS and OS than those with low expression level.Conclusions1.Increased TMB of HCC was associated with older age,male gender,and tumor diameter.2.Patients with a background of HBV or HCV infection had higher TMB and more gene aberrations in cell cycle control pathway.3.High TMB and genetic aberrations in cell cycle control pathway were associated with poor prognosis in HCC patients.