Association Of Mutant Gene With Tumor Mutation Load And Outcomes In Patients With Hepatocellular Carcinoma Based On Bioinformatics Analysis

OBJECTIVE:Based on bioinformatics analysis,Finding the mutated gene which was closely related with tumor mutation load and had prognostic significance as the biomarker predict response to Hepatocellular Carcinoma immunotherapy.Methods:Downloading dateset of mutated genes in patients with Hepatocellular Carcinoma from TCGA and ICGC datebase respectly and taking an intersetion for the highest frequency of top30 mutant genes of two datasets as Intersected Genes.Using the formula that tumor mutational burden(TMB)= number of non synonymous mutations/exome chip size(about 38 MB)to calculate every patient’s TMB,and an R package called Limma for differential analysis of TMB betweent patients who with wild Intersected Genes and mutant Intersected Genes,screening out the mutated gene associated with significantly different TMB as Candidate Genes.In additon,using R Survival package for Prognostic and Survival analysis to find the TargetGene that closely related with prognostic potentials.Then,using univariate and multivariate analysis to verify independent prognostic significance of the TargetGene.On the basis of the two dateset of mutated genes,downloading other two datesets from ICGC datebase(LICA-FR,LINC-JP)and studying the relationship between Target-Gene and the prognosis of all the patients of four datesets through meta analysis.Target-gene enrichment analysis through GSEA 4.1.0 and differential Analysis of immune infiltration not only between the group of HCC patients with mutant Target-Gene and wild Target-Gene but also high TMB and low TMB through CIBERSORT TOOL run by R language.Results: There were thirteen mutated genes significantly associated with TMB:TP53,TTN,MUC16,OBSCN,FLG,PCLO,LRP1 B,HMCN1,ADGRV1,USH2 A,XIRP2,CSMD3 and RYR2,among which LRP1 B was not only the most closely related to the prognosis of patients with Hepatocellular Carcinom but also had independent prognostic significance(P<0.05).Meta analysis showed that LRP1 B was an influencing factor for poor prognosis of HCC patients(HR = 1.37,95% CI(0.89,2.12)).The group of mutant LRP1 B enriched the metabolic pathway involving DNA Mismatch Repair and Glycosylphosphatidylinositol(GPI)Anchor Biosynthesis,and the group of wild-type LRP1 B enriched the pathway included Complement and Coagulation Cascades,Arachidonic Acid Metabolism and Nitrogen Metabolism.The analysis of immune cell infiltration showed that the group of patients with high TMB had more follivular helper T cells and patients with LRP1 B mutation had more Neutrophils and T cells CD4 naive(P<0.05)Conclusions:Most patients with high-frequency mutations genes of hepatocellular carcinoma had high TMB.LRP1 B mutation was not only closely related to high TMB but also poor prognosis of hepatocellular carcinoma patients.And LRP1 B was an independent prognostic factor for them.Mutations in LRP1 B were involved in essential DNA Mismatch Repair,Glycosylphosphatidylinositol(GPI)Anchor Biosynthesis,Arachidonic acid metabolism,Complement and Coagulation cascades and Nitrogen metabolism.In the same time,it had major impact on immune infiltrates in hepatocellular carcinoma.