Prognosis Analysis Of Gastric Cancer Based On Genomic Variations And Profiles Of Tumor Immune Microenvironment

Gastric cancer(GC)is one of the most common cancers worldwide.It is the fifth most common neoplasm and the third most deadly cancer.The risk factors for GC are diverse and complicated,leading to genomic structural variations and dysregulated gene expression,and accelerated tumorigenesis.Some comprehensive prospective studies have stratified the GC samples into distinct subtypes based on the clinical and pathological features or the genomic profiles.However,the association between genetic factors and the prognosis in GC has yet been studied and reported systemically.To explore the genetic factors of gastric cancer(GC)related to prognosis in the context of lower genetic heterogeneity,we focused on GC patients living in the middle geographical regions of Anhui Province("Jianghuai region").In this retrospective study,a total of 43 patients with primary GC were included based on the survival times after surgery,including 19 patients in the poor prognosis(PoP)group with survival time less than 1-year and 24 patients in the high prognosis(HiP)group with survival time more than 5 years(mean survival time of 7.3 years).The whole exome sequencing with high coverage was performed on the FFPE tumor sample of each patient,and the sequencing data was analyzed using a mutation detection pipeline optimized for the FFPE sample developed myself.The results showed that the mutation frequencies of 9 genes(PCDHA6,UBXN11,NBPF20,UPS6,SAMD1,TKBBP1,CSMD2,GPR98,ZIC3)were different between HiP and PoP and were associated with the prognosis.A total of 125 significantly mutated genes(SMGs)were identified,including 13 genes(ARID1A,ARID1B,BRD4,CSMD3,EP300,EPHB4,FAT1,LRP1B,RAD51,SH2B3,SOX17,TP53,ZNF384)reported as cancer-related genes in previous reports.Functional enrichment analysis of SMGs found that the genes in the Wnt signaling pathway were significantly enriched.Meanwhile,the genes in the axon guidance pathway were also overrepresented in the SMGs,implying the importance of the axon guidance pathway in cancer development.Cancer pathway analysis revealed that the mutation frequencies of another four genes(ZNRF3,ALK,PIK3CA,DNER)exhibited prognosis differences between the two groups.CNV analysis revealed that the amplified regions in chromosomes appeared to be consistent among GCs,in contrast with the heterogeneous deleted regions.Interestingly,12p12.1 chromosomal amplification and p13.3 deletion were found only in HiP and PoP,respectively.Mutational signature analysis revealed 2 differentially mutational signatures between two groups.The Sig4 associated with failure of homologous recombination DNA double-strand break repair was mainly observed in the HiP group,whereas the Sig3 with unknown causative mechanism occurred mainly in the PoP group.Neoantigen analysis showed that the presenting efficiency of neoantigens was decreased along with the increase in the patient’s age.The mean presenting efficiency of neoantigens in the HiP group was higher than that of the PoP group,implying patients with higher presenting efficiency of neoantigens have better prognosis.Immunotherapy emerged as a powerful treatment for gastric cancer patients.However,it is only effective in a limited fraction of patients.In this study,we evaluated the compositions of 22 tumor-infiltrating lymphocytes(TILs)in TCGA Stomach Adenocarcinoma(STAD)samples using a deconvolution-based method by analyzing the publicly available bulk tumor RNA-seq data.The patients were classified into high-TIL and low-TIL subtypes based on their immune cell profiles and prognosis outputs.The differentially expressed genes(DEGs)between the two subtypes were identified,and GO/KEGG analysis showed that broad immune genes,such as PD-L1 and PD-1,were highly expressed in the high-TIL subtype.A comprehensive protein-protein interaction(PPI)network centered on DEGs was built,and 16 hub genes of the network were further identified.Based on the hub genes,an elastic model with 11 gene signatures(NKG7,GZMB,IL2RB,CCL5,CD8A,IDO1,MYH1,GNLY,CXCL11,GBP5,and PRF1)was developed to predict the high-TIL subtype.In summary,several genetic factors related to prognosis were identified by comprehensively comparing the tumor mutation landscapes between HiP and PoP,which is useful for interpreting the genomic mutations and predicting the prognosis of GC patients.Our findings also showed that the compositions of TILs within the tumor immune microenvironment of stomach cancer patients are highly heterogeneous,and the profiles of TILs have the potential to be predictive markers of patients’ responses and overall survival outcomes.