Bioinformatics analyses for the identification of tumor antigens and immune subtypes of gastric adenocarcinoma

Shuxun Wei; Qiang Sun; Jinshui Chen; Xinxing Li; Zhiqian Hu

doi:10.3389/fgene.2022.1068112

Bioinformatics analyses for the identification of tumor antigens and immune subtypes of gastric adenocarcinoma

Front Genet. 2022 Dec 12:13:1068112. doi: 10.3389/fgene.2022.1068112. eCollection 2022.

Authors

Shuxun Wei¹, Qiang Sun¹, Jinshui Chen², Xinxing Li¹, Zhiqian Hu¹

Affiliations

¹ Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China.
² Department of General Surgery, The 991st Hospital of Joint Logistic Support Force of People's Liberation Army, Hubei, China.

Abstract

Background: Although mRNA vaccines have been effective against multiple cancers, their efficacy against stomach adenocarcinoma (STAD) remains undefined. Immunotyping can indicate the comprehensive immune status in tumors and their immune microenvironment, which is closely associated with therapeutic response and vaccination potential. The aim of this study was to identify potential antigens in STAD for mRNA vaccine development, and further distinguish immune subtypes of STAD to construct an immune landscape for selecting suitable patients for vaccination. Methods: The gene expression and clinicopathological features of patients with gastric cancer were downloaded from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression Program (GTEx). 729 samples from GSE66229 and GSE84437 were downloaded through GEO and were used as the validation cohorts. Differential gene expression, genetic alterations and prognosis were analyzed using the R package, cBioPortal program and Kaplan-Meier. The relationship between tumor antigens and immune cells was evaluated and plotted by TIMER. ConsensusClusterPlus was used for consistency matrix construction and data clustering, and graph learning-based dimensional reduction was used to depict immune landscape. WGCNA was used to estimate the relationship between the color modules and immune subtypes. Results: Two overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in STAD, including RAI14 and NREP. The immune subtypes showed distinct molecular, cellular and clinical characteristics. IS1 and IS2 exhibited immune-activated phenotypes and correlated to better survival compared to IS3, while IS3 tumors was immunologically cold. Immunogenic cell death modulators, immune checkpoints, and CA125, and CEA were also differentially expressed among the three immune subtypes. Finally, the immune landscape of STAD showed a high degree of heterogeneity between individual patients. Conclusion: RAI14 and NREP are potential antigens for developing anti-STAD mRNA vaccine, and patients with IS1 and IS3 tumors may be suitable for vaccination.

Keywords: immunotype; mRNA vaccine; raw letter analysis; stomach adenocarcinoma; tumor immune.