Identification and Validation of Immune-Related Prognostic Genes in the Tumor Microenvironment of Colon Adenocarcinoma

Shenghua Pan; Tingting Tang; Yanke Wu; Liang Zhang; Zekai Song; Sisi Yu

doi:10.3389/fgene.2021.778153

Identification and Validation of Immune-Related Prognostic Genes in the Tumor Microenvironment of Colon Adenocarcinoma

Front Genet. 2022 Jan 3:12:778153. doi: 10.3389/fgene.2021.778153. eCollection 2021.

Authors

Shenghua Pan¹, Tingting Tang¹, Yanke Wu¹, Liang Zhang¹, Zekai Song¹, Sisi Yu¹

Affiliation

¹ Department of Pathology, Ruian People's Hospital, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.

Abstract

The tumor microenvironment (TME) has been shown to be involved in angiogenesis, tumor metastasis, and immune response, thereby affecting the treatment and prognosis of patients. This study aims to identify genes that are dysregulated in the TME of patients with colon adenocarcinoma (COAD) and to evaluate their prognostic value based on RNA omics data. We obtained 512 COAD samples from the Cancer Genome Atlas (TCGA) database and 579 COAD patients from the independent dataset (GSE39582) in the Gene Expression Omnibus (GEO) database. The immune/stromal/ESTIMATE score of each patient based on their gene expression was calculated using the ESTIMATE algorithm. Kaplan-Meier survival analysis, Cox regression analysis, gene functional enrichment analysis, and protein-protein interaction (PPI) network analysis were performed. We found that immune and stromal scores were significantly correlated with COAD patients' overall survival (log rank p < 0.05). By comparing the high immune/stromal score group with the low score group, we identified 688 intersection differentially expressed genes (DEGs) from the TCGA dataset (663 upregulated and 25 downregulated). The functional enrichment analysis of intersection DEGs showed that they were mainly enriched in the immune process, cell migration, cell motility, Toll-like receptor signaling pathway, and PI3K-Akt signaling pathway. The hub genes were revealed by PPI network analysis. Through Kaplan-Meier and Cox analysis, four TME-related genes that were significantly related to the prognosis of COAD patients were verified in GSE39582. In addition, we uncovered the relationship between the four prognostic genes and immune cells in COAD. In conclusion, based on the RNA expression profiles of 1091 COAD patients, we screened four genes that can predict prognosis from the TME, which may serve as candidate prognostic biomarkers for COAD.

Keywords: OMICS data; colon adenocarcinoma; immune/stromal scores; protein–protein interaction network; tumor microenvironment.