Exploration of the relationship between tumor mutation burden and immune infiltrates in colon adenocarcinoma

Abstract

Background: Tumor mutation burden (TMB) was correlated with the immunotherapeutic response in various malignancies. We aimed to evaluate the TMB immune signature in colon adenocarcinoma (COAD). Methods: Gene expression profile, mutation and clinical data of COAD patients were obtained from The Cancer Genome Atlas (TCGA) database. The samples were divided into high and low TMB level groups to identify differentially expressed genes (DEGs). Functional enrichments analyzes were performed to identify the biological functions of the DEGs. Then, immune cell infiltration signatures were calculated by the CIBERSORT algorithm. Finally, Cox proportional hazard model was constructed to estimate the prognostic value of the identified immune-related genes. Results: Gene set enrichment analysis in the high-TMB level group showed that DEGS were enriched in immune-related pathways, such as antigen processing and presentation, Toll-like receptor signaling and natural killer cell-mediated cytotoxicity. A higher infiltration level of CD8+ T cells, CD4+ T cells, activated NK cells , M1 Macrophages and T follicular helper cells was observed in the high-TMB level group. Furthermore, a Cox regression model combined with survival analysis based on the expression level of four identified prognostic genes was constructed, validated anf revealed that higher risk-score levels conferred poor survival outcomes in COAD patients. Conclusions: Our data demonstrate that the high TMB levels are associated with an immune signature in COAD and deepen the molecular understanding of TMB function in tumor immunotherapy.

Keywords: Tumor mutation burden (TMB); colon adenocarcinoma (COAD); immune signature; prognosis.

Figure 1

Landscape of mutation profiles in COAD samples. Mutation information of each gene in each sample was shown in the waterfall plot, in which various colors with annotations at the bottom represented the different mutation types. The barplot above the legend exhibited the mutation burden.

Figure 2

Summary of the mutation information with statistical calculations. (A, B) Variant classification and type of genetic alterations in COAD. (C) The SNV class of COAD; (D) The coincident and exclusive associations across mutated genes. SNP, single nucleotide polymorphism; SNV, single nucleotide variants.

Figure 3

Comparisons of gene expression profiles in low- and high-TMB samples. (A) Top 30 DEGs were shown in heatmap plot; (B) Identification of TMB-related immune genes.

Figure 4

Functional enrichment in different TMB groups. (A,B) Functional enrichment pathway analysis of TMB-related DEGs in COAD, including biological processes (BP), cellular components (CC), molecular function (MF), and KEGG pathway. (C) Results of significantly enriched pathways in the high-TMB group by GESA. Enrichment scores (ES, green line) indicate the degree to which the genome is overexpressed at the top or bottom of the list of sequenced genes.

Figure 5

Immune cell infiltrations in COAD. (A) The specific 22 immune fractions represented by various colors in each sample were shown in barplot. (B) Comparisons of 22 immune cell infiltrations between the high‐TMB and low‐TMB groups.

Figure 6

Prognostic analysis based on risk score model of the 4 genes. (A) Kaplan-Meier curves for the low- and high-risk groups; (B) The receiver operating characteristic (ROC) curve validation of prognostic value by the risk score.

Figure 7

Evaluation of the prognostic value of the four-gene signature using Kaplan-Meier analysis.