A novel m7G-related lncRNA risk model for predicting prognosis and evaluating the tumor immune microenvironment in colon carcinoma

Abstract

N7-Methylguanosine (m7G) modifications are a common type of posttranscriptional RNA modifications. Its function in the tumor microenvironment (TME) has garnered widespread focus in the past few years. Long non-coding RNAs (lncRNAs) played an essential part in tumor development and are closely associated with the tumor immune microenvironment. In this study, we employed a comprehensive bioinformatics approach to develop an m7G-associated lncRNA prognostic model based on the colon adenocarcinoma (COAD) database from The Cancer Genome Atlas (TCGA) database. Pearson’s correlation analysis was performed to identify m7G-related lncRNAs. Differential gene expression analysis was used to screen lncRNAs. Then, we gained 88 differentially expressed m7G-related lncRNAs. Univariate Cox analysis and Lasso regression analysis were performed to build an eight-m7G-related-lncRNA (ELFN1-AS1, GABPB1-AS1, SNHG7, GS1-124K5.4, ZEB1-AS1, PCAT6, C1RL-AS1, MCM3AP-AS1) risk model. Consensus clustering analysis was applied to identify the m7G-related lncRNA subtypes. We also verified the risk prediction effect of a gene signature in the GSE17536 test set (177 patients). A nomogram was constructed to predict overall survival rates. Furthermore, we analyzed differentially expressed genes (DEGs) between high-risk and low-risk groups. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted with the analyzed DEGs. At last, single-sample gene set enrichment analysis (ssGSEA), CIBERSORT, MCP-COUNTER, and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithms were utilized to discover the relationship between the risk model and the TME. Consequently, the m7G-related lncRNA risk model for COAD patients could be a viable prognostic tool and treatment target.

A novel N7‐methylguanosine‐related long noncoding RNAs signature for predicting prognosis and immune microenvironment in gastric cancer patients

“…Recently, the role of lncRNA in m 7 G and their relationship to cancer were gradually clear. For example, some researchers have identified that the m 7 G-related lncRNA risk model can be an efficient prognostic tool and anti-tumor immunotherapy target for multiple cancer types, including colon carcinoma, 34 Lung Adenocarcinoma 35 and cutaneous melanoma. 36 In our study, the m 7 G-related lncRNAs risk model was constructed using three prognostic lncRNAs by bioinformatic analysis.…”

Role of long non-coding RNA ELFN1-AS1 in carcinogenesis

“…Age, lactate dehydrogenase (LDH) level, cell-of-origin, extranodal sites, and Eastern Cooperative Oncology Group performance status were correlated clinicopathological variables used in nomogram construction. Sheng Yang et al [ 83 ] identified eight N7-methylguanosine-related lncRNAs (consisting of ELFN1-AS1) and established a risk signature derived from TCGA and validated it in GEO (GSE17536 dataset) database patients with colon cancer. Based on the risk score and cluster analysis, patients were divided into three groups, of which group 1 had the worst prognosis.…”

Explore the prognostic characteristics of immunogenic cell death- related genes in colon carcinoma based on multi-constraint canonical correlation analysis

“…Yang et al developed eight risk models of m7G-related lncRNAs (ELFN1-AS1, PCAT6, etc.) to predict colon cancer prognosis and assess the tumour immune microenvironment [25].…”