Development and validation of an RBP gene signature for prognosis prediction in colorectal cancer based on WGCNA

作者：Lu Cao, Lili Duan, Rui Zhang, Wanli Yang, Ning Yang, Wenzhe Huang, Xuemin Chen, Nan Wang, Liaoran Niu, Wei Zhou, Junfeng Chen, Yiding Li, Yujie Zhang, Jinqiang Liu, Daiming Fan, Liu Hong · 发表于：Hereditas · 年份：2023 · DOI：10.1186/s41065-023-00274-z · 被引用次数：9 · 研究领域：Ferroptosis and cancer prognosis、Bioinformatics and Genomic Networks、RNA Research and Splicing

BACKGROUND: RNA binding proteins (RBPs) have been implicated in oncogenesis and progression in various cancers. However, the potential value of RBPs as prognostic indicators and therapeutic targets in colorectal cancer (CRC) requires further investigation. METHODS: Four thousand eighty two RBPs were collected from literature. The weighted gene co-expression network analysis (WGCNA) was performed to identify prognosis-related RBP gene modules based on the data attained from the TCGA cohorts. LASSO algorithm was conducted to establish a prognostic risk model, and the validity of the proposed model was confirmed by an independent GEO dataset. Functional enrichment analysis was performed to reveal the potential biological functions and pathways of the signature and to estimate tumor immune infiltration. Potential therapeutic compounds were inferred utilizing CMap database. Expressions of hub genes were further verified through the Human Protein Atlas (HPA) database and RT-qPCR. RESULTS: One thousand seven hundred thirty four RBPs were differently expressed in CRC samples and 4 gene modules remarkably linked to the prognosis were identified, based on which a 12-gene signature was established for prognosis prediction. Multivariate Cox analysis suggested this signature was an independent predicting factor of overall survival (P < 0.001; HR:3.682; CI:2.377-5.705) and ROC curves indicated it has an effective predictive performance (1-year AUC: 0.653; 3-year AUC:0.673; 5-year AUC: 0.77...