Identifying a new microRNA signature as a prognostic biomarker in colon cancer

• Published in: PloS one 2020-02, Vol.15 (2), p.e0228575-e0228575
• Main Authors: Lv, Yunxia, Duanmu, Jinzhong, Fu, Xiaorui, Li, Taiyuan, Jiang, Qunguang
• Format: Article
• Language: English
• Subjects: 1-Phosphatidylinositol 3-kinase; AKT protein; Analysis; Bioinformatics; Biology and life sciences; Biomarkers; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Cancer; Cancer genetics; Cancer patients; Chemotherapy; Colon; Colon cancer; Colonic Neoplasms - diagnosis; Colonic Neoplasms - genetics; Colonic Neoplasms - metabolism; Colorectal cancer; Development and progression; Diseases; Encyclopedias; Female; Focal Adhesion Protein-Tyrosine Kinases - genetics; Focal Adhesion Protein-Tyrosine Kinases - metabolism; Functional analysis; Gastrointestinal surgery; Gene expression; Gene Regulatory Networks; Genes; Genetic aspects; Genomes; Genomics; Humans; Male; MAP kinase; MAP Kinase Signaling System; Medical prognosis; Medicine and Health Sciences; MicroRNA; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; Middle Aged; miRNA; Nomograms; Nomographs; Novels; Ontology; Pathogenesis; Patients; Phosphatidylinositol 3-Kinases - genetics; Phosphatidylinositol 3-Kinases - metabolism; Physical Sciences; Proto-Oncogene Proteins c-akt - genetics; Proto-Oncogene Proteins c-akt - metabolism; Rank tests; Regression analysis; Regression models; Research and Analysis Methods; Ribonucleic acid; RNA; Survival; Survival analysis; Tissues; Training
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0228575

The aim was to identify a novel prognostic miRNA signature for colon cancer (CC) in silico. Data on the expression of miRNAs and relevant clinical information for 407 patients were obtained from The Cancer Genome Atlas (TCGA), and the samples were randomly split into a validation set (n = 203) and training set (n = 204). The differential expression of miRNAs between normal tissues and patients with CC was analyzed. We detected a miRNA expression signature in the training dataset by using a Cox proportional hazard regression model. Then, we verified the signature in the validation set. Association of the miRNA signature with overall survival was assessed in the validation cohort and combined cohort by log-rank test and based on Kaplan-Meier curves. The receiver operating characteristic and disease-free survival analyses were performed to evaluate the miRNA signature of CC in the combined cohort. Multivariate and univariate Cox analyses related to survival for the miRNA signature were performed, and a nomogram was built as a prognostic model for CC. To explore the function of target genes of the miRNA signature, Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used. Between the matched normal tissues and colon cancer tissues, 267 differentially expressed miRNAs were detected, and a single-factor CoxPH model showed that 13 miRNAs were related to overall survival in the training cohort. Then, a five-miRNA signature was identified using a CoxPH regression model with multiple factors. The five-miRNA signature had significant prognostic value in the training cohort and was validated in the validation cohort and combined cohort. A total of 193 target genes of the miRNA signature were identified. According to the results of functional analysis of the target genes, the signaling pathways MAPK, AMPK and PI3K-Akt, focal adhesion, and microRNAs in cancer were remarkably enriched. A five-miRNA signature had increased prognostic value for CC, which may provide important biological insights for the discovery and development of molecular predictors to improve the prognosis of patients with CC.