Identification of a stemness-related prognostic model in Pancreatic ductal adenocarcinoma by Weighted gene co-expression network analysis
Abstract Objective: Aim of this study was to identify the stemness-related genes in Pancreatic ductal adenocarcinoma (PDAC). Methods: The RNA-seq data of PADC were downloaded from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. mRNA expression base-index (mRNAsi) and epigenetically regulated mRNAsi (EREG-mRNAsi) of PADC were evaluated. The mRNAsi-based gene sets in PADC were identified by Weighted gene co-expression network analysis (WGCNA). Functional Enrichment Analyses were performed with key genes. Kaplan–Meier survival analysis and the Cox proportional hazards model were used to evaluate the prognostic value of the key genes. Prognosis-associated hub genes were applied to establish nomograms. The receiver operating characteristic curves (ROC) and concordance index (C-index) were utilized to assess the discrimination and accuracy of the nomogram. Finally, these results were validated in the Gene Expression Omnibus (GEO) database and immunohistochemistry (IHC). Results: 36 key genes associate with mRNAsi were screened via WGCNA. Next a five-gene signature compromised TPX2, NCAPH, UBE2C, CCNB2, CEP55. Based on the expression of the signature, the PADC patients were classify patients into high- and low-risk groups. Cox regression analysis revealed that the high-risk group was significantly positive with overall survival (OS). Moreover, the nomogram has better sensitivity and specificity for predicting the OS. And the ROC, C-index indicated good performance of the prognostic signature in the TCGA and GEO dataset. Conclusion: Prognostic model associated with cancer stem cells (CSCs) reliably predict OS in PADC. this might be beneficial for the treatment of PADC patients.