Identifying multi-omics biomarkers for ovarian cancer survival estimation

Abstract

Ovarian cancer is among the deadliest gynecologic malignancies, and its molecular heterogeneity limits accurate prognostic stratification. Although multi-omics approaches have improved predictive modeling, many prioritize predictive performance over biological interpretability, limiting their clinical translation. We developed an interpretable three-stage machine learning framework integrating mRNA, microRNA, DNA methylation, copy number variation, and protein expression data from The Cancer Genome Atlas. Hierarchical feature selection was combined with a weighted ensemble of ElasticNet, ridge regression, support vector regression, XGBoost, and random forest models to estimate overall survival time in patients with ovarian cancer. Multi-omics integration outperformed every single-modality model, achieving a Pearson correlation of 0.752, a concordance index of 0.779, and a mean absolute error of 8.57 months between estimated and observed survival time, compared with 0.48 for the best single modality. The framework identified a 20-biomarker signature dominated by tumor-associated macrophage and complement genes. In an independent survival analysis, VSIG4 and CD163 remained significant after false discovery rate correction, and the signature raised the concordance index over clinical covariates alone from 0.615 to 0.686Enrichment analysis implicated PI3K-Akt, MAPK, focal adhesion, hypoxia, apoptosis, and p53 signaling pathways. This framework couples improved prognostic estimation with biological interpretability supporting multi-omics biomarker discovery in ovarian cancer.