Integrating Multi-Omics and Machine Learning to Reveal a Prognostic Model for Prostate Cancer Metastatic Recurrence Associated with Epithelial–Mesenchymal Transition Features

Background: Prostate cancer (PCa) is a leading cause of cancer-related mortality worldwide, highlighting the need for improved prognostic tools. The integration of artificial intelligence (AI) and machine learning (ML) with multi-omics data offers new opportunities for biomarker discovery and risk stratification. Methods: We integrated bulk transcriptomic data from GSE116918 (training, n = 248) and three cross-cohort consistency evaluation cohorts (TCGA-PRAD, GSE70769, GSE46602), focusing on 1087 epithelial–mesenchymal transition (EMT)-associated genes. Using consensus clustering, weighted gene co-expression network analysis (WGCNA), and 91 machine learning algorithm combinations (including Random Forest, Lasso, and CoxBoost), we constructed a prognostic signature. SHAP analysis was used for model interpretability. Single-cell RNA sequencing (scRNA-seq, GSE268307, 10,672 cells) and spatial transcriptomics (10× Genomics Visium FFPE) provided hypothesis-generating evidence; spatial analysis was based on one tissue section. Results: A three-gene signature (INHBA, FAP, ITGBL1) effectively stratified patients into high- and low-risk groups, with the high-risk group showing significantly worse metastasis-free survival (HR = 1.61, 95% CI: 1.39–1.87; 4-year AUC = 0.93 in the training cohort; external AUCs ranged from 0.62 to 0.77). CytoTRACE inferred high differentiation potential of COMP+ fibroblasts, and Monocle3 inferred a transcriptional transition from COMP+ toward NELL2+ fibroblasts. BayesPrism deconvolution suggested that high inferred COMP+ fibroblast abundance was associated with poor prognosis and advanced T stage. NicheNet analysis prioritized BMP7 as a key upstream ligand, with downstream targets enriched in TGF-β signaling and stem cell pluripotency pathways. Conclusions: This study presents a machine learning-based multi-omics framework for prostate cancer risk stratification. The three-gene signature provides a new exploratory prognostic model while inferring a COMP+ to NELL2+ transcriptional transition. These findings may inform future hypothesis-driven studies of treatment sensitivity, pending experimental validation, and demonstrate the value of AI-driven multi-omics integration for precision oncology.