Integration of single‐cell and bulk RNA‐sequencing data reveals the prognostic potential of epithelial gene markers for prostate cancer

Abstract

Prognostic transcriptomic signatures for prostate cancer (PCa) often overlook the cellular origin of expression changes, an important consideration given the heterogeneity of the disorder. Current clinicopathological factors inadequately predict biochemical recurrence, a critical indicator guiding post-treatment strategies following radical prostatectomy. To address this, we conducted a meta-analysis of four largescale PCa datasets to identify consistent up-regulation of 33 previously reported PCaassociated genes in prostate tumours. By analysing single-cell RNA-seq data, we found these genes predominantly as markers in epithelial cells. Subsequently, we applied 97 advanced machine learning algorithms across five PCa cohorts and developed an 11-gene epithelial expression signature. This signature robustly predicted biochemical recurrence-free survival (BCRFS) and stratified patients into distinct risk categories, with high-risk patients showing worse survival and altered immune cell populations. The signature outperformed traditional clinical parameters in larger cohorts and was overall superior to published PCa signatures for BCRFS. By analysing peripheral blood data, four of our signature genes showed potential as biomarkers for radiation response in localised patients and effectively stratified castration-resistant patients for overall survival. In conclusion, this study developed a novel epithelial marker gene-based signature that enhanced BCRFS prediction and enabled effective risk stratification compared to existing clinical and gene expression derived prognostic tools. Furthermore, a set of genes from the signature demonstrated potential utility in peripheral blood, a tissue amenable to minimally invasive sampling in a primary care setting, offering significant prognostic value for PCa patients without requiring a tumour biopsy.