Prognostic and immunological implications of a mitophagy-associated gene signature in bladder cancer

The pronounced heterogeneity of bladder cancer (BLCA) drives divergent patient outcomes and therapy responses. Mitophagy, a pivotal cellular quality-control and metabolic mechanism, modulates the dynamics of the tumor microenvironment (TME). Its prognostic significance and potential for guiding precision oncology, however, remain incompletely defined. This investigation aimed to evaluate the translational utility of mitophagy-associated signatures for the risk stratification of BLCA, profiling of TME, and prediction of therapeutic response.

Using The Cancer Genome Atlas (TCGA)-BLCA cohort, a prognostic signature was established via least absolute shrinkage and selection operator (LASSO) and multivariable Cox regression analyses. The robustness of the signature was externally validated using two independent cohorts from the Gene Expression Omnibus (GSE32894, n=224; GSE31684, n=93). A nomogram was established to estimate survival probability. A multi-faceted analysis of TME features was conducted to compare the subgroups, integrating three algorithms: Cell-Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT), Tumor Immune Dysfunction and Exclusion (TIDE), and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE). Drug sensitivity and molecular alteration profiles were interrogated to identify potential personalized therapeutic avenues.

A five-core-gene signature (NTN4, AKR1B1, FBXW7, MYH10, and IGF2BP3) was established. Across all cohorts, high-risk individuals exhibited notably shorter overall survival (OS) (TCGA-BLCA: P<0.001; GSE32894: P=0.003; GSE31684: P=0.03). The areas under the curves (AUCs) for 1-, 3-, and 5-year survival were 0.645-0.654 (TCGA-BLCA), 0.625-0.785 (GSE32894), and 0.567-0.651 (GSE31684). The TME analysis suggested that high-risk tumors were associated with elevated stromal scores, enrichment of M2 macrophages, and a predicted T-cell exclusion phenotype. Conversely, low-risk individuals exhibited an 'immune-inflamed' profile, marked by elevated microsatellite instability (MSI) and infiltration of CD8⁺ T cells. The profiling of drug sensitivity indicated that the low-risk subgroup might be more susceptible to cisplatin, whereas high-risk cases showed potential responsiveness to epidermal growth factor receptor (EGFR) and mechanistic target of rapamycin (mTOR) inhibitors.

This research developed a mitophagy-derived signature that predicts survival and is associated with a potential 'stromal barrier and immune-excluded' phenotype underlying therapy resistance in high-risk BLCA. The model offers a stratification framework for therapeutic decisions. Standard chemotherapy or immune checkpoint blockade (ICB) may lead to benefits in the low-risk subgroup, whereas high-risk individuals likely require novel combinatorial strategies targeting microenvironmental remodeling. However, as these results represent predictive associations derived from public datasets, further experimental validation is warranted to confirm the underlying biological mechanisms.