CDKN2A copy number alteration in bladder cancer: integrative analysis in patient-derived xenografts and cancer patients

Bladder cancer (BlCa) is an extensively heterogeneous disease that leads to great variability in tumor evolution scenarios and lifelong patients’ surveillance, emphasizing the need for modern minimally-invasive precision medicine. Herein, we have explored the clinical significance of copy-number alterations (CNAs) in BlCa. CNAs profiling was performed in 15 patient-derived xenografts (PDXs) and validated in TCGA-BLCA (n=408) and Lindgren et al. (n=143) cohorts. CDKN2A copy-number loss was identified as the most frequent CNA in bladder tumors, associated with reduced CDKN2A expression, tumors of papillary phenotype and prolonged PDX survival. Study’s screening cohort consisted of 243 BlCa patients and CDKN2A copy-number was assessed in genomic DNA and cell-free DNA (cfDNA) from 217 tumors and 189 pre-treatment serum samples, respectively. CDKN2A copy-number loss was correlated with superior disease-free and progression-free survival of non-muscle-invasive bladder cancer (NMIBC) patients. Moreover, higher CDKN2A index (CDKN2A/LEP ratio) in pre-treatment cfDNA was associated with advanced tumor stage, grade and short-term NMIBC progression to invasive disease, while multivariate models fitted for CDKN2A index in pre-treatment cfDNA offered superior risk-stratification of T1/high grade and EORTC high-risk patients, enhancing prediction of treatment outcome. CDKN2A copy-number status could serve as minimally-invasive tool in improving risk-stratification and supporting personalized prognosis in BlCa.