Exploring vertical genomic heterogeneity and chemotherapy response using targeted genomic sequencing in muscle-invasive bladder cancer

We performed a targeted genomic sequence of muscle-invasive bladder cancer (MIBC) tissues to investigate vertical intratumoral heterogeneity, invasion processes, and potential biomarkers of platinum-based neoadjuvant chemotherapy (NAC) efficacy in MIBC. Mutations in key genes thought to be associated with MIBC were investigated using deep amplicon sequencing of tissue samples from 34 Japanese patients with MIBC, including paired superficial and deep layers from seven patients. Genetic mutations linked to the NAC response were identified by stratifying patients into NAC responder and non-responder groups. Somatic mutations were detected in 91.2% of cases, with TP53 mutations being the most common (50%). Pathogenic mutations in superficial and deep layers were concordant only in 2 of the 7 cases, and the concordance disappeared when including non-pathogenic mutations. In one case, TP53 mutations were found only in deep layer. Immunohistochemical staining revealed differential expression of epithelial–mesenchymal transition-related molecules in the superficial and deep layers. ERCC excision repair 2 gene (ERCC2) mutations were identified more frequently in NAC responders compared with non-responders (50% vs. 0%), whereas the reverse was true for TP53 mutations (16.7% vs. 42.9%). Our results suggest that ERCC2 and TP53 mutations are potential biomarkers of the response to NAC and that evaluating deep tumor layers may be considered to care about vertical heterogeneity.