Development and analytical validation of a multiplex diagnostic qPCR-array as a potential application in predicting the response to neoadjuvant chemotherapy in muscle invasive bladder cancer

Bladder cancer (BC) remains a common malignancy, with muscle-invasive bladder cancer (MIBC) comprising 20 % of cases and a poor 5-year survival rate of ∼50 %. While neoadjuvant chemotherapy (NAC) followed by radical cystectomy is the standard treatment for locally advanced disease, NAC is limited by toxicity and non-response in many patients. Predictive biomarkers are urgently needed to guide treatment decisions. We developed and analytically validated a multiplex qPCR array to measure mRNA expression of 10 NAC response-associated biomarkers in MIBC. RNA from 8 formalin-fixed paraffin-embedded (FFPE) and 4 fresh-frozen (FF) MIBC specimens was analyzed to assess the effects of tissue type, necrosis, and pre-analytical variables on assay performance. The assay showed high concordance between FF and FFPE samples, with stable performance using FFPE curls stored at ≤4 °C for up to two weeks. It remained robust across RNA input levels (5–100 ng) and required a minimum quality threshold (DV200 >15 %). Necrosis had minimal impact on gene expression, and reproducibility was confirmed across technicians and time points. In conclusion, this qPCR array-based assay offers a reliable platform for evaluating key biomarkers in FFPE tissues and holds promise as a potential clinical tool to predict NAC response in MIBC patients.