What question did this study set out to answer?

The research aims to improve monitoring and treatment selection for non–muscle-invasive bladder cancer using urine tumor DNA analysis.

March 6, 2026

Strategy to Analyze Urine Tumor DNA Predicts Outcomes in Bladder Cancer

Key Points

The research aims to improve monitoring and treatment selection for non–muscle-invasive bladder cancer using urine tumor DNA analysis.
Developed a novel approach combining uCAPP-seq and RePhyNERX to enhance specificity in urine DNA analysis.
Analyzed urine samples for oncogenic mutations and their association with patient age.
Evaluated treatment responses based on pre- and post-surgical urine DNA levels.
Assessed T cell-to-stroma enrichment scores for predicting BCG therapy response.
Detection of specific bladder cancer mutations in urine correlated with treatment responses.
Higher tumor mutation burden and immune signaling characterized patients responding to BCG therapy.
Clonal cystopoiesis identified in non-cancerous patients, suggesting ongoing mutation processes.
Urine samples contained more cancer DNA than plasma, indicating a practical monitoring approach.

Abstract

Analysis of urine tumor DNA (utDNA) holds great promise as a tool to monitor non–muscle-invasive bladder cancer (NMIBC). However, the presence of mutant DNA from normal urothelium, which arises in a phenomenon termed field cancerization, limits the specificity of such analyses. Additionally, previous studies have not distinguished biomarkers of response to surgery versus adjuvant Bacillus Calmette-Guerin (BCG) therapy, which are both used for treatment of intermediate- and high-risk tumors. In this study, Shi, Liu, and colleagues developed a novel approach that combines urine cancer personalized profiling by deep sequencing (uCAPP-seq) with a statistical approach that removes field effect mutations, called RePhyNERX (“refiner X”), to increase the specificity of utDNA analysis for disease monitoring. In patients without bladder cancer, uCAPP-seq analysis revealed the incidence of putative oncogenic mutations in PLEKHS1, TERT, KMT2D, and FGFR3 that increased with age, a phenomenon they termed “clonal cystopoiesis” given its parallels with clonal hematopoiesis. Using RePhyNERX-enhanced uCAPP-seq, mutations arising from bladder cancers were detected in urine from patients with NMIBC, and utDNA concentrations were found to associate with distinct treatment responses and outcomes. While presurgical utDNA levels did not correlate with recurrence or survival, detection of utDNA following surgery or subsequent BCG induction increasingly associated with recurrence. BCG responders, identified based on utDNA decrease after treatment, were characterized by higher tumor mutation burden and enhanced immune signaling compared to non-responders. Moreover, a positive T cell–to-stroma enrichment (TSE) score signified an increased likelihood of response to BCG. Finally, urine displayed increased abundance of bladder cancer DNA compared to plasma in patients with NMIBC, suggesting the high potential clinical relevance of the method in this clinical setting. Altogether, this study details the development and validation of a novel approach to utDNA analysis that can aid in treatment selection, response evaluation, and possibly the management of additional cancer types.Shi WY, Liu KJ, Esfahani MS, Mach KE, Phillips NA, Almanza D, et al. Field-effect-informed urine liquid biopsy for bladder cancer. Cell 2026 Jan 27 Epub ahead of print.Note: Research Watch is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details. For more Research Watch, visit Cancer Discovery online at https://aacrjournals.org/cdnews.

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