utDNA–guided MRD assessment may predict response to BCG in NMIBC

A field-effect–informed urine tumor DNA (utDNA) assay may help distinguish which patients with non–muscle invasive bladder cancer (NMIBC) benefit from intravesical BCG, according to findings from a study published in Cell.¹

The approach, which accounts for age-related background mutations in the urothelium, demonstrated the ability to identify minimal residual disease (MRD) and stratify patients by likelihood of recurrence following surgery and adjuvant therapy.

The findings address a clinical gap in NMIBC management, where clinicians lack reliable tools to determine which patients require BCG after transurethral resection of bladder tumor (TURBT). Given the persistent global shortage of BCG, improved risk stratification could have meaningful implications for treatment selection and resource allocation.

“Our test can detect minimal residual disease non-invasively after bladder cancer treatment, while accounting for mutations present in normal urothelium that has complicated prior studies,” said co-senior author Joseph C. Liao, MD, the Kathryn Simmons Stamey Professor of Urology at Stanford University, in a news release on the findings.² “For the first time, we were able to distinguish patients likely cured by BCG from those cured by surgery.”

For the study, investigators from Stanford Medicine analyzed 261 urine and tissue samples collected from patients with intermediate- and high-risk NMIBC undergoing TURBT followed by BCG. The study introduced a refined utDNA assay designed to filter out mutations arising from nonmalignant urothelial cells—a phenomenon termed “clonal cystopoiesis” or field effect—which can confound conventional liquid biopsy approaches. The investigators found that these mutations become more common with age.

Using the filtration method, patients were categorized into 3 molecular response groups: those whose tumor DNA cleared after surgery alone (surgical responders), those with persistent disease after surgery but clearance following BCG (BCG responders), and those with persistent or increasing tumor DNA despite both interventions (non-responders). Filtering out the background mutations were critical to these distinctions.

“By correcting for the field effect, a known confounder of mutation-based bladder cancer detection, we improved the specificity of urine tumor DNA liquid biopsies,” explained co-lead author William Shi, an MD/PhD student at Stanford School of Medicine, in the news release.² “This allowed us to molecularly distinguish the relative contributions of surgery and BCG to disease control.”

When applied to a prospectively enrolled cohort, the assay demonstrated strong prognostic performance. Detectable utDNA after completion of BCG induction was highly associated with high-grade recurrence-free survival (log rank test, HR, 12.8; 95% CI, 3.7 to 44.1, P < .001; Cox proportional hazards regression, P = .0005), whereas patients with clearance of utDNA experienced favorable outcomes. Notably, molecular evidence of residual disease was detected in some patients with negative cystoscopy findings, suggesting the approach may identify recurrence earlier than current surveillance modalities.

Biological properties of responders

Beyond its predictive utility, the study provides insight into the biological determinants of treatment response.

“The ability to distinguish responders from non-responders to the 2 treatments also allowed us to study which molecular properties make tumors more likely to benefit from each therapy,” said co-senior author Maximilian Diehn, MD, PhD, the Jack, Lulu, and Sam Willson Professor of Radiation Oncology.

Tumors responsive to BCG were characterized by higher mutational burden and evidence of pre-existing immune activation. In contrast, tumors resistant to surgery exhibited gene expression patterns associated with proliferation and invasion.

Limitations and next steps

The authors noted several limitations to the study, including the relatively modest sample size. Further, all patients in the study received adjuvant BCG, limiting the ability to determine whether patients who were utDNA-negative after TURBT could safely omit BCG without compromising outcomes. Additional limitations include the need to establish generalizability of the field-effect–informed approach (RePhyNERX) across tumor types and biofluids, as well as technical constraints related to sequencing methodology.

Based on the current findings, the authors suggest that patients with persistent utDNA after BCG may be candidates for early treatment escalation with novel therapies. Further, the approach may allow for prioritization of BCG for patients who are most likely to benefit from adjuvant treatment, although prospective validation is warranted.

“These kinds of predictive biomarkers are critical,” concluded Eila C. Skinner, MD, the Thomas A. Stamey Research Professor of Urology and Chair of Stanford’s Department of Urology. “We have new treatments that are costly and carry risk of [adverse] effects. We would love to personalize therapy to ensure each patient receives the best treatment for their individual cancer.”

REFERENCES
1. Shi WY, Liu KJ, Esfahani MS, et al. Field-effect-informed urine liquid biopsy for bladder cancer. Cell. 2026;189(4):1024-1038.e9. doi: 10.1016/j.cell.2025.12.054

2. A urine test that could change the course of bladder cancer care. News release. Stanford Medicine. April 7, 2026. Accessed April 8, 2026. https://www.eurekalert.org/news-releases/1123201