Noninvasive urine test improves prediction of bladder cancer treatment outcomes

Bladder cancer arises from the lining of the bladder, the organ that stores urine, and is one of the most common cancers in the United States. Most patients are diagnosed at an early stage called non-muscle invasive bladder cancer (NMIBC), in which the tumors are confined to the inner layers of the bladder. Despite early detection, the disease frequently returns.

For the more than 60,000 patients diagnosed each year with NMIBC, the treatment path is both routine and uncertain, as bladder cancer has a high recurrence rate. After a surgery called transurethral resection of bladder tumor, patients with high-risk features are recommended to receive six weekly instillations of bacillus Calmette-Guérin (BCG), a decades-old immunotherapy, in their bladder to reduce the risk of recurrence. Some patients may be cured by surgery alone, while others will relapse despite the addition of BCG. Until now, doctors have had no reliable way to tell the difference.

The stakes are high. BCG can cause significant side effects and there is a recurrent global shortage in supply. And for patients who are destined to relapse, waiting for tumors to visibly return can mean lost time, and lost opportunity.

A new study published in Cell from a team of investigators from the Stanford Departments of Urology and Radiation Oncology, in close collaboration with colleagues from Stanford Cancer Institute, offers a powerful new approach: using a non-invasive urine test to determine, at a molecular level, who benefits from additional therapy – and who does not. The findings suggest that clinicians may soon be able to personalize treatment decisions, escalate therapy early for patients at highest risk, and spare others from unnecessary intervention. The research was primarily supported by funding from the National Cancer Institute.

A smarter way to detect hidden cancer

Liquid biopsies are highly sensitive tests that detect fragments of tumor DNA in bodily fluids, hold the strong potential to transform cancer monitoring. In bladder cancer, tumor DNA can be measured in urine, offering a noninvasive window into whether disease remains after treatment.

But the Stanford team uncovered an important biological complication: even healthy people can carry cancer-related mutations in the lining of the bladder, and these become more common with age. The researchers called this “clonal cystopoiesis.” Because these non-cancerous cells can release altered DNA into urine, highly sensitive tests may mistake it for cancer. To solve this problem, the team created a statistical method that filters out these background mutations, allowing the test to more accurately detect true signs of remaining cancer.

“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 Joseph Liao, MD, the Kathryn Simmons Stamey Professor of Urology and co-senior author of the study. “For the first time, we were able to distinguish patients likely cured by BCG from those cured by surgery.”

When applied to a prospective group of patients undergoing surgery followed by BCG, the refined urine test proved strikingly predictive. Patients with detectable tumor DNA after completing BCG had an almost certain risk of recurrence. Those whose tumor DNA cleared had excellent outcomes.

In many cases, the urine test identified recurrence risk even when routine cystoscopy exams appeared normal – suggesting it may detect relapse earlier than current standard surveillance.

Three Distinct Treatment Response Patterns

By analyzing urine samples before surgery, after surgery, and after immunotherapy, the researchers identified three clear molecular response patterns: 1) surgery responders: patients whose tumor DNA disappeared after surgery alone; 2) BCG responders: patients with residual tumor DNA after surgery that decreased following immunotherapy; and 3) non-responders: patients whose tumor DNA persisted or increased after BCG.

Correcting for the field effect proved central to this distinction. “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,” said William Shi, co-lead author and an MD/PhD student at Stanford School of Medicine. “This allowed us to molecularly distinguish the relative contributions of surgery and BCG to disease control.”

“The ability to distinguish responders from non-responders to the two treatments also allowed us to study which molecular properties make tumors more likely to benefit from each therapy,” said Max Diehn, MD/PhD, the Jack, Lulu, and Sam Willson Professor of Radiation Oncology and co-senior author of the study. This analysis revealed that the biology driving response to surgery is different from that driving response to immunotherapy. Tumors resistant to surgery showed gene activity associated with cell growth and invasion. In contrast, tumors that responded to BCG had higher mutation burdens and pre-existing immune activity – essentially appearing more “visible” to the immune system.

The authors hypothesized that the inability of prior studies to be able to distinguish surgical cures from immunotherapy responders hampered their ability to identify reliable biomarkers of BCG response.

Why this matters – clinically and beyond

The real-world implications are profound.

Today, nearly all intermediate, and high-risk patients receive BCG after surgery because clinicians cannot reliably identify who still harbors microscopic disease. This study suggests that a field-effect-informed urine test could: 1) spare patients who are molecularly cured after surgery from unnecessary immunotherapy; 2) prioritize BCG for those most likely to benefit – especially important during global shortages; 3) escalate treatment early for patients at highest risk, before visible tumors return; 4) guide enrollment in clinical trials for novel therapies; and 5) reduce anxiety and invasive procedures caused by false-positive results.

“These kinds of predictive biomarkers are critical,” said Eila 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 side effects. We would love to personalize therapy to ensure each patient receives the best treatment for their individual cancer.”

In practical terms, this means acting sooner for patients whose cancer is likely to recur, potentially preventing progression to more aggressive disease, while reducing overtreatment for others.

Beyond bladder cancer, the findings also carry broader scientific implications. The “field effect” phenomenon has been observed in other tissues, including lung and colon epithelium. As liquid biopsies expand across cancer types and biofluids, accounting for age-related background mutations may be essential for maximizing test accuracy.

If validated in larger studies, this approach could shift bladder cancer care from a one-size-fits-all strategy to a truly personalized model – where a routine urine sample helps determine who can safely stop treatment, and who needs more aggressive intervention before it is too late.