We asked, what will the bladder cancer test of the future look like - could it use genome-wide biomarker signatures rather than focusing on biomarker panels; could such a test discriminate between a myriad of benign conditions, other malignancies, and field effects, potentially grade and subtype of disease, and perhaps even outperform flexis? DNA methylation is very cell-type specific, exerts higher-order regulation than genetic mutations, and can go awry in diseases such as cancer. Genome-wide methylation changes in urine are likely to be highly informative of disease processes in the urinary tract and are more amenable to longitudinal monitoring than tumour biopsies. However, it was unclear if genome-wide methylation (and other genomic events such as genomic copy number changes) could be detected comprehensively in urine samples using third-generation sequencing technology.
In this week’s issue of Clinical Epigenetics,3 we publish a pilot study that shows that Oxford Nanopore Technologies' long-read sequencing of urine DNA with direct methylation calling can be used to detect non-muscle invasive bladder cancer. With this technology, single DNA molecules (kilobases in length) are fed through pores in a membrane, and the DNA sequence, including mutations and methylation changes, is recorded for each constituent base in real time without requiring any prior chemical treatment. In our study, we were able to gain complete epigenomic information of the actual cancer from urine. The technology is cheap, highly portable, and in conjunction with advanced bioinformatic approaches, could enable rapid testing (as has been demonstrated for brain cancer subtyping).4
Our proof-of-principle study gives us hope that we can, in the future, develop a comprehensive, non-invasive, clinical test with capabilities beyond the current state-of-the-art tests. However, much work remains to be done to reach that point. The next steps for us are to expand the patient cohort and develop robust methods to identify disease-specific signatures from the highly complex data. This may take several years. In the meantime, patients should be benefiting from the current generation of accurate DNA-based diagnostic urine tests to reduce the personal burden of bladder cancer diagnosis and surveillance.
Written by: Anshita Goel, PhD, Benjamin J. Tura, PhD, Douglas G. Ward, PhD, Richard T. Bryan, PhD, and Roland Arnold, PhD
- The Bladder Cancer Research Centre, Department of Cancer and Genomic Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- Ward DG, Baxter L, Ott S, Gordon NS, Wang J, Patel P, Piechocki K, Silcock L, Sale C, Zeegers MP, Cheng KK, James ND, Bryan RT; BladderPath Trial Management Group. Highly Sensitive and Specific Detection of Bladder Cancer via Targeted Ultra-deep Sequencing of Urinary DNA. Eur Urol Oncol. 2023 Feb;6(1):67-75. doi: 10.1016/j.euo.2022.03.005. Epub 2022 Apr 8. PMID: 35410825.
- D'Andrea D, Soria F, Zehetmayer S, Gust KM, Korn S, Witjes JA, Shariat SF. Diagnostic accuracy, clinical utility and influence on decision-making of a methylation urine biomarker test in the surveillance of non-muscle-invasive bladder cancer. BJU Int. 2019 Jun;123(6):959-967. doi: 10.1111/bju.14673. Epub 2019 Feb 5. PMID: 30653818; PMCID: PMC6850401.
- Goel, A., Tura, B.J., Stockton, J.D. et al. Detection of genome-wide methylation changes in bladder cancer by long-read sequencing of urinary DNA. Clin Epigenet 17, 141 (2025).
- Brändl B, Steiger M, Kubelt C, Rohrandt C, Zhu Z, Evers M, Wang G, Schuldt B, Afflerbach AK, Wong D, Lum A, Halldorsson S, Djirackor L, Leske H, Magadeeva S, Smičius R, Quedenau C, Schmidt NO, Schüller U, Vik-Mo EO, Proescholdt M, Riemenschneider MJ, Zadeh G, Ammerpohl O, Yip S, Synowitz M, van Bömmel A, Kretzmer H, Müller FJ. Rapid brain tumor classification from sparse epigenomic data. Nat Med. 2025 Mar;31(3):840-848. doi: 10.1038/s41591-024-03435-3. Epub 2025 Feb 28. PMID: 40021833; PMCID: PMC11922770.