The latest results: 2022 update
Last July we announced that Nonacus and the University of Birmingham had partnered to develop a non-invasive test for bladder cancer. The test uses highly sensitive liquid biopsy technology developed by Nonacus, and a panel of biomarkers validated by Dr Rik Bryan and Dr Douglas Ward from the University’s Bladder Cancer Research Centre, to diagnose the disease from urine samples. Now, less than a year later, the first results are in.1
The latest data shows that the urine test was able to successfully detect 144 out of the 165 people with bladder cancer that had experience haematuria. The test showed an overall sensitivity of 87.3% – a measure of how often a test correctly generates a positive result for people who had bladder cancer – and a specificity of 84.8% – a measure of the test’s ability to correctly generate a negative result for people who didn’t have bladder cancer.
The team also looked at using the test in patients 293 patients who were already being treated for bladder cancer and were being monitored for the cancer returning. In this setting, the test returned a higher proportion of false positive results compared to when used in the haematuria clinic (37.5% vs 15.2%), with 99 positive urine tests without a tumour being seen by cystoscopy on the same day. However, during their follow up monitoring, the patients who had those positive results had almost 3-times higher (11% vs 4%) rates of the cancer returning within 24 months, suggesting that the test could help detect recurrent disease before it is visible by cystoscopy.
Background: the need for a sensitive, non-invasive urine test
Bladder cancer is the seventh most common cancer in the developed world2. In the UK, over 100,000 people a year are referred to hospital clinics that investigate for bladder cancer, usually after passing blood in their urine (haematuria). The first stage of investigation is usually cystoscopy, which involves inserting a camera into the bladder. Of these 100,000 patients, around 12% are subsequently diagnosed with bladder cancer, normally after a second invasive procedure to extract a biopsy.
Dr Bryan, Director of the Bladder Cancer Research Centre, commented:
“While blood visible in the urine should always be investigated, over 80% of people who have a cystoscopy at a haematuria clinic are diagnosed with non-malignant conditions or have no abnormality. Unfortunately, the remaining 20% will need a further invasive procedure to confirm diagnosis. What is required is a highly sensitive and specific, non-invasive test that can rapidly determine those who need a biopsy and those who do not, and a urine test is the obvious place to start.”
While the ‘liquid biopsy’ approach is attractive, the low levels of tumour DNA in a background of DNA from normal tissues requires highly sensitive analytical techniques to obtain accurate results. However, researchers at the University started their work in the knowledge that Nonacus had successfully pioneered commercial non-invasive prenatal tests to identify low-levels of fetal DNA in maternal blood samples. Moreover, the company was developing methods to allow confident and sensitive calling of mutations from as little as 10ng of DNA.
The researchers used ‘deep sequencing’ of tumour DNA to identify mutations that are present in the majority of urothelial bladder cancers (UBCs). Their work, which was funded by Cancer Research UK and an MRC Confidence in Concept grant, involved sequencing 23 genes from tumour samples collected from 956 newly diagnosed, treatment-naïve patients. This deep sequencing of genes identified 451 unique mutations that were present in over 96% of tumours. The researchers also demonstrated that these mutations were identifiable in urine samples collected at the same time as tumour sampling2.
As the researchers have shown, mutated DNA in a urine sample can be extracted from cancer cells shed into the urine from the lining of the urinary tract, or can be found as cell-free DNA fragments3. However, extracting DNA from the cancer cells provides more reliable amounts of DNA for the test, especially when only small volumes of urine may be available. Coupling the mutation panel with the unique molecular identifiers and the proprietary target capture technology provided by the Nonacus Cell3 Target™ will provide a much more sensitive test than the existing PCR-based approach. The researchers are already working on validating this combination in a further 600 cases (including non-cancer cases) and they expect to publish data on sensitivity and specificity within six months.
Nonacus intends to launch the new bladder cancer test as soon as possible, and the final product will include access to bioinformatics software to help with analysis. The test will provide high sensitivity for all stages and grades of disease, with plans to make it available worldwide to laboratories, hospitals and clinics.
Promisingly, the original research also determined the influence of the mutations on cancer progression, time to recurrence, and overall and disease-specific survival in patients with non-muscle-invasive bladder cancer (NMIBC), and disease-specific survival in patients with muscle-invasive bladder cancer (MIBC), raising the possibility that the test could be used to stratify patients according to risk.
Chris Sale, CEO of Nonacus, commented: “We expect this partnership to deliver better care and outcomes for patients by reducing the number of invasive procedures, providing earlier diagnosis and speeding up access to treatment for people with bladder cancer.”
Tony Hickson, Chief Business Officer at Cancer Research UK, said: "As funders of much of the world-class, cutting-edge cancer research happening in the UK, we offer unique opportunities to commercial partners looking for early involvement in new discoveries. Having Nonacus on board to help transform promising findings in the lab into a new non-invasive test to diagnosis bladder cancer is a testament to how commercial collaborations have the potential to transform the lives of patients. We are looking forward to seeing the next steps as the test is developed and rolled out to the UK and beyond.”
Allen Knight, Chair of Trustees, Action Bladder Cancer UK, said: “This really is very exciting and has the potential to make an incredible difference for patients and for Bladder Cancer treatment. Currently urine tests do not accurately pick up bladder cancer, and invasive tests are required to confirm a diagnosis. A urine test that can rapidly determine who needs these tests will be a very welcome development. Many patients, myself included, find cystoscopies very uncomfortable at best, and they can have lasting side effects. This research could pave the way for routine screening, common in other cancers, but unavailable at present for Bladder Cancer."
- Ward, D. et al. Highly Sensitive and Specific Detection of Bladder Cancer via Targeted Ultra-deep Sequencing of Urinary DNA. Eur Urol 2022; 03. 005
- Antoni, S. et al. Bladder cancer incidence and mortality: a global overview and recent trends. Eur Urol 2017; 71: 96–108.
- Bryan, RT. et al. Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA: a 23 gene panel with utility for non-invasive diagnosis and risk stratification. BJU Int 2019: 124; 532-544.
As a first step towards enabling further research, Nonacus has developed a translational and clinical research panel targeting 451 somatic mutations found in 96% of bladder cancer cases.
Based on the ultra sensitive Cell3™ Target chemistry developed by Nonacus, the new Cell3 Target: Bladder Cancer panel enables researchers to sequence the tumor DNA found in the urine of bladder cancer patients to raw read depths in excess of 20,000x. This depth of coverage provides the sensitivity and accuracy needed to offer a viable genomic alternative to flexible cystoscopy for the profiling of bladder cancer.