Urine Liquid Biopsy Detects 95 Percent of Localized Bladder Cancers
Researchers at Stanford Medicine and the VA Palo Alto Health Care System have developed a urine-based liquid biopsy that detects 95% of localized bladder cancers at 90% specificity. The test, named uRARE-seq (urine random priming and affinity capture of cell-free RNA fragments for enrichment analysis by sequencing), analyzes cell-free RNA (cfRNA) fragments released into urine rather than tumor-associated DNA mutations. In a study published in Nature Medicine encompassing 683 urine samples from 515 individuals, the approach mapped gene expression across thousands of genes to evaluate tumor biology and treatment response.
Gene Expression Sequencing Versus DNA Testing
Unlike FDA-cleared tests like NMP22, which detects a protein, or UroVysion, which identifies chromosomal abnormalities, uRARE-seq sequences thousands of active genes. The detection model incorporated 381 genes. The test showed higher pretreatment sensitivity than urine cytology and a tumor-naive urine tumor DNA assay, while matching the performance of a targeted tumor-informed DNA approach without requiring prior sequencing of a patient’s tumor.
Predicting Patient Response to Intravesical BCG
The assay provides a precision medicine tool for selecting treatments in patients with non-muscle-invasive bladder cancer who receive intravesical Bacillus Calmette-Guérin (BCG) after surgery. Pretreatment urine from patients who achieved a complete molecular response to BCG displayed stronger T-cell and immune-related expression signatures. Conversely, patients with molecular residual disease showed higher expression of proliferation-associated genes.
Institutional Review Boards Approve Sample Collection Protocols
All human participant samples were collected under protocols approved by Institutional Review Boards at Stanford University, Stanford Health Care, and the Veterans Affairs Palo Alto Health Care System. Bladder cancer cases were gathered under IRB 55427, while control cohorts utilized IRBs 55427, 12597, and 18225. Renal cell carcinoma samples fell under IRB 12597 and prostate cancer samples under IRB 49693. Participants provided written informed consent for the research use of their biospecimens and clinical data, which included self-reported smoking history and sex extracted from medical records.
Researchers Extract RNA from Bladder Tumor Blocks
Formalin-fixed paraffin-embedded (FFPE) bladder tumor blocks were examined by a pathologist to select tumor regions for comparison against urine cfRNA. Core punches from these blocks yielded RNA extracted via the CELLDATA DNAstorm/RNAstorm 2.0 Combination Kit, followed by DNase I treatment to remove residual DNA. Researchers synthesized double-stranded cDNA using New England Biolabs modules, hydrolyzed single-stranded regions with S1 nuclease, and prepared sequencing libraries with the KAPA Hyper Prep kit. Whole-coding transcriptome capture utilized the Twist Biosciences Comprehensive Exome Hybridization kit, with libraries sequenced on Illumina HiSeq4000 or NovaSeq6000 instruments targeting roughly 30 million read pairs.
Future Validation Plans for Multicenter Trials
The findings indicate that urine cfRNA can deliver multiple diagnostic layers from a single noninvasive sample, identifying cancer presence, tumor characteristics, residual disease after treatment, and optimal therapy selection. To establish clinical utility, the research team plans to validate uRARE-seq in larger, prospective, multicenter clinical trials.
What Does uRARE-Seq Stand For?
How many urine samples were analyzed in the study?
The research evaluated 683 urine samples collected from 515 individuals.
Which institutional review boards approved the sample collection protocols?
Collection protocols were approved by Institutional Review Boards at Stanford University, Stanford Health Care, and the Veterans Affairs Palo Alto Health Care System under specific protocol numbers including IRB 55427, 12597, 18225, and 49693.