title: Deep Sequencing of Urinary RNAs for Bladder Cancer Molecular Diagnostics.
abstract: Purpose:The majority of bladder cancer patients present with localized disease and are managed by transurethral resection. However, the high rate of recurrence necessitates lifetime cystoscopic surveillance. Developing a sensitive and specific urine-based test would significantly improve bladder cancer screening, detection, and surveillance.Experimental Design:RNA-seq was used for biomarker discovery to directly assess the gene expression profile of exfoliated urothelial cells in urine derived from bladder cancer patients (n= 13) and controls (n= 10). Eight bladder cancer specific and 3 reference genes identified by RNA-seq were quantitated by qPCR in a training cohort of 102 urine samples. A diagnostic model based on the training cohort was constructed using multiple logistic regression. The model was further validated in an independent cohort of 101 urines.Results:A total of 418 genes were found to be differentially expressed between bladder cancer and controls. Validation of a subset of these genes was used to construct an equation for computing a probability of bladder cancer score (PBC) based on expression of three markers (ROBO1, WNT5A, andCDC42BPB). Setting PBC= 0.45 as the cutoff for a positive test, urine testing using the three-marker panel had overall 88% sensitivity and 92% specificity in the training cohort. The accuracy of the three-marker panel in the independent validation cohort yielded an AUC of 0.87 and overall 83% sensitivity and 89% specificity.Conclusions:Urine-based molecular diagnostics using this three-marker signature could provide a valuable adjunct to cystoscopy and may lead to a reduction of unnecessary procedures for bladder cancer diagnosis.Clin Cancer Res; 23(14); 3700-10. ©2017 AACR.
authors.affiliation: Department of Urology, Stanford University School of Medicine, Stanford, California.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
authors.forename: Mandy L Y
authors.initials: MLY
authors.lastname: Sin
authors.affiliation: Department of Urology, Stanford University School of Medicine, Stanford, California.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
authors.forename: Kathleen E
authors.initials: KE
authors.lastname: Mach
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California.
authors.forename: Rahul
authors.initials: R
authors.lastname: Sinha
authors.affiliation: Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
authors.forename: Fan
authors.initials: F
authors.lastname: Wu
authors.affiliation: Department of Urology, Stanford University School of Medicine, Stanford, California.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
authors.forename: Dharati R
authors.initials: DR
authors.lastname: Trivedi
authors.affiliation: Department of Urology, Stanford University School of Medicine, Stanford, California.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Altobelli
authors.affiliation: Veterans Affairs Palo Alto Health Care System, Palo Alto, California.|Department of Pathology, Stanford University School of Medicine, Stanford, California.
authors.forename: Kristin C
authors.initials: KC
authors.lastname: Jensen
authors.affiliation: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, California.
authors.forename: Debashis
authors.initials: D
authors.lastname: Sahoo
authors.affiliation: Veterans Affairs Palo Alto Health Care System, Palo Alto, California.|Department of Biomedical Data Science and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California.
authors.forename: Ying
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Urology, Stanford University School of Medicine, Stanford, California. jliao@stanford.edu.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Liao
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000652:urine*; D003558:Cystoscopy / Q000379:methods; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009364:Neoplasm Recurrence, Local / Q000473:pathology / Q000652:urine; D057089:Pathology, Molecular; D012313:RNA / Q000235:genetics / Q000652:urine*; D001749:Urinary Bladder Neoplasms / Q000235:genetics / Q000473:pathology / Q000652:urine*
chemical_list: D014408:Biomarkers, Tumor; D012313:RNA