Abstract 548: Urine biopsy as dynamic marker to enhance clinical staging of urothelial carcinoma
Authors: Satyal Uttam , Liu David , Slifker Michael , Alpaugh R K. , Lallas Costas D. , Trabulsi Eduoard , Hoffman-Censits Jean H. , Mouw Kent W. , Ibragimova Ilsiya , Cairns Paul , Van Allen Eliezer M. , Plimack Elizabeth R. , Kutikov Alexander , Abbosh Philip 
Published: July 2021

Abstract
Introduction: Neoadjuvant chemotherapy results in 30-40% complete response rates in patients undergoing radical cystectomy (RC) for bladder cancer. There is significant interest in identifying complete responders prior to RC in order to potentially avoid removal of a pathologically benign bladder. However, clinical restaging after neoadjuvant chemotherapy (NAC) with cystoscopy and imaging techniques is highly inaccurate. Since, bladder tumors are known to shed DNA into the urine, we hypothesized that mutations from tumor tissue (MT) would be detectable in urine DNA (uDNA) using NGS methods and that the presence or absence of urinary mutations (MU) after NAC would correlate with presence or absence of residual disease at the time of RC, respectively.
Results: MU were benchmarked against MT by comparing the mutation profiles from 15 patients enrolled in clinical trial NCT01611662 (‘The AMVAC trial'; NCT01031420) who underwent whole exome sequencing of their pre-NAC tumor tissue and had available urine supernatant. We were able to detect 46 of 76 (61%) MT as MU that included 6 of 14 (43%) subclonal MT being detected as MU. Residual MU status correlated with residual disease status based on mutations present in pre-RC urine supernatant from 22 patients in this trial (13/13 patients with residual MU had residual disease; 9/9 patients with absence of MU achieved pathological complete response). Residual MU status correlated with residual disease status (p&lt;0.0001). However, &gt;20% of samples were nondiagnostic because of low DNA quantity/quality and/or poor library composition/sequencing. We validated the correlation between mutation persistence and residual disease in pre-RC urine pellets from clinical trial NCT02968732 (‘The pT0 trial'). DNA from Urine pellets yielded a much lower nondiagnostic rate (&lt;10%). In analyzing the patients who underwent NAC, we found that 17 of 22 patients with residual MU were confirmed to have residual disease while 4 of 9 patients with pathologic complete response had no detectable mutation. Overall, the accuracy was 77%, and sensitivity and specificity were 86% and 63%, respectively. The positive and negative predictive value was 79% and 72%, respectively. Residual MU status correlated closely with residual disease status (p&lt;0.0003).
Conclusions: MU are representative of MT and thus can be used to enhance clinical staging of urothelial carcinoma. Urine biopsy may be a reliable tool that can be further developed to identify complete response to neoadjuvant chemotherapy. This prospect would facilitate safe radical cystectomy avoidance and could also be used as a surveillance tool to detect recurrence. The optimal urine compartment for accuracy appears to be the supernatant, however, there is a high nondiagnostic rate with these samples. Further refinements to DNA isolation protocols or library preparation may decrease the nondiagnostic rate.*PHA has applied patent based on this technology.
Citation Format: Uttam Satyal, David Liu, Michael Slifker, R K. Alpaugh, Costas D. Lallas, Eduoard Trabulsi, Jean H. Hoffman-Censits, Kent W. Mouw, Ilsiya Ibragimova, Paul Cairns, Eliezer M. Van Allen, Elizabeth R. Plimack, Alexander Kutikov, Philip Abbosh. Urine biopsy as dynamic marker to enhance clinical staging of urothelial carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 548.