Optimization of urinary DNA deep sequencing tests to enhance clinical staging of bladder cancer patients

PROJECT SUMMARY/ABSTRACT
Muscle-invasive bladder cancer (MIBC) is optimally treated with neoadjuvant chemotherapy followed by
radical cystectomy (RC), whereby ~35% of patients will have a pathologic complete response (pCR). Given the
morbid, complicated, and expensive nature of RC and the well-established pCR rate, there is a groundswell of
interest in RC avoidance for patients achieving pCR. However, identifying pCR clinically (as opposed to
pathologically) is an inaccurate process. In published studies, patients who avoid RC after being deemed clinical
complete responders have a 25-60% likelihood of recurrence, metastasis, or bladder cancer mortality. Better
tools to assess residual disease status are needed.
To address this need, we developed a urine biopsy test which we call UTeRD (Urine Test for Residual
Disease). In UTeRD, DNA is isolated from urine and subjected to next generation sequencing to detect point
mutations in a targeted panel of genes. Using UTeRD, most mutations in tumor tissue are detectable as
mutations in urine. Further, presence or absence of residual MU after completion of chemotherapy strongly
associates with residual disease or pCR at the time of RC, respectively. Therefore, UTeRD could be used after
neoadjuvant therapy to better identify patients for RC avoidance.
Although UTeRD performs well in distinguishing patients with pCR from residual disease, the negative
predictive value (NPV) of UTeRD is only 76%, some urine samples were nondiagnostic, and a urinary DNA
preservation protocol needs to be developed in order for the test to be widely adopted. Pre-analytical factors
and methodology improvements which we believe will increase the NPV and decrease nondiagnostic rates will
be studied in Aim 1. In Aim 2, we will determine if urine preservatives can be used to facilitate shipping to a
centralized lab without loss of fidelity of the test. Lastly, in Aim 3, we will determine if the absence of mutations
from a urine biopsy is associated with pCR regardless of the pre-surgical therapy. To answer this question,
samples obtained on 5 prospective MIBC clinical trials from multiple institutions will be studied using the
optimized protocols identified through this research.
The research team is comprised of a urologist, medical oncologists, a radiation oncologist, a statistician,
a computational biologist who are experts in their fields. The skills and contributions of the team are
complimentary and will culminate in the development of a unique and robust biomarker that addresses a
significant clinical need using a one-of-a-kind sample cohort. UTeRD may enhance the ability of a bladder cancer
clinician to answer highly relevant clinical question, namely, “Does this patient have residual disease after pre-
surgical therapy, and therefore, will he/she benefit from RC?”

Grant Number: 5U01CA260369-05
NIH Institute/Center: NIH
Principal Investigator: Philip Abbosh