Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer

Abstract

Purpose: Targeted agents and immunotherapies promise to transform the treatment of metastatic bladder cancer, but therapy selection will depend on practical tumor molecular stratification. Circulating tumor DNA (ctDNA) is established in several solid malignancies as a minimally invasive tool to profile the tumor genome in real-time, but is critically underexplored in bladder cancer.Experimental Design: We applied a combination of wholeexome sequencing and targeted sequencing across 50 bladder cancer driver genes to plasma cell-free DNA (cfDNA) from 51 patients with aggressive bladder cancer, including 37 with metastatic disease.Results: The majority of patients with metastasis, but only 14% of patients with localized disease, had ctDNA proportions above 2% of total cfDNA (median 16.5%, range 3.9%-72.6%). Twelve percent of estimable samples had evidence of genome hypermutation. We reveal an aggressive mutational landscape in metastatic bladder cancer with 95% of patients harboring deleterious alterations to TP53, RB1, or MDM2, and 70% harboring a mutation or disrupting rearrangement affecting chromatin modifiers such as ARID1A. Targetable alterations in MAPK/ERK or PI3K/AKT/ mTOR pathways were robustly detected, including amplification of ERBB2 (20% of patients) and activating hotspot mutations in PIK3CA (20%), with the latter mutually exclusive to truncating mutations in TSC1. A novel FGFR3 gene fusion was identified in consecutive samples from one patient.Conclusions: Our study demonstrates that ctDNA provides a practical and cost-effective snapshot of driver gene status in metastatic bladder cancer. The identification of a wide spectrum of clinically informative somatic alterations nominates ctDNA as a tool to dissect disease pathogenesis and guide therapy selection in patients with metastatic bladder cancer.

Frequent mutation of the FOXA1 untranslated region in prostate cancer

“…Breast and bladder cancer express the second and third highest levels of FOXA1 , respectively. Using a published bladder cancer focused approach 21 , we assessed the FOXA1 mutation rate in 71 advanced bladder cancer patients. Although the bladder cancer panel achieved high sequencing depth throughout the FOXA1 3′-UTR (Supplementary Fig.…”

Circulating Tumor Cells Identify Patients with Super-High-Risk Non-Muscle-Invasive Bladder Cancer: Updated Outcome Analysis of a Prospective Single-Center Trial

“…Besides, in the last few years, it became clear that specific molecular differences exist between high‐ and low‐grade NMIBC and that the genetic alterations found in high‐grade NMIBC more closely resemble those present in MIBC . Recent studies have demonstrated that cancer‐associated mutations and other DNA alterations can be detected in body fluids, thus providing impetus to the technological advances for circulating tumor DNA analysis in blood and urine from patients with bladder cancer . Given the increasingly complex mutational landscape and intratumor heterogeneity of the disease, it is unlikely that a single biomarker will able to fill the gap in the discrimination of patients at the highest risk of progression to muscle‐invasive disease and/or metastatic dissemination.…”

Using plasma cell‐free DNA to monitor the chemoradiotherapy course of cervical cancer

“…A previous study, that evaluated gene mutations using ddPCR in the plasma of 150 patients with primary invasive cervical cancer, reported that two mutations in the PIK3CA gene, p.E542K and p.E545K were found to be significantly associated with both reduced disease‐free survival and overall survival . Other studies have been confined to measuring cfDNA levels (copies/ml or ng/l) in patient plasma samples or estimating the fraction of ctDNA in cfDNA according to the allelic fractions of somatic autosomal mutations . Our approach makes it possible to determine the mutant fraction of each single position in the target region, and therefrom compare the overall distance of mutation fraction between control sample (WBC) and cfDNA by ECDF and AFD.…”