Next-generation Sequencing of Nonmuscle Invasive Bladder Cancer Reveals Potential Biomarkers and Rational Therapeutic Targets

Abstract

Background

Molecular characterization of nonmuscle invasive bladder cancer (NMIBC) may provide a biologic rationale for treatment response and novel therapeutic strategies.

Objective

To identify genetic alterations with potential clinical implications in NMIBC.

Design, setting, and participants

Pretreatment index tumors and matched germline DNA from 105 patients with NMIBC on a prospective Institutional Review Board-approved protocol underwent targeted exon sequencing analysis in a Clinical Laboratory Improvement Amendments-certified clinical laboratory.

Outcome measurements and statistical analysis

Comutation patterns and copy number alterations were compared across stage and grade. Associations between genomic alterations and recurrence after intravesical bacillus Calmette-Guérin (BCG) were estimated using Kaplan-Meier and Cox regression analyses.

Results and limitations

TERT promoter mutations (73%) and chromatin-modifying gene alterations (69%) were highly prevalent across grade and stage, suggesting these events occur early in tumorigenesis. ERBB2 or FGFR3 alterations were present in 57% of high-grade NMIBC tumors in a mutually exclusive pattern. DNA damage repair (DDR) gene alterations were seen in 30% (25/82) of high-grade NMIBC tumors, a rate similar to MIBC, and were associated with a higher mutational burden compared with tumors with intact DDR genes (p < 0.001). ARID1A mutations were associated with an increased risk of recurrence after BCG (hazard ratio = 3.14, 95% confidence interval: 1.51–6.51, p = 0.002).

Conclusions

Next-generation sequencing of treatment-naive index NMIBC tumors demonstrated that the majority of NMIBC tumors had at least one potentially actionable alteration that could serve as a target in rationally designed trials of intravesical or systemic therapy. DDR gene alterations were frequent in high-grade NMIBC and were associated with increased mutational load, which may have therapeutic implications for BCG immunotherapy and ongoing trials of systemic checkpoint inhibitors. ARID1A mutations were associated with an increased risk of recurrence after BCG therapy. Whether ARID1A mutations represent a predictive biomarker of BCG response or are prognostic in NMIBC patients warrants further investigation.

Patient summary

Analysis of frequently mutated genes in superficial bladder cancer suggests potential targets for personalized treatment and predictors of treatment response, and also may help develop noninvasive tumor detection tests.

Introduction

Of the estimated 429 000 people to be diagnosed with bladder cancer in the industrialized world each year, 70–80% will have nonmuscle invasive bladder cancer (NMIBC) [1], [2]. Half of all NMIBC patients will experience tumor recurrence within 5 yr, and 20–30% will progress to secondary MIBC [3]. Ultimately, as many as 10–15% of patients presenting with NMIBC will die of bladder cancer [4].

Previous investigations into NMIBC genetics have been limited by their inability to comprehensively profile tumors for multiple cancer-associated genes [5]. More recently, MIBC were comprehensively investigated by The Cancer Genome Atlas (TCGA) and other groups using next-generation sequencing (NGS), leading to the identification of potential biomarkers and targets for therapeutic intervention [6], [7]. However, very few NMIBC tumors have been examined with NGS methods to date, and these investigations have been limited by a lack of clinical annotation, the absence of restaging transurethral resection (TUR) to ensure appropriate tumor staging, or a failure to differentiate between primary and recurrent tumors [8], [9], [10], [11].

In this study, we examined primary treatment-naive index tumors from a cohort of patients with NMIBC using a massively parallel, targeted, exon capture-based NGS platform to define the prevalence of genetic alterations and their potential clinical implications.