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.

Keywords: AT-Rich interaction domain 1A; Bacillus Calmette-Guérin; DNA damage repair; Genomics; Immunotherapy; Nonmuscle invasive bladder cancer; Targeted therapy.

Fig. 1

An overview of the genomic landscape of NMIBC by grade and stage with comparison to MIBC. HGTa = high-grade Ta; LGTa = low-grade Ta; MIBC = muscle invasive bladder cancer; MSK-IMPACT = Memorial Sloan Kettering Cancer Center-Integrated Mutation Profiling of Actionable Cancer Targets; NMIBC = nonmuscle invasive bladder cancer; TCGA = The Cancer Genome Atlas.

Fig. 2

(A) A comparison of DNA damage repair gene alterations found in high and low grade NMIBC. (B) Box and whisker plot comparing mutational burden per megabase between low-grade NMIBC (n = 23), high-grade NMIBC (n = 82), and MIBC (n = 40). (C) Box and whisker plot comparing mutational burden per megabase between high-grade NMIBC tumors with altered and unaltered DNA damage repair genes (n = 82). DDR = DNA damage repair; MB = megabase; MIBC = muscle invasive bladder cancer; MSK-IMPACT = Memorial Sloan Kettering Cancer Center-Integrated Mutation Profiling of Actionable Cancer Targets; NMIBC = nonmuscle invasive bladder cancer.

Fig. 3

(A) Volcano plot of effect size (log odds ratio) by significance (−log10 p value) for the association between specific genomic alterations and recurrence after bacillus Calmette-Guérin (BCG). Results are from Cox regression analysis (n = 62). The horizontal dotted line indicates an adjusted p-value <0.05. Bubble size is proportional to the total number of alterations. (B) Kaplan-Meier curve for recurrence after BCG Therapy for tumors with ARID1A truncating mutations compared to ARID1A wild-type (n = 62).