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.

Molecular changes during progression from nonmuscle invasive to advanced urothelial carcinoma

“…Previous studies have indicated that homozygous deletions of CDKN2A , a hallmark of advanced Uro tumors, correlate with progression and occur late in development . We did not observe this pattern, possibly due to difficulty to discriminate homozygous loss from single‐copy loss of chromosome 9, a universal event also in very early bladder tumors . To definitively test the accuracy of inferring copy number alterations would require copy‐number data from a similar series of recurrences, which was not possible due to the quality and amount of DNA obtained.…”

Genomic landscape of inverted urothelial papilloma and urothelial papilloma of the bladder

“…Only one of the cases, a UP, harbored oncogenic FGFR3 or TERT promoter mutations. This tumor, which also had oncogenic PIK3CA , KMT2D , and CDKN1A mutations, had a mutational profile common to that observed in urothelial carcinoma . While morphologic evaluation of this tumor, which consisted of a single small papillary lesion, was compatible with the diagnosis of papilloma, it arose in a patient who had several low‐grade non‐invasive papillary urothelial carcinomas prior and subsequent to the index UP tumor.…”

Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency

“…We also hypothesise that mutations in DNA repair genes play a larger role than we detected. Mutations in ERCC2 were reported recently in 11 of 32 high-grade Ta samples (Pietzak et al, 2017). We found one missense mutation in ERCC2 , one in ATM , one in FANCD2 and two in FANCM in exome-sequenced samples.…”