Evaluation of the Methylation Status of Tumour Suppressor Genes for Predicting Bacillus Calmette-Guérin Response in Patients With T1G3 High-Risk Bladder Tumours

BackgroundBacillus Calmette-Guérin (BCG) is a standard treatment for reducing tumour recurrence and delaying progression of high-risk non–muscle-invasive bladder tumours. However, it is not clear yet which patients are more likely to respond to BCG.ObjectiveTo evaluate the role of the methylation of 25 tumour suppressor genes (TSG) as clinical outcome predictive biomarkers in T1G3 bladder tumours treated with BCG.Design, setting, and participantsA retrospective design included 91 paraffin-embedded tumours of patients with T1G3 primary non–muscle-invasive disease undergoing nonmaintenance BCG treatment.MeasurementsThe methylation status of 25 TSGs was measured using a methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay. Recurrence, progression into muscle-invasive tumours, and disease-specific survival (DSS) rates were analysed using univariate and multivariate tests.Results and limitationsThe genes most frequently methylated included STK11 (94.5%), MSH6 (81.3%), BRCA1 (72.5%), PAX5A (68.1%), MGMT (67.0%), CDH13 (62.6%), and IGSF4 (61.5%). Methylation was newly identified in T1G3 tumours for TP73, MSH6, ESR1, PAX5A, WT1, CD44, ATM, IGSF4, CHFR, BRCA2, THBS1, PYCARD, STK11, and GATA5. Methylation for several TSGs was significantly associated with multifocality and tumour size. Patients with different methylation statuses of TSGs showed differential recurrence rates (PAX6: p = 0.025), progression rates (MSH6: p = 0.040; RB1: p = 0.042; THBS1: p = 0.041; PYCARD: p = 0.048; TP73: p = 0.048; ESR1: p = 0.036; and GATA5: p = 0.019), and DSS rates (GATA5: p = 0.037). Several combinations improved prediction for progression. Multivariate analyses indicated that among the combinations remaining as independent predictors, two genes—MSH6 and THBS1—already provided the most significant predictive assessment for progression (p = 0.004). The major limitation of this study is related to its retrospective design.ConclusionsThe methylation status of TSGs was associated with the clinical outcome of patients with T1G3 tumours undergoing BCG treatment under three clinical end points: recurrence, progression, and DSS. The methylation status of TSGs distinguished patients responding to BCG from those who may require a more aggressive therapeutic intervention.