Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

Abstract

PURPOSE Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy. PATIENTS AND METHODS We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses. RESULTS Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence ( P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging ( P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods. CONCLUSION ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.

Liquid Biopsies to Select Patients for Perioperative Chemotherapy in Muscle-invasive Bladder Cancer: A Systematic Review

“…Christensen et al [46] presented promising results. They analyzed longitudinal cfDNA samples of 68 patients with localized MIBC before NAC, after NAC, and after RC.…”

Low Abundance of Circulating Tumor DNA in Localized Prostate Cancer

“…Comprehensive cancer panels, as well as whole genome and exome sequencing, can also be used to interrogate somatic copy number alterations (SCNAs) from plasma DNA, with varying resolution depending on the sequence modality and depth [18,19]. Personalized, bespoke sequencing assays have shown sensitivity for the detection of urothelial and colorectal cancers [20,21]. The success of these approaches has been thought to depend upon high tumor burden and the propensity of the tumor to shed circulating tumor DNA (ctDNA) into the bloodstream with proportional contribution of subclones to the ctDNA pool [22,23].…”

Genomic profile of urine has high diagnostic sensitivity compared to cytology in non‐invasive urothelial bladder cancer

“…A recent study showed ultra-deep sequencing (median 10500-fold coverage depth) of plasma detected tumor-identical mutations in localized advanced BC. 30 To detect low VAF mutations in plasma cfDNA, high-coverage depth data would be need. Our data suggested that high VAF mutant could be detected in urine of urothelial BC, but not in plasma.…”