Association Of Plasma And Urinary Mutant DNA With Clinical Outcomes In Muscle Invasive Bladder Cancer

Abstract

Muscle Invasive Bladder Cancer (MIBC) has a poor prognosis. Whilst patients can achieve a 6% improvement in overall survival with Neo-Adjuvant Chemotherapy (NAC), many do not respond. Body fluid mutant DNA (mutDNA) may allow non-invasive identification of treatment failure. We collected 248 liquid biopsy samples including plasma, cell pellet (UCP) and supernatant (USN) from spun urine, from 17 patients undergoing NAC. We assessed single nucleotide variants and copy number alterations in mutDNA using Tagged-Amplicon- and shallow Whole Genome- Sequencing. MutDNA was detected in 35.3%, 47.1% and 52.9% of pre-NAC plasma, UCP and USN samples respectively, and urine samples contained higher levels of mutDNA (p = <0.001). Longitudinal mutDNA demonstrated tumour evolution under the selective pressure of NAC e.g. in one case, urine analysis tracked two distinct clones with contrasting treatment sensitivity. Of note, persistence of mutDNA detection during NAC predicted disease recurrence (p = 0.003), emphasising its potential as an early biomarker for chemotherapy response.

Comprehensive characterisation of cell-free tumour DNA in plasma and urine of patients with renal tumours

“…Comparison of plasma, USN and UCP data did not reveal a clear relationship in detection amongst these compartments (Fig. 2C), confirming previous observations in bladder cancer [13,21] . Considering only those patients for which we had access to plasma and urine, the detection rate increased to 9/21 (42.9%).…”

“…As sampling of biofluids collected in close proximity to the tumour site may improve detection [13,19] , we analysed urine supernatant (USN) samples from 21 DIAMOND cohort patients. Applying tMAD to urine for the first time (Fig.…”

“…In addition to USN, we had access to urine cell pellet (UCP) DNA for these 21 patients. UCP DNA is not cell-free but allows non-invasive detection of tumour DNA [13,20] . UCP tMAD analysis revealed 3/20 (15%) patients with detected ctDNA, including one with localised ccRCC, the largest tumour of the cohort with a diameter of 23cm.…”

“…As such, there remains an unmet need for the characterisation of the levels, and potential clinical utility, of ctDNA in renal cancers of differing stage and subtype. Furthermore, whilst evidence suggests ctDNA in the urine can be informative in urological cancers [12,13] , no previous study has assessed the presence of ctDNA in the urine of RCC patients. Here we aimed to determine the presence, levels, heterogeneity and potential clinical applications of ctDNA in plasma and urine of 90 patients with renal tumours ranging from benign oncocytomas through to metastatic RCCs using both untargeted genome-wide, and targeted sequencing approaches.…”

Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA: a 23‐gene panel with utility for non‐invasive diagnosis and risk stratification

“…Other workers have also utilised cpDNA and targeted deep sequencing for the identification of genomic alterations in urine samples from patients with UBC [7,9,30]; however, few studies have directly compared cpDNA and cfDNA by targeted deep sequencing in this setting [11,31]. Although cpDNA is conventionally utilised for urinary biomarker studies (principally due to higher yields than cfDNA), we have shown that SM detection in urinary cfDNA works as well as (or marginally better than) SM detection in cpDNA.…”