Circulating cell-free methylated DNA (cfmeDNA) to predict postoperative recurrence in patients with muscle-invasive bladder cancer (MIBC).

Authors

null

Pier Vitale Nuzzo

Dana-Farber Cancer Institute, Boston, MA

Pier Vitale Nuzzo , Sandor Spisak , Norbert Solymosi , Ankur Chakravarthy , Shu Yi Shen , Mark Pomerantz , Francesco Boccardo , Amin Nassar , Gwo-Shu Mary Lee , Guru Sonpavde , Toni K. Choueiri , Daniel De Carvalho , Matthew L Freedman

Organizations

Dana-Farber Cancer Institute, Boston, MA, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, Centre for Bioinformatics, University of Veterinary Medicine Budapest, Hungary, Budapest, Hungary, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Academic Unit of Medical Oncology, IRCCS San Martino University Hospital - IST National Cancer Research Institute, Genoa, Italy, Brigham and Women's Hospital, Boston, MA, Department of Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA

Research Funding

Other

Background: CfmeDNA is a promising non-invasive biomarker to assess solid tumor burden: i) CpG island methylation changes in cfDNA are stable ii) methylation is tissue- and tumor- specific iii) methylation target size is larger and more sensitively detected than genomic alterations. CfmeDNA Immunoprecipitation and high throughput sequencing (cfMeDIP-seq) is an innovative assay for genome-wide bisulfite-free plasma DNA methylation profiling, that permits CpG enrichment. We tested the feasibility of cfmeDNA to predict recurrence of MIBC post- radical cystectomy (RC). Methods: We selected 12 pts who underwent RC for MIBC: 6 pts who had recurrent disease within 2-3yrs after RC (A) and 6 pts who did not (B). 119 healthy pts without BC were controls. cfDNA isolated from 1ml of plasma samples collected after RC and before recurrence (A) or during follow-up in those who did not recur (B) was analyzed by the cfMeDIP-seq using 10ng cfDNA. The data were analyzed using the MEDIPS program and differentially methylated regions (DMR) between the cohorts were studied. ENCODE ChIP-seq analytical pipeline was used for fastq file processing and peak calling. Results: The average cfDNA isolated from 1ml of plasma was 13.1 ng (6.4-19.7) in A and 17.1 ng (13.6-21.2) in B. The median time from RC to plasma collection were respectively 9.3 mos (3.4-91.3) vs 12.3 mos (2.9-150). Median time from plasma collection to recurrence was 21.9 mos (0.25-141.3). We identified ~137,000 peaks in ≥1 sample. The supervised classification identified 61 DMR (FDR<0.050), predominantly located in intergenic region, which distinguished A from B. Randomized sample tests proved the discriminatory power of the identified set. Supervised analysis comparing the status of the identified DMRs relative to healthy controls showed 28 regions were differentially methylated (logFC > +/- 1, FDR < 0.05). The study is limited by retrospective design and sample size. Conclusions: This is the first study to demonstrate that cfmeDNA can be readily harvested from MIBC pts to detect cancer-specific methylation patterns and predict recurrence post-RC. Prospective validation will enable the selection of suitable pts for adjuvant therapy.

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Abstract Details

Meeting

2019 Genitourinary Cancers Symposium

Session Type

Poster Session

Session Title

Poster Session B: Prostate Cancer; Urothelial Carcinoma; Penile, Urethral, Testicular, and Adrenal Cancers

Track

Urothelial Carcinoma,Prostate Cancer,Penile, Urethral, Testicular, and Adrenal Cancers

Sub Track

Urothelial Carcinoma

Citation

J Clin Oncol 37, 2019 (suppl 7S; abstr 454)

DOI

10.1200/JCO.2019.37.7_suppl.454

Abstract #

454

Poster Bd #

K3

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