ASCO 2022: Exploratory Data From a Prospective Collection of Plasma Testing Cell-Free Methylated DNA as a Predictor of Response to Neoadjuvant Chemotherapy for Patients With Muscle-Invasive Bladder Cancer in SWOG S1314

(UroToday.com) Though platinum-based neoadjuvant chemotherapy is a standard of care in muscle-invasive bladder cancer, the overall benefit from this toxic therapy is modest, and robust biomarkers to identify patients that benefit the most are lacking. Several prior studies have identified factors like ERCC2 mutation, ERBB2 mutation, or a p53-like molecular subtype as potentially related to response. The randomized phase 2 SWOG S1314 study was designed to specifically evaluate a gene expression-based approach (Coexpression extrapolation or COXEN) as a predictor of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer. The schema of this trial is shown below.

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In this presentation, Dr. Flaig presented exploratory data from prospective collection of plasma to test the hypothesis that cell-free methylated DNA (cfmeDNA) could predict responders to neoadjuvant chemotherapy. This biomarker has previously been studied as a marker for cancer detection or minimal residual disease in other contexts. Specifically, cfmeDNA was isolated from 73 pre-treatment (C1D1) and 57 on-treatment (C2D1) plasma samples, bisulfite converted, and analyzed using bisulfite conversion and the Infinium MethylationEPIC BeadChip array, which assays 850,000 methylation sites across the genome.

 

As a feasibility study, the authors showed that reasonable results could be obtained using yields of 10-50 ng of DNA isolated from plasma, which is much lower than the quanitities typically isolated from tissue (500 ng or more).

 

The characteristics of the patients analyzed in this exploratory biomarker study are shown below. Techincal quality control data such as yields of cell-free DNA and number of high quality probes on the methylation array were comparable between response groups.

 

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No single methylation locus statistically correlated with response to neoadjuvant chemotherapy after adjusting for multiple testing. However, when utilizing the the 500 most-differentially methylated DNA loci and t-districuted stochastic neighbor embedding (t-SNE) to dimensionally reduce the 850,000 probe sets, the authors found that these 500 loci somewhat separated out non-responders from responders. To build on this finding, they created an “mR-score” using random forest machine learning applied to methylation levels at all 850,000 assayed genomic loci.

 

The mR-score was higher in non-responders relative to patients experiencing a complete or partial response, with an AUC of 63.6%.

 

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cfmeDNA profiles using the mR-score did not seem to fluctuate drastically with one cycle of chemotherapy.

 

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Interestingly, the authors also determined the percentage of circulating methylated DNA originated in the bladder using previously published tissue methylation profiles. The percentage of circulating bladder DNA did not seem to correlate with the mR-score, suggesting that this metric could be an independent biomarker for response to chemotherapy.

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Overall, when stratifying the patients assayed in this study by pre-treatment mR-score as well as proportion of circulating bladder DNA, 79% of patients were correctly classified into their chemotherapy response category. Dr. Flaig concluded that this exploratory study provides technical proof of principle for cfmeDNA as a response predictor for neoadjuvant chemotherapy in bladder cancer, but this requires future validation in larger patient cohorts. If validated, this may be an especially useful tool across multiple disease settings, especially the metastatic setting where tissue biopsy is performed less frequently and circulating biomarkers may have greater applicability.

 

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Presented by: Thomas Flaig, MD, Medical Oncologist and Vice-Chancellor of Research for the University of Colorado Denver and University of Colorado Anschutz Medical Campus, Denver, CO 

Written by: Alok K. Tewari, MD, PhD, medical oncologist at the Dana-Farber Cancer Institute, @aloktewar on Twitter during the 2022 American Society of Clinical Oncology (ASCO) Annual Meeting, Chicago, IL, Fri, June 3 – Mon, June 7, 2022.