Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer.

Objective: Mutations in cell-free circulating DNA (cfDNA) have been studied for tracking disease relapse in colorectal cancer (CRC). This approach requires personalised assay design due to the lack of universally mutated genes. In contrast, early methylation alterations are restricted to defined genomic loci allowing comprehensive assay design for population studies. Our objective was to identify cancer-specific methylated biomarkers which could be measured longitudinally in cfDNA (liquid biopsy) to monitor therapeutic outcome in patients with metastatic CRC (mCRC).
Design: Genome-wide methylation microarrays of CRC cell lines (n=149) identified five cancer-specific methylated loci ( EYA4 , GRIA4 , ITGA4 , MAP3K14-AS1, MSC ). Digital PCR assays were employed to measure methylation of these genes in tumour tissue DNA (n=82) and cfDNA from patients with mCRC (n=182). Plasma longitudinal assessment was performed in a patient subset treated with chemotherapy or targeted therapy.
Results: Methylation in at least one marker was detected in all tumour tissue samples and in 156 mCRC patient cfDNA samples (85.7%). Plasma marker prevalence was 71.4% for EYA4 , 68.5% for GRIA4 , 69.7% for ITGA4 , 69.1% for MAP3K14-AS1% and 65.1% for MSC . Dynamics of methylation markers was not affected by treatment type and correlated with objective tumour response and progression-free survival.
Conclusion: This five-gene methylation panel can be used to circumvent the absence of patient-specific mutations for monitoring tumour burden dynamics in liquid biopsy under different therapeutic regimens. This method might be proposed for assessing pharmacodynamics in clinical trials or when conventional imaging has limitations.
Competing Interests: Competing interests: AB reports personal fees (scientific advisory board member) from Horizon Discovery, personal fees (scientific advisory board member) from Biocartis, personal fees (Consultant) from Novartis, personal fees (Consultant) from Roche, personal fees (Consultant) from Illumina. AB and FDN reports grants from Trovagene, outside the submitted work. In addition, FDN and PZ have a patent 102017000072650 pending. All the other authors have nothing to disclose.
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