Exploration of Euchromatin Cell-Free DNA Methylation in Breast Cancer

Abstract

Circulating cell-Free DNA (cfDNA) is emerging as a non-invasive liquid biopsy biomarker for personalized and precision cancer management. While extensive tissue-based DNA methylation profiling at global and gene levels have been documented, studies regarding methylation status of cfDNA at the sub-genome scale as well as correlation with that of tissue-derived genomic DNA have yet to be explored. The ability to specifically interrogate DNA methylation status of the transcriptionally active regions within chromosomes, i.e., euchromatin, not only fulfills the knowledge gap but also provides a much needed longitudinal and real-time insight for early cancer detection and intervention. We have developed a proprietary technology for selective enrichment of euchromatin cfDNA and analyzed the 5-methylcytosine (5-mC) content in these circulating nucleocomplexes. Paired tissue and plasma DNA (n=28) were obtained from breast cancer patients at various stages with ages and genders matched to the control arm (n=21). Quantitative measurement of DNA methylation was determined by ELISA-based assays. Our results revealed significant lower methylation levels from breast cancer cohort as compared to the cancer-free group (P<0.01). Most importantly, the methylation quantification dataset from euchromatin cfDNA strongly correlated with that of tissue genomic DNA (R²=0.72). This is the first report on euchromatin cfDNA methylation and provides promising outcomes for its future clinical application.