The diagnostic potential of plaque-specific methylation patterns in cell-free dna

Abstract

Background and Aims : There is an urgent and unmet need for early, non-invasive diagnosis of atherosclerosis that can identify high-risk patients with potentially symptomatic plaques. Recent breakthroughs in the use of circulating fragments of cell-free DNA (cfDNA), have provided major advances in early cancer detection. Furthermore, it has been shown that, using tissue-specific methylation patterns, the contribution of different tissue origins to cfDNA can be quantified. Here we aim to identify plaque-specific methylation patterns and unravel the biological processes behind this epigenetic signature. We hypothesize that an increased contribution of plaque-derived cfDNA, as a proxy for the accumulation of atherosclerotic plaque, can be measured in cardiovascular disease patients.Methods: DNA methylation patterns were obtained for plaque samples from 50 female and 50 male patients that underwent carotid endarterectomy (CEA) from the Athero-Express Biobank using the Infinium HumanMethylation450 Beadchip Array. cfDNA methylation from 18 patients, spanning three cardiovascular clinical cohorts, was measured using the NEBNext Enzymatic Methyl-seq kit.Results: We were able to identify a plaque-specific methylation signature encompassing 200 CpG sides, of which a portion was found to be involved in atherosclerotic processes. Furthermore, we built a comprehensive human methylation atlas using methylation data on 18 different tissue and cell types, including plaque, which is used for the deconvolution of cfDNA.Conclusions: Our plaque-centric methylation atlas together with our well-established biobanks, offer the unique opportunity to investigate cfDNA composition in patients spanning various types of cardiovascular disease. We believe this comprehensive methylation framework would help unravel the potential of cfDNA as an innovative non-invasive biomarker for cardiovascular disease. Background and Aims : There is an urgent and unmet need for early, non-invasive diagnosis of atherosclerosis that can identify high-risk patients with potentially symptomatic plaques. Recent breakthroughs in the use of circulating fragments of cell-free DNA (cfDNA), have provided major advances in early cancer detection. Furthermore, it has been shown that, using tissue-specific methylation patterns, the contribution of different tissue origins to cfDNA can be quantified. Here we aim to identify plaque-specific methylation patterns and unravel the biological processes behind this epigenetic signature. We hypothesize that an increased contribution of plaque-derived cfDNA, as a proxy for the accumulation of atherosclerotic plaque, can be measured in cardiovascular disease patients. Methods: DNA methylation patterns were obtained for plaque samples from 50 female and 50 male patients that underwent carotid endarterectomy (CEA) from the Athero-Express Biobank using the Infinium HumanMethylation450 Beadchip Array. cfDNA methylation from 18 patients, spanning three cardiovascular clinical cohorts, was measured using the NEBNext Enzymatic Methyl-seq kit. Results: We were able to identify a plaque-specific methylation signature encompassing 200 CpG sides, of which a portion was found to be involved in atherosclerotic processes. Furthermore, we built a comprehensive human methylation atlas using methylation data on 18 different tissue and cell types, including plaque, which is used for the deconvolution of cfDNA. Conclusions: Our plaque-centric methylation atlas together with our well-established biobanks, offer the unique opportunity to investigate cfDNA composition in patients spanning various types of cardiovascular disease. We believe this comprehensive methylation framework would help unravel the potential of cfDNA as an innovative non-invasive biomarker for cardiovascular disease.