Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation

Abstract

Acute coronary syndromes (ACS) remain a major cause of worldwide mortality. ACS diagnosis is done by a combination of factors, such as electrocardiogram and plasma biomarkers. These biomarkers, however, lack the power to accurately stratify patients into different risk groups. Instead, we used changes in the circulating cell-free DNA (ccfDNA) methylation profiles to estimate the extent of heart injury and the severity of ACS. Our approach relies on the fact that dying cells in acutely damaged tissue release DNA into the blood, causing an increase in the ccfDNA. In addition, each cell type has a distinct DNA methylation profile. We leverage cell type/state specificity of DNA methylation to deconvolute the cell types of origin for ccfDNA and also find DNA methylation-based biomarkers that stratify patient cohorts. The cohorts consisted of healthy subjects, and patients from three ACS conditions: ST-segment elevation myocardial infarction (STEMI), non-ST-segment elevation myocardial infarction (NSTEMI) and unstable angina (UA). We have used two cohorts of patients - discovery, and validation, both consisting of the same conditions. We have sequenced the ccfDNA from the discovery cohort using Whole Bisulfite Genome Sequencing (WBGS), to obtain an unbiased overview of plasma DNA methylation profiles. We have found a total of 1,614 differential methylated regions (DMRs) in the three ACS groups. Many of the regions are associated with genes involved in cardiovascular conditions and inflammation. Using linear models, we were able to narrow down to 254 DMRs significantly associated with ACS severity. The reduced list of DMRs enabled a more accurate stratification of ACS patients. The predictive power of the DMRs was validated in the confirmation cohort using targeted methylation sequencing of the validation cohort.

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

“…Fast sample prep and sequencing times can allow a complete methylation analysis from sample preparation to computational classification in as little as 1-3 h, enabling real-time medical applications in cancer [11,12]. Because DNA methylation can differentiate non-cancer cell types as well, Nanopore liquid biopsy could be used to monitor collateral damage to adjacent tissue in cancer [23] or urgent conditions in other areas of medicine such as myocardial infarction, sepsis, and COVID-19 [4][5][6]42].…”

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

“…Fast sample prep and sequencing times can allow a complete methylation analysis from sample preparation to computational classification in as little as 1-3 hours, enabling real-time medical applications in cancer (11,12). Because DNA methylation can differentiate non-cancer cell types as well, Nanopore liquid biopsy could be used to monitor collateral damage to adjacent tissue in cancer (23), or urgent conditions in other areas of medicine such as myocardial infarction, sepsis, and COVID-19 (4)(5)(6)41).…”

Comment on: “Plasma Cell-Free DNA Is a Potential Biomarker for Diagnosis of Calcific Aortic Valve Disease”

“…However, it is imperious to adopt a prudent stance when interpreting and evaluating the implications of these results. Further investigation is needed to ascertain the potential of cfDI as not solely a diagnostic indicator but also as a means of monitoring disease progression [7]. In addition to the advantage above, it is worth noting that cfDI has the potential to contribute significantly to the evaluation of disease severity, thereby facilitating healthcare professionals in their pivotal.…”