5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic and predictive biomarkers for coronary artery disease

Chaoran Dong,Jian Lin,Hangyu Chen,Feng Gao,Yupeng Liu,Zilong He,Yiming Liang,Jiemei Chen,Haibo Zhu,Jie Long,Qianhui Zhu,Songnian Hu,Yida Tang,Jilin Zheng,Chuan He,Tao Yu

doi:10.1186/s13148-020-0810-2

Abstract

BackgroundThe 5-hydroxymethylcytosine (5hmC) DNA modification is an epigenetic marker involved in a range of biological processes. Its function has been studied extensively in tumors, neurodegenerative diseases, and atherosclerosis. Studies have reported that 5hmC modification is closely related to the phenotype transformation of vascular smooth muscle cells and endothelial dysfunction. However, its role in coronary artery disease (CAD) has not been fully studied.ResultsTo investigate whether 5hmC modification correlates with CAD pathogenesis and whether 5hmC can be used as a biomarker, we used a low-input whole-genome sequencing technology based on selective chemical capture (hmC-Seal) to firstly generate the 5hmC profiles in the circulating cell-free DNA(cfDNA) of CAD patients, including stable coronary artery disease (sCAD) patients and acute myocardial infarction (AMI) patients. We detected a significant difference of 5hmC enrichment in gene bodies from CAD patients compared with normal coronary artery (NCA) individuals. Our results showed that CAD patients can be well separated from NCA individuals by 5hmC markers. The prediction performance of the model established by differentially regulated 5hmc modified genes were superior to common clinical indicators for the diagnosis of CAD (AUC = 0.93) and sCAD (AUC = 0.93). Specially, we found that 5hmC markers in cfDNA showed prediction potential for AMI (AUC = 0.95), which was superior to that of cardiac troponin I, muscle/brain creatine kinase, and myoglobin.ConclusionsOur results suggest that 5hmC markers derived from cfDNA can serve as effective epigenetic biomarkers for minimally noninvasive diagnosis and prediction of CAD.

Highlights

The 5-hydroxymethylcytosine (5hmC) DNA modification is an epigenetic marker involved in a range of biological processes
Since non-invasive biomarkers for coronary artery disease (CAD) diagnosis and prediction are needed and 5hmC is involved in atherosclerosis, we investigate whether 5hmC modification correlates with CAD pathogenesis and whether 5hmC in Cell-free DNA (cfDNA) can be used as a biomarker
Genome-wide 5hmC profiles of cfDNA differ among stable coronary artery disease (sCAD), acute myocardial infarction (AMI), and normal coronary artery (NCA) groups We firstly used a low-input whole-genome sequencing technology based on hmC-Seal technology [14] to generate the 5hmC profile in cfDNA of CAD patients

Summary

Introduction

The 5-hydroxymethylcytosine (5hmC) DNA modification is an epigenetic marker involved in a range of biological processes. Its role in coronary artery disease (CAD) has not been fully studied. Coronary artery disease (CAD) remains a leading cause of mortality worldwide and was responsible for an estimated 8.14 million deaths (16.8%) in 2013 [1]. Clinical diagnosis of CAD is currently based on symptoms, electrocardiograms (ECGs), cardiac markers, stress testing, coronary computed tomographic angiography (CTA), and coronary angiography (CAG) are used for [2,3,4]; all these methods have limitations. Many individuals who undergo invasive CAG are found to have normal coronary arteries [6]. In other noninvasive approaches to diagnose CAD, such as CTA, high sensitivity can only be achieved in the case of severe coronary stenosis, while early-stage atherosclerosis cannot be diagnosed. The dependence on particular equipment and requirement for experience in interpreting the results limits the largescale use of these techniques

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