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

Abstract

Background: The 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. Results: To 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. Conclusions: Our results suggest that 5hmC markers derived from cfDNA can serve as effective epigenetic biomarkers for minimally noninvasive diagnosis and prediction of CAD.

A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation

“…Previous studies have shown that 5hmC-modified loci can serve as excellent biomarkers for the diagnosis and prognosis of human diseases including cancer [19][20][21][23][24][25][26] . These data suggest that 5hmC may mark specific genes or promoter/enhancers in disease samples that undergo concerted changes representative of the disease pathogenesis in question.…”

“…Moreover, 5hmC modifications co-localize with gene bodies and enhancers are known to mark for transcription activation 6,17,18 . Notably, in several recent studies, the 5hmC-modified loci have been shown to serve as informative biomarkers for a variety of human cancers and other complex diseases [19][20][21][22][23][24][25][26] . Interestingly, two early studies that investigated the 5hmC in circulating cell-free DNA from patients with solid tumors suggested that 5hmC had the potential to be specific biomarkers for human cancers arising from different tissue origins 19,20 .…”

5‐Hydroxymethylcytosine signature in circulating cell‐free DNA as a potential diagnostic factor for early‐stage colorectal cancer and precancerous adenoma

“…The DNA modification of 5-hydroxymethylcytosine (5hmC) is a significant DNA epigenetic alteration that affects global gene expression and is involved in tumors, neurodegenerative diseases, and atherosclerosis [12][13][14]. Genome-wide 5hmC distributions and dynamics in various human tissues have shown that it is mainly enriched in the gene body region and has a potential role in gene regulation in mammalian development and cell differentiation [15]. 5hmC was recently determined to be a potential cfDNA biomarker for nonsmall-cell lung cancer and esophageal cancer [16,17].…”

Cancer Biomarkers Discovery of Methylation Modification With Direct High-Throughput Nanopore Sequencing

“…In the detection of 5hmC, Han et al (2016) developed 5hmC selective chemical labeling technology (hmC-Seal) by combining chemical synthesis technology with modern biological technology. It opens the door for the research and clinical transformation of 5hmc ( Gao et al, 2019 ; Dong et al, 2020 ). However, this method is unable to obtain specific 5hmc modification sites at a single-base level.…”