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Investigating Coronary Artery Disease methylome through targeted bisulfite sequencing.

Authors
  • Ghose, Subhoshree1
  • Ghosh, Sourav1
  • Tanwar, Vinay Singh1
  • Tolani, Priya2
  • Kutum, Rintu1
  • Sharma, Anju2
  • Bhardwaj, Nitin2
  • Shamsudheen, K V1
  • Verma, Ankit2
  • Jayarajan, Rijith2
  • Dash, Debasis1
  • Sivasubbu, Sridhar1
  • Scaria, Vinod1
  • Seth, Sandeep3
  • Sengupta, Shantanu4
  • 1 CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. , (India)
  • 2 CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India. , (India)
  • 3 Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India. , (India)
  • 4 CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India. Electronic address: [email protected] , (India)
Type
Published Article
Journal
Gene
Publication Date
Dec 30, 2019
Volume
721
Pages
144107–144107
Identifiers
DOI: 10.1016/j.gene.2019.144107
PMID: 31499127
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Gene environment interactions leading to epigenetic alterations play pivotal role in the pathogenesis of Coronary Artery Disease (CAD). Altered DNA methylation is one such epigenetic factor that could lead to altered disease etiology. In this study, we comprehensively identified methylation sites in several genes that have been previously associated with young CAD patients. The study population consisted of 42 healthy controls and 33 young CAD patients (age group <50 years). We performed targeted bisulfite sequencing of promoter as well as gene body regions of several genes in various pathways like cholesterol synthesis and metabolism, endothelial dysfunction, apoptosis, which are implicated in the development of CAD. We observed that the genes like GALNT2, HMGCR were hypermethylated in the promoter whereas LDLR gene promoter was hypomethylated indicating that intracellular LDL uptake was higher in CAD patients. Although APOA1 did not show significant change in methylation but APOC3 and APOA5 showed variation in methylation in promoter and exonic regions. Glucokinase (GCK) and endothelial nitric oxide synthase 3 (NOS3) were hyper methylated in the promoter. Genes involved in apoptosis (BAX/BCL2/AKT2) and inflammation (PHACTR1/LCK) also showed differential methylation between controls and CAD patients. A combined analysis of the methylated CpG sites using machine learning tool revealed 14 CpGs in 11 genes that could discriminate CAD cases from controls with over 93% accuracy. This study is unique because it highlights important gene methylation alterations which might predict the risk of young CAD in Indian population. Large scale studies in different populations would be important for validating our findings and understanding the epigenetic events associated with CAD. Copyright © 2019 Elsevier B.V. All rights reserved.

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