Genome-wide DNA methylation encodes cardiac transcriptional reprogramming in human ischemic heart failure

Lab Invest. 2019 Mar;99(3):371-386. doi: 10.1038/s41374-018-0104-x. Epub 2018 Aug 8.

Abstract

Ischemic cardiomyopathy (ICM) is the clinical endpoint of coronary heart disease and a leading cause of heart failure. Despite growing demands to develop personalized approaches to treat ICM, progress is limited by inadequate knowledge of its pathogenesis. Since epigenetics has been implicated in the development of other chronic diseases, the current study was designed to determine whether transcriptional and/or epigenetic changes are sufficient to distinguish ICM from other etiologies of heart failure. Specifically, we hypothesize that genome-wide DNA methylation encodes transcriptional reprogramming in ICM. RNA-sequencing analysis was performed on human ischemic left ventricular tissue obtained from patients with end-stage heart failure, which enriched known targets of the polycomb methyltransferase EZH2 compared to non-ischemic hearts. Combined RNA sequencing and genome-wide DNA methylation analysis revealed a robust gene expression pattern consistent with suppression of oxidative metabolism, induced anaerobic glycolysis, and altered cellular remodeling. Lastly, KLF15 was identified as a putative upstream regulator of metabolic gene expression that was itself regulated by EZH2 in a SET domain-dependent manner. Our observations therefore define a novel role of DNA methylation in the metabolic reprogramming of ICM. Furthermore, we identify EZH2 as an epigenetic regulator of KLF15 along with DNA hypermethylation, and we propose a novel mechanism through which coronary heart disease reprograms the expression of both intermediate enzymes and upstream regulators of cardiac metabolism such as KLF15.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Animals
  • Cell Line
  • CpG Islands
  • DNA Methylation*
  • Enhancer of Zeste Homolog 2 Protein / genetics
  • Enhancer of Zeste Homolog 2 Protein / metabolism
  • Epigenesis, Genetic
  • Gene Expression Profiling
  • Genome, Human
  • Heart Failure / genetics*
  • Heart Failure / metabolism
  • Heart Ventricles / metabolism
  • Humans
  • Kruppel-Like Transcription Factors / genetics
  • Kruppel-Like Transcription Factors / metabolism
  • Male
  • Middle Aged
  • Models, Cardiovascular
  • Myocardial Ischemia / genetics*
  • Myocardial Ischemia / metabolism
  • Myocardium / metabolism
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Rats
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Sequence Analysis, RNA

Substances

  • KLF15 protein, human
  • Kruppel-Like Transcription Factors
  • Nuclear Proteins
  • Recombinant Proteins
  • EZH2 protein, human
  • Enhancer of Zeste Homolog 2 Protein