DNA methylation profiling allows for characterization of atrial and ventricular cardiac tissues and hiPSC-CMs

Clin Epigenetics. 2019 Jun 11;11(1):89. doi: 10.1186/s13148-019-0679-0.


Background: Cardiac disease modelling using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) requires thorough insight into cardiac cell type differentiation processes. However, current methods to discriminate different cardiac cell types are mostly time-consuming, are costly and often provide imprecise phenotypic evaluation. DNA methylation plays a critical role during early heart development and cardiac cellular specification. We therefore investigated the DNA methylation pattern in different cardiac tissues to identify CpG loci for further cardiac cell type characterization.

Results: An array-based genome-wide DNA methylation analysis using Illumina Infinium HumanMethylation450 BeadChips led to the identification of 168 differentially methylated CpG loci in atrial and ventricular human heart tissue samples (n = 49) from different patients with congenital heart defects (CHD). Systematic evaluation of atrial-ventricular DNA methylation pattern in cardiac tissues in an independent sample cohort of non-failing donor hearts and cardiac patients using bisulfite pyrosequencing helped us to define a subset of 16 differentially methylated CpG loci enabling precise characterization of human atrial and ventricular cardiac tissue samples. This defined set of reproducible cardiac tissue-specific DNA methylation sites allowed us to consistently detect the cellular identity of hiPSC-CM subtypes.

Conclusion: Testing DNA methylation of only a small set of defined CpG sites thus makes it possible to distinguish atrial and ventricular cardiac tissues and cardiac atrial and ventricular subtypes of hiPSC-CMs. This method represents a rapid and reliable system for phenotypic characterization of in vitro-generated cardiomyocytes and opens new opportunities for cardiovascular research and patient-specific therapy.

Keywords: 450K array; Bisulfite pyrosequencing; Cardiac tissue-specific DNA methylation; DNA methylation; Engineered heart tissue (EHT); Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • CpG Islands
  • DNA Methylation*
  • Female
  • Heart Atria / chemistry
  • Heart Atria / cytology*
  • Heart Defects, Congenital / genetics
  • Heart Defects, Congenital / pathology*
  • Heart Ventricles / chemistry
  • Heart Ventricles / cytology*
  • Humans
  • Induced Pluripotent Stem Cells / chemistry
  • Induced Pluripotent Stem Cells / cytology
  • Male
  • Models, Biological
  • Myocytes, Cardiac / chemistry
  • Myocytes, Cardiac / cytology*
  • Organ Specificity
  • Sequence Analysis, DNA
  • Tissue Engineering