DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling

Clin Epigenetics. 2018 Jan 29;10:13. doi: 10.1186/s13148-018-0440-0. eCollection 2018.


Background: Genetic predisposition and epigenetic alterations are both considered to contribute to sporadic neurodegenerative diseases (NDDs) such as Parkinson's disease (PD). Since cell reprogramming and the generation of induced pluripotent stem cells (iPSCs) are themselves associated with major epigenetic remodeling, it remains unclear to what extent iPSC-derived neurons lend themselves to model epigenetic disease-associated changes. A key question to be addressed in this context is whether iPSC-derived neurons exhibit epigenetic signatures typically observed in neurons derived from non-reprogrammed human embryonic stem cells (hESCs).

Results: Here, we compare mature neurons derived from hESC and isogenic human iPSC generated from hESC-derived neural stem cells. Genome-wide 450 K-based DNA methylation and HT12v4 gene array expression analyses were complemented by a deep analysis of selected genes known to be involved in NDD. Our studies show that DNA methylation and gene expression patterns of isogenic hESC- and iPSC-derived neurons are markedly preserved on a genome-wide and single gene level.

Conclusions: Overall, iPSC-derived neurons exhibit similar DNA methylation patterns compared to isogenic hESC-derived neurons. Further studies will be required to explore whether the epigenetic patterns observed in iPSC-derived neurons correspond to those detectable in native brain neurons.

Keywords: DNA methylation; Isogenic stem cells; iPS cell-derived neurons.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation
  • Cells, Cultured
  • DNA Methylation*
  • Epigenesis, Genetic
  • Gene Expression Profiling
  • Human Embryonic Stem Cells / chemistry
  • Human Embryonic Stem Cells / cytology*
  • Humans
  • Induced Pluripotent Stem Cells / chemistry
  • Induced Pluripotent Stem Cells / cytology*
  • Neurons / chemistry*
  • Oligonucleotide Array Sequence Analysis
  • Sequence Analysis, DNA
  • alpha-Synuclein / genetics


  • SNCA protein, human
  • alpha-Synuclein