Differential X Chromosome Inactivation Patterns During the Propagation of Human Induced Pluripotent Stem Cells

Keio J Med. 2017 Mar 25;66(1):1-8. doi: 10.2302/kjm.2016-0015-OA. Epub 2017 Jan 20.


Human induced pluripotent stem cells (hiPSCs) represent a potentially useful tool for studying the molecular mechanisms of disease thanks to their ability to generate patient-specific hiPSC clones. However, previous studies have reported that DNA methylation profiles, including those for imprinted genes, may change during passaging of hiPSCs. This is particularly problematic for hiPSC models of X-linked disease, because unstable X chromosome inactivation status may affect the detection of phenotypes. In the present study, we examined the epigenetic status of hiPSCs derived from patients with Rett syndrome, an X-linked disease, during long-term culture. To analyze X chromosome inactivation, we used a methylation-specific polymerase chain reaction (MSP) to assay the human androgen receptor locus (HUMARA). We found that single cell-derived hiPSC clones exhibit various states of X chromosome inactivation immediately after clonal isolation, even when established simultaneously from a single donor. X chromosome inactivation states remain variable in hiPSC clones at early passages, and this variability may affect cellular phenotypes characteristic of X-linked diseases. Careful evaluation of X chromosome inactivation in hiPSC clones, particularly in early passages, by methods such as HUMARA-MSP, is therefore important when using patient-specific hiPSCs to model X-linked disease.

MeSH terms

  • Cell Differentiation
  • Cell Proliferation
  • Cellular Reprogramming
  • Child
  • Clone Cells
  • DNA Methylation
  • Epigenesis, Genetic*
  • Female
  • Fibroblasts / metabolism
  • Fibroblasts / pathology
  • Genetic Loci
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Humans
  • Induced Pluripotent Stem Cells / metabolism*
  • Induced Pluripotent Stem Cells / pathology
  • Karyotyping
  • Lentivirus / genetics
  • Lentivirus / metabolism
  • Polymerase Chain Reaction / methods
  • Primary Cell Culture
  • Receptors, Androgen / genetics*
  • Receptors, Androgen / metabolism
  • Rett Syndrome / genetics*
  • Rett Syndrome / metabolism
  • Rett Syndrome / pathology
  • Skin / metabolism
  • Skin / pathology
  • Transduction, Genetic
  • Twins, Monozygotic
  • X Chromosome Inactivation*


  • AR protein, human
  • Receptors, Androgen