Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells

Michael Lenz, Roman Goetzke, Arne Schenk, Claudia Schubert, Jürgen Veeck, Hatim Hemeda, Steffen Koschmieder, Martin Zenke, Andreas Schuppert, Wolfgang Wagner*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Quality control of human induced pluripotent stem cells (iPSCs) can be performed by several methods. These methods are usually relatively labor-intensive, difficult to standardize, or they do not facilitate reliable quantification. Here, we describe a biomarker to distinguish between pluripotent and non-pluripotent cells based on DNA methylation (DNAm) levels at only three specific CpG sites. Two of these CpG sites were selected by their discriminatory power in 258 DNAm profiles - they were either methylated in pluripotent or non-pluripotent cells. The difference between these two β-values provides an Epi-Pluri-Score that was validated on independent DNAm-datasets (264 pluripotent and 1,951 non-pluripotent samples) with 99.9% specificity and 98.9% sensitivity. This score was complemented by a third CpG within the gene POU5F1 (OCT4), which better demarcates early differentiation events. We established pyrosequencing assays for the three relevant CpG sites and thereby correctly classified DNA of 12 pluripotent cell lines and 31 non-pluripotent cell lines. Furthermore, DNAm changes at these three CpGs were tracked in the course of differentiation of iPSCs towards mesenchymal stromal cells. The Epi-Pluri-Score does not give information on lineage-specific differentiation potential, but it provides a simple, reliable, and robust biomarker to support high-throughput classification into either pluripotent or non-pluripotent cells.

Original languageEnglish
Pages (from-to)8973
JournalScientific Reports
Publication statusPublished - 2015


  • Biomarkers
  • Cell Differentiation
  • Cell Line
  • Cells, Cultured
  • CpG Islands
  • DNA Methylation
  • Epigenesis, Genetic
  • Humans
  • Induced Pluripotent Stem Cells
  • Mesenchymal Stromal Cells
  • Octamer Transcription Factor-3


Dive into the research topics of 'Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells'. Together they form a unique fingerprint.

Cite this