title: Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells.
abstract: 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.
authors.affiliation: 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Lenz
authors.affiliation: Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Roman
authors.initials: R
authors.lastname: Goetzke
authors.affiliation: 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Bayer Technology Services GmbH, Leverkusen, Germany.
authors.forename: Arne
authors.initials: A
authors.lastname: Schenk
authors.affiliation: Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Schubert
authors.affiliation: Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Veeck
authors.affiliation: Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Hatim
authors.initials: H
authors.lastname: Hemeda
authors.affiliation: Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Koschmieder
authors.affiliation: 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Zenke
authors.affiliation: 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Bayer Technology Services GmbH, Leverkusen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schuppert
authors.affiliation: 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wagner
mesh_terms: D015415:Biomarkers; D002454:Cell Differentiation / Q000235:genetics; D002460:Cell Line; D002478:Cells, Cultured; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D059630:Mesenchymal Stem Cells / Q000378:metabolism; D050814:Octamer Transcription Factor-3 / Q000235:genetics
chemical_list: D015415:Biomarkers; D050814:Octamer Transcription Factor-3; C494173:POU5F1 protein, human