title: Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors.
abstract: The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.
authors.affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Morphology, Piracicaba Dental School, University of Campinas, Piracicaba, SP Brazil.
authors.forename: Aline C
authors.initials: AC
authors.lastname: Planello
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario M4G 0A3 Canada ; Center of Stem Cell and Developmental Biology, Zhejiang University, Hangzhou, Zhejiang Province 310058 China.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Ji
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario M4G 0A3 Canada ; National Cancer Institute, NIH, Bethesda, MD 20892 USA.
authors.forename: Vivek
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada.
authors.forename: Rajat
authors.initials: R
authors.lastname: Singhania
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario M4G 0A3 Canada.
authors.forename: Faridah
authors.initials: F
authors.lastname: Mbabaali
authors.affiliation: Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Müller
authors.affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2 M9 Canada.
authors.forename: Javier A
authors.initials: JA
authors.lastname: Alfaro
authors.affiliation: Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany ; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria ; Department of Laboratory Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria.
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
authors.affiliation: Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2 M9 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2 M9 Canada.
authors.forename: Daniel D
authors.initials: DD
authors.lastname: De Carvalho
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario M4G 0A3 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2 M9 Canada.
authors.forename: Nizar N
authors.initials: NN
authors.lastname: Batada