title: The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.
abstract: Induced pluripotent stem cells (iPSCs) are commonly generated by transduction of Oct4, Sox2, Klf4, and Myc (OSKM) into cells. Although iPSCs are pluripotent, they frequently exhibit high variation in terms of quality, as measured in mice by chimera contribution and tetraploid complementation. Reliably high-quality iPSCs will be needed for future therapeutic applications. Here, we show that one major determinant of iPSC quality is the combination of reprogramming factors used. Based on tetraploid complementation, we found that ectopic expression of Sall4, Nanog, Esrrb, and Lin28 (SNEL) in mouse embryonic fibroblasts (MEFs) generated high-quality iPSCs more efficiently than other combinations of factors including OSKM. Although differentially methylated regions, transcript number of master regulators, establishment of specific superenhancers, and global aneuploidy were comparable between high- and low-quality lines, aberrant gene expression, trisomy of chromosome 8, and abnormal H2A.X deposition were distinguishing features that could potentially also be applicable to human.
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel. Electronic address: yossibug@ekmd.huji.ac.il.
authors.forename: Yosef
authors.initials: Y
authors.lastname: Buganim
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Styliani
authors.initials: S
authors.lastname: Markoulaki
authors.affiliation: European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, the Netherlands.
authors.forename: Niek
authors.initials: N
authors.lastname: van Wietmarschen
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Heather
authors.initials: H
authors.lastname: Hoke
authors.affiliation: Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Kibibi
authors.initials: K
authors.lastname: Ganz
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Batool
authors.initials: B
authors.lastname: Akhtar-Zaidi
authors.affiliation: Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Yupeng
authors.initials: Y
authors.lastname: He
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Abraham
authors.affiliation: European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, the Netherlands.
authors.forename: David
authors.initials: D
authors.lastname: Porubsky
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Kulenkampff
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Dina A
authors.initials: DA
authors.lastname: Faddah
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Linyu
authors.initials: L
authors.lastname: Shi
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Gao
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Sovan
authors.initials: S
authors.lastname: Sarkar
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Malkiel
authors.initials: M
authors.lastname: Cohen
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Johanna
authors.initials: J
authors.lastname: Goldmann
authors.affiliation: Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Schultz
authors.affiliation: Genomic Analysis Laboratory, Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Xiao
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
authors.affiliation: European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, AV Groningen 9713, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Lansdorp
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Skolkovo Institute of Science and Technology (Skoltech), Novaya strazha 100, Skolkovo Moscow Region 143025, Russia. Electronic address: jaenisch@wi.mit.edu.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Jaenisch
mesh_terms: D000818:Animals; D002460:Cell Line; D065150:Cellular Reprogramming; D002678:Chimera; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000235:genetics; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D006657:Histones / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D000090062:Kruppel-Like Factor 4; D008810:Mice, Inbred C57BL; D008811:Mice, Inbred DBA; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014314:Trisomy / Q000235:genetics
chemical_list: D006657:Histones; D000090062:Kruppel-Like Factor 4; D012333:RNA, Messenger; D014157:Transcription Factors; C000715467:KLF4 protein, human; C000715468:Klf4 protein, mouse; C475961:gamma-H2AX protein, mouse