Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast

Cell Stem Cell. 2013 Dec 5;13(6):663-75. doi: 10.1016/j.stem.2013.11.015.


Human embryonic stem cells (hESCs) are derived from the inner cell mass of the blastocyst. Despite sharing the common property of pluripotency, hESCs are notably distinct from epiblast cells of the preimplantation blastocyst. Here we use a combination of three small-molecule inhibitors to sustain hESCs in a LIF signaling-dependent hESC state (3iL hESCs) with elevated expression of NANOG and epiblast-enriched genes such as KLF4, DPPA3, and TBX3. Genome-wide transcriptome analysis confirms that the expression signature of 3iL hESCs shares similarities with native preimplantation epiblast cells. We also show that 3iL hESCs have a distinct epigenetic landscape, characterized by derepression of preimplantation epiblast genes. Using genome-wide binding profiles of NANOG and OCT4, we identify enhancers that contribute to rewiring of the regulatory circuitry. In summary, our study identifies a distinct hESC state with defined regulatory circuitry that will facilitate future analysis of human preimplantation embryogenesis and pluripotency.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blastocyst / drug effects
  • Blastocyst / metabolism*
  • Cell Line
  • Cell Proliferation / drug effects
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / drug effects
  • Embryonic Stem Cells / metabolism
  • Epigenesis, Genetic / drug effects
  • GATA6 Transcription Factor / metabolism
  • Gene Regulatory Networks* / drug effects
  • Germ Layers / drug effects
  • Germ Layers / metabolism*
  • Homeodomain Proteins / metabolism
  • Humans
  • Leukemia Inhibitory Factor / pharmacology
  • Mice
  • Models, Biological
  • Nanog Homeobox Protein
  • Pluripotent Stem Cells / cytology*
  • Pluripotent Stem Cells / drug effects
  • Pluripotent Stem Cells / metabolism*
  • Signal Transduction / drug effects
  • Signal Transduction / genetics
  • Small Molecule Libraries / pharmacology
  • Transcriptome / drug effects
  • Transcriptome / genetics


  • GATA6 Transcription Factor
  • GATA6 protein, human
  • Homeodomain Proteins
  • Leukemia Inhibitory Factor
  • NANOG protein, human
  • Nanog Homeobox Protein
  • Small Molecule Libraries