Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Cell Syst. 2019 May 22;8(5):427-445.e10. doi: 10.1016/j.cels.2019.03.012. Epub 2019 May 8.


Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naive and primed, are well characterized, but our understanding of the intermediate states and transitions between them remains incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre- to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naive to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of the kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, with cell-state-specific surface markers tracking pluripotent state transitions. Our data provide new insights into multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions (

Keywords: EpiLC; MAPK/ERK; embryonic development; embryonic stem cells; epiblast; formative pluripotency; mTOR; pluripotency; protein phosphorylation; signaling.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation / physiology
  • Cell Lineage
  • Embryonic Stem Cells / cytology
  • Epigenome / genetics
  • Gene Expression Regulation, Developmental
  • Germ Layers / cytology
  • Germ Layers / metabolism
  • Humans
  • Pluripotent Stem Cells / metabolism*
  • Pluripotent Stem Cells / physiology*
  • Proteome / metabolism
  • Signal Transduction
  • Transcriptome / genetics


  • Proteome