Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3

Cell Stem Cell. 2019 Feb 7;24(2):257-270.e8. doi: 10.1016/j.stem.2018.11.021. Epub 2018 Dec 27.


Self-renewal and differentiation of pluripotent murine embryonic stem cells (ESCs) is regulated by extrinsic signaling pathways. It is less clear whether cellular metabolism instructs developmental progression. In an unbiased genome-wide CRISPR/Cas9 screen, we identified components of a conserved amino-acid-sensing pathway as critical drivers of ESC differentiation. Functional analysis revealed that lysosome activity, the Ragulator protein complex, and the tumor-suppressor protein Folliculin enable the Rag GTPases C and D to bind and seclude the bHLH transcription factor Tfe3 in the cytoplasm. In contrast, ectopic nuclear Tfe3 represses specific developmental and metabolic transcriptional programs that are associated with peri-implantation development. We show differentiation-specific and non-canonical regulation of Rag GTPase in ESCs and, importantly, identify point mutations in a Tfe3 domain required for cytoplasmic inactivation as potentially causal for a human developmental disorder. Our work reveals an instructive and biomedically relevant role of metabolic signaling in licensing embryonic cell fate transitions.

Keywords: Flcn; Rag GTPases; Ragulator; Tfe3; developmental disorder; differentiation; embryonic stem cell; mTOR; pluripotency.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / metabolism*
  • Cell Differentiation*
  • Cell Self Renewal
  • Female
  • GTP Phosphohydrolases / metabolism
  • Genome
  • Humans
  • Lysosomes / metabolism*
  • Male
  • Mice
  • Mouse Embryonic Stem Cells / cytology
  • Mouse Embryonic Stem Cells / metabolism
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism
  • Phosphorylation
  • Point Mutation / genetics
  • Protein Binding
  • Signal Transduction*
  • Transcription, Genetic


  • Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
  • Tcfe3 protein, mouse
  • GTP Phosphohydrolases