RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1 + Roof-Plate-Derived Cells

Stem Cell Reports. 2019 May 14;12(5):1159-1177. doi: 10.1016/j.stemcr.2019.04.001. Epub 2019 Apr 25.


Anamniotes, rodents, and young humans maintain neural stem cells in the ependymal zone (EZ) around the central canal of the spinal cord, representing a possible endogenous source for repair in mammalian lesions. Cell diversity and genes specific for this region are ill defined. A cellular and molecular resource is provided here for the mouse and human EZ based on RNA profiling, immunostaining, and fluorescent transgenic mice. This uncovered the conserved expression of 1,200 genes including 120 transcription factors. Unexpectedly the EZ maintains an embryonic-like dorsal-ventral pattern of expression of spinal cord developmental transcription factors (ARX, FOXA2, MSX1, and PAX6). In mice, dorsal and ventral EZ cells express Vegfr3 and are derived from the embryonic roof and floor plates. The dorsal EZ expresses a high level of Bmp6 and Gdf10 genes and harbors a subpopulation of radial quiescent cells expressing MSX1 and ID4 transcription factors.

Keywords: Msx1; ependyma; ependymal cells; floor plate; neural stem cells; niche; radial glial cells; regionalization; roof plate; spinal cord; transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism*
  • Ependymoglial Cells / cytology
  • Ependymoglial Cells / metabolism
  • Female
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Developmental*
  • Humans
  • MSX1 Transcription Factor / genetics
  • MSX1 Transcription Factor / metabolism
  • Male
  • Mice
  • Mice, Transgenic
  • Microscopy, Fluorescence
  • Middle Aged
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism
  • RNA / genetics*
  • RNA / metabolism
  • Spinal Cord / cytology
  • Spinal Cord / metabolism*
  • Stem Cell Niche
  • Stem Cells / cytology
  • Stem Cells / metabolism*
  • Young Adult


  • MSX1 Transcription Factor
  • RNA