SOX9 Is an Astrocyte-Specific Nuclear Marker in the Adult Brain Outside the Neurogenic Regions

J Neurosci. 2017 Apr 26;37(17):4493-4507. doi: 10.1523/JNEUROSCI.3199-16.2017. Epub 2017 Mar 23.


Astrocytes have in recent years become the focus of intense experimental interest, yet markers for their definitive identification remain both scarce and imperfect. Astrocytes may be recognized as such by their expression of glial fibrillary acidic protein, glutamine synthetase, glutamate transporter 1 (GLT1), aquaporin-4, aldehyde dehydrogenase 1 family member L1, and other proteins. However, these proteins may all be regulated both developmentally and functionally, restricting their utility. To identify a nuclear marker pathognomonic of astrocytic phenotype, we assessed differential RNA expression by FACS-purified adult astrocytes and, on that basis, evaluated the expression of the transcription factor SOX9 in both mouse and human brain. We found that SOX9 is almost exclusively expressed by astrocytes in the adult brain except for ependymal cells and in the neurogenic regions, where SOX9 is also expressed by neural progenitor cells. Transcriptome comparisons of SOX9+ cells with GLT1+ cells showed that the two populations of cells exhibit largely overlapping gene expression. Expression of SOX9 did not decrease during aging and was instead upregulated by reactive astrocytes in a number of settings, including a murine model of amyotrophic lateral sclerosis (SOD1G93A), middle cerebral artery occlusion, and multiple mini-strokes. We quantified the relative number of astrocytes using the isotropic fractionator technique in combination with SOX9 immunolabeling. The analysis showed that SOX9+ astrocytes constitute ∼10-20% of the total cell number in most CNS regions, a smaller fraction of total cell number than previously estimated in the normal adult brain.SIGNIFICANCE STATEMENT Astrocytes are traditionally identified immunohistochemically by antibodies that target cell-specific antigens in the cytosol or plasma membrane. We show here that SOX9 is an astrocyte-specific nuclear marker in all major areas of the CNS outside of the neurogenic regions. Based on SOX9 immunolabeling, we document that astrocytes constitute a smaller fraction of total cell number than previously estimated in the normal adult mouse brain.

Keywords: SOX9; astrocyte marker; astrocytes; transcriptome.

Publication types

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

MeSH terms

  • Adult
  • Aging
  • Animals
  • Astrocytes / metabolism*
  • Biomarkers
  • Brain Ischemia / genetics
  • Brain Ischemia / metabolism
  • Excitatory Amino Acid Transporter 2 / metabolism
  • Gene Expression Regulation / genetics
  • Gene Expression Regulation / physiology
  • Humans
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Neural Stem Cells / metabolism
  • Neurogenesis
  • RNA / biosynthesis
  • SOX9 Transcription Factor / genetics
  • SOX9 Transcription Factor / metabolism*
  • Stroke / genetics
  • Stroke / metabolism
  • Transcriptome / genetics


  • Biomarkers
  • Excitatory Amino Acid Transporter 2
  • SOX9 Transcription Factor
  • SOX9 protein, human
  • Slc1a2 protein, mouse
  • Sox9 protein, mouse
  • RNA