The glial cell-specific proteome

The function of the central nervous system (CNS) is to receive, process, and execute the coordinated higher functions of perception, motion, and cognition that signify human life. The retina is an extension of the CNS responsible specifically for vision. The cellular components of the underlying and highly complex network of transmitted signals include supporting glial cells as well as neurons.

  • 3491 elevated genes
  • 187 enriched genes
  • 513 group enriched genes
  • Main function: Homeostasis maintenance

Transcriptome analysis shows that 74% (n=14889) of all human proteins (n=20090) are detected in glial cells and 3491 of these genes show an elevated expression in any glial cells compared to other cell type groups. In-depth analysis of the elevated genes in glial cells using scRNA-seq and antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in the following types of glial cells: astrocytes, oligodendrocyte precursor cells, oligodendrocytes, microglial cells, Muller glia cells.

The glial cell transcriptome

The scRNA-seq-based glial cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in each specific glial cell type compared to other cell types (Table 1). Genes with an elevated expression are divided into three subcategories:

  • Cell type enriched: At least four-fold higher mRNA level in a certain cell type compared to any other cell type.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-10 cell types compared to any other cell type.
  • Cell type enhanced: At least four-fold higher mRNA level in a cell certain cell type compared to the average level in all other cell types.

Table 1. Number of genes in the subdivided specificity categories of elevated expression in Muller glia cells.

Cell type Tissue origin Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Astrocytes Brain 37 213 933 1183
Oligodendrocyte precursor cells Brain 22 351 1219 1592
Oligodendrocytes Brain 90 211 1290 1591
Microglial cells Brain 16 129 633 778
Muller glia cells Eye 22 63 393 478
Any glial cells 187 513 2791 3491


As shown in Table 1, 1183 genes are elevated in astrocytes compared to other cell types. Astrocytes are glial cells in the brain and spinal cord that fulfill many support functions like providing nutrients to the nerve cells and regulation of cerebral blood flow. One astrocyte enriched gene is the glial fibrillary acidic protein (GFAP) which is an intermediate filament protein specific for astrocytes. Another gene strongly enriched in astrocytes is glypican 5 (GPC5), a cell surface proteoglycan that may play a role in cell division and growth regulation.

GFAP - brain

GFAP - brain

GFAP - cerebral cortex

GPC5 - brain

GPC5 - brain

GPC5 - cerebral cortex

Oligodendrocyte precursor cells

As shown in Table 1, 1592 genes are elevated in oligodendrocyte precursor cells compared to other cell types. PTPRZ1 negatively regulates oligodendrocyte precursor proliferation in the embryonic spinal cord and is required for normal differentiation of the precursor cells into mature, fully myelinating oligodendrocytes.

PTPRZ1 - brain

PTPRZ1 - brain

PTPRZ1 - caudate


As shown in Table 1, 1591 genes are elevated in oligodendrocytes compared to other cell types. Oligodendrocytes are involved in myelination, such as the compact myelin proteins myelin basic protein (MBP), which contributes to stabilization and formation of the myelin throughout the CNS and the peripheral nervous system (PNS).

MBP - brain

MBP - brain

MBP - cerebral cortex

Microglial cells

As shown in Table 1, 778 genes are elevated in microglial cells compared to other cell types. Microglial cells are a specialized type of macrophage only found in the central nervous system. Genes enriched in microglial cells are for example purinergic receptor P2RY12 required for platelet aggregation and blood coagulation. Another example of a protein expressed in microglia is the integrin subunit alpha M (ITGAM), which can be found in the immune system.

P2RY12 - brain

P2RY12 - brain

P2RY12 - cerebral cortex

ITGAM - brain

ITGAM - brain

ITGAM - cerebral cortex

Muller glia

As shown in Table 1, 478 genes are elevated in Muller glia cells compared to other cell types. Muller glia is a type of glial cell found only in the retina. It buffers potassium and neurotransmitters essential for the normal function of different types of neuronal cells of the retina, as well as maintains the structural integrity of the retina. An example of a protein with elevated expression in Muller glia is retinaldehyde binding protein 1 (RLBP1). It carries 11-cis-retinaldehyde, or 11-cis-retinal, molecules that are essential for the conversion of light into neuronal signals in the photoreceptor cells. The function of RLBP1 in Muller glia cells is yet to be characterized.

RLBP1 - eye

RLBP1 - eye

RLBP1 - retina

Glial cell function

Glial cells maintain the microenvironment essential for neuronal activity. An ion and water flow homeostasis is essential for the generation of the action potential by the neuronal cells. This homeostasis is mainly managed by astrocytes and oligodendrocytes that form an intricate network, called panglial syncytium. While in the retina, Mueller glial cells buffer potassium ions. The action potential is propagated along neuronal axons and to increase the speed of transmission, axons are insulated by myelin sheaths, which are produced by oligodendrocytes.

Neuronal cells release neurotransmitters, e.g. glutamate, at the synapses and the neurotransmitters are recycled by glial cells (Mueller glia in retina and astrocytes in other parts of CNS), that maintain contact with the synapses. Neurotransmitters are captured by glial cells, transformed into inactive forms, and shuttled back to the synapses where they can be re-used by neuronal cells. This process requires a great amount of energy (ATP) and since the glial cells shoulder this task, the energy expenditure of neuronal cells is decreased. Certain molecules, e.g. glucose required for energy, pass through the blood-brain barrier, while harmful substances are prevented from entering the brain. Endothelial cells, pericytes, and astrocyte end-feet together comprise the blood-brain barrier. The end-feet ensheath the capillary and regulate the passage of molecules by affecting e.g. tight-junction formation and expression of different transporters. Astrocytes associated with capillaries also capture molecules, e.g. glucose, and process them into metabolites usable by neuronal cells. Pathogens that do pass the blood-brain barrier, as well as damaged neurons and harmful aggregations of proteins (plaques) are removed by microglia, a type of glial cell that is related to macrophages outside the brain.

The histology of organs that contain glial cells, including interactive images, is described in the Protein Atlas Histology Dictionary.


Here, the protein-coding genes expressed in glial cells are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in different glial cell types.

The transcript profiling was based on publicly available genome-wide expression data from scRNA-seq experiments covering 25 tissues and peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering, resulting in a total of 444 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The scRNA-seq data from each cluster of cells was aggregated to mean normalized protein-coding transcripts per million (nTPM) and the normalized expression value (nTPM) across all protein-coding genes. A specificity and distribution classification was performed to determine the number of genes elevated in these single cell types, and the number of genes detected in one, several or all cell types, respectively.

It should be noted that since the analysis was limited to datasets from 25 tissues and PBMC only, not all human cell types are represented. Furthermore, some cell types are present only in low amounts, or identified only in mixed cell clusters, which may affect the results and bias the cell type specificity.

Relevant links and publications

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Sjöstedt E et al., An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. (2020)
PubMed: 32139519 DOI: 10.1126/science.aay5947

Menon M et al., Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nat Commun. (2019)
PubMed: 31653841 DOI: 10.1038/s41467-019-12780-8