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. 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. Transcriptome analysis shows that 62% (n=12166) of all human proteins (n=19670) are detected in glial cells and 747 of these genes show an elevated expression in any glial cells compared to other cell type groups.

  • 747 elevated genes
  • 69 enriched genes
  • 169 group enriched genes
  • Main function: Homeostasis maintenance

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 Cell type enrichedGroup enrichedCell type enhancedTotal elevated
Muller glia cells 69 169 509 747

Protein expression of genes elevated in glial cells

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 different types of glial cells: Muller glia cells and other glial cells.

Muller glia - eye

As shown in Table 1, 747 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

Other glial cells

Different types of glial cells are specialized in certain functions. The most common subdivision of glial cells are astrocytes, oligodendrocytes and microglia based on their morphology and function. A common astrocyte marker is the glial fibrillary acidic protein (GFAP) that distinctly stains astrocytes throughout several brain regions. Several genes expressed in 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). Microglia are derived from hematopoietic stem cells invading the brain during embryonic development or macrophages that enter the brain from the bloodstream later in life. An example of a protein expressed in microglia is the integrin subunit alpha M (ITGAM), which can be found in the immune system.

GFAP - cerebral cortex

MBP - cerebral cortex

ITGAM - cerebral cortex

Glial cell function

Glial cells maintain the microenvironment essential for neuronal activity. An ion and water flow homeostasis is essential for the generation of 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. 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 13 different normal tissues, as well as analysis of human peripheral blood mononuclear cells (PBMCs). All datasets (unfiltered read counts of cells) were clustered separately using louvain clustering and the clusters obtained were gathered at the end, resulting in a total of 192 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 average normalized protein-coding transcripts per million (pTPM) 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 13 organs 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