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The glial cell-specific proteomeThe glial cell transcriptomeAstrocytesBergmann gliaMüller gliaPituicytes/FSCsOligodendrocyte precursor cellsOligodendrocytesSchwann cellsMicrogliaDeep Visual Proteomics analysis of glial cellAstrocytes and neuropilMicroglia and neuropilGlial cell functionBackgroundRelevant links and publications
Single cell type methods
DVP methods
The glial cell-specific proteomeThe function of the nervous system is to receive, process and execute the coordinated higher functions of perception, motion and cognition that signify human life. The nervous system is divided into a central nervous system (CNS), including the brain and the spinal cord, and a peripheral nervous system (PNS), including nerves branching out from the spinal cord to all parts of the body. Retina is an extension of the CNS responsible specifically for vision. The cellular components of this highly complex signal network include neurons and supportive glial cells. Glial cells are the main support cells of the nervous system, essential for maintaining homeostasis, protecting neurons, and ensuring efficient communication. Together, astrocytes, Bergmann glia, Müller glia, and pituicytes provide structural and metabolic support; oligodendrocytes and Schwann cells insulate axons with myelin; oligodendrocyte precursor cells enable regeneration and repair; and microglia serve as the brain’s immune defenders. Transcriptome analysis shows that 67% (n=13603) of all human proteins (n=20162) are detected in glial cells and 2411 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, Bergmann glia, Muller glia, pituicytes/FSCs, oligodendrocyte precursor cells, oligodendrocytes, Schwann cells and microglia. In addition, we utilized proteomic data from a mass spectrometry (MS)-based, cell type–resolved atlas of the human body, generated via Deep Visual Proteomics (DVP), a spatial proteomics platform that combines imaging-guided cell selection with high-resolution protein analysis. The analysis includes several glial cell types, including astrocytes and microglia where both cell type shapes include a portion of neuropil (mix of neuronal projections and synapses). Out of a total of 14361 detected proteins in all cell types, 7640 were detected in at least one of the glial cell types, and 1684 were classified as elevated in at least one glial cell types. Further details on cell type specific proteome profiles, as well as examples of enriched proteins across different glial cells, are provided below. The glial cell transcriptomeThe 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:
Table 2. Number of genes in the subdivided specificity categories of elevated expression in the different types of glial cell types, compared to all other cell types.
Among the genes with glial elevated expression, there are several genes specific to certain types of glial cells, such as the oligodendrocyte specific myelin oligodendrocyte glycoprotein MOG but also more general glial markers, such as S100 calcium-binding protein B (S100B), involved in the proliferation and differentiation of glial cells in the CNS as well as the PNS (Schwann cells).
AstrocytesAstrocytes are glial cells in the central nervous system that maintain the blood–brain barrier, regulate neurotransmitters and ions, and provide metabolic support to neurons. They also contribute to synapse formation and repair after injury. As shown in Table 2, 1161 genes show elevated expression in astrocytes compared to other cell types. An example of astrocyte enriched gene, often used as cell marker for astrocytes, is the glial fibrillary acidic protein (GFAP) which is an intermediate filament protein specific for astrocytes.
Bergmann gliaSpecialized radial astroglia in the cerebellum that guide neuronal migration and support Purkinje cells. They regulate extracellular potassium and glutamate to stabilize cerebellar circuits and share many proteins with astrocytes. As shown in Table 2, 1202 genes show elevated expression in Bergmann glia compared to other cell types. GRID2 is an example of gene with enriched expression in Bergmann glia.
Müller gliaMüller glia cells are a type of glial cell found only in the retina that 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. As shown in Table 2, 489 genes are elevated in Müller glia cells compared to other cell types. An example of a protein with elevated expression in Müller glia cells 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.
Pituicytes/FSCsThese are the glial‑like support cells of the pituitary: pituicytes in the posterior lobe modulate neurosecretory axons, while folliculostellate cells (FSCs) in the anterior lobe provide paracrine and structural support. Together they regulate hormone release and tissue homeostasis. As shown in Table 2, 383 genes show elevated expression in Pituicytes/FSCs compared to other cell types. Examples of genes with elevated expression in pituicytes/FSCs are beta-1,3-galactosyltransferase 1 (B3GALT1), an enzyme involved in glycosylation, and Endothelin 3 (EDN3) a peptide that acts through endothelin receptors to regulate vascular tone and neural crest cell development are two exmaples of proteins with enriched expression in the pituicytes/FSCs, neither with know connection to the pituitary gland.
Oligodendrocyte precursor cellsAlso called Oligodendrocyte preogenitor cells, shortened OPC, are proliferative precursors in the CNS that generate myelinating oligodendrocytes. OPCs are more than percursor cells, they also survey the parenchyma, respond to injury, and remodel myelin during learning and repair. Additionally, there are studies indicating OPCs play a part in synaptic pruning and might even receive synaptic input. As shown in Table 2, 1323 genes show elevated expression in oligodendrocyte precursor cells compared to other cell types. An examples is PTPRZ1, that 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.
OligodendrocytesOligodendrocytes are the glial cells of the CNS that wrap axons with myelin to accelerate action potential conduction. They also provide trophic and metabolic support to neurons. As shown in Table 2, 1241 genes show elevated expression in oligodendrocytes compared to other cell types. The myelinsation involves proteins 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).
Schwann cellsSchwann cells are a type of glial cell found in the PNS surrounding and supporting the neurons throughout the body, involved in the production of the myelin sheaths that sometimes cover and insulate the axons. As shown in Table 2, 307 genes show elevated expression in Schwann cells compared to other cell types. An example of a protein with elevated expression in Schwann cells is myelin protein zero (MPZ). It is a large transmembrane protein that is necessary for the formation of normal myelination of nerves in the PNS.
MicrogliaResident immune cells of the CNS that act as macrophages, clearing debris and pruning synapses. They constantly survey the brain environment and orchestrate neuroinflammatory responses. As shown in Table 1, 1013 genes are elevated in microglial cells compared to other cell types. 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.
Deep Visual Proteomics analysis of glial cellProteomic data from a mass spectrometry (MS)-based, cell type–resolved atlas of the human body, generated via Deep Visual Proteomics (DVP), a spatial proteomics platform that combines imaging-guided cell selection with high-resolution protein analysis, is integrated to the Single Cell Type resrouce. This enables exploration of global protein detection profiles with RNA expression profiles. The DVP data includes 13496 detected proteins and covers 27 cell types which is grouped into 24 main cell types used for classification and the RNA comparison. The cell type specificity categories were applied to the protein data. Here, we describe the included glial cell and show examples of proteins with elevated detection. The glial cell representation in the DVP data includes astrocytes and microglia, both includes neuropil, due to the shape of the mask used for the cell shape. Occational neuronal cell bodies may also be included in the sample, Read more about the sampling here, and look at zoom-able images of the mask used for the samples. Astrocytes and neuropilDVP resulted in 1206 proteins classified as elevated in Astrocytes and neuropil. In total, 6592 proteins were detected in Astrocytes and neuropil, out of these, 27 were only detected in Astrocytes and neuropil, compared to the other 24 DVP samples. The 68 proteins enriched is consistent with strong astrocytic enrichment, highlighted by the presence of canonical astrocyte-associated proteins including AQP4, GFAP, and MLC1. AQP4 and MLC1 are characteristic components of perivascular astrocytic endfeet involved in ion and water homeostasis, while GFAP reflects the astrocytic intermediate filament network. SLC7A11 and SLC15A2 further support astrocyte-associated metabolic and transporter functions, although these transporters are not generally considered core or highly specific astrocyte marker proteins in the same way as AQP4 or GFAP. In addition to astrocytic proteins, the dataset also contains several prominent oligodendrocyte and myelin-associated proteins, including MOBP, MOG, MBP, and ERMN, likely reflecting the sampling approach, which includes surrounding neuropil enriched in myelinated processes. These findings suggest that the sample is astrocyte-enriched but retains substantial contributions from adjacent neuropil and myelin-rich oligodendrocyte processes. Aquaporin-4 (AQP4) is a major water channel in the brain, highly expressed in astrocyte endfeet around blood vessels. In the brain, it helps regulate water movement, contributes to maintaining water balance, and plays an important role in the development and resolution of cerebral edema as well as fluid clearance through the glymphatic system. In the lung, AQP4 is expressed at lower levels, mainly in certain airway epithelial cells, where it contributes to water transport across membranes and may help in regulating airway surface fluid and edema, although other aquaporins (especially AQP1 and AQP5) have a more dominant role in pulmonary water movement. The precise function of MLC1 is still not fully resolved, but it is widely thought to play an important role in ion and water homeostasis in astrocytes, particularly at perivascular endfeet where it colocalizes with proteins such as AQP4. MLC1 is an astrocyte-specific membrane protein enriched at astrocyte–astrocyte junctions and perivascular regions, and it is suggested to contributes to regulation of cell volume, potassium buffering, and fluid exchange in the brain. However, unlike classical ion channels or transporters, MLC1 does not yet have a clearly defined molecular transport function, and its exact mechanistic role remains under investigation. Microglia and neuropilDVP resulted in 1433 proteins classified as elevated in microglia and neuropil. In total, 7421 proteins were detected in microglia and neuropil, out of these, 67 were only detected in microglia and neuropil, compared to the other 24 DVP samples. The 109 proteins enriched in microglia relative to other cell types, includes a mix of proteins, including canonical microglia markers such as CX3CR1, consistent with microglial enrichment. However, the list also contains proteins that are not microglia-specific, likely reflecting the sampling approach, as microglial isolates can include associated neuronal elements and surrounding neuropil. Accordingly, neuronal and synaptic proteins such as GRIK4, GNAL, and GABRG3, as well as potassium channels (e.g., KCNC4) and multiple solute carriers (SLC17A6, SLC24A4, SLC5A7), are detected alongside additional membrane proteins like TMEM145, supporting the notion that components of neurites and synapses are co-isolated with microglial material. Among the 1433 microglia elevated proteins, 46 are also elevated in microglia based on the single nuclei RNAseq data. In this list we can find known markers such as P2RY12. Interestingly, the marker used for identifying the DVP microglia, TMEM119, is not classified as microglia elevated. Although it is a robust and well-extablished marker, the function is unknown and it is suggested by both RNA and protein data that there is more to it than microglia marker. Glial cell functionGlial 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. In the CNS this homeostasis is mainly managed by astrocytes and oligodendrocytes that form an intricate network, called panglial syncytium, while in the retina, Muller 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 in the CNS, and by Schwann cells in the PNS. 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. BackgroundHere, 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 and snRNA-seq experiments (36 datasets) covering 34 tissues. All datasets (unfiltered read counts of cells) were clustered independenty using leiden clustering, resulting in a total of 1175 different cell type clusters. The clusters were then manually annotated based on a survey of known tissue and cell type-specific markers. The RNA-seq data from each cluster of cells was aggregated to mean normalized protein-coding counts per million (nCPM) for all protein-coding genes. A specificity and distribution classification was performed for both single cell types individually, as well as grouped into 53 main cell type groups. The specificity classification determined the number of elevated genes, while the distribution determined whether genes are detected in one, several or all cell types or cell type groups. It should be noted that since the analysis was limited to datasets representing 34 tissue types, 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) |
The Human Protein Atlas project is funded
