The glial cell-specific proteomeThe function of the brain, and the central nervous system, is to receive, process and execute the coordinated functions of perception, motion and cognition that signify human life. The cellular components of the underlying and highly complex network of transmitted signals include neurons and supportive glial cells. Glial cells include several different cell types with specialized functions and morphology, and activation of glial cells, such as astrocytes and microglia, is part of the brains defense system associated with stress, injury and disease. Gliomas, cancer origination from glial cells, accounts for over two thirds of primary intracranial tumors. Transcriptome analysis shows that 78% (n=15821) of all human proteins (n=20162) are detected in glial cells and 3901 of these genes show an elevated expression in any glial cells compared to other brain cell types. The main glial cell types are sometimes limited to Astrocytes, oligodendrocytes and microglia. Additionally, oligodendrocyte precursor cells (OPCs) and committed oligodendrocyte precursor cells are the predecessors to oligodendrocytes. Microglia and central nervous system macrophages are the local immune cells of the brain, not sharing the glial developmental origin. Bergmann glia are specialized radial glial cells, closely related to astrocytes, located in the cerebellum. Finally, ependymal cells are ciliated cells lining the ventricular system of the brain and central canal of the spinal cord, choroid plexus epithelial cells are a specialized type of ependymal cells surrounding the network of capillaries that is the choroid plexus, responsible for generating cerebral spinal fluid (CSF).
The glial cell transcriptomeThe snRNA-seq-based glial cell transcriptome can be analyzed with regard to specificity, illustrating the number of genes with elevated expression in glial cell type compared to other brain cell types (Table 1). Genes with an elevated expression are divided into three subcategories:
AstrocyteAstrocytes are specialized in transportation and enzymatic activity due to the important job of cleaning up and recycling several of the neurotransmitters at the synaptic cleft, as well as boarder control at the blood brain barrier, surrounding the brain vasculature with its endfeet. As shown in Table 1, 602 genes show elevated expression in astrocytes compared to other brain cell types. The glial fibrillary acidic protein (GFAP) is an intermediate filament protein specific for astrocytes, often used as a label of astrocytes. Another popular astrocyte marker is Aldehyde dehydrogenase 1 family member A1(ALDH1A1) which is expressed in astrocytes and Bergmann glia in the brain, and also expressed by several different cells and peripheral tissue types. Solute carrier family 1 member 2 (SLC1A2), also called EAAT2, is a transporter protein specifically detected in astrocytes and is often used as an astrocyte marker.
Exploring the astrocyte clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The astrocyte cluster can be explored to further investigate subtypes of astrocytes across the different brain regions.
Bergmann gliaBergmann glia, a type of radial glia with an important role in the developing cerebellum, as well as the adult cerebellum, are located in the Purkinje cell layer and molecular layer of the cerebellar cortex. As shown in Table 1, 526 genes are elevated in Bergmann glia compared to other brain cell. MAP2K6 show Bergmann glia enriched expression levels compared to other brain cells, it is a MAP kinase expressed in several tissue types. GPR37L1, classified as enhanced based on expression in brain cell types, a rather uncharacterized G-protein coupled receptor with elevated expression in the brain compared to peripheral tissue types. Within the brain, GPR37L1 is also expressed by other glial cells, such as astrocytes and OPCs.
The expression profile of Bergmann glia overlaps with the expression of astrocytes. They share several genes classified as group enriched, such as MLC1 and ACSBG1. GRID2 is an example of Bergmann glia expression combined with two neuronal cell clusters, the miscellaneous and cerebellar inhibitory cluster cells. Exploring the Bergmann glia clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The Bergmann glia cluster can be explored in further details.
Central nervous system macrophageThe local macrophages of the brain share developmental origin and can be divided into; microglia and barrier-associated macrophages, such as perivascular, leptomeningeal, choroid plexus and dural macrophages. As shown in Table 1, 1100 genes show elevated expression in brain macrophages compared to other brain cell types. Well characterized markers for microglia are purinergic receptor P2RY12, the integrin subunit alpha M (ITGAM) and Allograft inflammatory factor 1AIF1, also called IBA1,all classified as enriched in microglia compared to other cell types in the brain. CD68, a macrophage and monocyte marker, show selective expression in microglia and brain macrophages, and has been related to aging and lesions (Waller R et al. (2019)).
As mentioned, there are microglia and there are barrier-associated macrophages. The perivascular marcrophages reside within the perivascular space, and in the list of genes with elevated expression in central nervous system macrophage compared to other brain cell types, we can find several proteins detected in the peripheral macrophages, such as TREML1 and CD163.
Exploring the microglia clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The microglia cluster can be explored specificity for the microglia elevated genes, and by looking at the top enriched genes, most seems to be only detected in a subset of cells, compared to P2RY12 and SALL1 that are generally expressed within the cluster. Markers for perivascular macrophages, such as CD163 and LYVE1 show expression in the smaller sub cluster - further supporting the expression in perivascular macrophages.
Oligodendrocyte precursor cellOligodendrocyte precursor cells (OPC) persist as a subset of glial cells in the adult brain, making up less than a tenth of all glial cells. They are found in both gray and white matter and differentiate into oligodendrocytes, through maturation and cell cycle exits. OPCs has more functions than the precursor cell of oligodendrocyte, they are involved in remyelination, axonal remodeling, neuromodulation and immunomodulation. OPCs are found to eliminate neuronal synapses by phagocytic engulfment (Buchanan J et al. (2022)). As shown in Table 1, 329 genes are elevated in oligodendrocyte precursor cells compared to other brain cell types. Chondroitin sulfate proteoglycan 4 (CSPG4). also called NG2, is a well characterized OPC marker, also expressed by pericytes and vascular smooth muscle cells. While the OPC marker Platelet derived growth factor receptor alpha, PDGFRA, is expressed by fibroblast. The shared expression profile with committed oligodendrocyte precursor is observed when exploring the genes with enriched expression level in OPC, GALR1 and MYT1 are both highly expressed in OPC, and committed OPCs show second highest expression level. The Oligodendrocyte transcription factor 1, OLIG1, highlights the shared expression profile among the three oligodendrocyte lineage cell clusters, with a similar profile for the Oligodendrocyte transcription factor 2, OLIG2
Committed oligodendrocyte precursorCommitted oligodendrocyte precursor cells are a recently defined cell group, a critical intermediate cell population between the newly formed oligodendrocytes and OPCs (Fang M et al. (2023), a review to read more about this). As shown in Table 1, 302 genes are elevated in committed oligodendrocyte precursor cells compared to other brain cell types. As mentioned above, related to OPCs, there is a big overlap between all three cell types of the oligodendrocyte lineage. However, the 6 genes classified as enriched in committed oligodendrocyte precursor cells shows a distinction of these cells from both OPC and oligodendrocytes. The G protein-coupled receptor 17 (GPR17) is an example of a gene classified as enriched in committed oligodendrocyte precursor cells, and thanks to immunohistochemical images in the Tissue Atlas we can observed the morphology of the GPR17 positive cells.
OligodendrocyteOligodendrocytes are the cells responsible for producing myelin, a protective sheath that surrounds axonal nerve fibers, enhancing the speed of action potential propagation. Myelin is produced by oligodendrocytes in the central nervous system, while Schwann cells perform this function in the peripheral nervous system. As shown in Table 1, 616 genes are elevated in oligodendrocytes compared to other brain cell types. In line with the function of oligodendrocytes, myelin related proteins are found among the list of elevated genes in this cluster. Myelin associated oligodendrocyte basic protein (MOBP) is one example. As well as DBNDD2 and ERMN, both highly expressed by oligodendrocytes, and on protein level detected in oligodendrocytes and white matter of all brain regions.
Exploring the oligodendrocyte clusterIn the Human Brain Cell Atlas v1.0 you can explore the specific clusters of cells and their expression in single cell level. The oligodendrocyte cluster can be explored further.
Ependymal cellEpendymal cells create a thin, ciliated layer of neuroepithelial tissue that lines the ventricles of the brain and the central canal of the spinal cord. As shown in Table 1, 1029 genes are elevated in ependymal cells compared to other brain cell types. Out of those, 357 genes are also classified as cell type elevated in ciliated cells of other tissue types throughout the body. Since ependymal cells are highly different from other glial cells in the brain, there are high numbers of genes with elevated expression when comparing cells within the brain. And as mentioned, there is a high overlap with markers for ciliated cells, such as STOML3, ANKRD66 and CDHR4 all ciliated enriched and also enriched in ependymal cells in the brain. Additionally, ODAD1 is ciliated enriched in peripheral tissues and classified as group enriched in ependymal cells and choroid plexus epithelial cells of the brain. Thanks to immunohistochemistry we can confirm the location of ciliated proteins in the ependymal cells. CFAP53 and SPAG6 are both classified as group enriched in ependymal cells and choroid plexus epithelial cells, detected at protein level in the ependymal cells present in the caudate nucleus sample, representing basal ganglia of the brain.
Choroid plexus epithelial cellChoroid plexus epithelial cells are a specialized type of ependymal cell, but they exhibit unique characteristics. Choroid plexus cells and ependymal cells form adjacent single-cell layers that meet at a transitional zone. Unlike ependymal cells, the choroid plexus is supported by a basal lamina and possesses barrier properties. Ependymal cells play a vital role in producing and circulating cerebrospinal fluid (CSF), which supports the central nervous system. As shown in Table 1, 784 genes are elevated in Choroid plexus epithelial cells compared to other brain cell types. A serotonin receptor, 5-hydroxytryptamine receptor 2C (HTR2C) is expressed in several clusters of the brain cells, however, shows highest expression level in choroid plexus epithelial cells. Other examples of highly enriched genes are TTR, SLC13A4, KCNJ13 and SLC39A12. The sodium/iodide cotransporter SLC5A5 is highly expressed in choroid plexus epithelial cells, and detected on protein level by immunohistochemistry.
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. 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. BackgroundSingle nuclei RNAseq dataSiletti K et al. (2023) published single nuclei RNA sequencing result, based on over 3 million cells from multiple brain regions, in Science magazine and created an interactive portal (The Human Brain Cell Atlas v1.0 ) available for single cell exploration across human gene expression in healthy brain cells. The Human Protein Atlas aims to generate a comprehensive resource representing the human body and its complexity, and with a need for better representation of the different cell types of the human brain, we imported the expression profiles and grouped them based on our cell type- strategy (providing bar charts of pooled data for each cell type cluster and calculating the average normalized protein-coding transcripts per million). We based the cell type clusters on the 31 superclusters, as well as the provided assigned cell types, and the data is shown as 34 different "supercluster cell types". The expression profile of the different clusters are shown for each of the 11 different brain regions. More details, related to number of M reads and number of cells per brain region/UMAP can be found here. The published cerebral cortex data is represented by a larger number of cells and we only included a random selection of 500 thousand cells. In total, expression data for 2526725 brain cells is displayed in the Brain single nuclei resource, for browsing the gene expression and provide easy comparison to cell type expression in peripheral tissues.
Relevant publications Uhlén M et al., Tissue-based map of the human proteome. Science (2015) |