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CerebellumAnatomical divisionsRegionally elevated protein expression in humanSpatial resolved protein expression in the main layers and cell types of the human cerebellumRegionally elevated protein expression in mouseRegionally elevated protein expression in pigExtended information
Brain methods
CerebellumSummaryThe developmental origin of the cerebellum is the hindbrain, together with the brainstem (midbrain, pons, and medulla oblongata). The cerebellum is attached to the pons and all communication in and out of the cerebellum goes through pons. The cerebellum is located underneath the cerebrum in the back of the head (see Figure 1). It is involved in movements and coordination. The transcriptome analysis shows that 81% (n=16305) of all human protein-coding genes (n=20162) are expressed in the human cerebellum. Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 12054 of all mouse one-to-one orthologues (n=16679) are expressed in the mouse cerebellum and that 13564 of all pig orthologues (n=16614) are expressed in the pig cerebellum. Gene classification based on regional RNA expression in human, pig and mouse cerebellum defines 196 genes as cerebellum enriched in either of the three species, and 59 out of those genes show highest expression levels in cerebellum in all three species.
Figure 1. Schematic drawing of the human brain, indicating the location of cerebellum from a sagittal view. Anatomical divisionsThe cerebellum has, similar to cerebrum, two hemispheres and a folded cortical surface, which in cerebellum has parallel groves. The brain section contains cerebellar cortex, Vermis and Flocculonodular lobe characterized by their distinct cellular organization in three layers; the molecular layer, Purkinje layer and granular layer. All three layers include a large number of specialized neurons, making the cerebellum the most neuronal dense region of the human brain. It is estimated to include 80% of all the neurons in the brain, but it only represents 10% of the brain volume. The cerebellar nucleus is located deep in the white matter and has a different cellular organization compared to the regions of the cerebellar cortex. The Purkinje cells are one of the largest neurons in the human body, the cell body of Purkinje cells are located in the Purkinje layer while the dendritic tree of the Purkinje cells stretches out in the molecular layer and the axon of Purkinje cells projects through the granular layer and further to deep cerebellar nuclei. Two examples of proteins specifically located to the Purkinje cells are MYH10, labeling the cell body and the stem of the dendritic tree, and HOMER3 which shows the extensive dendritic tree as well as the axonal projection. The Purkinje cell receives input from both the parallel fibers from the granular cell, projecting into the molecular layer, as well as stellate and basket cells located in the molecular layer. The synaptic inter-connections between basket cells and the initial segment of the Purkinje cell axon are clearly visualized by the protein detection of KIT. An example of a protein specifically located to the cells of the molecular layer is BHLHE22. Granular cells are highly abundant neurons in the cerebellum with round nucleus tightly packed, and with synaptic glomeruli formed by granular cells, golgi cells and mossy fibers (one of the major inputs to cerebellum from cerebral cortex and other regions). GABRB2 show synaptic positivity, including the synaptic glomeruli in granular layer. Bergmann glia are radial astrocytes specific for cerebellum located in the Purkinje layer with processes through the molecular layer all the way to the pial surface of the cerebellar cortex. An example of protein specifically detected in Bergman glia is QKI. Above examples show the human cerebellum, and similar cell types and proteins can also be detected in the mouse cerebellum. For example, QKI show selective positivity in Bergmann glia, KCNIP4 show staining of the synaptic glomeruli in the granular layer and MX1 is located in the dendritic processes of Purkinje cells. Regionally elevated protein expression in human
Figure 2. Schematic drawing of the human brain, indicating the location of cerebellum from a coronal perspective. The transcriptome analysis shows that 81% (n=16305) of all human proteins (n=20162) are expressed in the cerebellum, 14715 of all genes detected in the brain are also detected in cerebellum.
Table 1: Number of genes within the different categories of regionally elevated expression, in human cerebellum
Elevated expression in cerebellum compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in cerebellum compared to all other regions), group enriched (at least four-fold higher mRNA levels in a group of 2-5 regions) and regionally enhanced (at least four-fold higher mRNA levels in cerebellum compared to the average of all regions). The number of genes in the individual category is shown in Table 1. In Table 2, the 12 genes with the highest level of regional specificity among the 64 enriched genes are listed. Table 2. The 12 genes with the highest level of enriched expression in human cerebellum. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.
Spatial resolved protein expression in the main layers and cell types of the human cerebellum
The cerebellum is segmented into the molecular layer (ml) containing interneurons and dendrites of Purkinje cells, the Purkinje layer (pl) with the soma of Purkinje cells and Bergmann glia, the granular layer (gl) mainly containing granule cells and white matter (WM) containing oligodendrocytes and whitematter astrocytes. The cell-type masks for each cell types is color coded. The zoomable images below provide an overview of the cell type mask in 3 human cerebellum crops. The tables on the right provide an overview of genes enriched in the neurons (all neuron types), Purkinje cells, astrocytes, microglia, oligodendroctyes and cells associated with brain vasculature. Details on the the method and calculations can be found in the spatial transcriptomics resource. A major advantage of spatial transcriptomics is the ability to link protein coding genes to cell types even if the protein distribution does not reveal a cell morphology when using immunohistochemstry (IHC). To illustrate this several IHC examples are shown below the tables. Top 12 cerebellum neuron elevated genes
This set of protein coding genes is dominated by proteins expressed by different neuron types in the cerebellum including granule cells, interneurons and Purkinje cells.
Top 12 Purkinje elevated This set of proteing coding genes are elevated in Purkinje cells and code for protiens located in the soma FGL2 , dendritesGNG13 or axons (mossy fibers) PANX2 or a combination.
Top 12 cerebellum astrocyte elevated genes This set contains protein coding genes expressed by Bergmann glia like AQP4 and SLC1A2.
Top 12 cerebellum microglia mask enriched genes These contain many general marker genes for microglia cells and other immune cells that can be found throught the brain.
Top 12 cerebullum vasculature elevated Thes include protein coding genes expressed by endothelia cells like SLC2A1 and CLDN5, but also transcripts found in blood cells like HBB.
Regionally elevated protein expression in mouseThe mouse cerebellum is anatomically similar to the human cerebellum, with folded cortex and the three distinct layers of cells; granular layer, Purkinje layer and molecular layer, all containing different neuronal cell types. The transcriptome analysis shows that 60% (n=12054) of all mouse genes with one-to-one human orthologue (n=16679) are expressed in the cerebellum. 182 genes show an elevated expression in cerebellum compared to other regions of the brain. Table 3: Number of genes within the different categories of regionally elevated expression, in mouse cerebellum
Figure 3.Schematic drawing of the mouse brain, indicating the location of cerebellum from a sagittal view. Elevated expression in cerebellum compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in cerebellum compared to all other regions), group enriched (at least four-fold higher mRNA levels in a group of 2-5 regions) and regionally enhanced (at least four-fold higher mRNA levels in cerebellum compared to the average of all regions). The number of genes in the individual category is shown in Table 3. In Table 4, the 12 genes with the highest level of regional specificity among the 94 enriched genes are listed. Table 4: The 12 genes with the highest level of enriched expression in mouse cerebellum. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.
One example of protein specifically localized to cerebellum is CBLN3 with a synaptic location most abundant in the molecular layer. Regionally elevated protein expression in pigThe pig cerebellum is anatomically similar to the human cerebellum, with folded cortex and the three distinct layers of cells; granular layer, Purkinje layer and molecular layer, all containing different neuronal cell types. The transcriptome analysis shows that 67% (n=13564) of all pig genes (n=16614) are expressed in the cerebellum. 165 genes show an elevated expression in cerebellum compared to other regions of the brain. Table 5: Number of genes within the different categories of regionally elevated expression, in pig cerebellum
Figure 4. Schematic drawing of the pig brain, indicating the location of cerebellum from a sagittal view. Elevated expression in cerebellum compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in cerebellum compared to all other regions), group enriched (at least four-fold higher mRNA levels in a group of 2-5 regions) and regionally enhanced (at least four-fold higher mRNA levels in cerebellum compared to the average of all regions). The number of genes in the individual category is shown in Table 5. In Table 6, the 12 genes with the highest level of regional specificity among the 79 enriched genes are listed. Table 6: The 12 genes with the highest level of enriched expression in pig cerebellum. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.
Extended informationProteins specifically localized in human cerebellumProteins with elevated expression in cerebellum compared to the other brain regions were detected in the different cell types and layers of cerebellum. Protein specifically detected in cell of molecular layer (SCGN), the granular cells (PAX6) and the synaptic glomeruli of the granular layer (TMEM266) were all identified among the cerebellum elevated genes. Several genes with cerebellum elevated expression were localized to Purkinje cells, for example ARHGEF33 and PPP1R17. Proteins detected in Bergmann glia were also found among the cerebellum elevated genes, for example DAO. Detailed annotation of the human cerebellumA refined characterization of the protein location in the cerebellum of 900 genes was performed by taking 19 different cellular compartments into consideration in the annotation, unlike the standard annotation which includes cells of the three different layers (molecular, Purkinje and granular). Large sections of human cerebellumThe standard setup in the Tissue Atlas, that profiles human tissues, is based on Tissue Micro array technique, saving valuable tissue material as well as reagents and still providing a good tissue representation for protein profiling. However, due to the complex nature of the brain, with different cell types and subfields, we occasionally include a larger tissue sample to better understand the protein location. In table 7, the selected targets used for profiling on extended tissue material is listed. Table 7. The following 9 genes have been analyzed using extended cerebellum samples. |
The Human Protein Atlas project is funded
