The cerebellum-specific proteomeCerebellum is involved in movments and coordination. The developmental origin of cerebellum is hindbrain, together with the brainstem (midbrain, pons and medulla oblangata). Cerebellum is attached to the Pons and all communication in and out of the cerebellum goes through Pons. Cerebellum is located underneath the cerebrum in the back of the head (see Figure 1). The cerebellum has, similar to cerebrum, two hemispheres and a folded cortical surface, which in cerebellum has parallel groves. The cerebellar cortex includes three distinct 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 transcriptome analysis shows that 79% (n=15629) of all human protein-coding genes (n=19670) are expressed in the human cerebellum. Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 11380 of all mouse one-to-one orthologues (n=15160) are expressed in the mouse cerebellum and that 12381 of all pig orthologues (n=14656) are expressed in the pig cerebellum.
Figure 1. Schematic drawing of the human brain, indicating the location of cerebellum from a sagittal veiw. Gene classification based on regional RNA expression in human, pig and mouse cerebellum defines 345 genes as cerebellum enriched in either of the three speces, and 95 out of those genes show highest expression levels in cerebellum in all three species. Cell types specific for cerebellumThe 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 streches 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 paralell 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 is especially clear by the protein detection of KIT. Example of a protein speclfically located to the cells of 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. Example of protein specifically detected in Bergmanglia 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 dendrictic processes of Purkinje cells. Regionally elevated expression in human cerebellum
Figure 2. Schematic drawing of the human brain, indicating the location of cerebellum from a coronal perspective. The transcriptome analysis shows that 79% (n=15629) of all human proteins (n=19670) are expressed in the cerebellum, 13188 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 individaul category is shown in Table 1. In Table 2, the 12 genes with the highest level of regional specificity among the 214 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.
Proteins 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. Regionally elevated expression in mouse cerebellumThe 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 58% (n=11380) of all mouse genes with one-to-one human orthologue (n=15160) are expressed in the cerebellum. 179 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 2.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 101 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 expression in pig cerebellumThe 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 63% (n=12381) of all pig genes (n=14656) are expressed in the cerebellum. 150 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 3. 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 96 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 human cerebellum tissue sectionThe 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 provide 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 3 genes have been analyzed using extended cerebellum samples. |
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The Human Protein Atlas
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