The cerebral cortex, located in the dorsal part of the forebrain (telencephalon), is the largest region of the human brain and is greatly involved in information processing. The cortical subregions are important for generating voluntary motor output and processing of sensory information, or are involved in the control of cognitive functions. The cerebral cortex mainly consists of excitatory pyramidal projection neurons, organized in 6 distinct layers, and inhibitory interneurons that form local networks, and acts as a relay system, where information from subcortical regions is filtered and projected back to subcortical regions that generate the behavioral output. Many of the human higher cognitive abilities depend on this brain structure, and neurodegenerative disease (e.g. Alzheimer's disease) or developmental abnormalities affecting the cerebral cortex often result in cognitive impairments.
The transcriptome analysis shows that 84% (n=16993) of all human protein-coding genes (n=20162) are expressed in the human cerebral cortex. Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 12540 of all mouse one-to-one orthologues (n=16679) are expressed in the mouse cerebral cortex and that 14138 of all pig orthologues (n=16614) are expressed in the pig cerebral cortex.
Figure 1. Schematic drawing of the human brain, indicating the location of cerebral cortex from a sagittal view.
Frontal lobe: This area of the brain is important for voluntary motor behavior, language and higher cognitive functions. The human frontal cortex data contains protein expression data from 12 cortical areas including premotor and motor areas. During primate evolution the size of the prefrontal cortex increased in the great apes and humans. Extended information on the prefrontal cortex based on 20 areas of the prefrontal cortex can be found below.
Cingulate gyrus: The cingulate cortex is part of the limbic system and important for emotional behavior. Six areas of the cingulate cortex covering anterior, middle and posterior areas of the cingulate cortex are included.
Insular cortex: The insular cortex in human is located in the temporal sulcus and not visible from the surface. The area of the cortex is important for sensory processing and linking sensory information to emotions. Anterior dorsal, Anterior ventral and posterior areas of the insular cortex are represented.
Parietal lobe: Fourteen areas of the parietal cortex are represented and these include the postcentral gyrus involved in the processing of sensory information and parietal association cortex involved in internal representation.
Retrosplenial cortex: Retrosplenial cortex is located in the medial posterior part of the cortex. This association cortex is involved in processing of spatial information.
Occiptal lobe: The main function of the occiptal cortex is visual perception. The area striata also known as the primary visual cortex (V1) is the main input site for information from the retina. The area parastriata is also known as the secondary visual cortex (V2). The eight areas represented in the occiptal cortex also contain the lingual cortex, important for recognition of words and transition areas between occiptal lobe and parietal and temporal lobes. These were assigned to the occiptal cortex group based on similarities in gene expression profiles.
Temporal lobe: This cortical region is important for the processing of auditory and other sensory information. Eight areas of the temporal cortex are analysed including the superior temporal gyrus (primary auditory cortex), middle temporal gyrus (association auditory cortex), transverse temporal gyrus involved in processing and interpretation of auditory information. The fusiform is involved in processing of visual information including face recognition.
Claustrum: The claustrum is a thin sheet of neurons located between the cortex and basal ganglia. Based on the similarity in gene expression with cortical samples the claustrum was grouped under cerebral cortex. The claustrum has connections to many cortical and subcortical structures and plays an important role in modulation and synchronization of activity in different cortical areas.
Paleocortex: This medial ventral area of the cortex contains the olfactory area, olfactory tubercle and piriform cortex, important for the perception and processing of olfactory information and discrimination of odors.
Cellular organization of the cerebral cortex: The main neuronal cell types in the cerebral cortex are glutamatergic pyramidal neurons and inhibitory (mainly GABA-ergic) interneurons (neuronal cells). These cells are organized in six cellular layers, based on cell densities, morphology, electrophysiological properties and connections. The cerebral cortex receives its main excitatory input from the thalamus. The neuronal networks, organized in columns spanning all layers of the cerebral cortex, process this information and output signals are send back to thalamus and other subcortical structures. The white matter, approximately 40% of the cerebral cortex, contains the myelinated input axons originating from subcortical structures and myelinated axons originating from cortical pyramidal neurons projecting to subcortical areas of the brain. In addition, the human white matter contains some sparsely distributed neurons including a population of large neurons expressing the calcium binding protein CALHM1.
Figure 2. Above an example of a large neuron located in the cortical whitematter expressing the protein CALHM1. To the right example of tripple labeling of the human cortex indicating cells located in the different layers.Yellow color show staining of TPPP3, green color represent NECAB1, red color is the labeling of PCP4 and blue is DAPI counterstaining.
Regionally elevated protein expression in human
The transcriptome analysis shows that 84% (n=16993) of all human proteins (n=20162) are expressed in the cerebral cortex and 180 genes show an elevated expression in cerebral cortex compared to other regions of the brain.
Table 1: Number of genes within the different categories of regionally elevated expression, in human cerebral cortex
Elevated expression in cerebral cortex compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in cerebral cortex 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 cerebral cortex compared to the average of all regions), The number of genes in the individual category is shown in Table 1. Very few genes are classified as regionally enriched in cerebral cortex, examples of interesting genes are DUSP2, FMN1, HECW1 and KCNS2. Proteins with elevated expression in cerebral cortex compared to all the other brain regions were often group enriched due to the similarity to other forebrain regions. Examples of group enriched expression in cerebral cortex are NPTXR, CDH9 and NRGN.
Regionally elevated protein expression in mouse
Figure 4. Schematic drawing of the mouse brain, indicating the location of cerebral cortex from a sagittal view and a coronal perspective.
The transcriptome analysis shows that 12540 of all mouse one-to-one orthologues (n=16679) are expressed in the mouse cerebral cortex and 1 genes are classified as regionally enriched genes and in total 55 regionally elevated. Elevated expression in cerebral cortex compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in cerebral cortex 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 cerebral cortex compared to the average of all regions), The number of genes in the individual category is shown in Table 2.
Table 2: Number of genes within the different categories of regionally elevated expression, in mouse cerebral cortex
The expression value representing cerebral cortex in the regional classification is defined as the highest expression (nTPM) in either of the subregions included. Subregions of the mouse cerebral cortex included in the brain atlas are: frontal cortex (prefrontal and motor cortex sampled together), retrosplenial and cingulate cortex as one sample, somatosensory cortex and visual (occipital) cortex, in total 4 different cortical samples. The entorhinal cortex is also included but grouped together with hippocampus as part of the hippocampal formation.
Regionally elevated protein expression in pig
The transcriptome analysis shows that 14138 of all pig one-to-one orthologues (n=16614) are expressed in the pig cerebral cortex and 0 genes are classified as regionally enriched genes and in total 109 regionally elevated. Elevated expression in cerebral cortex compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in cerebral cortex 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 cerebral cortex compared to the average of all regions), The number of genes in the individual category is shown in Table 3.
Table 3: Number of genes within the different categories of regionally elevated expression, in pig cerebral cortex
Figure 5. Schematic drawing of the pig brain, indicating the location of cerebral cortex from a sagittal view.
Extended human protein expression map of the prefrontal cortex
The mammalian frontal lobe contains the motor, pre-motor and prefrontal areas. From all cortical regions, the human prefrontal cortex is special and more developed, compared to other mammalian species. During evolution, its size increased rapidly in primates, especially in great apes and humans. This development has been associated with specialized higher cognitive functions such as language, attention and complex decision-making, involving prediction, imagination and planning. The prefontal cortex is divided in the dorsolateral, dorsomedial, ventrolateral, ventromedial and orbitofrontal regions. These regions can be further subdivided based on gyrification (folding of the brain) or cellular organization of the cortical layers.
The dorsolateral prefrontal cortex is important for the storage of working memory in the processing and preparation of all forthcoming actions and includes the superior frontal (SFG) and the dorsal middle frontal gyrus (MFG). The dorsomedial prefrontal cortex is involved in social cognition and processing of mental states and includes the superior frontal gyrus (SFG) and the dorsal and ventral anterior cingulate parts of cortex (aCGpd & aCGpv). The ventrolateral prefrontal cortex is involved in decision making by processing the behavioral significance of external events and includes the frontomarginal cortex, the medial frontal gyrus (MFG), the inferior frontal gyrus (IFGorb), and the Broca areas that are involved in speech production). The ventromedial prefrontal cortex is important for empathy, making of value-based decision and regulation of negative emotions and contains the frontopolar cortex (FP), the rostral gyrus (ROG), the dorsal and ventral pregenual (aCGpd & aCGpv) and subgenual (aCGs) part of the anterior cingulate cortex and the subcallosal gyrus (SCG). The orbibtofrontal part of the prefrontal cortex is located just above the eye sockets (orbital bone), is involved in emotional associative learning and includes the gyrus rectus (GR), and the medial (OrGm), anterior (OrGa), posterior (OrGp) and lateral (OrGl) areas of the orbitofrontal gyrus. Overall, the cingulate cortex, with its anterior, middle and posterior parts, is involved in the regulation of emotion. A detailed analysis comparing 17 areas of the human prefrontal cortex (Zhong W et al. (2022)) revealed the heterogenic molecular organization of the prefrontal cortex. The results suggest that the well-established anatomical and functional heterogeneity of human PFC is also reflected in the expression pattern of the neuropeptides.
Figure 6. Schematic drawing of the lateral, medial and orbital view of the cerebral cortex outlining the regions of the dorsolater (yellow), ventrolateral (blue), dorsomedial (green), ventromedial (purple) and orbitofrontal parts (orange/red) prefrontal cortex.
Extended human cerebral cortex tissue section
The standard setup in the Tissue Atlas, which profiles human tissues, is based on Tissue Micro array technique, saving valuable tissue material as well as reagents and provide a good tissue representation for protein profiling. However, due to the complex nature of the brain, with different cell types and subfeilds, larger tissue sample is occationally used to better understand the protein location. In Table 4, the selected targets used for protein profiling on extended tissue material are listed.
Table 4. The following 71 genes have been analyzed using extended cerebral cortex samples.