The pig brain proteome Regional classification based on RNA expression Pig Atlas Project

The pig brain proteome

Within mammalian evolution, the brain has undergone changes that resulted in increased capacities to process information and perform higher cognitive functions in primates and humans. These evolutionary processes not only involve size expansion, but also variation in gene-expression. To discover human specific molecular features of the brain we need to first identify the shared molecular architecture of the mammalian brain. Therefore, in addition to our mouse brain efforts, we have included the pig brain as a brain that in size and structural organization is closer to that of the human than the mouse. Many of the pig proteins have high homology with human orthologues, allowing us to explore and compare pig and human brain. The regional organization of brain anatomy separates the brain into regions, sub regions, nuclei, and layers of specialized cells, enabling the specific function of each individual region. Transcriptomic data from the different regions facilitates classification of the regional expression variation within pig brain. Here we analyse the pig brain in a similar manner as the human and mouse brain, enabling transcriptomic comparison between the three different mammalian species.

Figure 1. Sagittal schematic drawing of the pig brain indicating the regional organzation in different colors

Regional classification based on RNA expression

The transcriptome analysis shows that 15047 of the human orthologues (n=16614) are expressed in the pig brain, and 836 of these genes show a regionally elevated expression. 3548 human genes are missing pig one-to-one orthologue and is therefore missing pig expression data in the human protein atlas, expression data based on pig genes are downloadable here.

14211 genes are classified as low regional specificity in pig brain
Only 295 are regionally enriched
Cerebellum is the region with most regionally enriched genes (n=79)
Many group enriched genes are shared among the forebrain regions, see Figure 2.

Table 1. The 15 regions of the brain and numbers of genes detected above cut off, indicating expression in that brain region, as well as number of genes classified as elevated in each region compared to the others based on transcript abundance in the individual regions (max nTPM of sub regions is used as representative). Same classification rules are used for the regional classification as the classification based on tissue types.

	Pig
Brain region	Detected	Regionally elevated
Cerebral cortex	14138	109
Cerebellum	13564	165
Olfactory bulb	13937	89
Basal ganglia	14256	157
Thalamus	13915	31
Hypothalamus	14061	45
Midbrain	14335	114
White matter	13612	4
Amygdala	13954	49
Pons	13950	41
Medulla oblongata	13995	37
Hippocampal formation	14236	121
Spinal cord	14089	236

Table 2. The 12 genes with the highest level of regional enriched expression within the pig brain and the regional distribution category. Regional distribution indicates if protein is detected in a single or multiple regions of the pig brain. The mRNA column provides the highest nTPM vallue of the region with highest expression. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.

Gene	Description	Regional distribution	mRNA (region)	RS-score
HOXC10	Homeobox C10	Detected in single	41.7	418
HOXA9	Homeobox A9	Detected in single	19.0	191
HOXB9	Homeobox B9	Detected in single	19.0	190
SLC6A3	Solute carrier family 6 member 3	Detected in some	393.2	152
HOXC8	Homeobox C8	Detected in single	14.3	144
HOXA10	Homeobox A10	Detected in single	24.4	140
HOXD9	Homeobox D9	Detected in single	10.5	105
HOXD8	Homeobox D8	Detected in single	45.9	71
HOXD10	Homeobox D10	Detected in single	6.6	67
HCRT	Hypocretin neuropeptide precursor	Detected in some	146.5	60
FAT2	FAT atypical cadherin 2	Detected in many	313.3	58
HOXA11	Homeobox A11	Detected in single	5.6	56

In order to illustrate the relation of the different brain regions, a network plot was generated, displaying the number of genes shared between different regions. The majority of group enriched genes are shared between the forebrain regions. Cerebellum and basal ganglia are the regions with largest number of regionally enriched genes. For more information and examples about the regionally elevated expression in the different regions, please visit the individual summary pages; olfactory bulb, cerebral cortex, hippocampal formation, amygdala, basal ganglia, hypothalamus, thalamus, midbrain, pons, medulla, cerebellum, spinal cord and white matter .

Figure 2. An interactive network plot of the regionally enriched and group enriched genes connected to their respective enriched region (black circles). Red nodes represent the number of regionally enriched genes and orange noders represesnt the numcer of genes that are group enriched. The sizes of the red and orange nides are related to the number of genes displayed within the node. Each node is cliacle and results in a list of all enriched genes connected to the hightlighted edges. The netwoek is limited to group enriched genes in combinations up to 4 regions, but the resulting lists show the compleate set of group enriched genes in the particular region

Pig Atlas Project

The pig brain transcriptomics project is a collaborative project between The Human Protein Atlas and the Lars Bolund Institute of Regenerative Medicine (Dr. Yonglun Luo), BGI-Qingdao, China.

The protein atlas of the pig provides a full body overview of mRNA expression in all major organ and tissues types including the brain regions also presented in the human protein atlas. The pig RNAatlas is pig-gene centric including all known protein coding genes of the pig.