The human brain proteome

The function of the brain, defined as the central nervous system, is to receive, process and execute the coordinated higher 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. Brain tissue includes different cells types as well as the space between the cell bodies, often referred to as neuropil, the meshwork of exons, dendrites, synapses and extracellular matrix that embed the central nervous system cells.

Protein-coding genes are classified based on RNA expression in brain from two different perspectives:

  1. A whole-body perspective, comparing gene expression in the brain to peripheral organ and tissue types
  2. A brain-centric point of view comparing gene expression in the various regions of the brain


Brain expression is compared to other organs and tissues by using the highest expression value of all brain regions. For the regional classification the brain is divided into 13 anatomically defined regions, color coded in Figure 1. The transcriptome analysis shows that 82% (n=16507) of all human proteins (n=20090) are expressed in the brain (based on 13 brain regions, spinal cord and corpus callosum). Regional classification was based on 16507 genes are detected in the brain and included in all used external datasets. Out of the genes with regional expression classification, 822 are categorized as genes with a regionally eleveted expression. Regional specific summary pages including lists of regional elavated genes can be found here: cerebral cortex, olfactory bulb, hippocampal formation, amygdala, basal ganglia, thalamus, hypothalamus, midbrain, cerebellum, pons, medulla oblongata, spinal cord as well as white matter.

Figure 1. Midsagittal schematic drawing of the different regions of the human brain, color coded according to the 13 regions.

In addition to the basic regional distribution of gene expression in the human brain, a more detailed overview of gene expression is available. This dataset is based on RNAseq analysis of 1324 samples from several donors, providing a detailed overview of protein expression in more than 200 subregions of the human brain. Gene expression in each subregion can be explored on the gene summary page.

The brain elevated genes, comparing brain to other organs and tissue types

Out of the 16507 genes detected above cut off in the human brain, 2709 genes have an elevated expression in the brain compared to other tissue types. Tissue specificity category defines protein coding genes with elevated expression levels in the brain, while the tissue distribution category indicate transcript detection above cut off (nTPM≥1). The fraction of all protein coding genes in each category is shown Figure 2 and Table 1.

A

B

Figure 2. (A) The distribution of all genes across the five categories based on transcript abundance in brain as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (nTPM≥1) in brain as well as in all other tissues.

Brain expression is determined by expression above cut off (nTPM≥1).

  • Detected in single: Detected only in brain (204)
  • Detected in some: Detected in brain and at least one more tissue, but less than one-third of tissues (2029)
  • Detected in many: Detected in at least a third but not all tissues including brain (5435)

Elevated expression in brain compared to other tissue types is divided into three different categories;

  • Tissue enriched: At least four-fold higher mRNA level in brain compared to any other tissues (517)
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-5 tissues compared to any other tissue (637).
  • Tissue enhanced: At least four-fold higher mRNA level in brain compared to the average level in all other tissues (1555).


Table 1. Number of genes in the subdivided categories of elevated expression in the brain (based on transcript abundance) and the tissue distribution (based on expression above cut off) in the brain.

Distribution in the 36 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Specificity
Tissue enriched 12523613521 517
Group enriched 040720129 637
Tissue enhanced 75449748283 1555
Total 20010921084333 2709


Table 2. The 12 genes with the highest level of enriched expression in the brain and the tissue distribution category for the gene. "mRNA (tissue)" shows the transcript level as nTPM, TS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second-highest tissue.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
HCRT hypocretin neuropeptide precursor Detected in single 352.2 1460
CDR1 cerebellar degeneration related protein 1 Detected in many 38856.0 1159
AVP arginine vasopressin Detected in some 5271.0 860
BARHL1 BarH like homeobox 1 Detected in single 34.3 334
TPH2 tryptophan hydroxylase 2 Detected in single 117.3 256
TMEM88B transmembrane protein 88B Detected in some 416.1 186
GPR101 G protein-coupled receptor 101 Detected in single 12.7 128
F8A2 coagulation factor VIII associated 2 Detected in single 11.6 116
GABRA6 gamma-aminobutyric acid type A receptor subunit alpha6 Detected in single 68.4 109
USP17L15 ubiquitin specific peptidase 17 like family member 15 Detected in single 14.6 102
ANKRD63 ankyrin repeat domain 63 Detected in single 20.2 101
PMCH pro-melanin concentrating hormone Detected in some 97.3 91


Protein localization of genes with elevated expression in the brain compared to other tissues

In-depth analysis of the elevated genes in the brain, using antibody-based protein profiling, allowed us to understand the distribution of the brain specific genes and their protein location. Proteins expressed by the different cell types of the brain were identified among the genes with elevated expression.

Proteins specifically detected in neurons

Neurons are functional entities in the brain and based on location, morphology and neurotransmitter phenotype divided in many subclasses. In the cerebral cortex ELAV-like protein 3 (ELAVL3) is expressed in all neurons. In contrast, glutamate decarboxylase 1 (GAD1), an essential enzyme in the biosynthesis of GABA, is expressed by cortical GABAergic interneurons only. Protocadherin alpha-1 (PCDHA1) is expressed in cerebral cortex and can be detected in a few sparsely distributed interneuron-like neurons.


ELAVL3

GAD1

PCDHA1

Detailed immunohistochemical analysis of proteins with known molecular functions shows that many brain-elevated proteins are involved in synaptic signaling, such as docking of synaptic vesicles (e.g. synaptophysin (SYP)). Also various known post-synaptic proteins including the GABA B receptor subunit 2 (GABBR2) and proteins involved in organizing and maintaining synaptic connections, such as cell adhesion molecule 2 (CADM2) are encountered. These data underline that events associated with synaptic transmission require specialized proteins, most often with an enriched expression level in the brain compared to peripheral tissue types.


SYP

GABBR2

CADM2

Proteins specifically detected in glial cells

Glial cells can be subdivided into astrocytes, oligodendrocytes and microglia based on morphology and functions (https://dev.www.proteinatlas.org/humanproteome/single+cell+type/glial+cells).

The well-known astrocyte marker GFAP as well as the unexplored gene TAFA1 are detected in astrocytes of both the white and grey matter. In contrast, the water transporter AQP4 is mainly detected in the grey matter and reveals a neuropil-like staining pattern due to the localization of the protein in numerous glia endfeet.


GFAP

TAFA1

AQP4

Several genes expressed in oligodendrocytes are involved in myelination, such as the compact myelin proteins myelin basic protein (MBP) and proteolipid protein 1 (PLP1). In contrast to the oligodendrocyte transcription factor OLIG2, none of the other investigated myelin sh components are brain specific. MBP and PLP1 are enriched but this is mainly due to the sample composition containing 25% densely myelinated white matter. Expression above cut off is found in several peripheral tissue types and immunohistochemical analysis reveals that this expression mainly represents Schwann cells in peripheral nerves.


MBP

PLP1

OLIG2

The third type of glial cells 'populating' the brain is microglia. These cells are derived from hematopoietic stem cells invading the brain during embryonic development or macrophages that enter the brain from the bloodstream later in life. The well-known microglia genes integrin alpha M chain (ITGAM) and allograft inflammatory factor 1 (AIF1) are not specific nor enriched in the brain but are also expressed, for example, in cells populating the lymph node and bone marrow, the main site of hematopoiesis. Based on our immunohistochemistry analysis we can only identify one microglia gene, purinoceptor P2RY12, enhanced in brain tissue, with low expression in lymph node and bone marrow. These data show the close relationship of microglia and hematopoietic cells reflecting the common developmental origin of microglia and macrophages.


ITGAM

AIF1

P2RY12


Regional expression within the brain

The regional organization of the 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 additional classification of the expression within brain. Identical strategy, as used for the tissue type classification, was applied to the regional data resulting in regionally elevated genes (separated into regionally enriched, group enriched and regionally enhanced).

  • 822 genes classified as regionally elevated
  • 378 genes are brain elevated as well as regionally elevated
  • Cerebellum has the most regionally enriched genes (n=17)
  • 385 regionally elevated genes are elevated in other tissues than brain

Figure 3. 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 nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations up to 2 genes and 5 regions, but the resulting lists show the complete set of group enriched genes in the particular region.

Table 3, The 13 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 for that specific region is used as representative). Same classification rules are used for the regional classification as the tissue specificity classification based on tissue types

Table 4. The 12 genes with the highest level of regional enriched expression within the brain and the regional distribution category. "mRNA (region)" shows the transcript level as nTPM values, RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.

Gene Description Predicted location RS-score
MTRNR2L10 MT-RNR2 like 10 Intracellular,Secreted 43
AGRP Agouti related neuropeptide Secreted 40
HSPA1A Heat shock protein family A (Hsp70) member 1A Intracellular 39
GPR151 G protein-coupled receptor 151 Membrane 37
EDN3 Endothelin 3 Intracellular,Secreted 32
AL359092.3 Novel protein Intracellular 27
TRBV7-2 T cell receptor beta variable 7-2 Intracellular 18
CCL18 C-C motif chemokine ligand 18 Secreted 17
SLC6A3 Solute carrier family 6 member 3 Membrane 17
CST2 Cystatin SA Secreted 13
CYP4B1 Cytochrome P450 family 4 subfamily B member 1 Intracellular,Membrane 13
SPATA31E1 SPATA31 subfamily E member 1 Membrane 13


Proteins elevated in some regions of the brain


PNOC - Cerebral cortex

ADORA2A - Caudate (basal ganglia)

HDC - Hypothalamus


SLC6A3 - Substantia nigra (midbrain)

TPH2 - Dorsal raphe (midbrain)

ARHGEF33 - Cerebellum


Comparing tissue classification with regional expression in the brain

The majority of brain elevated genes are classified as low regional specificity (n=2331) and 378 genes are brain elevated as well as regionally elevated. Among the genes classified as brain elevated and low regional specificity several glial specific proteins are found, for example GFAP and AQP4 as well as MBP. In contrast, neuronal proteins are more often found among the regionally elevated genes, such as ADORA2A and AVP. Interestingly, there are many brain interesting proteins classified as elevated in other tissues than brain, such as ANK1 elevated in skeletal muscle and TFAP2B elevated in epididymis, as well as the widely expressed CRYAB localized to white matter that is elevated in heart and skeletal muscle. This highlights the importance of mapping expression and localization from multiple perspectives to better understand the biology and brain physiology.


ANK1

TFAP2B

CRYAB

Table 5. Overlap between tissue classification, indicating elevated expression in the brain or not, with the regional specificity within the brain. (The regional classification of human brain expression is limited by available external data, thus do not cover all human protein-coding genes.

Regionally elevated Low regional specificity Missing regional classification Total
Elevated in brain 378 2331 0 2709
Elevated in other tissue but expressed in brain 385 5245 0 5630
Low tissue specificity 59 8109 65 8233
Total 822 15685 1113 16270

Gene expression shared between brain and other tissues

There are 637 group enriched genes expressed in the brain. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including brain, compared to all other tissues.

In order to illustrate the relation of brain tissue to other tissue types, a network plot was generated, displaying the number of genes shared between different tissue types. The common origin of neuroectoderm is a plausible reason for the relatively high number of genes connecting brain with adrenal gland and pancreas. However, a clear connection for the large number of genes shared between testis and brain could not be revealed, neither by gene ontology analysis or immunohistochemical analysis and further investigations are needed. The network plot reveals that most group enriched genes are shared with the testis (n=122). The large number of group enriched genes related to brain and skeletal muscle is possibly due to shared signaling functions. The group enriched genes shared with pituitary gland is expected since half of the pituitary gland (posterior lobe) originates from the brain and both neuronal and glial cells are located in the gland. Several group enriched genes are shared with the fallopian tube, mainly related to ciliated cells that are found in the ependymal cells of the ventricle walls.

Figure 4. An interactive network plot of the brain enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of brain enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.


SH3GL3 is implicated in neuronal endocytosis, and group enriched in brain and testis. Immunohistochemical analysis shows the encoded protein to be expressed in sperm cells and neuropil.


SH3GL3 - testis

SH3GL3 - cerebral cortex

AQP4 is also group enriched and show highest expression value in brain and lung.


AQP4 - cerebral cortex

AQP4 - lung

SPTB is group enriched and show high expression value in brain and skeletal muscle, located to the membrane of neurons as well as skeletal muscle.
SPTB - skeletal muscle

SPTB - cerebellum

Ciliated cells in fallopian tube and respiratory epithelium share several proteins with the ciliated ependymal cells in the brain, resulting in several genes classified as group enriched, such as FOXJ1 and RSPH1.


FOXJ1 - caudate

FOXJ1 - fallopian tube

FOXJ1 - bronchus


RSPH1 - caudate

RSPH1 - fallopian tube

RSPH1 - bronchus

Relevant links and publications

Sjöstedt E et al., An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. (2020)
PubMed: 32139519 DOI: 10.1126/science.aay5947

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Yu NY et al., Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res. (2015)
PubMed: 26117540 DOI: 10.1093/nar/gkv608

Sjöstedt E et al., Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PLoS One. (2015)
PubMed: 26076492 DOI: 10.1371/journal.pone.0130028

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600