Midbrain

Summary

The midbrain is located between forebrain and hindbrain and is commonly segmented into tectum, aqueduct, tegmentum, basis pedunculi. Developmentally, midbrain emerges from the second vesicle of neural tube and does not sub-divide further, in comparison to other brain regions. The midbrain is involved in functions such as the processing of visual and auditory information, facilitating homeostatic reflexes and motor coordination.

The transcriptome analysis shows that 73% (n=14641) of all human protein-coding genes (n=20090) are expressed in the human midbrain (represented by RNA expression in substantia nigra). Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 12147 of all mouse one-to-one orthologues (n=16320) are expressed in the mouse midbrain and that 13335 of all pig orthologues (n=15829) are expressed in the pig midbrain.

Gene classification based on regional RNA expression in human, pig and mouse midbrain defines 43 genes as midbrain enriched in either of the three species, and 11 out of those genes show highest expression levels in midbrain in all three species.

Figure 1. Schematic drawing of the human brain, indicating the location of midbrain from a sagittal view.

Anatomical divisions

The midbrain grey matter can be divided into the pretectal region, tegmentum, and tectum. The pretectal area, situated close to the forebrain, is part of the mediation of pupal reflexes and is indicated in the induction of REM sleep. Within the tegmentum resides periaqueductal grey (anterior, dorsal, and lateral part) which envelops the cerebral aqueduct and is involved in the visual system as well as implicated in pain suppression. Other important nuclei in the midbrain are the dorsal raphe and median raphe nucleus. The dorsal raphe nucleus projects to amygdala, cerebral cortex, caudate, putamen and olfactory bulb. While the median raphe nucleus outputs target the hippocampus and are involved in long-term memory formation. Both nuclei are implicated in depression.


TPH2 - Dorsal raphe

SLC6A4 - Dorsal raphe

PAK1 - Dorsal raphe

SNCG - Median raphe

Moreover, in tegmentum is the ventral tegmental area which is the largest centre for production of dopamine in the brain. It has outputs targeting several brain regions e.g., the hippocampal formation, amygdala, and olfactory bulb. It is implicated in functions concerning the reward system and addiction, cognition, and psychiatric disorders. The cuneiform nucleus and the pedunculopontine tegmental nucleus are part of the mesencephalic locomotor region and are in the dorsolateral portion of tegmentum. Centrally in the tegmentum is the large structure the red nucleus that is involved in motor coordination. Another area of tegmentum involved in motor functions as well as the reward system is the substantia nigra. The substantia nigra is divided into two parts: 1) pars compacta (that projects to the caudate nucleus and putamen via the dopaminergic nigrostriatal pathway); 2) pars reticulata (that receives inputs from basal ganglia, via the direct and indirect pathway). It is a large group of pigmented dopaminergic neurons that together with globus pallidus, caudate nucleus, and putamen form the striatum. Additionally, the substantia nigra is implicated in Parkinson’s disease.


TH - Ventral tegmental area

SNCG - Substantia nigra

DRD2 - Substantia nigra

SLC6A3 - Substantia nigra

Tectum is the dorsal part of the midbrain. A major part of tectum is comprised of the superior colliculus and inferior colliculus which, respectively, play a role in the processing of visual and auditory information

Regionally elevated protein expression in human

The transcriptome analysis shows that 73% (n=14641) of all human proteins (n=20090) are expressed in the midbrain. 77 genes show an elevated expression level in midbrain compared to other regions of the brain.

  • 23 regionally enriched genes
  • 77 regionally elevated genes in total
  • 43 of the midbrain elevated genes are elevated in other tissues than the brain.
  • 34 of the midbrain elevated genes are elevated in the brain.


Table 1: Schematic drawing of the human brain, indicating the location of midbrain from a coronal perspective or sagittal view.

Specificity Number of Human elevated genes
Region enriched 23
Group enriched 23
Region enhanced 31
Elevated 77

Elevated expression in midbrain compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in midbrain 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 midbrain 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 amongof the 23 genes with high level of regional specificity are listed.

Table 2. The 12 genes with the highest level of enriched expression in human midbrain. "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.

Gene Description Predicted location RS-score
GPR151 G protein-coupled receptor 151 Membrane 37
TRBV7-2 T cell receptor beta variable 7-2 Intracellular 18
SLC6A3 Solute carrier family 6 member 3 Membrane 17
AIPL1 Aryl hydrocarbon receptor interacting protein like 1 Intracellular 12
IGKV1D-33 Immunoglobulin kappa variable 1D-33 Intracellular,Secreted 11
PITX3 Paired like homeodomain 3 Intracellular 11
NEUROG1 Neurogenin 1 Intracellular 10
TPH1 Tryptophan hydroxylase 1 Intracellular 10
COL6A5 Collagen type VI alpha 5 chain Intracellular,Secreted 9
NEUROD4 Neuronal differentiation 4 Intracellular 9
CRX Cone-rod homeobox Intracellular 8
IMPG2 Interphotoreceptor matrix proteoglycan 2 Membrane,Secreted 8


SLC6A3 - Substantia nigra

SLC6A3 - Caudate nucleus

Regionally elevated protein expression in mouse

The whole mouse midbrain was dissected and used for this analysis, mean value of the 2 male and 2 female mice is used as representative of the midbrain.

The transcriptome analysis shows that 60% (n=12147) of all mouse one-to-one human orthologue genes (n=16320) are expressed in the midbrain and 45 genes show an elevated expression in midbrain compared to other regions of the brain.

Table 3: Number of genes within the different categories of regionally elevated expression, in mouse midbrain

Specificity Number of Mouse elevated genes
Region enriched 8
Group enriched 27
Region enhanced 10
Elevated 45


Figure 2. Schematic drawing of the mouse brain, indicating the location of midbrain from a sagittal view.

Table 4: The 8 genes with the highest level of enriched expression in mouse midbrain. "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 tissue.

Gene Description Predicted location RS-score
PAX7 Paired box 7 Intracellular 17
PAX5 Paired box 5 Intracellular 11
GATA3 GATA binding protein 3 Intracellular 6
POU4F2 POU class 4 homeobox 2 Intracellular 6
EN1 Engrailed homeobox 1 Intracellular 5
TAL1 TAL bHLH transcription factor 1, erythroid differentiation factor Intracellular 5
SLC6A4 Solute carrier family 6 member 4 Membrane 4
TFAP2D Transcription factor AP-2 delta Intracellular 4


PAX5

SLC6A4

Regionally elevated protein expression in pig

Figure 3. Schematic drawing of the pig brain, indicating the location of midbrain from a sagittal view.

Elevated expression in midbrain compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in midbrain 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 midbrain compared to the average of all regions).

The substantia nigra, superior colliculus and periaqueductal gray were dissected out as separate areas of the midbrain and analyzed separately from the remaining midbrain area. The highest expression value of the 4 midbrain samples was used as representative for midbrain in the regional expression comparison.

The transcriptome analysis shows that 66% (n=13335) of all pig one-to-one human orthologue genes (n=15829) are expressed in the midbrain. 106 genes show an elevated expression in midbrain compared to other regions of the brain.


Table 5: Number of genes within the different categories of regionally elevated expression, in pig midbrain

Specificity Number of Pig elevated genes
Region enriched 18
Group enriched 37
Region enhanced 51
Elevated 106

Table 6: The 12 genes with the highest level of enriched expression in pig midbrain. "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.

Gene Description Predicted location RS-score
SLC6A3 Solute carrier family 6 member 3 Membrane 152
TH Tyrosine hydroxylase Intracellular 20
FERD3L Fer3 like bHLH transcription factor Intracellular 16
INS Insulin Secreted 13
ASB4 Ankyrin repeat and SOCS box containing 4 Intracellular 10
FOXA2 Forkhead box A2 Intracellular 9
SPDEF SAM pointed domain containing ETS transcription factor Intracellular 7
TTC6 Tetratricopeptide repeat domain 6 Intracellular 7
ALDH1A1 Aldehyde dehydrogenase 1 family member A1 Intracellular 6
CHRNA6 Cholinergic receptor nicotinic alpha 6 subunit Intracellular,Membrane 6
EN1 Engrailed homeobox 1 Intracellular 6
FOXA1 Forkhead box A1 Intracellular 6

Extended information

Table 7. The following 5 genes have been analyzed using extended midbrain samples.

Gene Gene description Tissue Staining pattern
DBH Dopamine beta-hydroxylase Dorsal raphe Strong synaptic and projection staining, membranous staining in neurons.
PRPH Peripherin Dorsal raphe Cytoplasmic positivity in a subset of neurons.
SLC6A3 Solute carrier family 6 member 3 Dorsal raphe Rare projection positivity.
SLC6A3 Solute carrier family 6 member 3 Substantia nigra Strong cytoplasmic staining in neurons.
SLC6A4 Solute carrier family 6 member 4 Dorsal raphe Strong membrane staining in a few neurons. Synaptic and projection staining.
TPH2 Tryptophan hydroxylase 2 Dorsal raphe Strong neuronal staining.

Substantia nigra and Parkinsson's disease

This movie shows 3D light sheet microscopy scans of the neurons that are affected by Parkinson´s disease, the dopamine producing neurons located in the substantia nigra. Interview: Prof Per Svenningsson, Karolinska Institutet.