Hypothalamus

Summary

The hypothalamus is a part of the diencephalon, together with the thalamus, epithalamus, subthalamus and meta-thalamus. The hypothalamus develops from the embryonic diencephalon and is located at the bottom of the diencephalon. In humans, it is an almond-like structure. The hypothalamus is the center of the vegetative nervous system as well as a key regulator of the endocrine system.

The transcriptome analysis has revealed that 74% (n=14773) of all human protein-coding genes (n=20090) are expressed in the human hypothalamus. Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 12272 of all mouse one-to-one orthologues (n=16320) are expressed in the mouse hypothalamus and that 13044 of all pig orthologues (n=15829) are expressed in the pig hypothalamus.

Gene classification based on regional RNA expression in human, pig and mouse hypothalamus defines 75 genes as hypothalamus enriched in either of the three species, and 20 out of those genes show highest expression levels in hypothalamus in all three species.

Figure 1. Schematic drawing of the human brain, indicating the location of hypothalamus below the thalamus, at the bottom of diencephalon from a sagittal view.

Anatomical divisions

Anatomically, the hypothalamus can be divided into anterior, tuberal and posterior parts. The anterior part involves the preoptic nucleus (thermoregulation), the medial preoptic nucleus (releases GnRH hormone), supraoptic nucleus (releases oxytocin - OXT and vasopressin - AVP), the paraventricular nucleus (releases the thyrotropin releasing hormone - TRH, corticotropin releasing factor - CRH, oxytocin, vasopressin and somatostatin hormones), the anterior hypothalamic nucleus (involved in thermoregulation) and the suprachiasmatic nucleus (involved in the regulation of the circadian rhythms). The tuberal hypothalamus consists of a medial and a lateral part. The medial part involves the dorsomedial- (regulation of blood pressure and heart rate), ventromedial- (regulation of satiety) and arcuate nucleus (regulation of food intake, among others). The lateral part of the tuberal hypothalamus is a complex hub of neuronal networks; it contains, among others, the orexin and MCH neurons that regulate food intake and the sleep/wake cycle. The lateral hypothalamus partially extends also to the anterior and posterior hypothalamus. The posterior hypothalamus consists of the mammillary nuclei, the lateral nucleus (that is involved in the regulation of blood pressure) and the tuberomammillary nucleus (that is involved in the regulation of arousal, energy balance, learning-memory processes and sleep).


GNRH1

TRH

PMCH

Histologically, the hypothalamus could be divided into magnocellular and microcellular neurosecretory neurons and non-secretory neurons. The magnocellular neurons release oxytocin and vasopressin in the neurohypophysis. The axons of these magnocellular neurons form the suproopticohyphophyseal tract. The microcellular neurons secrete the ‘releasing’ and ‘release inhibiting’ hormones to the portal veins that will transport these hormones to the adenohypophysis. The axons of the microcellular neurons form the tuberoinfundibular tract. The non-secretory neurons are involved in the regulation of multiple and complex vegetative functions. The tuberomammillary and mammillary nuclei are important parts of the limbic-system. The hypothalamic neurons express several neuropeptides and several hypothalamic neuronal populations and sub-populations can be identified by their neuropeptide markers (e.g. orexin- and MCH-expressing neurons in the lateral hypothalamus; NPY- and POMC-expressing neurons in the arcuate nucleus etc.)


GAL

GAL

NUCB2

Galanin (GAL) is a physiologically active neuropeptide that is implicated in nociception, feeding and energy homeostasis, osmotic regulation and water balance. Galanin immunoreactivity can be observed in the tuberal hypothalamus. Nucleobindin 2 (NUCB2) is a calcium-binding protein and has a role in eating regulation in the hypothalamus NUCB2 immunoreactivity is observed in the hypothalamic paraventricular nucleus.

Regionally elevated protein expression in human

The transcriptome analysis shows that 74% (n=14773) of all human proteins (n=20090) are expressed in the hypothalamus. 152 genes show an elevated expression level in hypothalamus compared to other regions of the brain.


  • 55 regionally enriched genes
  • 152 regionally elevated genes in total
  • 96 of the hypothalamus elevated genes are elevated in other tissues than the brain.
  • 56 of the hypothalamus elevated genes are elevated in the brain.


Table 1: Number of genes within the different categories of regionally elevated expression, in human hypothalamus.

Specificity Number of Human elevated genes
Region enriched 55
Group enriched 37
Region enhanced 60
Elevated 152

Elevated expression in hypothalamus compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in hypothalamus 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 hypothalamus 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 among the 55 enriched genes are listed.

Table 2. The 12 genes with the highest level of enriched expression in human hypothalamus. "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
AGRP Agouti related neuropeptide Secreted 40
EDN3 Endothelin 3 Intracellular,Secreted 32
CST2 Cystatin SA Secreted 13
CYP4B1 Cytochrome P450 family 4 subfamily B member 1 Intracellular,Membrane 13
AVP Arginine vasopressin Secreted 12
GHRH Growth hormone releasing hormone Secreted 12
LEFTY2 Left-right determination factor 2 Secreted 12
PRG4 Proteoglycan 4 Secreted 12
PGAP1 Post-GPI attachment to proteins inositol deacylase 1 Intracellular,Membrane 11
GAL Galanin and GMAP prepropeptide Secreted 10
LIF LIF interleukin 6 family cytokine Intracellular,Secreted 10
IL6 Interleukin 6 Intracellular,Secreted 9



HCRT

AVP

OTP


AGRP

HDC

The (HCRT) gene produces two neuropeptides, orexin A and orexin B, and are implicated in the regulation of sleep and might also play a role in feeding behavior and homeostasis. Vasopressin (AVP) is synthesized in the supraoptic nucleus and paraventricular nucleus of the hypothalamus and is transported to the nerve endings in the neurohypophysis. When secreted into the bloodstream, vasopressin acts as an antidiuretic hormone in the kidneys. OTP is a transcription factor involved in the development of the hypothalamus. The agouti related neuropeptide (AGRP) has a role in feeding control and weight homeostasis. The HDC protein controls several processes such as gastric acid secretion and smooth muscle contraction.


Regionally elevated protein expression in mouse

The mouse hypothalamus is anatomically similar to the human hypothalamus, with similar topography of nuclei and similar neurochemical character (e.g. neuropeptide-expression) of the homologous nuclei.

The transcriptome analysis shows that 61% (n=12272) of all mouse one-to-one human orthologue genes (n=16320) are expressed in the hypothalamus and 97 genes show an elevated expression in hypothalamus compared to other regions of the brain.

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

Specificity Number of Mouse elevated genes
Region enriched 25
Group enriched 39
Region enhanced 33
Elevated 97



Figure 2. Schematic drawing of the mouse brain, indicating the location of hypothalamus from a sagittal perspective.

Elevated expression in hypothalamus compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in hypothalamus 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 hypothalamus 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 25 enriched genes are listed.

Table 4: The 12 genes with the highest level of enriched expression in mouse hypothalamus. "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
NR5A1 Nuclear receptor subfamily 5 group A member 1 Intracellular 52
NKX2-4 NK2 homeobox 4 Intracellular 23
NPVF Neuropeptide VF precursor Secreted 18
AGRP Agouti related neuropeptide Secreted 16
SIX6 SIX homeobox 6 Intracellular 14
FEZF1 FEZ family zinc finger 1 Intracellular 11
FOXB2 Forkhead box B2 Intracellular 11
AVP Arginine vasopressin Secreted 10
HIGD1C HIG1 hypoxia inducible domain family member 1C Membrane 10
GHRH Growth hormone releasing hormone Secreted 9
SIM1 SIM bHLH transcription factor 1 Intracellular 8
OTP Orthopedia homeobox Intracellular 7


HCRT

AVP

OTP

Orexin (HCRT) immunostaining in the lateral hypothalamus. Vasopressin (AVP) peptide immunostaining in the paraventricular hypothalamic nucleus. Orthopedia homeobox protein (OTP) localization in the hypothalamic paraventricular nucleus.


Regionally elevated protein expression in pig

The pig hypothalamus is anatomically similar to the human hypothalamus, with similar topography of nuclei and similar neurochemical character (e.g. neuropeptide-expression) of the homologous nuclei.

The transcriptome analysis shows that 65% (n=13044) of all pig one-to-one human orthologue genes (n=15829) are expressed in the hypothalamus. 42 genes show an elevated expression in hypothalamus compared to other regions of the brain.

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

Specificity Number of Pig elevated genes
Region enriched 11
Group enriched 20
Region enhanced 11
Elevated 42

Figure 3. Schematic drawing of the pig brain, indicating the location of hypothalamus from a sagittal perspective.

Elevated expression in hypothalamus compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in hypothalamus 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 hypothalamus 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 11 enriched genes are listed.

Table 6: The 12 genes with the highest level of enriched expression in pig hypothalamus. "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
CGA Glycoprotein hormones, alpha polypeptide Secreted 40
PMCH Pro-melanin concentrating hormone Secreted 34
HCRT Hypocretin neuropeptide precursor Secreted 21
FEZF1 FEZ family zinc finger 1 Intracellular 14
SIX6 SIX homeobox 6 Intracellular 12
NKX2-4 NK2 homeobox 4 Intracellular 11
BSX Brain specific homeobox Intracellular 10
GPR50 G protein-coupled receptor 50 Membrane 10
NPVF Neuropeptide VF precursor Secreted 8
NR5A1 Nuclear receptor subfamily 5 group A member 1 Intracellular 8
POMC Proopiomelanocortin Secreted 5


Extended information

3D imaging of mouse brain

This video demonstrates the 3D distribution of orexin immunostaining (HCRT) in the mouse lateral hypothalamus (iDISCO volume immunostaining). A descriptive movie including more details and an interview with Dr. Csaba Adori, Karolinska Institute, related Orexin and Narcolepsy is found here.


List of proteins stained on human hypothalamus tissue section

The standard setup in the Tissue Atlas, which profiles the human tissues, is based on Tissue Micro array technique, thus saving valuable tissue material and reagents. The TMA technique provides a wide tissue representation for protein profiling. Cerebral cortex, caudate nucleus, hippocampus and cerebellum are the four brain regions in the standard human brain profiling. In-depth analysis of the elevated genes in hypothalamus and literature search for hypothalamus-associated proteins served as a strategy when selecting which proteins to analyze in human hypothalamus samples.

Table 7. The following 41 genes have been analyzed using extended hypothalamus samples.

Gene Gene description Staining pattern
ADCYAP1 Adenylate cyclase activating polypeptide 1 Synaptic staining.
AGRP Agouti related neuropeptide Strong staining of synapses and neuronal projections
ARHGAP36 Rho GTPase activating protein 36 Strong in neuronal cells, synapses and projections.
AVP Arginine vasopressin Strong cytoplasmic staining in magnocellular neurosecretory neurons.
CALCR Calcitonin receptor Strong membranous staining in neurons.
CALY Calcyon neuron specific vesicular protein Cytoplasmic staining in neurons.
CARTPT CART prepropeptide Neuronal projections and synaptic positivity.
CCK Cholecystokinin Strong neuronal projection and extracellular staining.
CNGA3 Cyclic nucleotide gated channel subunit alpha 3 Stains in neural projections and neuronal cell bodies.
CRABP1 Cellular retinoic acid binding protein 1 Strong in a subset of hypothalamic neurons.
DDX25 DEAD-box helicase 25 Strong staining processes and in subsets of astrocyte-like cells.
ECEL1 Endothelin converting enzyme like 1 Strong in neurons.
FEZF1 FEZ family zinc finger 1 Distinct positivity in processes and neuropil of hypothalamus.
GAL Galanin and GMAP prepropeptide Strong cytoplasmic positivity in neuronal cells and projections.
GATA2 GATA binding protein 2 Nuclear staining in a few neurons.
GNRH1 Gonadotropin releasing hormone 1 Strong cytoplasmic staining in a subset of hypothalamic neuronal cells.
GRIN2D Glutamate ionotropic receptor NMDA type subunit 2D Membranous and cytoplasmic staining in neurons. Projections and synapses are also positive.
HCRT Hypocretin neuropeptide precursor Strong staining in a subset of hypothalamic neurons.
HCRTR1 Hypocretin receptor 1 Positive projections and synapses.
HDC Histidine decarboxylase Strong staining in neurons of hypothalamus.
HMX2 H6 family homeobox 2 Strong staining in neurons and projections/synapses.
HTR7 5-hydroxytryptamine receptor 7 Cytoplasmic in a subset of neurons. Distinct staining in neuronal projections.
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