Extended brain samples



The Tissue atlas is based on immunohistochemical staining of tissue microarrays from 44 different normal tissue types. In addition to the standard setup, extended tissue profiling is performed for selected proteins, to give a more complete overview on where the protein is expressed. Extended tissue samples include mouse brain, human lactating breast, eye, thymus and additional samples of adrenal gland, skin and brain. For extended brain samples, both tissue microarrays with 1 mm diameter cores and tissue section samples are used.

The full list of proteins analyzed in extended brain samples is found in Table 1.


Cerebral cortex


The cerebral cortex (also known as the neocortex) is a complex, multilayered (six layers), highly organized structure, and the outer layer of the brain in humans and most mammals. The cerebral cortex contains a high number of different neuronal and glial cells types. The cortical neurons comprise mainly of two classes: the interneurons and the pyramidal (projection) neurons, which can further be classified based on morphological and molecular signatures. The cerebral cortex is included in the standard tissue microarray setup. Extended protein profiling, using a tissue section (15 x 20 mm) from human cerebral cortex frontal lobe, was performed in order to give a wider perspective of the protein localization and assess protein expression in cells that are not included in the standard setup due to tissue sampling. The gene tachykinin precursor 1 (TAC1) encodes several forms of active peptide hormones which function in neuronal excitation, and as vasodilators and secretagogues. TAC1 is expressed in a subset of cortical neurons (Figure 1).

Figure 1. Immunohistochemical staining of human cerebral cortex using an antibody toward TAC1 shows strong cytoplasmic staining in a subset of neuronal cells.

Hypothalamus and pituitary gland


The hypothalamus, a part of the diencephalon (interbrain), is located below the thalamus and above the pituitary gland. The hypothalamus is considered to be the link between the nervous and endocrine system, and plays an essential role in metabolism and homeostasis – by regulating the autonomic nervous system, production of hormones (via the pituitary gland), and controlling body temperature. The hypothalamus is also involved in regulation of behavior, food intake and circadian rhythm. The hypothalamus can be divided into three different regions based on structure and function; the anterior, tuberal and posterior regions, which further can be structured into several nuclei and functional areas. Extended protein profiling in human hypothalamus was performed using large tissue sections (20 x 30 mm). Only images representing regions of interest are selected for inclusion on the Human Protein Atlas.

The pro-melanin concentrating hormone (PMCH) encodes a preproprotein, and is proteolytically processed to generate multiple proteins. PMCH is mainly expressed in a subset of hypothalamic neurons (Figure 2).

Figure 2. Immunohistochemical staining of human hypothalamus using an antibody toward PMCH shows strong cytoplasmic staining in neuronal cells.


The pituitary gland (also called hypophysis) consists of two glands, the anterior (adeno) pituitary gland, and the posterior (neuro) pituitary gland. The anterior pituitary gland is divided into three regions: pars distalis, pars tuberalis and pars intermedia. These structures consist mainly of hormone-producing epithelial cells that store hormones and other molecules in secretory granules, to later be released in the bloodstream to act on various tissues. One example is pleiotrophin (PTN), a secreted heparin-binding growth factor. PTN plays a significant role in cell growth, migration, angiogenesis and tumorigenesis. PTN is expressed in the anterior pituitary gland (Figure 3). The posterior pituitary gland consists mainly of unmyelinated axons of secretory neuronal cells located in the supraoptic and periventricular nuclei of the hypothalamus. The neurons produce a neurosecretory material, containing antidiuretic hormones and oxytocin, which travels along the axons from the hypothalamic neurons to the nerve endings in the posterior pituitary, specifically to the pars nervosa - the main structure of the posterior gland.

Extended protein profiling in human anterior pituitary gland was performed using a tissue microarray with 1 mm diameter cores.

Figure 3. Immunohistochemical staining of human pituitary gland toward PTN shows strong cytoplasmic positivity in endocrine cells.


Hippocampal formation


Located in the medial temporal lobes, surrounded by the entorhinal, parahippocampal and perirhinal cortices, lies the hippocampus. The hippocampus belongs to the limbic system. The dorsal part is involved in episodic memory and spatial navigation, while the ventral hippocampus is implicated in emotion-related connections. The hippocampus is included in the standard tissue microarray setup. Extended protein profiling of human hippocampus, using a tissue section (20 x 30 mm) which includes the dentate gyrus/hippocampal cornus ammonis (CA) areas, was performed in order to give a wider perspective of the protein localization and to assess protein expression in cells that are not included in the standard setup due to factors related to tissue sampling. The PTPRN gene encodes a member of the protein tyrosine phosphatase family, that regulates a variety of cellular processes including cell growth and differentiation. PTPRN is expressed in neuronal and neuroendocrine tissues, such as islets of Langerhans, and in hippocampal neurons (Figure 4). Only images representing regions of interest are selected for inclusion on the Human Protein Atlas.

Figure 4. Immunohistochemical staining of human hippocampus toward PTPRN shows moderate cytoplasmic positivity in neuronal cells.

Caudate nucleus and the basal ganglia


The caudate nucleus lies in the dorsal striatum, one of several subcortical nuclei, situated at the base of the forebrain, that constitutes the basal ganglia. The basal ganglia include dorsal striatum (caudate, putamen), ventral striatum (nucleus accumbens), substantia nigra, subthalamic nucleus and globus pallidus. The dorsal striatum receives glutamatergic signals from the cortex and projects mainly through dopaminergic signals to substantia nigra and globus pallidus. One important function of the basal ganglia is to initiate, stop and fine-tune movements. Disruptions in this system are found in diseases like Parkinson's disease and Huntington's disease. The SLC6A3 gene encodes the dopamine transporter 1 (DAT1), an important protein in the caudate. This membrane-bound protein will pump dopamine from the synaptic cleft back into the cytosol of the cell. DAT1 can be manipulated with different drugs, cocaine being the most apparent one where the pump function of this protein is inhibited.

Extended protein profiling of human caudate nucleus, using a tissue section (22 x 17 mm) was performed in order to give a wider perspective of the protein localization and to assess protein expression in areas of the caudate that are not included in the standard setup due to factors related to tissue sampling.

Figure 5. Immunohistochemical staining of human caudate nucleus toward SLC6A3 shows strong synaptic positivity.


Table 1. The following 107 genes have been analyzed using extended brain samples.

Gene Gene description Tissue Staining pattern
ADORA2A Adenosine A2a receptor Caudate Cytoplasmic positivity in subset of neurons. Synaptic and neuronal projection positivity.
ADRB3 Adrenoceptor beta 3 Caudate Strong neuronal projection positivity.
ARHGAP36 Rho GTPase activating protein 36 Pituitary gland Strong cytoplasmic staining in a subset of cells in anterior pituitary gland.
AVP Arginine vasopressin Hypothalamus Strong cytoplasmic staining in magnocellular neurosecretory neurons.
AVPR1B Arginine vasopressin receptor 1B Pituitary gland Strong membranous and cytoplasmic staining in anterior pituitary cells.
CALCR Calcitonin receptor Hypothalamus Strong membranous staining in neurons.
CALY Calcyon neuron specific vesicular protein Cerebral cortex Strong staining in neurons, neuronal projections and a subset of glial cells.
CALY Calcyon neuron specific vesicular protein Caudate Strong cytoplasmic staining in neurons.
CALY Calcyon neuron specific vesicular protein Hypothalamus Cytoplasmic staining in neurons.
CARTPT CART prepropeptide Hypothalamus Synaptic and axonal staining.
CCK Cholecystokinin Hypothalamus Strong neuronal projection and extracellular staining.
CDH9 Cadherin 9 Cerebral cortex Membranous and cytoplasmic staining in neurons.
CGA Glycoprotein hormones, alpha polypeptide Pituitary gland Anterior lobe of pituitary gland strongly stained.
CHGB Chromogranin B Pituitary gland Strong in anterior pituitary gland.
CHRNA5 Cholinergic receptor nicotinic alpha 5 subunit Cerebral cortex Strong staining in astrocytes.
CHRNA5 Cholinergic receptor nicotinic alpha 5 subunit Hippocampus Strong staining in astrocytes.
CHST14 Carbohydrate sulfotransferase 14 Pituitary gland Strong cytoplasmic staining in subsets of cells in anterior pituitary.
CHST8 Carbohydrate sulfotransferase 8 Pituitary gland Strong cytoplasmic positivity in anterior pituitary gland.
CNGA3 Cyclic nucleotide gated channel alpha 3 Hypothalamus Stains in neural projections and neuronal cell bodies.
COL22A1 Collagen type XXII alpha 1 chain Pituitary gland Strong intracellular staining in a subset of cells in anterior pituitary gland.
CRABP1 Cellular retinoic acid binding protein 1 Hypothalamus Strong in a subset of hypothalamic neurons.
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Relevant links and publications


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

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

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