THE HUMAN TISSUE PROTEOMES

The adipose tissue-specific proteome


Adipose tissue (fat) is a highly specialized loose connective tissue mainly formed by adipocytes and has a number of physiological functions including storage of energy and secretion of hormones such as leptin. Adipose tissue insulates and protects the organs. Fat is located around organs (visceral fat) and beneath the skin (subcutaneous). The transcriptome analysis shows that 68% of all human proteins (n=19628) are expressed in the adipose tissue and 166 of these genes show an elevated expression in adipose tissue compared to other tissue types. An analysis of the genes with elevated expression in the adipose tissue shows that several are involved in regulation of lipid metabolic processes, regulation of secretion, organ morphogenesis and regulation of transport.

  • 17 adipose tissue enriched genes
  • Most of the tissue enriched genes encode proteins involved in metabolism
  • 166 genes defined as elevated in the adipose tissue
  • Most group enriched genes share expression with the liver

Figure 1. The distribution of all genes across the five categories based on transcript abundance in adipose tissue as well as in all other tissues.


166 genes show some level of elevated expression in the adipose tissue compared to other tissues. The three categories of genes with elevated expression in adipose tissue compared to other organs are shown in Table 1. The list of tissue enriched genes (n=17) are well in-line with the function of the adipose tissue.

Table 1. The genes with elevated expression in adipose tissue

Category

Number of genes

Description

Tissue enriched 17 At least five-fold higher mRNA levels in a particular tissue as compared to all other tissues
Group enriched 34 At least five-fold higher mRNA levels in a group of 2-7 tissues
Tissue enhanced 115 At least five-fold higher mRNA levels in a particular tissue as compared to average levels in all tissues
Total 166 Total number of elevated genes in adipose tissue


Table 2. The 12 genes with the highest level of enriched expression in adipose tissue. "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. "mRNA (tissue)" shows the transcript level asáTPM values,áTS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.

Gene

Description

Predicted localization

mRNA (tissue)

TS-score

LIPE lipase, hormone-sensitive Intracellular 868.9 20
TUSC5 tumor suppressor candidate 5 Membrane 109.9 18
ADIPOQ adiponectin, C1Q and collagen domain containing Secreted 935.8 17
PLIN4 perilipin 4 Intracellular 810.9 14
PNPLA2 patatin-like phospholipase domain containing 2 Intracellular 419.8 13
CIDEA cell death-inducing DFFA-like effector a Intracellular 220.9 13
GYG2 glycogenin 2 Intracellular 161.7 13
LEP leptin Secreted 321.7 11
RP11-407P15.2 Membrane 6.1 11
PLIN1 perilipin 1 Intracellular,Membrane 1011.2 10
FP325317.1 Membrane 38.3 8
ACVR1C activin A receptor, type IC Membrane,Secreted 33.9 8

Some of the proteins predicted to be membrane-spanning are intracellular, e.g. in the Golgi or mitochondrial membranes, and some of the proteins predicted to be secreted can potentially be retained in a compartment belonging to the secretory pathway, such as the ER, or remain attached to the outer face of the cell membrane by a GPI anchor.

The adipose tissue transcriptome


An analysis of the expression levels of each gene makes it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 87% of the mRNA molecules in the adipose tissue correspond to housekeeping genes and only 4% of the mRNA pool corresponds to genes categorized to be either adipose tissue enriched, group enriched, or enhanced. Thus, most of the transcriptional activity in the adipose tissue relates to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.

Protein expression of genes elevated in adipose tissue


In-depth analysis of the elevated genes in adipose tissue using antibody-based protein profiling allowed us to create a map of where these proteins are expressed within the adipose tissue including the location of several plasma proteins, enzymes and transporters.

Proteins specifically expressed in adipose tissue


Adipose tissue is mainly formed by adipocytes (fat cells) but also consists of pre-adipocytes, fibroblasts, blood vessels and inflammatory cells. It is a specialized loose connective tissue with a number of functions including storage of energy, protection of organs and secretion of hormones.

Examples of proteins expressed in the adipose tissue include FABP4, involved in lipid transport, LIPE, hydrolyze the stored TAGs to free FAs, and PLIN1 and PLIN4, which have major roles in lipid droplet formation.



Plasma proteins


Plasma proteins are found in the blood plasma where red and white blood cells and platelets are suspended. Plasma proteins play a key role in the coagulation of blood, defense mechanisms of the body, transport of various substances and regulation of different functions within the human body. Differences in the levels of plasma proteins can lead to progression of various diseases. Hence, the levels of plasma proteins in the blood are widely used to gather information about the health and disease status of an individual.

Adipose tissue was at first characterized as a connective tissue that contained lipid droplets, without a link to the metabolism of the organism. After the discovery of adipose-derived serum factors, like leptin (LEP), and adiponectin (ADIPOQ), adipose tissue is now regarded as an endocrine organ at the center of energy homeostasis. 38 plasma proteins are identified in the adipose tissue elevated gene lists.

Examples of plasma proteins with elevated expression in adipose tissue include LEP, which play a major role in the regulation of body weight by decreasing food intake and increasing energy expenditure, ADIPOQ, involved in modulating a number of metabolic processes including glucose regulation and lipid oxidation.



Enzymes


Enzymes, speed up all vital biological processes, catalyze biochemical reactions and enable the building of chemical substances to the main components of the human body including proteins, carbohydrates and fats. These proteins require additional entities, co-enzymes, for functional activity. Co-enzymes are typically small molecules that accept or donate functional groups to assist in the enzymatic reaction.

An example of an enzyme with elevated expression in adipose tissue is LIPE, a hormone-sensitive lipase that in adipose tissue primarily hydrolyzes stored triglycerides to free fatty acids.



Transporters


The majority of biological solutes are charged organic or inorganic molecules and hydrophobic cellular membranes establish concentration gradients through the use of transporters. Transporters carry solutes across cell membranes and the energy required for these active transport processes is obtained from the cell ATP turnover.

One of the largest families of membrane proteins in the human genome are the solute carrier (SLC) family. Members of the SLC super family are present in large number of the cells and allow the transport of nutrients, amino acids, lipid structures, nucleosides, nucleotides, as well as diverse metabolites, both on the cell surface and on intracellular organelles.

An example of a transporter with elevated expression in adipose tissue is HAS1.



Genes shared between adipose tissue and other tissues


There are 34 group enriched genes expressed in the adipose tissue. Group enriched genes are defined as genes showing a 5-fold higher average level of mRNA expression in a group of 2-7 tissues, including adipose tissue, compared to all other tissues.

In order to illustrate the relation of adipose tissue to other tissue types, a network plot was generated, displaying the number of commonly expressed genes between different tissue types.

Figure 2. An interactive network plot of theáadipose tissueáenriched and group enriched genes connected to their respective enriched tissues (grey circles).áRedánodes represent the number ofáadipose tissue enriched genes andáorangeánodes 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 toá3átissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.



The adipose tissue shares a few genes with several other tissue types but has most shared group enriched genes with the liver (9 genes). A Gene ontology-based analysis of these genes shows that a majority are associated with regulation of secretion, organ morphogenesis and regulation of transport.

Example of group enriched genes shared between adipose tissue and liver include ADH1B, a member of the alcohol dehydrogenase family which plays a major role in ethanol catabolism.

ADH1B - liver
ADH1B - adipose tissue (soft tissue)


Adipose tissue function


Adipose tissue (fat) is a highly specialized loose connective tissue and has a number of physiological functions including storage of energy and secretion of hormones such as leptin. Protection of the organs in the body as well as insulation is other important features. Fat is located all over the human body but mainly around organs (visceral fat) and beneath the skin (subcutaneous). The adipose tissue is mainly formed by adipocytes but also consists of pre-adipocytes, fibroblasts, blood vessels and inflammatory cells. There are different types of adipose tissue including white adipose tissue (WAT) and brown adipose tissue (BAT). WAT has a major role in the progression of obesity and its adverse outcomes. Obesity has become a global pandemic and it is considered as one of the greatest threats to human health. Obesity is also associated with one or more co-morbidities, including type 2-diabetes, cardiovascular disease and increased risk of cancer.

Adipose tissue histology


Adipocytes are the main cell type in adipose tissue (fat). Adipose tissue is typically homogenous and finely divided by faint septa. Adipose tissue is spread throughout the body and surrounds most organs and tissues in the human body. In the skin, underlying adipose tissue forms the subcutaneous layer as an integral component of the skin. Microscopically adipose tissue is mainly composed of indistinct lobules of adipocytes surrounded by thin bands of collagen and small blood vessels. The cytoplasm of the adipocyte is compressed at the perimeter of the cell as it is displaced by a single lipid vacuole and only a thin rim of cell membrane is evident in the microscopic image. Adipocytes contain a small, thin and oval nucleus located peripheral to the dominating lipid vacuole, whereas nuclei of capillary endothelial cells are present at intersections between multiple adipocytes.

The histology of human adipose tissue including detailed images and information can be viewed in the Protein Atlas Histology Dictionary.

Background


Here, the protein-coding genes expressed in the adipose tissue are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the adipose tissue.

Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 172 individual samples corresponding to 37 different human normal tissue types. RNA sequencing results of 5 fresh frozen tissues representing normal adipose tissue was compared to 167 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in adipose tissue. A tissue-specific score, defined as the ratio between mRNA levels in adipose tissue compared to the mRNA levels in all other tissues, was used to divide the genes into different categories of expression. These categories include: genes with elevated expression in adipose tissue, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in adipose tissue, and genes not expressed in any tissue. Genes with elevated expression in adipose tissue were further sub-categorized as i) genes with enriched expression in adipose tissue, ii) genes with group enriched expression including adipose tissue and iii) genes with enhanced expression in adipose tissue.

Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank. All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board.


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Histology dictionary - adipocytes in soft tissue

An international consortium that seeks to identify genetic loci that modulate human body size and shape:
GIANT consortium

Encyclopedia of Sports Medicine and Science:
Adipose tissue