The skin-specific proteome

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

459 genes show some level of elevated expression in the skin compared to other tissues. The three categories of genes with elevated expression in skin compared to other organs are shown in Table 1.

Table 1. The genes with elevated expression in skin

Table 2. The 12 genes with the highest level of enriched expression in skin. "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 as TPM values, TS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.

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 skin transcriptome

An analysis of the expression levels of each gene made it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 79% of the mRNA molecules derived from skin corresponds to housekeeping genes and only 14% of the mRNA pool corresponds to genes categorized as skin enriched, group enriched or, skin enhanced. Thus, most of the transcriptional activity in the skin is related to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.

Gene Ontology-based analysis of all the genes defined as skin enriched (n=92), and group enriched with esophagus (n=34) indicate a clear overrepresentation of proteins associated with keratinization, epidermis development, epithelial development, epidermal cell differentiation and keratinocyte differentiation. Gene ontology terms that are specifically found in skin and not esophagus are genes related to establishment of skin barrier, regulation of water loss, and genes related to melanin biosynthesis.

Protein expression of genes elevated in skin

In-depth analysis of the elevated genes in skin using antibody-based protein profiling allowed us to create a portrait of where these proteins are expressed with regards to keratinocytes in different layers of the epidermis, e.g. stratum basale, stratum spinosum, stratum granulosum and stratum corneum, and other specific cell types present in the skin, e.g. melanocytes and Langerhans cells.

Proteins specifically expressed in stratum basale

The stratum basale is the inner-most single cell layer residing on the basement membrane that separates the epidermis from the underlying dermis. The basal layer contains epidermal stem cells and is the location for proliferation and renewal of keratinocytes. In addition to keratinocytes, melanocytes are also present in the basal layer. Proteins expressed in the basal layer include COL17A1 and TP73.

Proteins specifically expressed in stratum spinosum

Stratum spinosum is the layer in which post-mitotic keratinocytes are concurrently "pushed" towards the skin surface and differentiate. Squamous differentiation in skin involves keratinization, an active process that includes both morphological and biochemical differentiation centered on the generation of keratin proteins that aggregate together and provide strong connections between the keratinocytes through desmosomes. Examples of proteins expressed in the stratum spinosum include KRT10 and CASP14.

Proteins specifically expressed in stratum granulosum

In the stratum granulosum keratinocytes undergo terminal differentiation into non-viable corneocytes that lack nuclei and cellular organelles. In this layer, the connections between cells become tighter, and secreted lipids and proteins forms a hydrophobic barrier. Combined, these events constitute most of the skin's protective functions against the external world. Examples of proteins that are expressed in this layer include FLG and KPRP.

Proteins specifically expressed in stratum corneum

The stratum corneum is the outermost layer of the skin and functions as the actual barrier against dehydration, mechanical stress, pathogens and other burdens to the skin. Stratum corneum consists of dead, flattened and tightly coupled corneocytes that eventually are "pushed" to the surface and subsequently shed. Examples of proteins that are expressed in this layer include CDSN and KLK5.

Proteins specifically expressed by melanocytes

Melanocytes are located in the basal layer of the epidermis and their primary role is to produce and deliver melanin-pigment to basal keratinocytes through dendritic processes. The function of melanin is to absorb ultraviolet light and protect keratinocytes from mutagenic UV-B radiation. Genes specific for melanocytes include MLANA, DCT and TYR which encode proteins involved in melanin-synthesis pathways.

Proteins specifically expressed by Langerhans cells

Langerhans cells are specialized immune cells of the skin (and esophagus) that reside in stratum spinosum. Their main function is to present antigens to T-cells from either the skin itself or from invading pathogens. When there is an inflammation in the skin, Langerhans cells are activated and migrate away to lymph nodes. Proteins expressed on the surface of Langerhans cells include CD1A and CD207.

Genes shared between skin and other tissues

There are 126 group-enriched genes expressed in the skin. 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 skin, compared to all other tissues.

In order to illustrate the relation of skin tissue to other tissue types, a network plot (Figure 2) was generated to visualize the number of commonly expressed genes between different tissue types. The skin shares a striking amount of transcripts (n=34) with esophagus, which is a tissue coated by squamous epithelia that has a similar epithelial structure and function as the skin. Many of these skin and esophagus-specific genes belong to gene families that are important for normal squamous epithelial function. A Gene ontology analysis performed on these 34 genes shared between esophagus and skin reveal that the top shared categories are related to epidermal and epithelial development, as well as keratinocyte and epidermal cell differentiation.

Figure 2. An interactive network plot of the skin enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of skin 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 4 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

Several genes expressed both in skin and esophagus are previously well characterized in both tissue types, and are described as proteins important for the normal differentiation and function of squamous epithelia, e.g. keratins including KRT5, KRT8, KRT15, KRT17 and KRT31, and genes related to cell adhesion and squamous differentiation, e.g. desmoplakin 1 (DSP), envoplakin (EVPL), desmocollin 3 (DSC3), SLURP1 and KLK8.

The secreted LY6/PLAUR domain containing 1 (SLURP1) protein is a member of the Ly6/uPAR family of proteins but lacks a GPI-anchoring signal sequence. SLURP1 is suggested to be involved in late differentiation, predominantly expressed in the granular layer of skin. Moreover, SLURP1 is identified in several biological fluids such as sweat, saliva, tears, and urine. It is thought that this secreted protein exerts antitumor activity.

The poly(U)-specific endoribonuclease (ENDOU) protein is a secreted protein with protease activity previously reported to be expressed in placenta and also associated with various malignant tumors.

Interestingly, the skin also shares genes with other tissues, for example brain and testis. The protein tyrosine phosphatase receptor liprin alpha 3 (PPFIA3) is group enriched in brain and skin, and is previously known to be important for axon guidance and mammary gland development.

Skin function

The skin is the largest tissue in the human body and can be viewed as an encapsulating fabric that is in constant contact with the external environment. The constant exposure to the outside necessitates that the skin is capable of fulfilling a few basic but very important requirements. It needs to be resilient to mechanical, tension and other wearing forces. It needs to maintain a physical barrier to prevent pathogens from entering our bodies and to provide protection against damaging solar radiation. The skin also keeps our bodies from drying out by retaining water and regulates the body temperature by sweating or raises hairs to keep warm. Due to the constant wear and tear, the skin must also be able to renew itself and to heal wounds. Furthermore, the peripheral nerves in the skin convey the sense of touch that helps us to be aware of our surroundings, and to avoid injury through e.g. the sense of pain.

Skin histology

The skin is divided into three main parts: a) the epidermis, which is a quite thin epithelial sheet located in the outermost part of the skin. The epidermis is where new skin cells are generated and where the protective barriers are formed. b) The dermis, which is mainly composed of connective tissue and blood vessels that provide stability, elasticity and nutrition to the epidermis, and c) the subcutis, which is mainly composed of subcutaneous fat cells that provide isolation and functions as energy deposits. The skin also contains a variety of other cells with specialized functions like in the sebaceous and sweat glands, hair follicles, arrector pili muscles and nail plates.

The histology of human skin including detailed images and information about the different cell types can be viewed in the Protein Atlas Histology Dictionary.

Background

Here, the protein-coding genes expressed in the skin 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 skin.

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 3 fresh frozen tissues representing normal skin was compared to 169 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in skin. A tissue-specific score, defined as the ratio between mRNA levels in skin 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 skin, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in skin, and genes not expressed in any tissue. Genes with elevated expression in skin were further sub-categorized as i) genes with enriched expression in skin, ii) genes with group enriched expression including skin and iii) genes with enhanced expression in skin.

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.

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

Edqvist PH et al, 2015. Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. J Histochem Cytochem.
PubMed: 25411189 DOI: 10.1369/0022155414562646

Systematic identification and characterization of novel human skin-associated genes encoding membrane and secreted proteins

Large-scale identification of human genes implicated in epidermal barrier function

Anatomy and Physiology of the Skin

Dermnet - Skin Disease Atlas

Histology dictionary - skin