The skin-specific proteome

The skin transcriptome

Transcriptome analysis of the skin can be visualized with regard to the specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the skin compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

• Tissue enriched: At least four-fold higher mRNA level in skin compared to any other tissues.
• Group enriched: At least four-fold higher average mRNA level in a group of 2-5 tissues compared to any other tissue.
• Tissue enhanced: At least four-fold higher mRNA level in skin compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the skin compared to other tissues. As evident in Table 1, all genes elevated in skin are categorized as:

• Detected in single: Detected in a single tissue
• Detected in some: Detected in more than one but less than one-third of tissues
• Detected in many: Detected in at least a third but not all tissues
• Detected in all: Detected in all tissues

Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in skin as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (nTPM≥1) in skin as well as in all other tissues.

As shown in Figure 1, 612 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. In Table 2, the 12 genes with the highest enrichment in skin are defined.

Table 1. The number of genes in the subdivided categories of elevated expression in skin.

Table 2. The 12 genes with the highest level of enriched expression in skin. "Tissue distribution" describes the transcript detection (nTPM≥1) in skin as well as in all other tissues. "mRNA (tissue)" shows the transcript level in skin as nTPM values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in skin and the tissue with the second-highest expression level.

Protein expression of genes elevated in skin

In-depth analysis of the genes elevated in skin, using antibody-based protein profiling, allowed us to visualize the expression patterns of the corresponding proteins within skin tissue. Proteins specific for the 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 are shown below.

Proteins specifically expressed in stratum basale

The stratum basale is the innermost 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.

COL17A1
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.

KRT10
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 form a hydrophobic barrier. Combined, these events constitute most of the skin's protective functions. Examples of proteins that are expressed in this layer include FLG and KPRP.

FLG
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. The 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.

CDSN
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.

MLANA
DCT
TYR

Proteins specifically expressed by Langerhans cells

Langerhans cells are specialized immune cells of the skin (and esophagus) that reside in the 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.

CD1A
CD207

Proteins specifically expressed in hair

The hair can be divided into three layers, namely the medulla, cortex and cuticle layer. The hair follicle is an epidermal invagination that encloses the initial part of the hair shaft. The hair follicle is composed of two distinct layers: the internal and external root sheath. Proteins that play a significant role in hair formation include the type II cytoskeletal keratins 75 (KRT75), and 71 (KRT71). KRT75 is expressed in the outer root sheath, while KRT71 is expressed in the internal root sheath (Figure 2). The type I keratin 34 (KRT34) is a protein expressed in the cortex. KRT34 heterodimerizes with type II keratins to form hair.

KRT75
KRT34

Figure 2. Immunohistochemical staining of human hair follicles using an antibody toward KRT71 shows strong cytoplasmic staining in the internal root sheath.

Proteins specifically expressed in skin glands

The eccrine glands can be found throughout the body in varying densities, especially in thick skin, and are primarily involved in the cooling of the human body. The secretory unit is located in the dermis layer and consists of a coiled base that discharges a water-based secretion through a duct, which empties on the surface of the skin. An example of a protein expressed in eccrine sweat glands is dermcidin (DCD), previously known as an antimicrobial peptide important for the innate immune system (Figure 3).

Figure 3. Immunohistochemical staining of human skin using an antibody toward DCD shows strong membranous and cytoplasmic positivity in eccrine sweat duct cells and secretory cells.

The sebaceous glands are located in the upper part of the dermis. They produce an oily or waxy secretion called sebum. One function is to lubricate and protect the hair and skin from water and thus act as a protective barrier. This barrier function also results in the reduction of water loss from the skin surface. An example of a protein expressed in sebaceous glands is the elongation of very long chain fatty acids protein 3 (ELOVL3), which plays a role in the elongation of long chain fatty acids (Figure 4).

Figure 4. Immunohistochemical staining of human skin using an antibody toward ELOVL3 shows strong cytoplasmic positivity in cells in sebaceous gland.

Gene expression shared between skin and other tissues

There are 97 group enriched genes expressed in skin. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including skin, compared to all other tissues.

To illustrate the relation of skin tissue to other tissue types, a network plot was generated, displaying the number of genes with a shared expression between different tissue types.

Figure 5. 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 5 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

Skin mainly shares group enriched gene expression with esophagus (n= 34), which, like skin, contains stratified squamous epithelium. Several genes are also group enriched in skin and vagina, another tissue with stratified squamous epithelium. Proteins important for normal differentiation and function of squamous epithelia include; KRT15, LGALS7, DSC3 and SLURP1.

The keratin KRT15 (KRT15) is a component of the cytoskeleton and is associated with epidermis development and keratinization. The secreted LY6/PLAUR domain containing 1 (SLURP1) protein, a member of the Ly6/uPAR family of proteins, is suggested to be involved in late differentiation, predominantly expressed in the granular layer of skin.

KRT15 - skin
KRT15 - esophagus

KRT15 - vagina
KRT15 - breast

SLURP1 - skin
SLURP1 - esophagus

Galectin 7 (LGALS7) is a member of the family of beta-galactoside-binding proteins known for playing a role in cell-cell and cell-matrix interactions. This particular galectin is specific to keratinocytes. The desmocollin protein family is known to be mainly found in epithelial cells. DSC3, a member of this family, is a component of desmosomes and thus essential for cell-to-cell adhesion.

LGALS7 - skin
LGALS7 - esophagus

DSC3 - skin
DSC3 - esophagus
DSC3 - tonsil

Proteins analyzed in extended samples of skin

The standard setup in the Tissue Atlas is based on Tissue Microarray technique (TMA), thus saving valuable tissue material as well as reagents, and providing a good tissue representation for protein profiling. However, skin samples included in the standard TMA contains only the epidermis and superficial parts of the dermis, often excluding structures like hair, sweat glands and sebaceous glands. To fully understand protein location in skin, genes with literature suggesting a function in hair, sweat glands and sebaceous glands were analyzed in extended skin samples; 2 mm diameter TMA cores and larger tissue sections. The selected targets used for protein profiling with extended skin samples are listed in Table 3.

Table 3. Following 58 genes have been analyzed in skin.

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 as well as 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 raising hairs. Due to the constant wear and tear, the skin must also be able to renew itself and 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.

The duration of hair growth (anagen), growth arrest (catagen) and resting periods (telogen) are different throughout the body. Specifically, the growth of hair on the scalp and face is highly influenced by sex hormones, mainly androgens.

Skin histology

The skin is divided into three main parts: first the epidermis, which is a 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.

The epidermis is divided into several layers. Residing on the basement membrane is the basal layer of keratinocytes, stratum basale, that contains the proliferating basal cells. Keratinocytes that leave this layer undergo terminal differentiation. Stratum spinosum, the prickle cell layer, is located above the stratum basale, and in this layer, keratinocytes acquire more cytoplasm and well-formed bundles of keratin intermediate filaments. As the keratinocytes are pushed further outwards, proteins that constitute the cell envelope and keratohyalin granules of the stratum granulosum are synthesized. The end-stage of epidermal keratinocyte differentiation results in a dense keratinous layer, the cornified layer consisting of flake-like squames that are eventually shed. The second layer is the dermis, mainly composed of connective tissue and blood vessels that provide stability, elasticity and nutrition to the epidermis. The last layer, the subcutis, is mainly composed of subcutaneous fat cells that provide isolation and function 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.

Hair is found almost everywhere on the body and arises from hair follicles, which are epidermal derivatives present in the dermis. Hair can be divided into three layers, namely the medulla, cortex and cuticle layer, all originating from cells at the base of the hair bulb, the dermal papilla. The medulla consists of moderately keratinized cells, while the cortex is formed by compact, heavily keratinized cells, and the surrounding cuticle layer forms a protective layer for the hair shaft. Melanocytes, which are responsible for hair pigmentation, are present in the dermal papilla. The hair follicle is an epidermal invagination that encloses the initial part of the hair shaft. The hair follicle is composed of two distinct layers: the internal and external root sheath

As the hair follicles, skin glands also arise from down-growths of the epidermal epithelium. Sweat glands are tubular structures in the skin and can be separated into two main types: eccrine sweat glands and apocrine sweat glands. The secretory unit of eccrine glands is located in the dermis layer and consists of a coiled base that discharges a water-based secretion through a duct, which empties on the surface of the skin. The apocrine sweat glands are located at certain parts of the body e.g. armpits, ear canals and eyelids. These glands have also a coiled tubular structure but empty an oily secretion into hair follicles. The sebaceous glands are located in the upper part of the dermis. Similar to apocrine sweat glands, they produce an oily or waxy secretion called sebum.

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 skin are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in skin.

Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 54 different human normal tissue types. The final consensus normalized expression (nTPM) value for each tissue type was used for the classification of all genes according to the tissue-specific expression into two different categories, based on specificity or distribution.

Relevant links and publications

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

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

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

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

Histology dictionary - skin