Skin

The main function of the skin is to protect our body from environmental challenges, such as radiation and infectious agents. The skin also regulates body temperature, and can detect different sensations like heat, cold, pressure, contact and pain. The epidermis, which is dominated by keratinocytes, forms the skin barrier that protects the body against water loss and external physical, chemical, and biological insults. In the pig transcriptomic analysis, both skin from the back and groin area was included and used for quantitative RNA measurements, representing the skin. The gene classification strategy highlights genes with an elevated level of expression in one or a group of tissues compared to all other tissues.

526 genes are classified as skin elevated out of which 99 genes are highlighted as skin enriched.

The function of the skin is similar between the pig and human. Histological image of the pig tissues used in the analysis can be found in the pig tissue dictionary.

Gene expression in the skin is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 1 summarizes the number of genes in respective category. In total, 16246 genes are detected above cut of (1NX) in pig skin. The tissue distribution category highlights 39 genes only detected in skin while 526 genes are classified as skin elevated compared to other tissues. Table 1 shows the overlap for the skin elevated genes and tissue distribution category.

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 (NX≥1) in skin as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 1, Number of genes in the subdivided categories of elevated expression and tissue distribution in skin

Skin enriched expression

Among the genes with most enriched expression in skin compared to other tissues there are many that lack gene names and human orthologues. Further down the list of enriched expression, genes with human orthologues and genes are included, and here the functions of the skin-enriched proteins are clear: mainly keratin-associated proteins are found, as expected. KRTAP11-1, KRT77 and KRT85 are all examples of genes with skin enriched expression both in human and pig.

Table 2, The 10 genes with the highest level of enriched expression in skin. "mRNA (tissue)" shows the transcript level in skin as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in skin and the tissue with second highest expression level.

Noteworthy differences between human and pig skin is that melanocytes are less active in pig skin compared to human, exemplified by three examples of proteins specifically expressed in the skin melanocytes in human and highly expressed in human skin while pig show very low expression levels, MLANA, DCT and TYR.

DSC1 is an example with skin enriched expression while KRT10 is shared group enriched between mouth and skin.

Immunohistochemically stained pig skin DSC1 using HPA075379 (to the left) and KRT10 using HPA012014 (to the right).

Expression comparison between skin from the groin and back

The expression variation category enables further details related to expression heterogeneity within the tissues that include grouped samples. In this case, expression profile from skin of the groin is compared to the expression profile from skin from the back, resulting in 100 genes highlighted as variable between the two skin samples. It is likely that the variation in expression level is due to differences in amout of hair in the two locations.

Gene expression in the skin compared to other tissues

In order to illustrate the relation of the skin to other tissue types, a network plot was generated, displaying the number of genes shared between different tissue types. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, compared to all other tissues. Skin shares most group enriched genes with mouth and cornea, both tissues include squamous epithelium

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 tissue 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 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.