The Eye

816 genes are classified as retina elevated out of which 78 genes are highlighted as retina enriched. Based on the expression in lens, 900 genes are classified as lens elevated compared to other tissue types, out of which 146 genes are highlighted as tissue enriched in lens. RNA expression levels in cornea resulted in 407 genes classified as elevated in cornea compared to other tissue types, out of which 25 genes are highlighted as tissue enriched in cornea.

The eye is responsible for detecting light and converting it into the neuronal signals sent to the visual center of the brain. It consists of the eyeball and other eye appendages. Pig eyes are similar to human eyes in anatomy, vasculature and photoreceptor distribution. However, pigs have dichromatic vision, where only two pigment cones create colors, compared to the human trichromatic vision. This results in a less color rich world compared to human, although they can still differentiate colors. Histological image of the pig eye can be found in the pig tissue dictionary.

Retina

The retina is a multilayered neural tissue located in the eye that converts light into nerve signals that are transported to the visual centers in the brain by the optical nerve. The retina originates from neuroepithelium (an outpocketing of the diencephalon) and consists of a network of neuronal and glial cells connected to each other via synapses. Consequently, it shares the developmental origin and organization with other parts of the central nervous system (CNS). Transcriptome analysis shows that 15674 of all pig genes (n=22342) are expressed in the retina and 816 of these genes show an elevated expression in retina compared to other tissue types.

Gene expression in retina is categorized based on two classification strategies, tissue detection and tissue specificity. Figure 3 summarizes the number of genes in the respective category. The tissue distribution category highlights 23 genes only detected in retina while 78 genes are classified as retina enriched compared to other tissues. Table 1 shows the overlap between tissue specificity and distribution while Table 2 shows the top 10 genes, classified as retina enriched sorted on tissue specificity score (expression in retina divided by the second highest expression).

Figure 3. (A) The distribution of all genes across the five categories based on transcript specificity in retina as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX?1) in retina 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 retina

Retina elevated expression

The main function of retina is to transfer images into electrical neural impulses to the brain to form vision perception. To meet this need, light-sensitive protein, like rhodopsin (RHO), involved in visual phototransduction is abundantly expressed in photoreceptor cells. Neural retina leucine zipper (NRL), function as transcriptional activator to regulate the expression of RHO and is also among the highly abundant proteins expressed in the retina. S-antigen visual arrestin (SAG) binds to the photo-activated phosphorylated RHO and terminating RHO signaling by competing with G protein for the same binding site on RHO.

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

Lens

The lens is a major part of the eyeball, located in front of the vitreous body and surrounded by the lens ligament and the ciliary body. It is a transparent, biconvex intraocular and helps bringing rays of light to focus on the retina. The lens consists of three main parts, the capsule, epithelium and fibers. The lens capsule is the outer layer of the lens while the fibers form the inside of the lens. The epithelial layer, located between the capsule and the fibers is only located at the anterior part of the lens. The epithelial cells are the progenitor cells for new lens fibers, and also regulate the homeostasis of the lens.The lens lacks both nerves, blood vessels and connective tissue.

Gene expression in the lens is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 4 summarizes the number of genes in the respective category. In total, 13607 genes are detected above cutoff (NX=1) in pig lens. The tissue distribution category highlights 33 genes only detected in lens while 900 genes are classified as lens elevated compared to other tissues. Table 3 show the overlap between the lens elevated genes and tissue distribution category. Table 4 shows the top10 genes, classified as lens enriched sorted on tissue specificity score (expression in lens divided by the second highest expression).

Figure 4, (A) The distribution of all genes across the five categories based on transcript specificity in lens as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX?1) in lens as well as in all other tissues. The combination of the two categories is shown in table 3.

Table 3. Number of genes in the subdivided categories of elevated expression and tissue distribution in lens

Lens elevated expression

Crystalline is the dominant structural component of the vertebrate lens. Typical examples of crystallines are CRYBB1, CRYBB2, CRYBB3. They are extremely stable and retained throughout life and maintains the transparency and refractive index of the lens. Among the genes with lens-elevated expression, the majority are crystallines. The lens even accounts for the most abundant and most specific genes when comparing all tissue types due to the unique function of crystalline only expressed in the lens. Additionally, the easy sampling of a clean lens tissue sample, without any connective tissue results in a tissue sample highly enriched for a certain cell type.

Table 4, The 10 genes with the highest level of enriched expression in lens. "mRNA (tissue)" shows the transcript level in lens as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in lens and the tissue with second highest expression level.

Cornea

The cornea is a thin, transparent film on the front of the eye, which covers the iris, pupil and anterior chamber and provides most of an eye’s optical power. Its function is to let light enter and converge it. Besides the corneal epithelium, which is a non-keratinized squamous epithelium, the cornea includes a thick transparent stromal layer consisting of regularly arranged collagen fibers.

Gene expression in cornea is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 5 summarizes the number of genes in the respective category. In total, 15222 genes are detected above cut of (1NX) in pig cornea. The tissue distribution category highlights 8 genes only detected in cornea while 407 genes are classified as cornea elevated compared to other tissues. Table 5 shows the top 10 genes, classified as cornea enriched sorted on tissue specificity score (expression in cornea divided by the second highest expression).

Figure 5. (A) The distribution of all genes across the five categories based on transcript specificity in cornea as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX?1) in cornea as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 5. Number of genes in the subdivided categories of elevated expression and tissue distribution in cornea

Cornea elevated expression

Since the cornea includes a layer of squamous epithelium, most genes classified as cornea elevated are squamous epithelium related. The KRT12 gene, encoding the type I intermediate filament chain keratin 12, show high expression in pig cornea. Along with KRT3, which may play a main role in maintaining integrity and normal function of cornea. The keratan sulfate proteoglycan (KERA) is related to development and maintain the transparency of the cornea. ALDH3A1 encodes an aldehyde dehydrogenases, which can oxidize various aldehydes to the corresponding acids, protecting the cornea from UV and 4-hydroxy-2-nonenal-induced oxidative damage.

Table 6. The 10 genes with the highest level of enriched expression in cornea. "mRNA (tissue)" shows the transcript level in cornea as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in cornea and the tissue with second highest expression level.

Gene expression in the eye compared to other tissues

The shared developmental origin of retina and the brain is obvious when comparing the overlap of genes classified as group enriched with tissue types outside the eye. As already mentioned, lens holds a rather unique expression profile and therefore stands out compared to other tissue types based on gene expression. Cornea on the other hand shares several genes with other squamous epithelia tissue types such as skin and mouth.

Immunohistochemical labelling of DYNC1I1 in pig tissues using antibody HPA061689 shows strong positiity in retina, lens and brain (represented by cerebellum).

In order to illustrate the relation of eye tissue 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.

Figure 6. An interactive network plot of the eye enriched and group enriched genes connected to their respective enriched tissues (grey circles). Black circles show tissues representing the eye. 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.