The retina proteome
The retina is a multilayered neural tissue located in the eye and 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 79% (n=15630) of all human proteins (n=19670) are expressed in the retina and 310 of these genes show an elevated expression in retina compared to other tissue types.
Figure 1. Schematic overview of the organization of the retina. Pigment epithelium is located nearest the choroid, while the nerve fiber layer is closest to the vitreous humour of the eye.
Transcriptome analysis of the retina can be visualized with regard to specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the retina compared to other tissues. Elevated expression includes three subcategory types of elevated expression:
Distribution, on the other hand, visualizes how many genes that have, or do not have, detectable levels (NX≥1) of transcribed mRNA molecules in the retina compared to other tissues. As evident in Table 1, all genes elevated in retina are categorized as:
Figure 2. (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.
As shown in Figure 1, 310 genes show some level of elevated expression in the retina compared to other tissues. The three categories of genes with elevated expression in retina compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in retina are defined.
Table 1. Number of genes in the subdivided categories of elevated expression in retina.
Table 2. The 12 genes with the highest level of enriched expression in retina. "Tissue distribution" describes the transcript detection (NX≥1) in retina as well as in all other tissues. "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.
Protein expression of genes elevated in retina
In-depth analysis of the elevated genes in retina using antibody-based protein profiling allowed us to understand the distribution of the retina specific genes and their expression profiles. Proteins expressed in specific cell-types or in synapses were identified among the genes with elevated expression in the retina.
Proteins specifically expressed in retinal pigment epithelial cells
Cells in the retinal pigment epithelium (RPE) produce melanin in order to protect photoreceptor cells from UV-radiation. Our analysis revealed that, in addition to melanocytes in skin, melan-A (MLANA) is also expressed in the RPE. RPE cells are also involved in transport of nutrients and ions between photoreceptor cells and blood vessels in the choroid. Another protein identified in the RPE is bestrophin 1 (BEST1); it is known to form a bicarbonate transporting channel. Solute carrier family 16 member 8 (SLC16A8) plays a role in transport of molecules and here we show that it is located in the cell membrane of cells in the RPE.
Proteins specifically expressed in photoreceptor cells
An example of a protein located in the nuclei of photoreceptor cells is cone-rod homeobox (CRX), a transcription factor essential for normal photoreceptor function. The process of conversion of light to nerve signals, also called phototransduction, involves interaction between numerous proteins in the outer segments of photoreceptor cells. In rods, phototransduction begins when light activates rhodopsin (RHO), followed by interaction with the rod-specific transducin. A component of the latter is G protein subunit gamma transducin (GNGT1). Another protein expressed in the outer segments is cyclic GMP-phosphodiesterase 6G (PDE6G). It converts cyclic GMP into 5' GMP in rods, a process known to lead to hyperpolarization and subsequent nerve signaling. S-antigen visual arrestin (SAG) turns off phototransduction by preventing interaction between rhodopsin and transducin. This allows activated rods to recover and consequently adapt to low light conditions.
Proteins involved in phototransduction in cones include g protein subunit gamma transducin 2 (GNGT2), guanylate cyclase activator 1B (GUCA1B) and arrestin 3 (ARR3). GNGT2 is a component of the cone-specific transducin, and like its rod-specific relative GNGT1, it is located in the outer segments. GUCA1B is a calcium-binding protein that activates photoreceptor guanylate cyclases. ARR3 is the cone-specific equivalent of SAG, and it is involved in the deactivation of cones.
Proteins specifically expressed in the outer limiting membrane
The outer limiting membrane is a row of cell-junctions located where the inner and outer segments of photoreceptors connect, as illustrated by integrin subunit beta 8 (ITGB8), which is a component of integrin complex. Integrin complexes are important for cell to cell and cell to matrix interactions. Crumbs 2 (CRB2) is another protein expressed in the outer limiting membrane. CRB2 is component of the Crumbs cell polarity complex, a protein important for many cellular processes during embryonic development. Mutation in this gene has been reported to cause congenital disorders such as retinitis pigmentosa.
Proteins specifically expressed in the inner nuclear layer and ganglion cells
A transcription factor that may be involved in the development of cells in the inner nuclear layer (INL), horizontal cells in particular, is visual system homeobox 2 (VSX2). VSX2 is expressed in the nuclei of subset of cells in the INL. Recoverin (RCVRN), similarly to SAG, is known to block phototransduction in rods in darkness. Here we show that RCVRN is expressed in photoreceptor cells and in subset of cells in INL. Calcium binding protein 5 (CABP5), is a member of a protein family involved in intracellular signaling. However, the exact function of this gene is unknown. A mouse homolog has been found in the INL of mice. Our analysis shows that CABP5 is expressed in the INL and ganglion cells in human retina. The axons of ganglion cells are collected in the nerve fiber layer, as exemplified by PI16, and extend through the optic nerve to various visual centers in the central nervous system. PI16 is a peptidase inhibitor that has been reported to be involved in stress response in cardiac muscle and vasculature. Its function in retina is not yet characterized.
Proteins specifically expressed in the inner and outer plexiform layers
The outer and inner plexiform layers (OPL and IPL) contain synapses through which the nerve signals are transmitted between the different cells in retina. Anoctamin 2 (ANO2) encodes a calcium-activated chloride channel expressed exclusively in the OPL. CPLX4 is a protein located in the IPL and may be involved in synaptic vesicle exocytosis. Glutamate metabotropic receptor 6 (GRM6) is, as the name suggests, one of several types of metabotropic receptors that bind the neurotransmitter L-glutamate in the central nervous system. In retina, GRM6 is detected in both the OPL and IPL.
Gene expression shared between retina and other tissues
There are 79 group enriched genes expressed in the retina. 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 retina, compared to all other tissues.
In order to illustrate the relation of retina to other tissue types, a network plot was generated, displaying the number of genes shared between different tissue types (Figure 3).
Figure 3. An interactive network plot of the retina enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of retina 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.
Proteins analyzed in retina
Protein expression of selected genes with RNA expression elevated in retina or literature indicating function related to retina were analyzed in retina samples. The full list of genes used for protein profiling in retina is found in Table 3.
Table 3. Following 93 genes have been analyzed in retina.
The retina is a multilayered neural tissue that comprises the innermost layer of the eye, called the inner photosensitive layer. Similarly to other parts of the central nervous system, it originates from the neuroepithelium, an outpocketing of the diencephalon. In retina, light is converted into nerve signals that are transported to the visual centers in the brain by the optical nerve. As light enters the eye through the pupil and becomes refracted by the lens, it reaches the retina where it is absorbed. Photosensitive neuronal cells called photoreceptor cells transduce the light into nerve signals that are then transmitted to different types of interneurons that modulate the nerve signaling before it is collected in the optical nerve.
There are two types of photoreceptor cells: rods and cones. Rod photoreceptors cells register presence of light and allow vision during low light conditions while cones register red, green and blue colors and allow color vision. A layer of pigmented cells provide nutrients and protection against UV-radiation to the photoreceptor cells. Four types of interneurons modulate nerve signaling by inhibiting and/or activating the cells they interact with. Horizontal cells connect only to synapses of the photoreceptor cells, while bipolar cells transmit signals between photoreceptor cells and ganglion cells. Amacrine cells modulate signals coming from bipolar cells to ganglion cells. Ganglion cells are the last cells to receive and regulate molecular signals from the photoreceptor cells before nerve signals are collected in the optical nerve. They interact both with bipolar and amacrine cells. Müller glia, as the name suggest are glial cells. They maintain the structural integrity of the retina by stretching across all layers as well as buffer potassium and neurotransmitters.
Relevant links and publications
Uhlén M et al, 2015. Tissue-based map of the human proteome. Science