Transcriptome of the human retina, retinal pigmented epithelium and choroid

Abstract

The retina and its adjacent supporting tissues - retinal pigmented epithelium (RPE) and choroid - are critical structures in human eyes required for normal visual perception. Abnormal changes in these layers have been implicated in diseases such as age-related macular degeneration and glaucoma. With the advent of high-throughput methods, such as serial analysis of gene expression, cDNA microarray, and RNA sequencing, there is unprecedented opportunity to facilitate our understanding of the normal retina, RPE, and choroid. This information can be used to identify dysfunction in age-related macular degeneration and glaucoma. In this review, we describe the current status in our understanding of these transcriptomes through the use of high-throughput techniques.

Keywords: Age-related macular degeneration; Choroid; Glaucoma; RNA-Seq; Retina; Retinal pigmented epithelium; Serial analysis of gene expression; Transcriptome; cDNA microarray.

Figure 1. Chorioretinal tissue layers in human eye

A. Cross-section of a human eye. Green bracket shows extent of the posterior pole that is illustrated in panel B, including optic nerve head and macula with fovea. Light shines into this eye from the right. Schematic from David Fisher Designs. B. In vivo high-resolution imaging of a normal human retina (black bar) and choroid (white bar) shows tissue layers of the 6 mm diameter macula and adjacent optic nerve clearly. Light shines into this eye from above. The neurosensory retina contains multiple bands of alternating high and low reflectivity that coincide in part with the anatomical layers. Blue bar delimits layers occupied by photoreceptors. Arrowheads indicate a dip at the fovea, shown by histology in panel C. The choroidal vasculature contains lumens of large vessels. It is bounded externally by the sclera, which has a more homogeneous reflectivity. Swept-source optical coherence tomography scan, a 58 yr old male, courtesy of R.F. Spaide, MD. C. Ex vivo high-resolution histology of the fovea, which is located in the center of macula and is responsible for high acuity vision. The neurosensory retina including thickened photoreceptor layers and choroid are indicated by black, blue, and white arrows, respectively. A foveal pit is created by inner retinal neurons, Müller cells, and accompanying retinal vasculature being swept to the side of the visual axis. This facilitates light capture by tightly packed inner segments of cone photoreceptors on the opposite aspect of the retina. The photoreceptors and Müller cells (glial cells) have long fibers that together make a thick layer that is 14% of total retinal thickness in this region (Henle fiber layer). The RPE is a simple cuboidal epithelium that sits on Bruch’s membrane. Bruch’s membrane is the inner wall of the choroid and functions as a vessel wall between choriocapillaries and RPE, as well as substrate for RPE attachment. RPE maintains health of the photoreceptors and the choroid. RPE is visible clinically by its melanosomes and lipofuscin, which is autofluorescent due to long-lasting vitamin A byproducts. The choroidal vasculature contains fenestrated capillaries adjacent to the RPE and larger arteries and veins near the sclera. A 63-year-old female recovered <3 hour after death, osmium post-fixation, epoxy embedding, 1 µm thick section, and toluidine blue stain. Figure was prepared by J.D. Messinger, DC.

Figure 2. Distributions of gene expression values from microarray (Plier) and RNA-Seq (FPKM)

X axis shows the log2 value of the Plier number; Y axis shows a histogram of the number of genes.

Figure 3. Disease term enrichment of 24 genes near AMD disease loci

X axis shows the disease terms; Y axis shows the number of genes enriched in the specific disease term.

Figure 4. Functional enrichment analysis of 24 genes near AMD disease loci

X axis shows the biological function categories; Y axis shows the number of genes enriched in the specific function category.

Figure 5. Pathway analysis of 24 genes near AMD disease loci

X axis lists top 3 pathways; Y axis shows the number of genes enriched in the specific pathway.