Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE)

Abstract

We used the serial analysis of gene expression (SAGE) technique to catalogue and measure the relative levels of expression of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium (RPE) from one or both of two humans, aged 88 and 44 years. The cone photoreceptor contribution to all transcription in the retina was found to be similar in the macula versus the retinal periphery, whereas the rod contribution was greater in the periphery versus the macula. Genes encoding structural proteins for axons were found to be expressed at higher levels in the macula versus the retinal periphery, probably reflecting the large proportion of ganglion cells in the central retina. In comparison with the younger eye, the peripheral retina of the older eye had a substantially higher proportion of mRNAs from genes encoding proteins involved in iron metabolism or protection against oxidative damage and a substantially lower proportion of mRNAs from genes encoding proteins involved in rod phototransduction. These differences may reflect the difference in age between the two donors or merely interindividual variation. The RPE library had numerous previously unencountered tags, suggesting that this cell type has a large, idiosyncratic repertoire of expressed genes. Comparison of these libraries with 100 reported nonocular SAGE libraries revealed 89 retina-specific or enriched genes expressed at substantial levels, of which 14 are known to cause a retinal disease and 53 are RPE-specific genes. We expect that these libraries will serve as a resource for understanding the relative expression levels of genes in the retina and the RPE and for identifying additional disease genes. T he human retina is a highly specialized tissue that converts photons into neural signals that are communicated to the brain. This process involves different types of retinal cells, mainly neuronal cells (e.g., photoreceptors, bipolar cells, and others) and the nonneuronal retinal pigment epithelium (RPE). The set of genes expressed by the human neural retina has been elucidated partially, mainly through reported expressed sequence tag (EST) libraries [nonnormalized (1-3) or enriched (4, 5)] that contain over 16,000 EST sequences derived from less than 5,000 genes (6). Our knowledge of the set of genes expressed by the RPE is more rudimentary, because only 624 ESTs have been sequenced (refs. 4 and 7, and GenBank Library 6359). Little is known about the variation in gene expression between different regions of the retina (e.g., the retinal periphery versus the macula); only a few genes with a preferential expression in the fovea have been identified (1). There is no counterpart to these different retinal regions in mouse retinas. Knowledge of the set of genes expressed in these regions is valuable, because some common diseases of the retina can affect one region preferentially (e.g., age-related macular degeneration).The serial analysis of gene expression (SAGE) procedure, first described by Velculescu et al. (8), allows the comp...

A large-scale screening of the normalized mammalian mitochondrial gene expression profiles

“…Only one group of samples that fell entirely into a single cluster was identified within the course of analysis. Mitochondrial profiles of all 4 SAGE samples generated from human retina (NlaIII dataset; GSM571-574), including human retinal pigment epithelium (RPE), peripheral and central retina (Sharon et al, 2002), were found in Cluster 2 (Fig. 4).…”

New meaning in the message: Noncoding RNAs and their role in retinal development

“…Examination of public SAGE data indicates that this pri-miRNA is equally abundant in the human retina. Analysis of SAGE data also indicates that the pri forms of miR-124a-2 and miR-9 are abundant in both human and mouse retinas, though less so than pri-miR124a-1 (Sharon et al, 2002;Blackshaw et al, 2004). By contrast, the pri-form of the highly retinal-enriched miR-96/182/ 183 cluster is barely detectable even by RT-PCR, so abundance of some primiRNAs is unlikely to reflect general deficiencies in miRNA processing in retina .…”

Apolipoprotein B in Cholesterol-Containing Drusen and Basal Deposits of Human Eyes with Age-Related Maculopathy

“…Previous attempts to identify apo B mRNA in human RPE by RT-PCR gave inconsistent results, 46 and apo B has not appeared among RPEexpressed genes identified by other methods. [57][58][59] This may be due to low abundance of apo B mRNA and to difficulties in obtaining high quality RNA from native human RPE. These include variable postmortem delay to processing, potential contamination with blood, and the presence of melanin, an RT-PCR inhibitor.…”