A New Strategy to Identify and Annotate Human RPE-Specific Gene Expression

Abstract

Purpose: : To identify and functionally annotate cell type-specific gene expression of the human retinal pigment epithelium (RPE), a key tissue involved in age-related macular degeneration and retinitis pigmentosa.

Methods: : RPE, photoreceptor and choroidal cells were isolated from retinal cryo-sections of selected freshly frozen healthy human donor eyes, using laser microdissection. We isolated RNA and performed 44 K RNA microarray analysis (Agilent procedures). Bioinformatics was carried out using Rosetta Resolver, David and Ingenuity software.

Results: : Our previous 22K microarray analysis showed that the RPE has high levels of protein synthesis, strong energy demands, is exposed to high levels of oxidative stress and a variable degree of inflammation. We now used a complementary strategy aimed at the identification and functional annotation of RPE-specific expressed transcripts. This strategy takes advantage of the multilayered cellular structure of the retina and overcomes a number of limitations of previous studies. In triplicate, we compared the transcriptomes of RPE, photoreceptor and choroidal cells and we deduced RPE specific expression. We identified at least 114 entries with RPE-specific gene expression. Thirty-nine of these 114 genes also show high expression in the RPE. Comparison with the literature showed that 85% of these 39 were previously identified to be expressed in the RPE. In the group of 114 RPE specific genes there was an overrepresentation of genes involved in (membrane) transport, vision and ophthalmic disease.

Conclusions: : We identfied a substantial number of (new) RPE specific transcripts, which is intrumental for RPE disease gene identification and functional assesment of (disorders of) the human RPE.

Keywords: gene/expression • retinal degenerations: cell biology • age-related macular degeneration