Investigating Differential Gene Expression in Anatomical Compartments of the Human Eye Using cDNA Microarrays

Abstract

Abstract: : Purpose:In this study, we characterized the various eye compartments on a molecular level by identifying a distinct set of differentially expressed genes for each tissue. We used cDNA microarray technology, which allows genome–scale expression analysis of thousands of genes in parallel. We also present an approach to identifying candidate disease genes by combining our tissue–specific gene expression profiles with previous genetic mapping studies. Methods: The following tissues were dissected from seven cadaver eyes: cornea, lens, iris, ciliary body, retina, and optic nerve. RNA was isolated from each of these tissues, amplified, and converted into cDNA. These cDNA samples were then hybridized to microarrays that contained 43,198 elements (representing ∼30,000 genes). To explore gene expression relationships among the different eye tissues, we performed a combination of supervised and unsupervised statistical analyses of both the genes and samples. Results:Our analyses provided us with a "signature," or set of differentially expressed genes, for each eye tissue. Many of the genes contained within a particular signature recapitulated known aspects of the physiology of that eye tissue, while other genes had not previously been characterized within that tissue. For example, the ciliary body/iris gene signature contained numerous genes involved in the regulation of melanin production as would be expected in pigmented tissue; however, the same signature also contained a striking number of genes coding for immunological proteins. We also detected expression differences within the retinal compartment itself by comparing macula and peripheral retina samples. Finally, based on the hypothesis that disease genes affecting a particular eye tissue are likely to be expressed in that tissue, we combined our gene expression signatures with genetic mapping studies to identify candidate genes for a number of diseases affecting the cornea, lens, and retina. Conclusions: These cDNA microarray studies demonstrate that each eye tissue can be defined by a molecular signature of differentially expressed genes. These signatures will serve as a reference database for investigators interested in the physiology and pathophysiology of the eye. These signatures also provide a valuable tool for discovering candidate disease genes.

Keywords: candidate gene analysis • gene/expression • gene microarray