Differential Gene Expression in Human Fovea Compared with Peripheral Retina

Abstract

Abstract: : Purpose: The human retinal fovea is essential for precise visual acuity. In order to further understand its structure, function and pathology, a study was designed to find genes differentially expressed in human fovea compared with peripheral retina. Methods: Total RNA was extracted from 1.5mm foveal punches from twelve human donor eyes, from two 4mm foveo-macular punches, and from two sections of mid-peripheral retina. Paired RNA samples were reverse transcribed, one sample labeled with Cy3 and one with Cy5. The paired samples were then hybridized to a microarray of 14,000 70mers in duplicate from a named human probe set, derived from UniGene. Data were managed in an SQL database and analysed using scripts with the R statistics package. Results: Fourteen genes showed ten-fold increased expression in fovea compared with peripheral retina. These genes also appeared more highly differentially expressed in 1.5mm fovea than in 4mm fovea. Of these fourteen genes, one (RP2) is known to cause retinal disease. Conversely, only S-antigen (rod arrestin) was consistently (four-fold) over-expressed in peripheral retina compared with fovea. Rhodopsin was expressed twice as highly in peripheral retina than in 1.5mm fovea. Control experiments showed a variability of 1.5-fold, accounting for both intra-slide and inter-sample variation. Conclusions: This study has identified genes expressed differentially in fovea compared with peripheral retina, when accounting for the variability inherent in microarray analysis. The retinal function of a number of these genes has not so far been studied.

Keywords: retina • gene/expression • gene microarray