Micro Serial Analysis of Gene Expression in Normal Human Choroid and Retinal Pigment Epithelial Transcriptomes

Abstract

Purpose

To investigate the gene expression profile of the normal human choroid/retinal pigment epithelium(RPE) tissues.

Methods

Micro serial analysis of gene expression (Micro SAGE) was performed. A SAGE library was constructed from 110 µg of total RNA of normal human choroid/RPE tissue, and cloned tag concatemers transformed to E.coli were sequenced. The sequence data were analyzed by SAGE software and matched to GenBank and UniGene public databases. The sequence data were also compared with the choroid/RPE cDNA library of NEIBank.

Results

A total of 12 070 tags were sequenced; 3627 tags were unique. Of these 3627 tags, 2508 tags were encoded genes and 1119 tags were unknown tags in the UniGene database. The most frequently expressed tag was TCCCTATTAA, but the gene corresponding to this tag has not been identified yet. Other frequently expressed tags encoded a tissue inhibitor of matrix metalloproteinase 3, insulin-like growth factor binding protein-related protein 1, and transthyretin. These genes are notably different, with high expression frequencies when compared to the cDNA library of NEIBank.

Conclusions

This gene expression profile of the normal human choroid/RPE tissue should provide further understanding of the biological function of the choroid and the pathogenesis of diseases in which the choroid and RPE play a role, such as choroidal neovascularization. Jpn J Ophthalmol 2005;49:15–22 © Japanese Ophthalmological Society 2005