Purpose.: To determine whether differences in gene expression occur between areas of focal retinal ganglion cell (RGC) loss and of relative RGC preservation in the DBA/2 mouse retina and whether they can provide insight into the pathophysiology of glaucoma.

Methods.: Areas of focal RGC loss (judged by lack of Fluorogold labeling; Fluorochrome, Denver, CO), adjacent areas with relative RGC preservation in DBA/2 retina, and Fluorogold-labeled retina from DBA/2− pe (pearl) mice were dissected and used for microarray analysis. RT-PCR and immunoblot analysis were used to confirm differential gene expression. Bioinformatic analysis was used to identify gene networks affected in the glaucomatous retina.

Results.: Microarray analysis identified 372 and 115 gene chip IDs as up-and downregulated, respectively, by 0.5-fold in areas of RGC loss. Differentially expressed genes included those coding for cytoskeletal proteins, enzymes, transport proteins, extracellular matrix (ECM) proteins, and immune response proteins. Several genes were confirmed by RT-PCR. For at least two genes, differential protein expression was verified. Bioinformatics analysis identified multiple affected functional gene networks. Pearl mice appeared to have significantly different gene expression, even when compared with relatively preserved areas of the DBA/2 retina.

Conclusions.: Regional gene expression changes occur in areas of focal RGC loss in the DBA/2 retina. The genes involved code for proteins with diverse cellular functions. Further investigation is needed to determine the cellular localization of the expression of these genes during the development of spontaneous glaucoma in the DBA/2 mouse and to determine whether some of these gene expression changes are causative or protective of RGC loss.