Differential gene expression in anatomical compartments of the human eye

Jennifer J Diehn¹^,4 , Maximilian Diehn² , Michael F Marmor¹ and Patrick O Brown²^,3

¹Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA

²Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA

³Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA

⁴Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA

author email corresponding author email

Genome Biology 2005, 6:R74doi:10.1186/gb-2005-6-9-r74


Published:	17 August 2005

Subject areas: Physiology, Medicine, Molecular biology, Genome studies

Abstract

Background

The human eye is composed of multiple compartments, diverse in form, function, and embryologic origin, that work in concert to provide us with our sense of sight. We set out to systematically characterize the global gene expression patterns that specify the distinctive characteristics of the various eye compartments.

Results

We used DNA microarrays representing approximately 30,000 human genes to analyze gene expression in the cornea, lens, iris, ciliary body, retina, and optic nerve. The distinctive patterns of expression in each compartment could be interpreted in relation to the physiology and cellular composition of each tissue. Notably, the sets of genes selectively expressed in the retina and in the lens were particularly large and diverse. Genes with roles in immune defense, particularly complement components, were expressed at especially high levels in the anterior segment tissues. We also found consistent differences between the gene expression patterns of the macula and peripheral retina, paralleling the differences in cell layer densities between these regions. Based on the hypothesis that genes responsible for diseases that affect a particular eye compartment are likely to be selectively expressed in that compartment, we compared our gene expression signatures with genetic mapping studies to identify candidate genes for diseases affecting the cornea, lens, and retina.

Conclusion

Through genome-scale gene expression profiling, we were able to discover distinct gene expression 'signatures' for each eye compartment and identified candidate disease genes that can serve as a reference database for investigating the physiology and pathophysiology of the eye.