Profiling Gene Expression of Human Ocular Tissues

Abstract

Purpose:: To determine genome-wide gene expression patterns in human ocular tissues.

Methods:: Human donor eyes were preserved by submersion in RNAlater within 6 hr post mortem. RNA was extracted from 10 carefully dissected ocular tissues (cornea, iris, ciliary body, lens, trabecular meshwork, RPE/choroid, retina, optic nerve, optic nerve head, and sclera). Gene expression was profiled in pooled RNA from 3 to 12 donors by Affymetrix array (U133 set). Array data were analyzed by GeneSpring and GenMapp programs. Tissue specific genes were identified based on the following criteria: (1) present only in target tissue with normalized signal >1 and (2) absent/marginal in at least 8 other tissues with normalized signal <1 in at least 5-7 other tissues. Array data for selected genes were confirmed using RT-qPCR.

Results:: Expression of approximately 50% of 22283 genes was detected as present in all ten ocular tissues. Ciliary body had the highest rate of genes with "present" calls while optic nerve head had the lowest rate. Gene expression patterns were compared among the 10 ocular tissues by cluster analysis. Iris and ciliary body have the most representative expression patterns for ocular tissues, while lens, retina and cornea are the most distinct from other ocular tissues. The most similar gene expression patterns were observed between optic nerve and optic nerve head (r² = 0.81). Twenty and nineteen genes expressed preferentially for anterior and posterior tissues were identified respectively. There were fifteen to thirty-four tissue-specific genes identified for each individual tissue, including some genes that have not been previously identified as uniquely expressed in a specific ocular tissue. This ocular tissue gene expression database is a unique and complete resource because most other ocular gene expression databases are for whole eye or only for specific ocular tissues.

Conclusions:: We have established an ocular gene expression database from 10 ocular tissues using microarray technology. This database provides not only a molecular basis of the biology of the eye but also a useful resource for comparing expression profiles between normal and diseased tissues to better understand molecular mechanisms of eye diseases. Tissue-specific genes identified in each ocular tissue provide candidate genes that may be useful as molecular markers for characterizing tissue types, as well as tissue-specific promoters to generate ocular tissue specific transgenic animal models for eye disorders such as glaucoma and AMD.

Keywords: gene microarray • gene/expression • trabecular meshwork