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Sophie X. Deng, Martin N. Nakatsu, Lily Vartanyan, Xinmin Li; Gene Profiling and Biological Process Analysis in the Human Cornea. Invest. Ophthalmol. Vis. Sci. 2012;53(14):4223.
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To identify transcriptional differences in gene expression and cell processes in the human corneal epithelium by comparing directly to its adjacent structures, the limbus and conjunctiva.
Total RNA was isolated from the cornea, limbus and conjunctiva in human sclerocorneal tissues from 3 separate donors. The gene expression profile of each tissue type was analyzed through a human genome U133 Plus 2.0 microarray and candidate genes from each tissue were identified by expression levels two-fold or higher when compared to each other from the average expression levels of the 3 donors. Selected differentially expressed genes were confirmed by quantitative RT-PCR (qRT-PCR) and functional and pathways analyses of genes overexpressed in the cornea were performed by the web-based toolkit Database for Annotation, Visualization and Integrated Discovery (DAVID).
There were 594 differentially expressed (two-fold or higher) transcripts in the cornea in direct comparison to that in the limbus and conjunctiva. Expression of signature markers of the cornea, conjunctiva and limbus were present in their respective tissues in the microarray and were confirmed by qRT-PCR. A number of previously identified corneal genes were present in the list, such as keratin 3, dickkopf 3, extracellular matrix protein 1 and brain-derived neurotrophic factor. We identified several new corneal transcripts including, ATP-binding cassette sub-family G member 1, delta/notch-like EGF repeat containing, patched 1, Frizzled 8 and Wnt 3. Functional analysis of the corneal list of overexpressed genes included several biological groups involved in various cell processes and signaling, including cytoskeletal rearrangements, cell adhesion, cell division, cell migration, apoptosis, Wnt signaling and Hedgehog signaling.
These results demonstrate the possible role for these differentially expressed cornea genes in regulating corneal epithelial cell differentiation and migration.
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