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N. V. Strunnikova, J. Barb, C. Zhi, A. Maminishkis, P. Munson, S. Miller; Human Fetal and Adult RPE Gene Expression Signature: Function and Disease Association. Invest. Ophthalmol. Vis. Sci. 2009;50(13):2921.
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© ARVO (1962-2015); The Authors (2016-present)
Dysfunction of RPE cells plays a critical role in the development of a variety of ophthalmic disorders. Understanding the functional and genetic properties of native RPE is a necessary first step in the prevention and treatments of these disorders. Therefore we developed a genetic characterization that distinguishes RPE from all other tissues in the body.
Total RNA was isolated from RPE from 4 adult (59-79 yrs) and 4 fetal donors, 4 primary fetal cultures (P1) and adult cultures (ARPE-19). Gene expression profiling was done using HU133 Plus 2.0 chip from Affymetrix containing 54,675 probes. Data analysis was carried out using the MSCL Toolbox, Ingenuity and EASE software packages. Using all of these samples, a set of "RPE signature" genes was defined as those genes with mean expression values up-regulated 10 fold or more relative to the median gene expression values of the Novartis gene expression database (http://symatlas.gnf.org/SymAtlas). RT-PCR, western blot and immunocytochemistry were used for validation.
Expression levels of 150 RPE "signature" genes were determined and confirmed by Q-PCR. Expression of signature genes was used to successfully distinguish our RPE preparations from other human tissues. Significance of RPE signature genes was demonstrated by their role in variety of eye disorders. Analysis by Ingenuity software established that fifteen unrelated genes (TYRP1, SIL1, BEST1, COL8A2, EFEMP1, LOXL1, SERPINF1, BMP4, VEGFA, TIMP3, CHRNA3, PRNP, RPE65, CRX, GPNMB) were significantly associated (p < 10-19 to 10-4) with variety of ophthalmic disorders. Functional analysis demonstrated a large number of genes in the RPE signature (PDPN, SDC2, NAV3, SIL1, MFAP3L) associated with variety of cancers. We have begun to evaluate the RPE signature genes for possible association with AMD in a genome-wide association dataset.
Using hfRPE, native RPE, and Novartis expression data we determined a set of RPE specific genes. Our screening approach was able to determine a variety of critically important RPE specific disease-associated genes. This signature set can be used for the discovery of RPE candidate genes whose functions are not yet established in eye disorders.
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