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Lee Kiang, Jillian Huang, Thiran Jayasundera, Jeffrey Sundstrom; Expression of AMD Susceptibility Genes in Human Vitreous. Invest. Ophthalmol. Vis. Sci. 2014;55(13):5243.
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Using a systems biology approach, we previously inferred candidate genes associated with AMD or with AMD and smoking. We hypothesized that the vitreous may contain gene expression products associated with AMD and that expression or post-translational modification of these proteins may correlate with disease progression.
A literature review of studies of the human vitreous proteome was conducted. To be included in the analysis, a study was required to have identified at least 50 proteins in total. We investigated whether the gene products of established AMD susceptibility genes and of inferred candidate genes were identified in those studies, and determined the fraction of gene products of interest identified in those studies. In addition, we applied a new optimized and unbiased proteomics assay that allows for the identification of over 1000 proteins per human vitreous sample. Mass spectrometry was conducted using use an inline Waters NanoAcquity HPLC system coupled to a ThermoFisher Q-Exactive mass spectrometer (LC-ESI MS/MS). Protein identification was conducted with MS/MS spectra searching against a Uniprot database using SEQUEST in Proteome Discoverer (version 188.8.131.523). Spectral counts were performed as an index of protein abundance after normalization and correction with ABACUS (Fermin et al., 2011).
A literature review revealed that 7 of 16 established AMD-associated genes were previously identified in human vitreous while 5 of 15 inferred candidate genes were previously identified in human vitreous. This reflects a compilation of 8 studies. Application of an optimized unbiased proteomics assay revealed a total of 1120 proteins with a false discovery rate of < 1:1000. In this assay alone, gene products of 8 of 16 of the established AMD susceptibility genes were identified, and 9 of 15 of the inferred candidate gene products were identified.
Gene products of the majority of AMD susceptibility genes and inferred AMD candidate genes are present in human vitreous. These gene products are readily detectable in a single assay and suggest the plausibility of studies linking genotype, vitreous protein abundance/modification and disease progression.
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