AMD aq soma
Description
Analytic datasets for paper entitled "PROTEOMIC PROFILES IN THE AQUEOUS FOLLOWING ANTI-VEGF THERAPY IN TREATMENT NAÏVE NEOVASCULAR AGE-RELATED MACULAR DEGENERATION". Purpose: To determine: 1) the impact of anti-VEGF injections on the aqueous humor protein composition of VEGF-related proteins and other proteins in treatment naïve neovascular AMD patients and controls, and 2) if, among cases, the protein concentrations and signatures change over time among cases. Experimental design Cases were treatment naïve neovascular AMD patients. Controls were cataract patients with no AMD. Cases had a sample of aqueous collected immediately prior to starting the anti-VEGF intra-vitreal injection and at two follow-up visits month 1 and 2. Controls had aqueous collected at the time of cataract surgery. The samples were analyzed using an aptamer-based proteomic technology. Results: Comparison of the 9 cases and 11 controls revealed 56 proteins with significant differences in expression at the baseline visit. After treatment, there was a trend towards anonsignificant decline in aqueous VEGF concentrations as recorded from two aptamer reagents, while a third reagent recorded a significant increase. Interference studies demonstrated that the latter reagent measured both drug bound and free VEGF concentrations (total VEGF) while the others measured only free VEGF levels. Conclusions and clinical relevance: Several proteins changed in expression over the course of the study. These findings illustrate the importance of considering the protein interactome in analyzing proteomic data.
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Steps to reproduce
Somascan data provided is stored in long format. Protein signals obtained from the SomaScan assay were log (base 2) transformed. Signals (RFU) for each of the aptamers in the aqueous samples were compared between groups and over time using linear mixed effects regression that included a random subject intercept. Comparison of protein levels across groups and over time were evaluated using linear contrasts. P-values were adjusted for multiple comparisons using false discover rate (FDR) calculations.