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J. Sebag, Kenneth M. Yee, Michele C. Madigan, Lloyd P. Aiello, Alfredo A. Sadun; Bioinformatic Analysis of Embryonic Human Vitreomics. Invest. Ophthalmol. Vis. Sci. 2012;53(14):4928.
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© ARVO (1962-2015); The Authors (2016-present)
Embryonic vitreous vessels regress during the 2nd trimester. Proteomic analyses (Sebag et al ARVO 2010) during this time frame identified 294 proteins that changed 2 to 100-fold. Potential involvement of biological networks and canonical pathways in this data set were evaluated with bioinformatics.
Ingenuity Pathway Analysis (IPA; Ingenuity Systems, Redwood City, CA) was performed on 1000 proteins assayed by one-dimensional SDS-PAGE and nano-LC tandem mass spectrometry in each of 17 whole vitreous bodies from human embryos aged 14-20 weeks’ gestation. Protein ID, Spearman’s R, and p-value for each protein were analyzed and assigned a network score that indicates the likelihood that a set of genes in a network associate randomly (e.g. a score of 6 indicates a 1 in a million chance that the genes are associated due to chance). A score of 2 or higher represents at least 99% confidence of not being generated by random chance.
Top networks were protein synthesis (Score = 56; 30 proteins), free radical scavenging & molecular transport (Score = 48; 27 proteins), small molecule biochemistry (Score = 42; 25 proteins), and connective tissue (CT) disorders (Score = 38; 23 proteins). In the first 3 networks, most proteins were intracellular and decreased (27/30 = 90%; 23/27 = 85.2%; 24/25 = 96%; respectively) during the 2nd trimester. Only 5/23 (21.7%) proteins decreased in the CT disorder network (p=0.0001 for each of the first 3 networks compared to CT disorders). Of the 18 proteins that increased in the CT disorders network, 15 (83.3%) were extracellular. EIF2 signaling (p=3.0 E-7) and protein ubiquitination (p=9.6 E-6) were the top canonical pathways.
IPA of human embryo vitreomics during the period of hyaloid vessel regression demonstrated that protein synthesis, free radical scavenging & molecular transport, and small molecule biochemistry networks had markedly decreased protein expression, in contrast to increased protein expression in the CT disorder network. This is consistent with replacement of the cellular primary vitreous with the acellular secondary vitreous which is primarily a collagenous extracellular matrix. That protein ubiquitination (which induces protein degradation) increases concurrently with EIF2 signaling (needed for transcription, presumably for collagen synthesis) further supports this conclusion. This approach provides new insight into potential mechanisms of vascular regression in normal development with possible application to pathologic neovascularization.
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