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Genome-wide expression profiling of complex regional pain syndrome

ABSTRACT: we successfully identified pain-related genes through genome-wide expression profiling in blood from CRPS patients. We found that 80 genes were differentially expressed between 4 CRPS patients (2 CRPS I and 2 CRPS II) and 5 controls (cut-off value: 1.5-fold change and p < 0.05). Most of those genes were associated with signal transduction, developmental processes, cell structure and motility, and immunity and defense. The expression levels of 12 genes selected from the microarray were confirmed in 24 CRPS patients and 18 controls by quantitative reverse transcription-polymerase chain reaction. We focused on matrix metalloproteinase 9 (MMP9) that showed statistically significant difference from controls and the highest relative fold change in CRPS II patients to controls by qPCR validation (6.4 ± 2.47 times and p = 0.001).

ORGANISM(S): Homo sapiens

PROVIDER: GSE47603 | GEO | 2013/06/06

SECONDARY ACCESSION(S): PRJNA206506

REPOSITORIES: GEO

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Project description:This is the model described in the article: A biochemical model of matrix metalloproteinase 9 activation and inhibition. Vempati P, Karagiannis ED, Popel AS. J Biol Chem. 2007 Dec 28;282(52):37585-96. Pubmed ID: 17848556 , doi: 10.1074/jbc.M611500200 . Abstract: Matrix metalloproteinases (MMPs) are a class of extracellular and membrane-bound proteases involved in an array of physiological processes, including angiogenesis. We present a detailed computational model of MMP9 activation and inhibition. Our model is validated to existing biochemical experimental data. We determine kinetic rate constants for the processes of MMP9 activation by MMP3, MMP10, MMP13, and trypsin; inhibition by the tissue inhibitors of metalloproteinases (TIMPs) 1 and 2; and MMP9 deactivation. This computational approach allows us to investigate discrepancies in our understanding of the interaction of MMP9 with TIMP1. Specifically, we find that inhibition due to a single binding event cannot describe MMP9 inhibition by TIMP1. Temporally accurate biphasic inhibition requires either an additional isomerization step or a second lower affinity isoform of MMP9. We also theoretically characterize the MMP3/TIMP2/pro-MMP9 and MMP3/TIMP1/pro-MMP9 systems. We speculate that these systems differ significantly in their time scales of activation and inhibition such that MMP9 is able to temporarily overshoot its final equilibrium value in the latter. Our numerical simulations suggest that the ability of pro-MMP9 to complex TIMP1 increases this overshoot. In all, our analysis serves as a summary of existing kinetic data for MMP9 and a foundation for future models utilizing MMP9 or other MMPs under physiologically well defined microenvironments. This model was taken from the CellML repository and automatically converted to SBML. The original model is: Vempati, Karagiannis, Popel, 2007 version 1 The original CellML model was created and curated by: Catherine May Lloyd c.lloyd(at)auckland.ac.nz The University of Auckland, Bioengineering Institute This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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Genome-wide expression profiling of complex regional pain syndrome

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