Integrating metabolomics and phenomics with systems models of cardiac hypoxia.

Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Progress in Biophysics and Molecular Biology (Impact Factor: 3.38). 01/2008; 96(1-3):209-25. DOI: 10.1016/j.pbiomolbio.2007.07.014
Source: PubMed

ABSTRACT Hypoxia is the major cause of necrotic cell death in myocardial infarction. Cellular energy supply and demand under hypoxic conditions is regulated by many interacting signaling and transcriptional networks, which complicates studies on individual proteins and pathways. We apply an integrated systems approach to understand the metabolic and functional response to hypoxia in muscle cells of the fruit fly Drosophila melanogaster. In addition to its utility as a hypoxia-tolerant model organism, Drosophila also offers advantages due to its small size, fecundity, and short life cycle. These traits, along with a large library of single-gene mutations, motivated us to develop new, computer-automated technology for gathering in vivo measurements of heart function under hypoxia for a large number of mutant strains. Phenotype data can be integrated with in silico cellular networks, metabolomic data, and microarrays to form qualitative and quantitative network models for prediction and hypothesis generation. Here we present a framework for a systems approach to hypoxia in the cardiac myocyte, starting from nuclear magnetic resonance (NMR) metabolomics, a constraint-based metabolic model, and phenotypic profiles.

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