Biological control networks suggest the use of biomimetic sets for combinatorial therapies

Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks (transcription factors, microRNAs, and protein kinases) and a drug-target network. Certain network properties seem universal across systems and species, suggesting the existence of common control strategies in biology. The number of controllers is ~8% of targets and the density of links is 2.5% \pm 1.2%. Links per node are predominantly exponentially distributed, implying conservation of the average, which we explain using a mathematical model of robustness in control networks. These findings suggest that optimal pharmacological strategies may benefit from a similar, many-to-many combinatorial structure, and molecular tools are available to test this approach.Comment: 33 page

Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue

The fruit fly D. melanogaster is increasingly used as a model organism for studying acute hypoxia tolerance and for studying aging, but the interactions between these two factors are not well known. Here we show that hypoxia tolerance degrades with age in post-hypoxic recovery of whole-body movement, heart rate and ATP content. We previously used 1H NMR metabolomics and a constraint-based model of ATP-generating metabolism to discover the end products of hypoxic metabolism in flies and generate hypotheses for the biological mechanisms. We expand the reactions in the model using tissue- and age-specific microarray data from the literature, and then examine metabolomic profiles of thoraxes after 4 hours at 0.5% O2 and after 5 minutes of recovery in 40- versus 3-day-old flies. Model simulations were constrained to fluxes calculated from these data. Simulations suggest that the decreased ATP production during reoxygenation seen in aging flies can be attributed to reduced recovery of mitochondrial respiration pathways and concomitant over-dependence on the acetate production pathway as an energy source.Comment: 30 page

Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis

BACKGROUND: Cellular hypoxia is a component of many diseases, but mechanisms of global hypoxic adaptation and resistance are not completely understood. Previously, a population of Drosophila flies was experimentally selected over several generations to survive a chronically hypoxic environment. NMR-based metabolomics, combined with flux-balance simulations of genome-scale metabolic networks, can generate specific hypotheses for global reaction fluxes within the cell. We applied these techniques to compare metabolic activity during acute hypoxia in muscle tissue of adapted versus "naïve" control flies. RESULTS: Metabolic profiles were gathered for adapted and control flies after exposure to acute hypoxia using (1)H NMR spectroscopy. Principal Component Analysis suggested that the adapted flies are tuned to survive a specific oxygen level. Adapted flies better tolerate acute hypoxic stress, and we explored the mechanisms of this tolerance using a flux-balance model of central metabolism. In the model, adapted flies produced more ATP per glucose and created fewer protons than control flies, had lower pyruvate carboxylase flux, and had greater usage of Complex I over Complex II. CONCLUSION: We suggest a network-level hypothesis of metabolic regulation in hypoxia-adapted flies, in which lower baseline rates of biosynthesis in adapted flies draws less anaplerotic flux, resulting in lower rates of glycolysis, less acidosis, and more efficient use of substrate during acute hypoxic stress. In addition we suggest new specific hypothesis, which were found to be consistent with existing data

Search algorithms as a framework for the optimization of drug combinations

Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms, originally developed for digital communication, modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise capacity in Drosophila melanogaster, we found that search algorithms correctly identified optimal combinations of four drugs with only one third of the tests performed in a fully factorial search. In experiments identifying combinations of three doses of up to six drugs for selective killing of human cancer cells, search algorithms resulted in a highly significant enrichment of selective combinations compared with random searches. In simulations using a network model of cell death, we found that the search algorithms identified the optimal combinations of 6-9 interventions in 80-90% of tests, compared with 15-30% for an equivalent random search. These findings suggest that modified search algorithms from information theory have the potential to enhance the discovery of novel therapeutic drug combinations. This report also helps to frame a biomedical problem that will benefit from an interdisciplinary effort and suggests a general strategy for its solution.Comment: 36 pages, 10 figures, revised versio

Mapping an atlas of tissue-specific drosophila melanogaster metabolomes by high resolution mass spectrometry

Metabolomics can provide exciting insights into organismal function, but most work on simple models has focussed on the whole organism metabolome, so missing the contributions of individual tissues. Comprehensive metabolite profiles for ten tissues from adult Drosophila melanogaster were obtained here by two chromatographic methods, a hydrophilic interaction (HILIC) method for polar metabolites and a lipid profiling method also based on HILIC, in combination with an Orbitrap Exactive instrument. Two hundred and forty two polar metabolites were putatively identified in the various tissues, and 251 lipids were observed in positive ion mode and 61 in negative ion mode. Although many metabolites were detected in all tissues, every tissue showed characteristically abundant metabolites which could be rationalised against specific tissue functions. For example, the cuticle contained high levels of glutathione, reflecting a role in oxidative defence; the alimentary canal (like vertebrate gut) had high levels of acylcarnitines for fatty acid metabolism, and the head contained high levels of ether lipids. The male accessory gland uniquely contained decarboxylated S-adenosylmethionine. These data thus both provide valuable insights into tissue function, and a reference baseline, compatible with the FlyAtlas.org transcriptomic resource, for further metabolomic analysis of this important model organism, for example in the modelling of human inborn errors of metabolism, aging or metabolic imbalances such as diabetes

Systems biology of the cardiac hypoxia response in Drosophila

Drosophila is an emerging model for studying genetic influences on heart function, and has also been found to be highly tolerant to hypoxia. Strategies for controlling metabolism in the hypoxic adult fly heart may give clues to new therapies for myocardial ischemia in humans, however, the mechanisms of their hypoxic metabolic regulation are not well known. We adopt a systems biology approach to discover important hypoxia-tolerance strategies in ATP-generating metabolism in Drosophila heart. First, we built automation technology for rapidly screening the in vivo cardiac hypoxia response in adult flies, and proved its speed by characterizing the wild type over a range of conditions. The assay detected loss- of-function phenotypes in known hypoxia-sensitive mutants. Next we used ¹H NMR metabolomics to discover the major anaerobic end products (lactate, alanine, and acetate), which we built into a genome-wide reconstruction of central metabolism. We fit metabolomic data to the model and used it to examine the benefits of these pathways under hypoxia. The model was then used to predict the effects of a lactate dehydrogenase (LDH) mutant, which were supported by metabolomic, heart phenotype, and whole- body assays on an LDH mutant strain. The model was further refined with gene expression data and used with metabolomic profiling to study the effects of age on the hypoxia response. Recovery of heart rate, whole-body activity, and ATP concentration was delayed in older flies. After fitting the model to metabolomic data for young and old flies, flux-balance analysis pointed to impaired mitochondrial recovery, with excess pyruvate converted to acetate, as the major source of differences between the age groups. Gene expression and the literature on Drosophila aging supported these conclusions. This approach was repeated for a strain of flies that had been experimentally selected to survive chronic hypoxia. Flux- balance modeling suggested that adapted flies may better divert pyruvate flux through pyruvate dehydrogenase rather than pyruvate carboxylase in order to better tolerate acute hypoxia. Gene expression data from microarrays helped support this finding. The dissertation offers clues to hypoxia tolerance in flies, generating hypotheses for further research, and also provides a technology platform for a systematic perturbation analysi

Systems biology of the cardiac hypoxia response in Drosophila

Drosophila is an emerging model for studying genetic influences on heart function, and has also been found to be highly tolerant to hypoxia. Strategies for controlling metabolism in the hypoxic adult fly heart may give clues to new therapies for myocardial ischemia in humans, however, the mechanisms of their hypoxic metabolic regulation are not well known. We adopt a systems biology approach to discover important hypoxia-tolerance strategies in ATP-generating metabolism in Drosophila heart. First, we built automation technology for rapidly screening the in vivo cardiac hypoxia response in adult flies, and proved its speed by characterizing the wild type over a range of conditions. The assay detected loss- of-function phenotypes in known hypoxia-sensitive mutants. Next we used ¹H NMR metabolomics to discover the major anaerobic end products (lactate, alanine, and acetate), which we built into a genome-wide reconstruction of central metabolism. We fit metabolomic data to the model and used it to examine the benefits of these pathways under hypoxia. The model was then used to predict the effects of a lactate dehydrogenase (LDH) mutant, which were supported by metabolomic, heart phenotype, and whole- body assays on an LDH mutant strain. The model was further refined with gene expression data and used with metabolomic profiling to study the effects of age on the hypoxia response. Recovery of heart rate, whole-body activity, and ATP concentration was delayed in older flies. After fitting the model to metabolomic data for young and old flies, flux-balance analysis pointed to impaired mitochondrial recovery, with excess pyruvate converted to acetate, as the major source of differences between the age groups. Gene expression and the literature on Drosophila aging supported these conclusions. This approach was repeated for a strain of flies that had been experimentally selected to survive chronic hypoxia. Flux- balance modeling suggested that adapted flies may better divert pyruvate flux through pyruvate dehydrogenase rather than pyruvate carboxylase in order to better tolerate acute hypoxia. Gene expression data from microarrays helped support this finding. The dissertation offers clues to hypoxia tolerance in flies, generating hypotheses for further research, and also provides a technology platform for a systematic perturbation analysi

Results of flux-balance analysis on the model of ATP-generating metabolism

<p><b>Copyright information:</b></p><p>Taken from "Flexibility in energy metabolism supports hypoxia tolerance in flight muscle: metabolomic and computational systems analysis"</p><p></p><p>Molecular Systems Biology 2007;3():99-99.</p><p>Published online 17 Apr 2007</p><p>PMCID:PMC1865581.</p><p>Copyright © 2007, EMBO and Nature Publishing Group</p> () Proton production increases but then levels off at low oxygen levels as pyruvate begins to be fermented to alanine, acetate, and lactate. Glucose uptake is decreased during restricted oxygen. () When pyruvate is only allowed to be converted to lactate (pseudo-mammalian), proton production is much higher and glucose uptake remains constant during hypoxia, whereas () ATP production remains the same or better. Abbreviations: ac: acetate accumulation; ala: alanine accumulation; atp: ATP production; CO: CO production; glc: glucose uptake; h: proton production and lac: lactate accumulation