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      Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy

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          Abstract

          Muscle atrophy is a physiological response to disuse and malnutrition, but hibernating bears are largely resistant to this phenomenon. Unlike other mammals, they efficiently reabsorb amino acids from urine, periodically activate muscle contraction, and their adipocytes differentially responds to insulin. The contribution of myocytes to the reduced atrophy remains largely unknown. Here we show how metabolism and atrophy signaling are regulated in skeletal muscle of hibernating grizzly bear. Metabolic modeling of proteomic changes suggests an autonomous increase of non-essential amino acids (NEAA) in muscle and treatment of differentiated myoblasts with NEAA is sufficient to induce hypertrophy. Our comparison of gene expression in hibernation versus muscle atrophy identified several genes differentially regulated during hibernation, including Pdk4 and Serpinf1. Their trophic effects extend to myoblasts from non-hibernating species (including C. elegans), as documented by a knockdown approach. Together, these changes reflect evolutionary favored adaptations that, once translated to the clinics, could help improve atrophy treatment.

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          Most cited references39

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          Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

          Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a substantial update of this in silico toolbox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis methods developed since its original release. New functions include (i) network gap filling, (ii) (13)C analysis, (iii) metabolic engineering, (iv) omics-guided analysis and (v) visualization. As with the first version, the COBRA Toolbox reads and writes systems biology markup language-formatted models. In version 2.0, we improved performance, usability and the level of documentation. A suite of test scripts can now be used to learn the core functionality of the toolbox and validate results. This toolbox lowers the barrier of entry to use powerful COBRA methods.
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            Functional genomic analysis of C. elegans chromosome I by systematic RNA interference.

            Complete genomic sequence is known for two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and it will soon be known for humans. However, biological function has been assigned to only a small proportion of the predicted genes in any animal. Here we have used RNA-mediated interference (RNAi) to target nearly 90% of predicted genes on C. elegans chromosome I by feeding worms with bacteria that express double-stranded RNA. We have assigned function to 13.9% of the genes analysed, increasing the number of sequenced genes with known phenotypes on chromosome I from 70 to 378. Although most genes with sterile or embryonic lethal RNAi phenotypes are involved in basal cell metabolism, many genes giving post-embryonic phenotypes have conserved sequences but unknown function. In addition, conserved genes are significantly more likely to have an RNAi phenotype than are genes with no conservation. We have constructed a reusable library of bacterial clones that will permit unlimited RNAi screens in the future; this should help develop a more complete view of the relationships between the genome, gene function and the environment.
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              IKKbeta/NF-kappaB activation causes severe muscle wasting in mice.

              Muscle wasting accompanies aging and pathological conditions ranging from cancer, cachexia, and diabetes to denervation and immobilization. We show that activation of NF-kappaB, through muscle-specific transgenic expression of activated IkappaB kinase beta (MIKK), causes profound muscle wasting that resembles clinical cachexia. In contrast, no overt phenotype was seen upon muscle-specific inhibition of NF-kappaB through expression of IkappaBalpha superrepressor (MISR). Muscle loss was due to accelerated protein breakdown through ubiquitin-dependent proteolysis. Expression of the E3 ligase MuRF1, a mediator of muscle atrophy, was increased in MIKK mice. Pharmacological or genetic inhibition of the IKKbeta/NF-kappaB/MuRF1 pathway reversed muscle atrophy. Denervation- and tumor-induced muscle loss were substantially reduced and survival rates improved by NF-kappaB inhibition in MISR mice, consistent with a critical role for NF-kappaB in the pathology of muscle wasting and establishing it as an important clinical target for the treatment of muscle atrophy.
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                Author and article information

                Contributors
                gotthardt@mdc-berlin.de
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                27 December 2019
                27 December 2019
                2019
                : 9
                : 19976
                Affiliations
                [1 ]ISNI 0000 0001 1014 0849, GRID grid.419491.0, Neuromuscular and Cardiovascular Cell Biology, , Max Delbrück Center for Molecular Medicine, ; Berlin, Germany
                [2 ]ISNI 0000 0001 1014 0849, GRID grid.419491.0, Berlin Institute for Medical Systems Biology, , Max Delbrück Center for Molecular Medicine, ; Berlin, Germany
                [3 ]GRID grid.5603.0, Interfaculty Institute for Genetics and Functional Genomics, , University Medicine Greifswald, ; Greifswald, Germany
                [4 ]ISNI 0000 0001 2157 6568, GRID grid.30064.31, College of Veterinary Medicine and Department of Veterinary Clinical Science, , Washington State University, ; Pullman, Washington USA
                [5 ]ISNI 0000 0001 2157 6568, GRID grid.30064.31, School of the Environment and School of Biological Sciences, , Washington State University, ; Pullman, Washington USA
                [6 ]ISNI 0000 0004 5937 5237, GRID grid.452396.f, DZHK (German Centre for Cardiovascular Research), partner site Greifswald, ; Greifswald, Germany
                [7 ]ISNI 0000 0001 1014 0849, GRID grid.419491.0, Experimental and Clinical Research Center, , Charité & Max Delbrück Center for Molecular Medicine, ; Berlin, Germany
                [8 ]ISNI 0000 0001 2218 4662, GRID grid.6363.0, Charité Universitätsmedizin Berlin, ; Berlin, Germany
                [9 ]ISNI 0000 0004 5937 5237, GRID grid.452396.f, DZHK (German Center for Cardiovascular Research), partner site Berlin, ; Berlin, Germany
                Article
                56007
                10.1038/s41598-019-56007-8
                6934745
                31882638
                155a9ff6-a615-487e-a140-dc7e8d028ce4
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 September 2019
                : 5 December 2019
                Funding
                Funded by: TransCard PhD fellowship
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: CRG192
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                translational research,experimental models of disease,molecular medicine,skeletal muscle,cell signalling,mechanisms of disease,systems biology,metabolism,proteome

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