Patterns of gene expression in atrophying skeletal muscles: response to food deprivation

Jagoe, R. Thomas; Lecker, Stewart H.; Gomes, Marcelo; Goldberg, Alfred L.

doi:10.1096/fj.02-0312com

Cited by 344Muscle Physiology and DisordersMuscle metabolism and nutritionNutrition and Health in Aging

Patterns of gene expression in atrophying skeletal muscles: response to food deprivation

Jagoe, R. Thomas, Lecker, Stewart H., Gomes, Marcelo, Goldberg, Alfred L.·2002·The FASEB Journal

DOI 10.1096/fj.02-0312com

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Abstract

During fasting and many systemic diseases, muscle undergoes rapid loss of protein and functional capacity. To define the transcriptional changes triggering muscle atrophy and energy conservation in fasting, we used cDNA microarrays to compare mRNAs from muscles of control and food‐deprived mice. Expression of >94% of genes did not change, but interesting patterns emerged among genes that were differentially expressed: 1) mRNAs encoding polyubiquitin, ubiquitin extension proteins, and many (but not all) proteasome subunits increased, which presumably contributes to accelerated protein breakdown; 2) a dramatic increase in mRNA for the ubiquitin ligase, atrogin‐1, but not most E3s; 3) a significant suppression of mRNA for myosin binding protein H (but not other myofibrillar proteins) and IGF binding protein 5, which may favor cell protein loss; 4) decreases in mRNAs for several glycolytic enzymes and phosphorylase kinase subunits, and dramatic increases in mRNAs for pyruvate dehydrogenase kinase 4 and glutamine synthase, which should promote glucose sparing and gluconeogenesis. During fasting, metallothionein mRNA increased dramatically, mRNAs for extracellular matrix components fell, and mRNAs that may favor cap‐independent mRNA translation rose. Significant changes occurred in mRNAs for many growth‐related proteins and transcriptional regulators. These transcriptional changes indicate a complex adaptive program that should favor protein degradation and suppress glucose oxidation in muscle. Similar analysis of muscles atrophying for other causes is allowing us to identify a set of atrophy‐specific changes in gene expression.—Jagoe, R. T., Lecker, S. H., Gomes, M., Goldberg, A. L. Patterns of gene expression in atrophying skeletal muscles: response to food deprivation. FASEB J . 16, 1697–1712 (2002)

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Fasting produces changes in gene expression that are strikingly similar to the pattern of fat-induced changes observed in this study's high-fat diet experiments.
“Surprisingly, fasting produces changes in gene expression that are strikingly similar to the pattern of fat-induced changes observed in our studies of HFDs.”
From A High-Fat Diet Coordinately Downregulates Genes Required for Mitochondrial Oxidative Phosphorylation in Skeletal Muscle (2005) · cites this paper as Jagoe et al. (37)
Jagoe et al. found that CASQ2, NDUFS1, glycogen synthase, and pyruvate dehydrogenase kinase isoenzyme 4, four genes found on this study's microarray hit list and confirmed by quantitative RT-PCR, were similarly regulated by fasting in rodents.
“Jagoe et al. (37) found that CASQ2 (calsequestrin 2), NDUFS1, glycogen synthase, and pyruvate dehydrogenase kinase isoenzyme 4, four genes found on our microarray”
From A High-Fat Diet Coordinately Downregulates Genes Required for Mitochondrial Oxidative Phosphorylation in Skeletal Muscle (2005) · cites this paper as Jagoe et al. (37)

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Foxo transcription factors induce the atrophy-related ubiquitin ligase atrogin-1 and cause skeletal muscle atrophy.
Sandri, M., Sandri, C., Gilbert, A., Skurk, C., Calabria, E., Picard, A., Walsh, K., Schiaffino, S., Lecker, S. H., & Goldberg, A. L. (2004) · Cell · doi:10.1016/s0092-8674(04)00400-3 · Cited by 3,012 · see citing works
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Multiple types of skeletal muscle atrophy involve a common program of changes in gene expression
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Skeletal muscle atrophy and the E3 ubiquitin ligases MuRF1 and MAFbx/atrogin-1
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The Molecular Basis of Skeletal Muscle Atrophy
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PGC-1α protects skeletal muscle from atrophy by suppressing FoxO3 action and atrophy-specific gene transcription
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Myostatin reduces Akt/TORC1/p70S6K signaling, inhibiting myoblast differentiation and myotube size
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A High-Fat Diet Coordinately Downregulates Genes Required for Mitochondrial Oxidative Phosphorylation in Skeletal Muscle
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IGF-I stimulates muscle growth by suppressing protein breakdown and expression of atrophy-related ubiquitin ligases, atrogin-1 and MuRF1
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Rapid disuse and denervation atrophy involve transcriptional changes similar to those of muscle wasting during systemic diseases
Sacheck, J. M., Hyatt, J. K., Raffaello, A., Thomas Jagoe, R., Roy, R. R., Reggie Edgerton, V., Lecker, S. H., & Goldberg, A. L. (2007) · The FASEB Journal · doi:10.1096/fj.06-6604com · Cited by 585 · see citing works
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Targeting Proteins for Destruction by the Ubiquitin System: Implications for Human Pathobiology
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Molecular mechanisms modulating muscle mass
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New fundamental resistance exercise determinants of molecular and cellular muscle adaptations
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O-GlcNAc Modification Is an Endogenous Inhibitor of the Proteasome
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Mechanisms Regulating Neuromuscular Junction Development and Function and Causes of Muscle Wasting
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The eEF2 Kinase Confers Resistance to Nutrient Deprivation by Blocking Translation Elongation
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Control of the size of the human muscle mass
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The proteasomal system
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The FOXO3a Transcription Factor Regulates Cardiac Myocyte Size Downstream of AKT Signaling
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Suppression of autophagy in skeletal muscle uncovers the accumulation of ubiquitinated proteins and their potential role in muscle damage in Pompe disease.
Raben, N., Hill, V., Shea, L., Takikita, S., Baum, R., Mizushima, N., Ralston, E., & Plotz, P. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn292 · Cited by 352 · see citing works
Forkhead transcription factor FOXO1 (FKHR)-dependent induction of PDK4 gene expression in skeletal muscle during energy deprivation
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Proteolytic and lipolytic responses to starvation
Finn, P. F., & Dice, J. F. (2006) · Nutrition · doi:10.1016/j.nut.2006.04.008 · Cited by 321 · see citing works
A Caenorhabditis elegans nutrient response system partially dependent on nuclear receptor NHR-49
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Sirt3 regulates metabolic flexibility of skeletal muscle through reversible enzymatic deacetylation
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Inflammation induced loss of skeletal muscle
Londhe, P., & Guttridge, D. C. (2015) · Bone · doi:10.1016/j.bone.2015.03.015 · Cited by 276 · see citing works
The regulation of muscle mass by endogenous glucocorticoids
Braun, T. P., & Marks, D. L. (2015) · Frontiers in Physiology · doi:10.3389/fphys.2015.00012 · Cited by 273 · see citing works
Global analysis of gene expression patterns during disuse atrophy in rat skeletal muscle
Stevenson, E. J., Giresi, P. G., Koncarevic, A., & Kandarian, S. C. (2003) · The Journal of Physiology · doi:10.1111/j.1469-7793.2003.00033.x · Cited by 270 · see citing works
Regulation of myostatin expression and myoblast differentiation by FoxO and SMAD transcription factors
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Denervation Causes Fiber Atrophy and Myosin Heavy Chain Co-Expression in Senescent Skeletal Muscle
Rowan, S. L., Rygiel, K. A., Purves-Smith, F. M., Solbak, N. M., Turnbull, D. M., & Hepple, R. T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029082 · Cited by 246 · see citing works
Lysosomal proteolysis in skeletal muscle
Béchet, D., Tassa, A., Taillandier, D., Combaret, L., & Attaix, D. (2005) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2005.02.029 · Cited by 241 · see citing works
Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE
Caielli, S., Cardenas, J., de Jesus, A. A., Baisch, J., Walters, L., Blanck, J. P., Balasubramanian, P., Stagnar, C., Ohouo, M., Hong, S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.021 · Cited by 228 · see citing works
Central nervous system inflammation induces muscle atrophy via activation of the hypothalamic–pituitary–adrenal axis
Braun, T. P., Zhu, X., Szumowski, M., Scott, G. D., Grossberg, A. J., Levasseur, P. R., Graham, K., Khan, S., Damaraju, S., Colmers, W. F., et al. (2011) · Journal of Experimental Medicine · doi:10.1084/jem.20111020 · Cited by 213 · see citing works
Calpains in muscle wasting
Bartoli, M., & Richard, I. (2005) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2004.12.012 · Cited by 198 · see citing works
Proinflammatory cytokines and skeletal muscle
te, U. S., & Schulze, P. C. (2004) · Current Opinion in Clinical Nutrition & Metabolic Care · doi:10.1097/00075197-200405000-00005 · Cited by 187 · see citing works
Molecular determinants of skeletal muscle mass: getting the “AKT” together
Nader, G. A. (2005) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2005.02.026 · Cited by 182 · see citing works
S6 Kinase Deletion Suppresses Muscle Growth Adaptations to Nutrient Availability by Activating AMP Kinase
Aguilar, V. M., Alliouachene, S., Sotiropoulos, A., Sobering, A. K., Athéa, Y., Djouadi, F., Miraux, S., Thiaudière, E., Foretz, M., Viollet, B., et al. (2007) · Cell Metabolism · doi:10.1016/j.cmet.2007.05.006 · Cited by 182 · see citing works
Recent progress toward understanding the molecular mechanisms that regulate skeletal muscle mass
Goodman, C. A., Mayhew, D. L., & Hornberger, T. A. (2011) · Cellular Signalling · doi:10.1016/j.cellsig.2011.07.013 · Cited by 178 · see citing works
Resveratrol prevents TNF-α-induced muscle atrophy via regulation of Akt/mTOR/FoxO1 signaling in C2C12 myotubes
Wang, D., Yin, Y., Yang, Y., Lv, P.-J., Shi, Y. Q., Lu, L., & Wei, L.-B. (2014) · International Immunopharmacology · doi:10.1016/j.intimp.2014.02.002 · Cited by 176 · see citing works
Gene expression profile of omental adipose tissue in human obesity
Gómez‐Ambrosi, J., Catalán, V., Diez-Caballero, A., Martínez‐Cruz, L. A., Gil, M. J., García‐Foncillas, J., Cienfuegos, J. A., Salvador, J., Mato, J. M., & Frühbeck, G. (2003) · The FASEB Journal · doi:10.1096/fj.03-0591fje · Cited by 173 · see citing works
Proteomic analysis of bovine skeletal muscle hypertrophy
Bouley, J., Meunier, B., Chambon, C., SMET, S. D., Hocquette, J.-F. J.-F., & Picard, B. B. (2005) · PROTEOMICS · doi:10.1002/pmic.200400925 · Cited by 169 · see citing works
Waste management—Cytokines, growth factors and cachexia
Saini, A., Al‐Shanti, N., & Stewart, C. E. (2006) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2006.09.006 · Cited by 165 · see citing works
Modulation of gene expression in hibernating arctic ground squirrels
Yan, J., Barnes, B. M., Kohl, F., & Marr, T. G. (2007) · Physiological Genomics · doi:10.1152/physiolgenomics.00075.2007 · Cited by 163 · see citing works
Diet-induced obesity alters signalling pathways and induces atrophy and apoptosis in skeletal muscle in a prediabetic rat model: Diet-induced obesity and skeletal muscle
Sishi, B., Loos, B., Ellis, B., Smith, W., du Toit, E. F., & Engelbrecht, A.-M. (2011) · Experimental Physiology · doi:10.1113/expphysiol.2010.054189 · Cited by 162 · see citing works
JunB transcription factor maintains skeletal muscle mass and promotes hypertrophy
Raffaello, A., Milan, G., Masiero, E., Carnio, S., Lee, D., Lanfranchi, G., Goldberg, A. L., & Sandri, M. (2010) · Journal of Cell Biology · doi:10.1083/jcb.201001136 · Cited by 156 · see citing works
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Doxorubicin acts via mitochondrial ROS to stimulate catabolism in C2C12 myotubes
Gilliam, L. A. A., Moylan, J. S., Patterson, E. W., Smith, J. D., Wilson, A. S., Rabbani, Z., & Reid, M. B. (2011) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00217.2011 · Cited by 162 · see citing works
Stress and Growth
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Gene expression in Huntington's disease skeletal muscle: a potential biomarker
Strand, A. D., Aragaki, A. K., Shaw, D., Bird, T. D., Holton, J. L., Turner, C., Tapscott, S. J., Tabrizi, S. J., Schapira, A. H. V., Kooperberg, C. L., et al. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi192 · Cited by 160 · see citing works
Ubiquitin–protein ligases in muscle wasting
Cao, P., Kim, H. J., & Lecker, S. H. (2004) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2004.11.010 · Cited by 156 · see citing works
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Adaptation of muscle size and myofascial force transmission: a review and some new experimental results
Huijing, P. A., & Jaspers, R. T. (2005) · Scandinavian Journal of Medicine and Science in Sports · doi:10.1111/j.1600-0838.2005.00457.x · Cited by 157 · see citing works
Analysis of human skeletal muscle after 48 h immobilization reveals alterations in mRNA and protein for extracellular matrix components
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Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)
Martín, S., Douglas, A., Houlihan, D. F., & Secombes, C. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-418 · Cited by 151 · see citing works
Potential mechanisms underlying the role of chronic inflammation in age-related muscle wasting
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MuRF1/TRIM63, Master Regulator of Muscle Mass
Peris-Moreno, D., Taillandier, D., & Polge, C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21186663 · Cited by 142 · see citing works
A novel ubiquitin‐binding protein ZNF216 functioning in muscle atrophy
Hishiya, A., Iemura, S., Natsume, T., Takayama, S.-I. J., Ikeda, K., & Watanabe, K. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600945 · Cited by 140 · see citing works
Fuel economy in food‐deprived skeletal muscle: signaling pathways and regulatory mechanisms
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Muscle Wasting and Changes in Muscle Protein Metabolism in Chronic Obstructive Pulmonary Disease
Jagoe, R. T., & Engelen, M. P. K. J. (2003) · European Respiratory Journal · doi:10.1183/09031936.03.00004608 · Cited by 134 · see citing works
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Transcriptional pathways associated with skeletal muscle disuse atrophy in humans
Chen, Y., Gregory, C. M., Scarborough, M. T., Shi, R., Walter, G. A., & Vandenborne, K. (2007) · Physiological Genomics · doi:10.1152/physiolgenomics.00115.2006 · Cited by 134 · see citing works
Constitutive activation of MAPK cascade in acute quadriplegic myopathy
Giovanni, S. D., Molon, A., Broccolini, A., Melcon, G., Massimiliano Mirabella, A., Hoffman, E. P., & Servidei, S. (2003) · Annals of Neurology · doi:10.1002/ana.10811 · Cited by 129 · see citing works
The Transcription Factor ATF4 Promotes Skeletal Myofiber Atrophy during Fasting
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Muscle wasting and interleukin-6-induced atrogin-I expression in the cachectic Apc Min/+ mouse
Baltgalvis, K. A., Berger, F. G., Peña, M. M. O., Davis, J. M., White, J. P., & Carson, J. A. (2008) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-008-0574-6 · Cited by 125 · see citing works
The Role of Autophagy in Skeletal Muscle Diseases
Xia, Q., Huang, X., Huang, J., Zheng, Y., March, M., Li, J., & Wei, Y. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.638983 · Cited by 130 · see citing works
Satellite cell senescence underlies myopathy in a mouse model of limb-girdle muscular dystrophy 2H
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Differential gene expression profiling of short and long term denervated muscle
Batt, J. A. E., Bain, J. R., Gonçalves, J., Michalski, B., Plant, P. J., Fahnestock, M. L., & Woodgett, J. R. (2005) · The FASEB Journal · doi:10.1096/fj.04-3640fje · Cited by 119 · see citing works
Activation of serum/glucocorticoid‐induced kinase 1 (SGK1) is important to maintain skeletal muscle homeostasis and prevent atrophy
Andrés‐Mateos, E., Brinkmeier, H., Burks, T. N., Mejı́as, R., Files, D. C., Steinberger, M., Soleimani, A. A., Marx, R., Simmers, J. L., Lin, B., et al. (2012) · EMBO Molecular Medicine · doi:10.1002/emmm.201201443 · Cited by 111 · see citing works
Implications of chronic heart failure on peripheral vasculature and skeletal muscle before and after exercise training
Duscha, B. D., Schulze, P. C., Robbins, J. L., & Forman, D. E. (2007) · Heart Failure Reviews · doi:10.1007/s10741-007-9056-8 · Cited by 113 · see citing works
TNF induction of atrogin-1/MAFbx mRNA depends on Foxo4 expression but not AKT-Foxo1/3 signaling
Moylan, J. S., Smith, J. D., Chambers, M. A., McLoughlin, T. J., & Reid, M. B. (2008) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00041.2008 · Cited by 113 · see citing works
Alterations in mRNA expression and protein products following spinal cord injury in humans
Urso, M. L., Chen, Y., Scrimgeour, A. G., Lee, P. C., Lee, K. F., & Clarkson, P. M. (2007) · The Journal of Physiology · doi:10.1113/jphysiol.2006.118042 · Cited by 111 · see citing works
Powerful signals for weak muscles
Saini, A., Faulkner, S., Al-Shanti, N., & Stewart, C. (2009) · Ageing Research Reviews · doi:10.1016/j.arr.2009.02.001 · Cited by 109 · see citing works
High Fat Diet‐Induced Skeletal Muscle Wasting Is Decreased by Mesenchymal Stem Cells Administration: Implications on Oxidative Stress, Ubiquitin Proteasome Pathway Activation, and Myonuclear Apoptosis
Abrigo, J., Rivera, J. C., Aravena, J., Cabrera, D., Simon, F., Ezquer, F., Ezquer, M., & Cabello-Verrugio, C. (2016) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2016/9047821 · Cited by 109 · see citing works
Patterns of global gene expression in rat skeletal muscle during unloading and low-intensity ambulatory activity
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Self-citation

Authors: Jagoe, R. T., Lecker, S. H., Gomes, M., & Goldberg, A. L.
Affiliations: Harvard University (US)
Beth Israel Deaconess Medical Center (US)
ORCID: Jagoe, R. Thomas
Lecker, Stewart H.
Goldberg, Alfred L.
Venue: The FASEB Journal
Publisher: Wiley
Published: 2002-11
Volume: 16
Issue: 13
Pages: 1697-1712
ISSN: 0892-6638 (ISSN-L)
1530-6860
DOI: 10.1096/fj.02-0312com
OpenAlex: W2101050876
Cited by: 344
References: 102
Citations by year: 2026: 3 · 2025: 5 · 2024: 7 · 2023: 4 · 2022: 7 · 2021: 8 · 2020: 7 · 2019: 13 · 2018: 10 · 2017: 14 · 2016: 12 · 2015: 16 · 2014: 10 · 2013: 13 · 2012: 28
FWCI: 7.90
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: The FASEB Journal (publishedVersion)
PubMed (publishedVersion)
Funders: National Space Biomedical Research Institute
National Institutes of Health (DK02707)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Muscle Physiology and Disorders
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Muscle metabolism and nutrition
Health Sciences › Medicine › Physiology › Nutrition and Health in Aging
Keywords: skeletal muscle atrophy, fasting, food deprivation, gene expression, protein degradation, ubiquitin-proteasome system, atrogin-1, IGF binding protein-5, glycolytic enzymes, PDK4, glutamine synthetase, gluconeogenesis, glucose sparing, metallothionein, extracellular matrix, cap-independent translation, transcriptional regulation
MeSH terms: Animals, Atrophy, Body Weight, Cell Division, Creatine Kinase, Electron Transport, Food Deprivation, Gene Expression Regulation, Glutamate-Ammonia Ligase, Glycolysis, Male, Mice, Inbred C57BL, Endopeptidases, RNA, Messenger, Transcription Factors, Apoptosis, Muscle, Skeletal, Insulin-Like Growth Factor Binding Protein 5, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Carbonic Anhydrase III, Mice

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Patterns of gene expression in atrophying skeletal muscles: response to food deprivation

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