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Liu J, Jiang G, Zhang H, Zhang H, Jia X, Gan Z, Yu H. Effects of Hibernation on Colonic Epithelial Tissue and Gut Microbiota in Wild Chipmunks ( Tamias sibiricus). Animals (Basel) 2024; 14:1498. [PMID: 38791715 PMCID: PMC11117362 DOI: 10.3390/ani14101498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The gut microbiota plays a crucial role in the host's metabolic processes. Many studies have shown significant changes in the gut microbiota of mammals during hibernation to adapt to the changes in the external environment, but there is limited research on the colonic epithelial tissue and gut microbiota of the wild chipmunks during hibernation. This study analyzed the diversity, composition, and function of the gut microbiota of the wild chipmunk during hibernation using 16S rRNA gene high-throughput sequencing technology, and further conducted histological analysis of the colon. Histological analysis of the colon showed an increase in goblet cells in the hibernation group, which was an adaptive change to long-term fasting during hibernation. The dominant gut microbial phyla were Bacteroidetes, Firmicutes, and Proteobacteria, and the relative abundance of them changed significantly. The analysis of gut microbiota structural differences indicated that the relative abundance of Helicobacter typhlonius and Mucispirillum schaedleri increased significantly, while unclassified Prevotella-9, unclassified Prevotellaceae-UCG-001, unclassified Prevotellaceae-UCG-003 and other species of Prevotella decreased significantly at the species level. Alpha diversity analysis showed that hibernation increased the diversity and richness of the gut microbiota. Beta diversity analysis revealed significant differences in gut microbiota diversity between the hibernation group and the control group. PICRUSt2 functional prediction analysis of the gut microbiota showed that 15 pathways, such as lipid metabolism, xenobiotics biodegradation and metabolism, amino acid metabolism, environmental adaptation, and neurodegenerative diseases, were significantly enriched in the hibernation group, while 12 pathways, including carbohydrate metabolism, replication and repair, translation, and transcription, were significantly enriched in the control group. It can be seen that during hibernation, the gut microbiota of the wild chipmunk changes towards taxa that are beneficial for reducing carbohydrate consumption, increasing fat consumption, and adapting more strongly to environmental changes in order to better provide energy for the body and ensure normal life activities during hibernation.
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Affiliation(s)
- Juntao Liu
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Guangyu Jiang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Hongrui Zhang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Haiying Zhang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
| | - Xiaoyan Jia
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
| | - Zhenwei Gan
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Huimei Yu
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
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2
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Lewis CTA, Melhedegaard EG, Ognjanovic MM, Olsen MS, Laitila J, Seaborne RAE, Gronset M, Zhang C, Iwamoto H, Hessel AL, Kuehn MN, Merino C, Amigo N, Frobert O, Giroud S, Staples JF, Goropashnaya AV, Fedorov VB, Barnes B, Toien O, Drew K, Sprenger RJ, Ochala J. Remodeling of skeletal muscle myosin metabolic states in hibernating mammals. eLife 2024; 13:RP94616. [PMID: 38752835 PMCID: PMC11098559 DOI: 10.7554/elife.94616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to determine whether skeletal muscle myosin and its metabolic efficiency undergo alterations during hibernation to optimize energy utilization. We isolated muscle fibers from small hibernators, Ictidomys tridecemlineatus and Eliomys quercinus and larger hibernators, Ursus arctos and Ursus americanus. We then conducted loaded Mant-ATP chase experiments alongside X-ray diffraction to measure resting myosin dynamics and its ATP demand. In parallel, we performed multiple proteomics analyses. Our results showed a preservation of myosin structure in U. arctos and U. americanus during hibernation, whilst in I. tridecemlineatus and E. quercinus, changes in myosin metabolic states during torpor unexpectedly led to higher levels in energy expenditure of type II, fast-twitch muscle fibers at ambient lab temperatures (20 °C). Upon repeating loaded Mant-ATP chase experiments at 8 °C (near the body temperature of torpid animals), we found that myosin ATP consumption in type II muscle fibers was reduced by 77-107% during torpor compared to active periods. Additionally, we observed Myh2 hyper-phosphorylation during torpor in I. tridecemilineatus, which was predicted to stabilize the myosin molecule. This may act as a potential molecular mechanism mitigating myosin-associated increases in skeletal muscle energy expenditure during periods of torpor in response to cold exposure. Altogether, we demonstrate that resting myosin is altered in hibernating mammals, contributing to significant changes to the ATP consumption of skeletal muscle. Additionally, we observe that it is further altered in response to cold exposure and highlight myosin as a potentially contributor to skeletal muscle non-shivering thermogenesis.
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Affiliation(s)
| | | | - Marija M Ognjanovic
- Department of Biomedical Sciences, University of CopenhagenCopenhagenDenmark
| | - Mathilde S Olsen
- Department of Biomedical Sciences, University of CopenhagenCopenhagenDenmark
| | - Jenni Laitila
- Department of Biomedical Sciences, University of CopenhagenCopenhagenDenmark
| | - Robert AE Seaborne
- Department of Biomedical Sciences, University of CopenhagenCopenhagenDenmark
- Centre for Human and Applied Physiological Sciences, Faculty of Life Sciences & Medicine, King’s College LondonLondonUnited Kingdom
| | - Magnus Gronset
- Department of Cellular and Molecular Medicine, University of CopenhagenCopenhagenDenmark
| | - Changxin Zhang
- Department of Computational Medicine and Bioinformatics, University of MichiganAnn ArborUnited States
| | - Hiroyuki Iwamoto
- Spring-8, Japan Synchrotron Radiation Research InstituteHyogoJapan
| | - Anthony L Hessel
- Institute of Physiology II, University of MuensterMuensterGermany
- Accelerated Muscle Biotechnologies ConsultantsBostonUnited States
| | - Michel N Kuehn
- Institute of Physiology II, University of MuensterMuensterGermany
- Accelerated Muscle Biotechnologies ConsultantsBostonUnited States
| | | | | | - Ole Frobert
- Department of Clinical Medicine, Faculty of Health, Aarhus UniversityAarhusDenmark
- Faculty of Health, Department of Cardiology, Örebro UniversityÖrebroSweden
| | - Sylvain Giroud
- Energetics Lab, Department of Biology, Northern Michigan UniversityMarquetteUnited States
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine ViennaViennaAustria
| | - James F Staples
- Department of Biology, University of Western OntarioLondonCanada
| | - Anna V Goropashnaya
- Center for Transformative Research in Metabolism, Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
| | - Vadim B Fedorov
- Center for Transformative Research in Metabolism, Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
| | - Brian Barnes
- Center for Transformative Research in Metabolism, Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
| | - Oivind Toien
- Center for Transformative Research in Metabolism, Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
| | - Kelly Drew
- Center for Transformative Research in Metabolism, Institute of Arctic Biology, University of Alaska FairbanksFairbanksUnited States
| | - Ryan J Sprenger
- Department of Zoology, University of British ColumbiaVancouverCanada
| | - Julien Ochala
- Department of Biomedical Sciences, University of CopenhagenCopenhagenDenmark
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Sone M, Yamaguchi Y. Cold resistance of mammalian hibernators ∼ a matter of ferroptosis? Front Physiol 2024; 15:1377986. [PMID: 38725569 PMCID: PMC11079186 DOI: 10.3389/fphys.2024.1377986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Most mammals adapt thermal physiology around 37°C and large deviations from their range, as observed in severe hypothermia and hyperthermia, resulting in organ dysfunction and individual death. A prominent exception is mammalian hibernation. Mammalian hibernators resist the long-term duration of severe low body temperature that is lethal to non-hibernators, including humans and mice. This cold resistance is supported, at least in part, by intrinsic cellular properties, since primary or immortalized cells from several hibernator species can survive longer than those from non-hibernators when cultured at cold temperatures. Recent studies have suggested that cold-induced cell death fulfills the hallmarks of ferroptosis, a type of necrotic cell death that accompanies extensive lipid peroxidation by iron-ion-mediated reactions. In this review, we summarize the current knowledge of cold resistance of mammalian hibernators at the cellular and molecular levels to organ and systemic levels and discuss key pathways that confer cold resistance in mammals.
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Affiliation(s)
- Masamitsu Sone
- Hibernation Metabolism, Physiology and Development Group, Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Yoshifumi Yamaguchi
- Hibernation Metabolism, Physiology and Development Group, Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
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Dang K, Gao Y, Wang H, Yang H, Kong Y, Jiang S, Qian A. Integrated metabolomics and proteomics analysis to understand muscle atrophy resistance in hibernating Spermophilus dauricus. Cryobiology 2024; 114:104838. [PMID: 38097057 DOI: 10.1016/j.cryobiol.2023.104838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Hibernating Spermophilus dauricus experiences minor muscle atrophy, which is an attractive anti-disuse muscle atrophy model. Integrated metabolomics and proteomics analysis was performed on the hibernating S. dauricus during the pre-hibernation (PRE) stage, torpor (TOR) stage, interbout arousal (IBA) stage, and post-hibernation (POST) stage. Time course stage transition-based (TOR vs. PRE, IBA vs. TOR, POST vs. IBA) differential expression analysis was performed based on the R limma package. A total of 14 co-differential metabolites were detected. Among these, l-cystathionine, l-proline, ketoleucine, serine, and 1-Hydroxy-3,6,7-Trimethoxy-2, 8-Diprenylxanthone demonstrated the highest levels in the TOR stage; Beta-Nicotinamide adenine dinucleotide, Dihydrozeatin, Pannaric acid, and Propionylcarnitine demonstrated the highest levels in the IBA stage; Adrenosterone, PS (18:0/14,15-EpETE), S-Carboxymethylcysteine, TxB2, and 3-Phenoxybenzylalcohol demonstrated the highest levels in the POST stage. Kyoto Encyclopedia of Genes and Genomes pathways annotation analysis indicated that biosynthesis of amino acids, ATP-binding cassette transporters, and cysteine and methionine metabolism were co-differential metabolism pathways during the different stages of hibernation. The stage-specific metabolism processes and integrated enzyme-centered metabolism networks in the different stages were also deciphered. Overall, our findings suggest that (1) the periodic change of proline, ketoleucine, and serine contributes to the hindlimb lean tissue preservation; and (2) key metabolites related to the biosynthesis of amino acids, ATP-binding cassette transporters, and cysteine and methionine metabolism may be associated with muscle atrophy resistance. In conclusion, our co-differential metabolites, co-differential metabolism pathways, stage-specific metabolism pathways, and integrated enzyme-centered metabolism networks are informative for biologists to generate hypotheses for functional analyses to perturb disuse-induced muscle atrophy.
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Affiliation(s)
- Kai Dang
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Gao
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Huiping Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China; China Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi'an, 710069, China
| | - Huajian Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China; China Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi'an, 710069, China
| | - Yong Kong
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China; China Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi'an, 710069, China
| | - Shanfeng Jiang
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Airong Qian
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China; NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
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5
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Lewis CTA, Melhedegaard EG, Ognjanovic MM, Olsen MS, Laitila J, Seaborne RAE, Gronset MN, Zhang C, Iwamoto H, Hessel AL, Kuehn MN, Merino C, Amigo N, Frobert O, Giroud S, Staples JF, Goropashnaya AV, Fedorov VB, Barnes BM, Toien O, Drew KL, Sprenger RJ, Ochala J. Remodelling of Skeletal Muscle Myosin Metabolic States in Hibernating Mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.566992. [PMID: 38014200 PMCID: PMC10680686 DOI: 10.1101/2023.11.14.566992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to determine whether skeletal muscle myosin and its metabolic efficiency undergo alterations during hibernation to optimize energy utilization. We isolated muscle fibers from small hibernators, Ictidomys tridecemlineatus and Eliomys quercinus and larger hibernators, Ursus arctos and Ursus americanus. We then conducted loaded Mant-ATP chase experiments alongside X-ray diffraction to measure resting myosin dynamics and its ATP demand. In parallel, we performed multiple proteomics analyses. Our results showed a preservation of myosin structure in U. arctos and U. americanus during hibernation, whilst in I. tridecemlineatus and E. quercinus, changes in myosin metabolic states during torpor unexpectedly led to higher levels in energy expenditure of type II, fast-twitch muscle fibers at ambient lab temperatures (20°C). Upon repeating loaded Mant-ATP chase experiments at 8°C (near the body temperature of torpid animals), we found that myosin ATP consumption in type II muscle fibers was reduced by 77-107% during torpor compared to active periods. Additionally, we observed Myh2 hyper-phosphorylation during torpor in I. tridecemilineatus, which was predicted to stabilize the myosin molecule. This may act as a potential molecular mechanism mitigating myosin-associated increases in skeletal muscle energy expenditure during periods of torpor in response to cold exposure. Altogether, we demonstrate that resting myosin is altered in hibernating mammals, contributing to significant changes to the ATP consumption of skeletal muscle. Additionally, we observe that it is further altered in response to cold exposure and highlight myosin as a potentially contributor to skeletal muscle non-shivering thermogenesis.
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6
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Krishnan JKS, Rice S, Mikes M, Sugiura MH, Drew KL, Barati Z, Oliver SR. Pre-hibernation diet alters skeletal muscle relaxation kinetics, but not force development in torpid arctic ground squirrels. J Comp Physiol B 2024; 194:65-79. [PMID: 38219236 DOI: 10.1007/s00360-023-01527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/10/2023] [Accepted: 11/20/2023] [Indexed: 01/16/2024]
Abstract
During the hibernation season, Arctic ground squirrels (AGS) experience extreme temperature fluctuations (body temperature, Tb, as low as - 3 °C), during which they are mostly physically inactive. Once Tb reaches ~ 15 °C during interbout arousals, hibernators recruit skeletal muscle (SkM) for shivering thermogenesis to reach Tb of ~ 35 °C. Polyunsaturated fatty acids (PUFA) in the diet are known to influence SkM function and metabolism. Recent studies in the cardiac muscle of hibernators have revealed that increased levels of ω-6 and the ω-6:ω-3 PUFA ratio correlate with sarco/endoplasmic reticulum calcium ATPase (SERCA) activity and hibernation status. We hypothesized that diet (increased ω-6:ω-3 PUFA ratio) and torpor status are important in the regulation of the SERCA pump and that this may improve SkM performance during hibernation. Ex vivo functional assays were used to characterize performance changes in SkM (diaphragm) from AGS fed the following diets. (1) Standard rodent chow with an ω-6:ω-3 ratio of 5:1, or (2) a balanced diet with an ω-6:ω-3 ratio of 1:1 that roughly mimics wild diet. We collected diaphragms at three different stages of hibernation (early torpor, late torpor, and arousal) and evaluated muscle function under hypothermic temperature stress at 4 °C, 15 °C, 25 °C, and 37 °C to determine functional resilience. Our data show that torpid animals fed standard rodent chow have faster SkM relaxation when compared to the balanced diet animals. Furthermore, we discovered that standard rodent chow AGS during torpor has higher SkM relaxation kinetics, but this effect of torpor is eliminated in balanced diet AGS. Interestingly, neither diet nor torpor influenced the rate of force development (rate of calcium release). This is the first study to show that increasing the dietary ω-6:ω-3 PUFA ratio improves skeletal muscle performance during decreased temperatures in a hibernating animal. This evidence supports the interpretation that diet can change some functional properties of the SkM, presumably through membrane lipid composition, ambient temperature, and torpor interaction, with an impact on SkM performance.
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Affiliation(s)
- Jishnu K S Krishnan
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Sarah Rice
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Monica Mikes
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - M Hoshi Sugiura
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kelly L Drew
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Zeinab Barati
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - S Ryan Oliver
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Department of Chemistry, United States Naval Academy, Annapolis, MD, USA.
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7
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Perry BW, McDonald AL, Trojahn S, Saxton MW, Vincent EP, Lowry C, Evans Hutzenbiler BD, Cornejo OE, Robbins CT, Jansen HT, Kelley JL. Feeding during hibernation shifts gene expression toward active season levels in brown bears ( Ursus arctos). Physiol Genomics 2023; 55:368-380. [PMID: 37486084 PMCID: PMC10642923 DOI: 10.1152/physiolgenomics.00030.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/28/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
Hibernation in bears involves a suite of metabolical and physiological changes, including the onset of insulin resistance, that are driven in part by sweeping changes in gene expression in multiple tissues. Feeding bears glucose during hibernation partially restores active season physiological phenotypes, including partial resensitization to insulin, but the molecular mechanisms underlying this transition remain poorly understood. Here, we analyze tissue-level gene expression in adipose, liver, and muscle to identify genes that respond to midhibernation glucose feeding and thus potentially drive postfeeding metabolical and physiological shifts. We show that midhibernation feeding stimulates differential expression in all analyzed tissues of hibernating bears and that a subset of these genes responds specifically by shifting expression toward levels typical of the active season. Inferences of upstream regulatory molecules potentially driving these postfeeding responses implicate peroxisome proliferator-activated receptor gamma (PPARG) and other known regulators of insulin sensitivity, providing new insight into high-level regulatory mechanisms involved in shifting metabolic phenotypes between hibernation and active states.
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Affiliation(s)
- Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Anna L McDonald
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Michael W Saxton
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Ellery P Vincent
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Courtney Lowry
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | | | - Omar E Cornejo
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States
| | - Charles T Robbins
- School of the Environment, Washington State University, Pullman, Washington, United States
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, Washington, United States
| | - Joanna L Kelley
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States
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Kamata T, Yamada S, Sekijima T. Differential AMPK-mediated metabolic regulation observed in hibernation-style polymorphisms in Siberian chipmunks. Front Physiol 2023; 14:1220058. [PMID: 37664438 PMCID: PMC10468594 DOI: 10.3389/fphys.2023.1220058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Hibernation is a unique physiological phenomenon allowing extreme hypothermia in endothermic mammals. Hypometabolism and hypothermia tolerance in hibernating animals have been investigated with particular interest; recently, studies of cultured cells and manipulation of the nervous system have made it possible to reproduce physiological states related to hypothermia induction. However, much remains unknown about the periodic regulation of hibernation. In particular, the physiological mechanisms facilitating the switch from an active state to a hibernation period, including behavioral changes and the acquisition of hypothermia tolerance remain to be elucidated. AMPK is a protein known to play a central role not only in feeding behavior but also in metabolic regulation in response to starvation. Our previous research has revealed that chipmunks activate AMPK in the brain during hibernation. However, whether AMPK is activated during winter in non-hibernating animals is unknown. Previous comparative studies between hibernating and non-hibernating animals have often been conducted between different species, consequently it has been impossible to account for the effects of phylogenetic differences. Our long-term monitoring of siberian chipmunks, has revealed intraspecific variation between those individuals that hibernate annually and those that never become hypothermic. Apparent differences were found between hibernating and non-hibernating types with seasonal changes in lifespan and blood HP levels. By comparing seasonal changes in AMPK activity between these polymorphisms, we clarified the relationship between hibernation and AMPK regulation. In hibernating types, phosphorylation of p-AMPK and p-ACC was enhanced throughout the brain during hibernation, indicating that AMPK-mediated metabolic regulation is activated. In non-hibernating types, AMPK and ACC were not seasonally activated. In addition, AMPK activation in the hypothalamus had already begun during high Tb before hibernation. Changes in AMPK activity in the brain during hibernation may be driven by circannual rhythms, suggesting a hibernation-regulatory mechanism involving AMPK activation independent of Tb. The differences in brain AMPK regulation between hibernators and non-hibernators revealed in this study were based on a single species thus did not involve phylogenetic differences, thereby supporting the importance of brain temperature-independent AMPK activation in regulating seasonal metabolism in hibernating animals.
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Affiliation(s)
- Taito Kamata
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Shintaro Yamada
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
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Perry BW, Saxton MW, Jansen HT, Quackenbush CR, Evans Hutzenbiler BD, Robbins CT, Kelley JL, Cornejo OE. A multi-tissue gene expression dataset for hibernating brown bears. BMC Genom Data 2023; 24:33. [PMID: 37291509 PMCID: PMC10251632 DOI: 10.1186/s12863-023-01136-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/06/2023] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVES Complex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing transcriptomic resources for non-traditional model organisms with phenotypes of interest can provide a foundation for understanding the genomic basis of these phenotypes, and the degree to which these resemble, or contrast, those of traditional model organisms. Here, we present a one-of-a-kind gene expression dataset generated from multiple tissues of two hibernating brown bears (Ursus arctos). DATA DESCRIPTION This dataset is comprised of 26 samples collected from 13 tissues of two hibernating brown bears. These samples were collected opportunistically and are typically not possible to attain, resulting in a highly unique and valuable gene expression dataset. In combination with previously published datasets, this new transcriptomic resource will facilitate detailed investigation of hibernation physiology in bears, and the potential to translate aspects of this biology to treat human disease.
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Affiliation(s)
- Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Michael W Saxton
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99164, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | | | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
- School of the Environment, Washington State University, Pullman, WA, 99164, USA
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA.
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10
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Cahill T, Chan S, Overton IM, Hardiman G. Transcriptome Profiling Reveals Enhanced Mitochondrial Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle. Cells 2023; 12:1366. [PMID: 37408201 PMCID: PMC10216211 DOI: 10.3390/cells12101366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 07/07/2023] Open
Abstract
The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However, mounting evidence points to torpor-induced protective benefits from the main hazards of space travel, namely, exposure to radiation and microgravity. To determine the radio-protective effects of an induced torpor-like state we exploited the ectothermic nature of the Danio rerio (zebrafish) in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low-dose radiation (0.3 Gy) to simulate radiation exposure on long-term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition, DNA repair processes were downregulated in the muscle two days' post-irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of extracellular matrix and developmental genes. Upon radiation exposure, increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of immune-related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however, immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross-species comparison was performed with the muscle of hibernating Ursus arctos horribilis (brown bear) to define shared mechanisms of cold tolerance. Shared responses show an upregulation of protein translation and metabolism of amino acids, as well as a hypoxia response with the shared downregulation of glycolysis, ECM, and developmental genes.
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Affiliation(s)
- Thomas Cahill
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK;
| | - Sherine Chan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA;
- JLABS at the Children’s National Research and Innovation Campus, Washington, DC 20012, USA
| | - Ian M. Overton
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK;
| | - Gary Hardiman
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK;
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA;
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11
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Niu Y, Guan L, Wang C, Jiang H, Li G, Yang L. Aestivation induces widespread transcriptional changes in the African lungfish. Front Genet 2023; 14:1096929. [PMID: 36733343 PMCID: PMC9886888 DOI: 10.3389/fgene.2023.1096929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Aestivation is a special ability possessed by some animals to cope with hot and dry environments utilizing dormancy. At a macroscopic level, dormant animals stop moving and eating. At the microscopic level, the expression of a large number of genes in these animals is strictly controlled. However, little is known about what changes occur during aestivation, especially in fish. In this study, we used transcriptome analysis to examine what changes occur in the gills and lungs of the African lungfish (Protopterus annectens) during the maintenance phase of aestivation and speculated on their causes. We found that aestivating transcriptomes were highly similar between gills and lungs. We also found that some genes showed differential expression or alternative splicing, which may be associated with different organs. In addition, differential expression analysis revealed that the lungs maintained significantly higher bioactivity during aestivation, which suggests that the main respiratory organ in aestivating lungfish can transform. Our study provides a reference point for studying the relationship between aestivation and hibernation and further increases understanding of aestivation.
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Affiliation(s)
- Yuhan Niu
- College of Life Sciences, Qinghai Normal University, Xining, Qinghai, China,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
| | - Lihong Guan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guogang Li
- College of Life Sciences, Qinghai Normal University, Xining, Qinghai, China,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China,Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China,*Correspondence: Guogang Li, ; Liandong Yang,
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China,*Correspondence: Guogang Li, ; Liandong Yang,
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12
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Transcriptomic and proteomic time-course analyses based on Metascape reveal mechanisms against muscle atrophy in hibernating Spermophilus dauricus. Comp Biochem Physiol A Mol Integr Physiol 2023; 275:111336. [PMID: 36280225 DOI: 10.1016/j.cbpa.2022.111336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/19/2022]
Abstract
Hibernating Spermophilus dauricus is resistant to muscle atrophy. Comprehensive transcriptome and proteome time-course analyses based on Metascape can further reveal the underlying processes (pre-hibernation stage, PRE; torpor stage, TOR; interbout arousal stage, IBA; and post-hibernation stage, POST). Transcriptome analysis showed that the cellular responses to growth factor stimulus and discrete oxygen levels continuously changed during hibernation. Proteomic analysis showed that neutrophil degranulation, sulfur compound metabolic process, and generation of precursor metabolites and energy continuously changed during hibernation. Molecular complex detection (MCODE) analysis in both transcriptome and proteome indicated that smooth muscle contraction was involved in the POST versus IBA stage, and peroxisome proliferator-activated receptor delta (Ppard), Myc proto-oncogene (Myc), Sp1 transcription factor (Sp1), and nuclear factor Kappa B subunit 1 (NFκB1) are the common TFs during the hibernation process. Integrated transcriptome and proteome analyses found 18 molecules in the TOR versus PRE stage, 1 molecule in the IBA versus TOR stage, and 16 molecules in the POST versus IBA stage. Among these molecules, carnitine palmitoyltransferase 1A (Cpt1a), SET and MYND domain containing 2 (Smyd2), four and a half LIM domains 1(Fhl1), reactive oxygen species modulator 1 (Romo1), and translocase of the inner mitochondrial membrane 50 (Timm50) were testified by Western blot. In conclusion, novel muscle atrophy resistance mechanisms can be deciphered by time-course transcriptome and proteome analyses based on Metascape.
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13
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Miyazaki M, Shimozuru M, Kitaoka Y, Takahashi K, Tsubota T. Regulation of protein and oxidative energy metabolism are down-regulated in the skeletal muscles of Asiatic black bears during hibernation. Sci Rep 2022; 12:19723. [PMID: 36385156 PMCID: PMC9668988 DOI: 10.1038/s41598-022-24251-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Hibernating animals exhibit an unexplained physiological characteristic of skeletal muscles being atrophy resistance, in which case muscle mass and strength remain almost unchanged both before and after hibernation. In this study, we examined the alterations in the regulatory systems of protein and energy metabolism in the skeletal muscles of Asiatic black bears during hibernation. Skeletal muscle samples (vastus lateralis muscle) were collected from identical individuals (n = 8) during the active (July) and hibernating (February) periods, while histochemical and biochemical analyses were performed. We observed no significant alterations in body weight, muscle fiber size, and fiber type composition during the active and hibernating periods, indicating that the skeletal muscles of bears are very well preserved during hibernation. In hibernating bear skeletal muscles, both regulatory pathways of muscle protein synthesis (Akt/mechanistic target of rapamycin and mitogen-activated protein kinase systems) and proteolysis (ubiquitin-proteasome and autophagy systems) were down-regulated. Gene expression levels of factors regulating oxidative metabolism were also decreased in hibernating bear skeletal muscles. This is likely an adaptive strategy to minimize the energy wasting of amino acids and lipids during hibernation, which is accompanied by a prolonged period of disuse and starvation.
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Affiliation(s)
- Mitsunori Miyazaki
- grid.257022.00000 0000 8711 3200Department of Integrative Physiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima, 734-8553 Japan ,grid.412021.40000 0004 1769 5590Department of Physical Therapy, School of Rehabilitation Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Michito Shimozuru
- grid.39158.360000 0001 2173 7691Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Yu Kitaoka
- grid.411995.10000 0001 2155 9872Department of Human Sciences, Kanagawa University, Kanagawa, Japan
| | - Kenya Takahashi
- grid.26999.3d0000 0001 2151 536XDepartment of Sports Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshio Tsubota
- grid.39158.360000 0001 2173 7691Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
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14
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Ilyina TN, Baishnikova IV. Retinol and α-Tocopherol Content in the Liver and Skeletal Muscle of Bats (Chiroptera) during Hibernation and Summer Activity. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Saxton MW, Perry BW, Evans Hutzenbiler BD, Trojahn S, Gee A, Brown AP, Merrihew GE, Park J, Cornejo OE, MacCoss MJ, Robbins CT, Jansen HT, Kelley JL. Serum plays an important role in reprogramming the seasonal transcriptional profile of brown bear adipocytes. iScience 2022; 25:105084. [PMID: 36317158 PMCID: PMC9617460 DOI: 10.1016/j.isci.2022.105084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/30/2022] [Accepted: 09/01/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding how metabolic reprogramming happens in cells will aid the progress in the treatment of a variety of metabolic disorders. Brown bears undergo seasonal shifts in insulin sensitivity, including reversible insulin resistance in hibernation. We performed RNA-sequencing on brown bear adipocytes and proteomics on serum to identify changes possibly responsible for reversible insulin resistance. We observed dramatic transcriptional changes, which depended on both the cell and serum season of origin. Despite large changes in adipocyte gene expression, only changes in eight circulating proteins were identified as related to the seasonal shifts in insulin sensitivity, including some that have not previously been associated with glucose homeostasis. The identified serum proteins may be sufficient for shifting hibernation adipocytes to an active-like state. Hibernation in grizzly bears is marked by insulin resistance Bear adipocytes were stimulated with active and hibernating bear blood serum Serum elicited dramatic gene expression responses related to insulin signaling Eight serum proteins were implicated in driving this transcriptional response
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Affiliation(s)
- Michael W. Saxton
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Blair W. Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | | | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Alexia Gee
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Anthony P. Brown
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Charles T. Robbins
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
- School of the Environment, Washington State University, Pullman, WA 99163, USA
| | - Heiko T. Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99163, USA
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
- Corresponding author
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16
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Sullivan IR, Adams DM, Greville LJS, Faure PA, Wilkinson GS. Big brown bats experience slower epigenetic ageing during hibernation. Proc Biol Sci 2022; 289:20220635. [PMID: 35946154 PMCID: PMC9364000 DOI: 10.1098/rspb.2022.0635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Comparative analyses of bats indicate that hibernation is associated with increased longevity among species. However, it is not yet known if hibernation affects biological ageing of individuals. Here, we use DNA methylation (DNAm) as an epigenetic biomarker of ageing to determine the effect of hibernation on the big brown bat, Eptesicus fuscus. First, we compare epigenetic age, as predicted by a multi-species epigenetic clock, between hibernating and non-hibernating animals and find that hibernation is associated with epigenetic age. Second, we identify genomic sites that exhibit hibernation-associated change in DNAm, independent of age, by comparing samples taken from the same individual in hibernating and active seasons. This paired comparison identified over 3000 differentially methylated positions (DMPs) in the genome. Genome-wide association comparisons to tissue-specific functional elements reveals that DMPs with elevated DNAm during winter occur at sites enriched for quiescent chromatin states, whereas DMPs with reduced DNAm during winter occur at sites enriched for transcription enhancers. Furthermore, genes nearest DMPs are involved in regulation of metabolic processes and innate immunity. Finally, significant overlap exists between genes nearest hibernation DMPs and genes nearest previously identified longevity DMPs. Taken together, these results are consistent with hibernation influencing ageing and longevity in bats.
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Affiliation(s)
- Isabel R. Sullivan
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Danielle M. Adams
- Department of Biology, University of Maryland, College Park, MD 20742, USA,Department of Biological Sciences, Towson University, Towson, MD 21252, USA
| | - Lucas J. S. Greville
- Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, ON, Canada L8S 4K1,Department of Biology, University of Waterloo, Waterloo, ON, Canada N3 L 3G1
| | - Paul A. Faure
- Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, ON, Canada L8S 4K1
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17
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Tseng E, Underwood JG, Evans Hutzenbiler BD, Trojahn S, Kingham B, Shevchenko O, Bernberg E, Vierra M, Robbins CT, Jansen HT, Kelley JL. Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos). G3 (BETHESDA, MD.) 2022; 12:6472356. [PMID: 35100340 PMCID: PMC9210309 DOI: 10.1093/g3journal/jkab422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022]
Abstract
Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons in bears. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individual bears sampled during both active and hibernation seasons. The existing reference genome annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals were mapped to the new reference annotation to quantify differential isoform usage (DIU) between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of DIU with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that DIU, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.
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Affiliation(s)
| | | | - Brandon D Evans Hutzenbiler
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA.,School of the Environment, Washington State University, Pullman, WA 99164, USA
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Brewster Kingham
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Olga Shevchenko
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Erin Bernberg
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Charles T Robbins
- School of the Environment, Washington State University, Pullman, WA 99164, USA.,School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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18
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Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle. Commun Biol 2021; 4:1290. [PMID: 34782710 PMCID: PMC8592991 DOI: 10.1038/s42003-021-02819-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Mice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature. During torpor, the oxygen consumption rate in some animals drops to less than 30% of the normal rate without harming the body. This safe but severe reduction in metabolism is attractive for various clinical applications; however, the mechanism and molecules involved are unclear. Therefore, here we systematically analyzed the gene expression landscape on the level of the RNA transcription start sites in mouse skeletal muscles under various metabolic states to identify torpor-specific transcribed regulatory patterns. We analyzed the soleus muscles from 38 mice in torpid and non-torpid conditions and identified 287 torpor-specific promoters out of 12,862 detected promoters. Furthermore, we found that the transcription factor ATF3 is highly expressed during torpor deprivation and its binding motif is enriched in torpor-specific promoters. Atf3 was also highly expressed in the heart and brown adipose tissue during torpor and systemically knocking out Atf3 affected the torpor phenotype. Our results demonstrate that mouse torpor combined with powerful genetic tools is useful for studying active hypometabolism.
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19
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Cussonneau L, Boyer C, Brun C, Deval C, Loizon E, Meugnier E, Gueret E, Dubois E, Taillandier D, Polge C, Béchet D, Gauquelin-Koch G, Evans AL, Arnemo JM, Swenson JE, Blanc S, Simon C, Lefai E, Bertile F, Combaret L. Concurrent BMP Signaling Maintenance and TGF-β Signaling Inhibition Is a Hallmark of Natural Resistance to Muscle Atrophy in the Hibernating Bear. Cells 2021; 10:cells10081873. [PMID: 34440643 PMCID: PMC8393865 DOI: 10.3390/cells10081873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022] Open
Abstract
Muscle atrophy arises from a multiplicity of physio-pathological situations and has very detrimental consequences for the whole body. Although knowledge of muscle atrophy mechanisms keeps growing, there is still no proven treatment to date. This study aimed at identifying new drivers for muscle atrophy resistance. We selected an innovative approach that compares muscle transcriptome between an original model of natural resistance to muscle atrophy, the hibernating brown bear, and a classical model of induced atrophy, the unloaded mouse. Using RNA sequencing, we identified 4415 differentially expressed genes, including 1746 up- and 2369 down-regulated genes, in bear muscles between the active versus hibernating period. We focused on the Transforming Growth Factor (TGF)-β and the Bone Morphogenetic Protein (BMP) pathways, respectively, involved in muscle mass loss and maintenance. TGF-β- and BMP-related genes were overall down- and up-regulated in the non-atrophied muscles of the hibernating bear, respectively, and the opposite occurred for the atrophied muscles of the unloaded mouse. This was further substantiated at the protein level. Our data suggest TGF-β/BMP balance is crucial for muscle mass maintenance during long-term physical inactivity in the hibernating bear. Thus, concurrent activation of the BMP pathway may potentiate TGF-β inhibiting therapies already targeted to prevent muscle atrophy.
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Affiliation(s)
- Laura Cussonneau
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
- Correspondence: (L.C.); (L.C.); Tel.: +(33)4-7362-4824 (Lydie Combaret)
| | - Christian Boyer
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
| | - Charlotte Brun
- Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France; (C.B.); (S.B.); (F.B.)
| | - Christiane Deval
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
| | - Emmanuelle Loizon
- CarMen Laboratory, INSERM 1060, INRAE 1397, University of Lyon, F-69600 Oullins, France; (E.L.); (E.M.); (C.S.)
| | - Emmanuelle Meugnier
- CarMen Laboratory, INSERM 1060, INRAE 1397, University of Lyon, F-69600 Oullins, France; (E.L.); (E.M.); (C.S.)
| | - Elise Gueret
- Institut de Génomique Fonctionnelle (IGF), University Montpellier, CNRS, INSERM, 34094 Montpellier, France; (E.G.); (E.D.)
- Montpellier GenomiX, France Génomique, 34095 Montpellier, France
| | - Emeric Dubois
- Institut de Génomique Fonctionnelle (IGF), University Montpellier, CNRS, INSERM, 34094 Montpellier, France; (E.G.); (E.D.)
- Montpellier GenomiX, France Génomique, 34095 Montpellier, France
| | - Daniel Taillandier
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
| | - Cécile Polge
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
| | - Daniel Béchet
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
| | | | - Alina L. Evans
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, NO-2480 Koppang, Norway; (A.L.E.); (J.M.A.)
| | - Jon M. Arnemo
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, NO-2480 Koppang, Norway; (A.L.E.); (J.M.A.)
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Jon E. Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway;
| | - Stéphane Blanc
- Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France; (C.B.); (S.B.); (F.B.)
| | - Chantal Simon
- CarMen Laboratory, INSERM 1060, INRAE 1397, University of Lyon, F-69600 Oullins, France; (E.L.); (E.M.); (C.S.)
| | - Etienne Lefai
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
| | - Fabrice Bertile
- Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France; (C.B.); (S.B.); (F.B.)
| | - Lydie Combaret
- INRAE, Unité de Nutrition Humaine, Université Clermont Auvergne, UMR 1019, F-63000 Clermont-Ferrand, France; (C.B.); (C.D.); (D.T.); (C.P.); (D.B.); (E.L.)
- Correspondence: (L.C.); (L.C.); Tel.: +(33)4-7362-4824 (Lydie Combaret)
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20
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A biomimetic natural sciences approach to understanding the mechanisms of ageing in burden of lifestyle diseases. Clin Sci (Lond) 2021; 135:1251-1272. [PMID: 34037207 DOI: 10.1042/cs20201452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022]
Abstract
The worldwide landscape of an ageing population and age-related disease brings with it huge socio-economic and public healthcare concerns across nations. Correspondingly, monumental human and financial resources have been invested in biomedical research, with a mission to decode the mechanisms of ageing and how these contribute to age-related disease. Multiple hallmarks of ageing have been identified that are common across taxa, highlighting their fundamental importance. These include dysregulated mitochondrial metabolism and telomeres biology, epigenetic modifications, cell-matrix interactions, proteostasis, dysregulated nutrient sensing, stem cell exhaustion, inflammageing and immuno-senescence. While our understanding of the molecular basis of ageing is improving, it remains a complex and multifactorial process that remains to be fully understood. A key aspect of the shortfall in our understanding of the ageing process lies in translating data from standard animal models to humans. Consequently, we suggest that a 'biomimetic' and comparative approach, integrating knowledge from species in the wild, as opposed to inbred genetically homogenous laboratory animals, can provide powerful insights into human ageing processes. Here we discuss some particularities and comparative patterns among several species from the animal kingdom, endowed with longevity or short lifespans and unique metabolic profiles that could be potentially exploited to the understanding of ageing and age-related diseases. Based upon lessons from nature, we also highlight several avenues for renewed focus in the pathophysiology of ageing and age-related disease (i.e. diet-microbiome-health axis, oxidative protein damage, adaptive homoeostasis and planetary health). We propose that a biomimetic alliance with collaborative research from different disciplines can improve our understanding of ageing and age-related diseases with long-term sustainable utility.
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21
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Transcriptional changes and preservation of bone mass in hibernating black bears. Sci Rep 2021; 11:8281. [PMID: 33859306 PMCID: PMC8050052 DOI: 10.1038/s41598-021-87785-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/05/2021] [Indexed: 11/19/2022] Open
Abstract
Physical inactivity leads to losses of bone mass and strength in most mammalian species. In contrast, hibernating bears show no bone loss over the prolonged periods (4–6 months) of immobility during winter, which suggests that they have adaptive mechanisms to preserve bone mass. To identify transcriptional changes that underlie molecular mechanisms preventing disuse osteoporosis, we conducted a large-scale gene expression screening in the trabecular bone and bone marrow, comparing hibernating and summer active bears through sequencing of the transcriptome. Gene set enrichment analysis showed a coordinated down-regulation of genes involved in bone resorption, osteoclast differentiation and signaling, and apoptosis during hibernation. These findings are consistent with previous histological findings and likely contribute to the preservation of bone during the immobility of hibernation. In contrast, no significant enrichment indicating directional changes in gene expression was detected in the gene sets of bone formation and osteoblast signaling in hibernating bears. Additionally, we revealed significant and coordinated transcriptional induction of gene sets involved in aerobic energy production including fatty acid beta oxidation, tricarboxylic acid cycle, oxidative phosphorylation, and mitochondrial metabolism. Mitochondrial oxidation was likely up-regulated by transcriptionally induced AMPK/PGC1α pathway, an upstream stimulator of mitochondrial function.
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Chen X, Li M, Chen B, Wang W, Zhang L, Ji Y, Chen Z, Ni X, Shen Y, Sun H. Transcriptome sequencing and analysis reveals the molecular mechanism of skeletal muscle atrophy induced by denervation. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:697. [PMID: 33987395 PMCID: PMC8106053 DOI: 10.21037/atm-21-1230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background The molecular mechanism of denervated muscle atrophy is very complex and has not been elucidated to date. In this study, we aimed to use transcriptome sequencing technology to systematically analyze the molecular mechanism of denervated muscle atrophy in order to eventually develop effective strategies or drugs to prevent muscle atrophy. Methods Transcriptome sequencing technology was used to analyze the differentially expressed genes (DEGs) in denervated skeletal muscles. Unsupervised hierarchical clustering of DEGs was performed. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to analyze the DEGs. Results Results showed that 2,749 transcripts were up-regulated, and 2,941 transcripts were down-regulated in denervated tibialis anterior (TA) muscles after 14 days of denervation. The up-regulated expressed genes were analyzed through GO and the results demonstrated that biological processes of the up-regulated expressed genes included apoptotic process, cellular response to DNA damage stimulus, aging, and protein ubiquitination; the cellular component of the up-regulated expressed genes included cytoplasm, cytoskeleton, and nucleus; and the molecular function of the up-regulated expressed genes included ubiquitin-protein transferase activity and hydrolase activity. The KEGG pathway of the up-regulated expressed genes included ubiquitin mediated proteolysis, Fc gamma R-mediated phagocytosis, and transforming growth factor-beta (TGF-β) signaling pathway. The biological processes of the down-regulated expressed genes included angiogenesis, tricarboxylic acid cycle, adenosine triphosphate (ATP) biosynthetic process, muscle contraction, gluconeogenesis; the cellular component of the down-regulated expressed genes included mitochondrion, cytoskeleton, and myofibril; and the molecular function of the down-regulated expressed genes included nicotinamide adenine dinucleotide plus hydrogen (NADH) dehydrogenase (ubiquinone) activity, proton-transporting ATP synthase activity, ATP binding, electron carrier activity, cytochrome-c oxidase activity, and oxidoreductase activity. The KEGG pathway of the down-regulated expressed genes included oxidative phosphorylation, tricarboxylic acid cycle, glycolysis/gluconeogenesis, and the PI3K-Akt signaling pathway. Conclusions A huge number of DEGs were identified in TA muscles after denervation. The up-regulated expressed genes mainly involve in proteolysis, apoptosis, and ageing. The down-regulated expressed genes mainly involve in energy metabolism, angiogenesis, and protein synthesis. This study further enriched the molecular mechanism of denervation-induced muscle atrophy.
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Affiliation(s)
- Xin Chen
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, China
| | - Ming Li
- Department of Laboratory, People's Hospital of Binhai County, Yancheng, China
| | - Bairong Chen
- Department of Medical Laboratory, School of Public Health, Nantong University, Nantong, China
| | - Wei Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Lilei Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yanan Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Zehao Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xuejun Ni
- Department of Ultrasound, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuntian Shen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
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Bertile F, Habold C, Le Maho Y, Giroud S. Body Protein Sparing in Hibernators: A Source for Biomedical Innovation. Front Physiol 2021; 12:634953. [PMID: 33679446 PMCID: PMC7930392 DOI: 10.3389/fphys.2021.634953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Proteins are not only the major structural components of living cells but also ensure essential physiological functions within the organism. Any change in protein abundance and/or structure is at risk for the proper body functioning and/or survival of organisms. Death following starvation is attributed to a loss of about half of total body proteins, and body protein loss induced by muscle disuse is responsible for major metabolic disorders in immobilized patients, and sedentary or elderly people. Basic knowledge of the molecular and cellular mechanisms that control proteostasis is continuously growing. Yet, finding and developing efficient treatments to limit body/muscle protein loss in humans remain a medical challenge, physical exercise and nutritional programs managing to only partially compensate for it. This is notably a major challenge for the treatment of obesity, where therapies should promote fat loss while preserving body proteins. In this context, hibernating species preserve their lean body mass, including muscles, despite total physical inactivity and low energy consumption during torpor, a state of drastic reduction in metabolic rate associated with a more or less pronounced hypothermia. The present review introduces metabolic, physiological, and behavioral adaptations, e.g., energetics, body temperature, and nutrition, of the torpor or hibernation phenotype from small to large mammals. Hibernating strategies could be linked to allometry aspects, the need for periodic rewarming from torpor, and/or the ability of animals to fast for more or less time, thus determining the capacity of individuals to save proteins. Both fat- and food-storing hibernators rely mostly on their body fat reserves during the torpid state, while minimizing body protein utilization. A number of them may also replenish lost proteins during arousals by consuming food. The review takes stock of the physiological, molecular, and cellular mechanisms that promote body protein and muscle sparing during the inactive state of hibernation. Finally, the review outlines how the detailed understanding of these mechanisms at play in various hibernators is expected to provide innovative solutions to fight human muscle atrophy, to better help the management of obese patients, or to improve the ex vivo preservation of organs.
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Affiliation(s)
- Fabrice Bertile
- University of Strasbourg, CNRS, IPHC UMR 7178, Laboratoire de Spectrométrie de Masse Bio-Organique, Strasbourg, France
| | - Caroline Habold
- University of Strasbourg, CNRS, IPHC UMR 7178, Ecology, Physiology & Ethology Department, Strasbourg, France
| | - Yvon Le Maho
- University of Strasbourg, CNRS, IPHC UMR 7178, Ecology, Physiology & Ethology Department, Strasbourg, France.,Centre Scientifique de Monaco, Monaco, Monaco
| | - Sylvain Giroud
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
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24
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Fazzalari A, Basadonna G, Kucukural A, Tanriverdi K, Koupenova M, Pozzi N, Kakuturu J, Friedrich AKU, Korstanje R, Fowler N, Belant JL, Beyer DE, Brooks MB, Dickson EW, Blackwood M, Mueller C, Palesty JA, Freedman JE, Cahan MA. A Translational Model for Venous Thromboembolism: MicroRNA Expression in Hibernating Black Bears. J Surg Res 2021; 257:203-212. [PMID: 32858321 PMCID: PMC11026106 DOI: 10.1016/j.jss.2020.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/17/2020] [Accepted: 06/16/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Hibernating American black bears have significantly different clotting parameters than their summer active counterparts, affording them protection against venous thromboembolism during prolonged periods of immobility. We sought to evaluate if significant differences exist between the expression of microRNAs in the plasma of hibernating black bears compared with their summer active counterparts, potentially contributing to differences in hemostasis during hibernation. MATERIALS AND METHODS MicroRNA sequencing was assessed in plasma from 21 American black bears in summer active (n = 11) and hibernating states (n = 10), and microRNA signatures during hibernating and active state were established using both bear and human genome. MicroRNA targets were predicted using messenger RNA (mRNA) transcripts from black bear kidney cells. In vitro studies were performed to confirm the relationship between identified microRNAs and mRNA expression, using artificial microRNA and human liver cells. RESULTS Using the bear genome, we identified 15 microRNAs differentially expressed in the plasma of hibernating black bears. Of these microRNAs, three were significantly downregulated (miR-141-3p, miR-200a-3p, and miR-200c-3p), were predicted to target SERPINC1, the gene for antithrombin, and demonstrated regulatory control of the gene mRNA expression in cell studies. CONCLUSIONS Our findings suggest that the hibernating black bears' ability to maintain hemostasis and achieve protection from venous thromboembolism during prolonged periods of immobility may be due to changes in microRNA signatures and possible upregulation of antithrombin expression.
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Affiliation(s)
- Amanda Fazzalari
- Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts; The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | - Giacomo Basadonna
- Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Alper Kucukural
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, Massachusetts; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kahraman Tanriverdi
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Milka Koupenova
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Natalie Pozzi
- The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | - Jahnavi Kakuturu
- The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | | | - Ron Korstanje
- The Korstanje Lab, The Jackson Laboratory, Bar Harbor, Maine
| | - Nicholas Fowler
- Camp Fire Program in Wildlife Conservation, State University of New York College of Environmental Science and Forestry, Syracuse, New York
| | - Jerrold L Belant
- Camp Fire Program in Wildlife Conservation, State University of New York College of Environmental Science and Forestry, Syracuse, New York
| | - Dean E Beyer
- Department of Fisheries and Wildlife, College of Agriculture & Natural Resources, Michigan State University, East Lansing, Michigan; Michigan Department of Natural Resources, Marquette, Michigan
| | - Marjory B Brooks
- Comparative Coagulation Section, Cornell University Animal Health Diagnostic Center, Ithaca, New York
| | - Eric W Dickson
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Meghan Blackwood
- Mueller Lab for Gene Therapy, Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Chris Mueller
- Mueller Lab for Gene Therapy, Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J Alexander Palesty
- The Stanley J. Dudrick Department of Surgery, Saint Mary's Hospital, Waterbury, Connecticut
| | - Jane E Freedman
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Mitchell A Cahan
- Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts.
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25
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Rice SA, Ten Have GAM, Reisz JA, Gehrke S, Stefanoni D, Frare C, Barati Z, Coker RH, D'Alessandro A, Deutz NEP, Drew KL. Nitrogen recycling buffers against ammonia toxicity from skeletal muscle breakdown in hibernating arctic ground squirrels. Nat Metab 2020; 2:1459-1471. [PMID: 33288952 PMCID: PMC7744440 DOI: 10.1038/s42255-020-00312-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Hibernation is a state of extraordinary metabolic plasticity. The pathways of amino acid metabolism as they relate to nitrogen homeostasis in hibernating mammals in vivo are unknown. Here we show, using pulse isotopic tracing, evidence of increased myofibrillar (skeletal muscle) protein breakdown and suppressed whole-body production of metabolites in vivo throughout deep torpor. As whole-body production of metabolites is suppressed, amino acids with nitrogenous side chains accumulate during torpor, while urea cycle intermediates do not. Using 15N stable isotope methodology in arctic ground squirrels (Urocitellus parryii), we provide evidence that free nitrogen is buffered and recycled into essential amino acids, non-essential amino acids and the gamma-glutamyl system during the inter-bout arousal period of hibernation. In the absence of nutrient intake or physical activity, our data illustrate the orchestration of metabolic pathways that sustain the provision of essential and non-essential amino acids and prevent ammonia toxicity during hibernation.
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Affiliation(s)
- Sarah A Rice
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA
- Institute of Arctic Biology, Center for Transformative Research in Metabolism, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Gabriella A M Ten Have
- Center for Translational Research in Aging and Longevity, Department of Health and Kinesiology, Texas A&M University, College Station, TX, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sarah Gehrke
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Davide Stefanoni
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carla Frare
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA
- Institute of Arctic Biology, Center for Transformative Research in Metabolism, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Zeinab Barati
- Institute of Arctic Biology, Center for Transformative Research in Metabolism, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Robert H Coker
- Institute of Arctic Biology, Center for Transformative Research in Metabolism, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nicolaas E P Deutz
- Center for Translational Research in Aging and Longevity, Department of Health and Kinesiology, Texas A&M University, College Station, TX, USA
| | - Kelly L Drew
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Institute of Arctic Biology, Center for Transformative Research in Metabolism, University of Alaska Fairbanks, Fairbanks, AK, USA.
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Zhang J, Cai R, Liang J, Izaz A, Shu Y, Pan T, Wu X. Molecular mechanism of Chinese alligator (Alligator sinensis) adapting to hibernation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:32-49. [PMID: 33231934 DOI: 10.1002/jez.b.23013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/22/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022]
Abstract
Hibernation is a physiological state for Chinese alligators to cope with cold weather. In mammals, gene expression changes during hibernation and their regulatory mechanisms have been extensively studied, however, these studies in reptiles are still rare. Here, integrated analysis of messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) reveals the molecular mechanisms of the hypothalamus, liver, and skeletal muscle in hibernating and active individuals. During hibernation, the number of genes increased in the hypothalamus, liver, and skeletal muscle was 585, 282, and 297, while the number of genes decreased was 215, 561, and 627, respectively, as compared with active individuals. Through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, the differential expressed genes were mainly enriched in DNA damage repair, biological rhythm, energy metabolism, myoprotein degradation, and other related items and pathways. Besides, 4740 miRNAs were identified in three tissues. Through the comprehensive analysis of miRNA and mRNA abundance profiles, 12,291, 6997, and 8232 miRNA-mRNA pairs all showed a negative correlation in the hypothalamus, liver, and skeletal muscle, respectively. Some miRNA target genes were related tobiological rhythm and energy metabolism, suggesting that miRNA may play an important role in the physiological metabolism of the hibernating adaptability of Chinese alligators. Moreover, 402, 230, and 130 differentially expressed lncRNAs were identified in the hypothalamus, liver, and skeletal muscle, respectively. The targeting relationship of four lncRNA-mRNA pairs were predicted, with the main function of target genes involved in the amino acid transportation. These results are helpful to further understand the molecular regulatory basis of the hibernation adaptation in Chinese alligators.
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Affiliation(s)
- Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ruiqing Cai
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Juanjuan Liang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Ali Izaz
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Tao Pan
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Xiaobing Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
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Transcriptional changes in muscle of hibernating arctic ground squirrels (Urocitellus parryii): implications for attenuation of disuse muscle atrophy. Sci Rep 2020; 10:9010. [PMID: 32488149 PMCID: PMC7265340 DOI: 10.1038/s41598-020-66030-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/11/2020] [Indexed: 01/10/2023] Open
Abstract
Physical inactivity generates muscle atrophy in most mammalian species. In contrast, hibernating mammals demonstrate limited muscle loss over the prolonged intervals of immobility during winter, which suggests that they have adaptive mechanisms to reduce disuse muscle atrophy. To identify transcriptional programs that underlie molecular mechanisms attenuating muscle loss, we conducted a large-scale gene expression profiling in quadriceps muscle of arctic ground squirrels, comparing hibernating (late in a torpor and during torpor re-entry after arousal) and summer active animals using next generation sequencing of the transcriptome. Gene set enrichment analysis showed a coordinated up-regulation of genes involved in all stages of protein biosynthesis and ribosome biogenesis during both stages of hibernation that suggests induction of translation during interbout arousals. Elevated proportion of down-regulated genes involved in apoptosis, NFKB signaling as well as significant under expression of atrogenes, upstream regulators (FOXO1, FOXO3, NFKB1A), key components of the ubiquitin proteasome pathway (FBXO32, TRIM63, CBLB), and overexpression of PPARGC1B inhibiting proteolysis imply suppression of protein degradation in muscle during arousals. The induction of protein biosynthesis and decrease in protein catabolism likely contribute to the attenuation of disuse muscle atrophy through prolonged periods of immobility of hibernation.
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Liu B, Bai L, Yu Q, Hu F, Wu J, Zhao S, Wang R, Wang W, Tao Y, Fan J, Liu E. iMarmot: an integrative platform for comparative and functional genomics of marmots. BMC Genomics 2020; 21:266. [PMID: 32228437 PMCID: PMC7104516 DOI: 10.1186/s12864-020-6697-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/24/2020] [Indexed: 11/10/2022] Open
Abstract
Background Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integrative database is urgent needed. Description iMarmot is freely available on the web at http://www.marmotdb.org/ and currently contains the biological information of 14 marmots, genomic sequence of 6 marmots, syntenic relationship and orthologs among 3 marmots, and expression profiles of several hibernators and plague hosts. To assist with the genomic and transcriptomic analysis, we also integrated a set of analysis and visualization tools, such as KEGG or GO enrichment analysis, PCA, Blast, Muscle, GeneWise, Lastz, and JBrowse. Particularly, one DEGs (differentially expressed genes) module has been implemented in this database to visualize the gene expression changes in hibernators and plague hosts. Conclusion This database will provide comprehensive information and analysis platform for researchers interested in understanding the biological features of marmots.
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Affiliation(s)
- Baoning Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Liang Bai
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Qingqing Yu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Fang Hu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Jing Wu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Laboratory Animal Center, Ningxia Medical University, Yinchuan, 750004, Gansu, China
| | - Sihai Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Rong Wang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Weirong Wang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China.,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China
| | - Yuanqing Tao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, Qinghai, China
| | - Jianglin Fan
- Department of Molecular Pathology, Faculty of Medicine, Interdisciplinary Graduate School of Medicine, University of Yamanashi, Yamanashi, 409-3898, Japan
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, 710061, Shaanxi, China. .,Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, 710061, Shaanxi, China.
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Fröbert O, Frøbert AM, Kindberg J, Arnemo JM, Overgaard MT. The brown bear as a translational model for sedentary lifestyle-related diseases. J Intern Med 2020; 287:263-270. [PMID: 31595572 DOI: 10.1111/joim.12983] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sedentary lifestyle accelerates biological ageing, is a major risk factor for developing metabolic syndrome and is associated with cardiovascular disease, diabetes mellitus, kidney failure, sarcopenia and osteoporosis. In contrast to the linear path to worsening health in humans with metabolic syndrome, brown bears have developed a circular metabolic plasticity enabling these animals to tolerate obesity and a 'sedentary lifestyle' during hibernation and exit the den metabolically healthy in spring. Bears are close to humans physiology wise, much closer than rodents, the preferred experimental animals in medical research, and may better serve as translational model to develop treatments for lifestyle-related diseases. In this review, aspects of brown bear hibernation survival strategies are outlined and conceivable experimental strategies to learn from bears are described.
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Affiliation(s)
- O Fröbert
- Department of Cardiology, Faculty of Health, Örebro University, Örebro, Sweden
| | - A M Frøbert
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - J Kindberg
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.,Norwegian Institute for Nature Research, Trondheim, Norway
| | - J M Arnemo
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
| | - M T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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30
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Shen Y, Zhang R, Xu L, Wan Q, Zhu J, Gu J, Huang Z, Ma W, Shen M, Ding F, Sun H. Microarray Analysis of Gene Expression Provides New Insights Into Denervation-Induced Skeletal Muscle Atrophy. Front Physiol 2019; 10:1298. [PMID: 31681010 PMCID: PMC6798177 DOI: 10.3389/fphys.2019.01298] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/27/2019] [Indexed: 01/01/2023] Open
Abstract
Denervation induces skeletal muscle atrophy, accompanied by complex biochemical and physiological changes, with potentially devastating outcomes even an increased mortality. Currently, however, there remains a paucity of effective strategies to treat skeletal muscle atrophy. Therefore, it is required to understand the molecular mechanisms of skeletal muscle atrophy and formulate new treatment strategies. In this study, we investigated the transcriptional profile of denervated skeletal muscle after peripheral nerve injury in rats. The cDNA microarray analysis showed that a huge number of genes in tibialis anterior (TA) muscles were differentially expressed at different times after sciatic nerve transection. Notably, the 24 h of denervation might be a critical time point for triggering TA muscle atrophy. According to the data from self-organizing map (SOM), Pearson correlation heatmap, principal component analysis (PCA), and hierarchical clustering analysis, three nodal transitions in gene expression profile of the denervated TA muscle might partition the period of 0.25 h–28 days post nerve injury into four distinct transcriptional phases. Moreover, the four transcriptional phases were designated as “oxidative stress stage”, “inflammation stage”, “atrophy stage” and “atrophic fibrosis stage”, respectively, which was concluded from Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene ontology (GO) analyses at each transcriptional phase. Importantly, the differentially expressed genes at 24 h post sciatic nerve transection seemed to be mainly involved in inflammation, which might be a critical process in denervation-induced muscle atrophy. Overall, our study would contribute to the understanding of molecular aspects of denervation-induced muscle atrophy, and may also provide a new insight into the time window for targeted therapy.
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Affiliation(s)
- Yuntian Shen
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Ru Zhang
- The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, China
| | - Liang Xu
- Department of Surgery, Changshu Affiliated Hospital of Nanjing University of Chinese Medicine, Changshu Traditional Chinese Medicine Hospital, Changshu, China
| | - Qiuxian Wan
- Department of Medical Laboratory, School of Public Health, Nantong University, Nantong, China
| | - Jianwei Zhu
- Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Jing Gu
- Department of Medical Laboratory, School of Public Health, Nantong University, Nantong, China
| | - Ziwei Huang
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Wenjing Ma
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Mi Shen
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu, Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
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31
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Jansen HT, Trojahn S, Saxton MW, Quackenbush CR, Evans Hutzenbiler BD, Nelson OL, Cornejo OE, Robbins CT, Kelley JL. Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. Commun Biol 2019; 2:336. [PMID: 31531397 PMCID: PMC6744400 DOI: 10.1038/s42003-019-0574-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Revealing the mechanisms underlying the reversible physiology of hibernation could have applications to both human and animal health as hibernation is often associated with disease-like states. The present study uses RNA-sequencing to reveal the tissue and seasonal transcriptional changes occurring in grizzly bears (Ursus arctos horribilis). Comparing hibernation to other seasons, bear adipose has a greater number of differentially expressed genes than liver and skeletal muscle. During hyperphagia, adipose has more than 900 differentially expressed genes compared to active season. Hibernation is characterized by reduced expression of genes associated with insulin signaling, muscle protein degradation, and urea production, and increased expression within muscle protein anabolic pathways. Across all three tissues we find a subset of shared differentially expressed genes, some of which are uncharacterized, that together may reflect a common regulatory mechanism. The identified gene families could be useful for developing novel therapeutics to treat human and animal diseases.
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Affiliation(s)
- Heiko T. Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164 USA
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Michael W. Saxton
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Corey R. Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Brandon D. Evans Hutzenbiler
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164 USA
- School of the Environment, Washington State University, Pullman, WA 99164 USA
| | - O. Lynne Nelson
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164 USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Charles T. Robbins
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
- School of the Environment, Washington State University, Pullman, WA 99164 USA
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
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Capraro A, O'Meally D, Waters SA, Patel HR, Georges A, Waters PD. Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps. BMC Genomics 2019; 20:460. [PMID: 31170930 PMCID: PMC6555745 DOI: 10.1186/s12864-019-5750-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/29/2019] [Indexed: 12/30/2022] Open
Abstract
Background Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be lethal. Many studies have sought to elucidate the molecular mechanisms of mammalian hibernation, but detailed analyses are lacking in reptiles. Here we examine gene expression in the Australian central bearded dragon (Pogona vitticeps) using mRNA-seq and label-free quantitative mass spectrometry in matched brain, heart and skeletal muscle samples from animals at late hibernation, 2 days post-arousal and 2 months post-arousal. Results We identified differentially expressed genes in all tissues between hibernation and post-arousal time points; with 4264 differentially expressed genes in brain, 5340 differentially expressed genes in heart, and 5587 differentially expressed genes in skeletal muscle. Furthermore, we identified 2482 differentially expressed genes across all tissues. Proteomic analysis identified 743 proteins (58 differentially expressed) in brain, 535 (57 differentially expressed) in heart, and 337 (36 differentially expressed) in skeletal muscle. Tissue-specific analyses revealed enrichment of protective mechanisms in all tissues, including neuroprotective pathways in brain, cardiac hypertrophic processes in heart, and atrophy protective pathways in skeletal muscle. In all tissues stress response pathways were induced during hibernation, as well as evidence for gene expression regulation at transcription, translation and post-translation. Conclusions These results reveal critical stress response pathways and protective mechanisms that allow for maintenance of both tissue-specific function, and survival during hibernation in the central bearded dragon. Furthermore, we provide evidence for multiple levels of gene expression regulation during hibernation, particularly enrichment of miRNA-mediated translational repression machinery; a process that would allow for rapid and energy efficient reactivation of translation from mature mRNA molecules at arousal. This study is the first molecular investigation of its kind in a hibernating reptile, and identifies strategies not yet observed in other hibernators to cope stress associated with this remarkable state of metabolic depression. Electronic supplementary material The online version of this article (10.1186/s12864-019-5750-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Capraro
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present address: Center for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Shafagh A Waters
- School of Women's & Children's Health, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Canberra, 2601, ACT, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia
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33
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Chazarin B, Storey KB, Ziemianin A, Chanon S, Plumel M, Chery I, Durand C, Evans AL, Arnemo JM, Zedrosser A, Swenson JE, Gauquelin-Koch G, Simon C, Blanc S, Lefai E, Bertile F. Metabolic reprogramming involving glycolysis in the hibernating brown bear skeletal muscle. Front Zool 2019; 16:12. [PMID: 31080489 PMCID: PMC6503430 DOI: 10.1186/s12983-019-0312-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/08/2019] [Indexed: 12/17/2022] Open
Abstract
Background In mammals, the hibernating state is characterized by biochemical adjustments, which include metabolic rate depression and a shift in the primary fuel oxidized from carbohydrates to lipids. A number of studies of hibernating species report an upregulation of the levels and/or activity of lipid oxidizing enzymes in muscles during torpor, with a concomitant downregulation for glycolytic enzymes. However, other studies provide contrasting data about the regulation of fuel utilization in skeletal muscles during hibernation. Bears hibernate with only moderate hypothermia but with a drop in metabolic rate down to ~ 25% of basal metabolism. To gain insights into how fuel metabolism is regulated in hibernating bear skeletal muscles, we examined the vastus lateralis proteome and other changes elicited in brown bears during hibernation. Results We show that bear muscle metabolic reorganization is in line with a suppression of ATP turnover. Regulation of muscle enzyme expression and activity, as well as of circulating metabolite profiles, highlighted a preference for lipid substrates during hibernation, although the data suggested that muscular lipid oxidation levels decreased due to metabolic rate depression. Our data also supported maintenance of muscle glycolysis that could be fuelled from liver gluconeogenesis and mobilization of muscle glycogen stores. During hibernation, our data also suggest that carbohydrate metabolism in bear muscle, as well as protein sparing, could be controlled, in part, by actions of n-3 polyunsaturated fatty acids like docosahexaenoic acid. Conclusions Our work shows that molecular mechanisms in hibernating bear skeletal muscle, which appear consistent with a hypometabolic state, likely contribute to energy and protein savings. Maintenance of glycolysis could help to sustain muscle functionality for situations such as an unexpected exit from hibernation that would require a rapid increase in ATP production for muscle contraction. The molecular data we report here for skeletal muscles of bears hibernating at near normal body temperature represent a signature of muscle preservation despite atrophying conditions.
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Affiliation(s)
- Blandine Chazarin
- 1Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France.,10Centre National d'Etudes Spatiales, CNES, F-75001 Paris, France
| | - Kenneth B Storey
- 2Department of Biology, Carleton University, Ottawa, ON K1S 5B6 Canada
| | - Anna Ziemianin
- 1Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France.,10Centre National d'Etudes Spatiales, CNES, F-75001 Paris, France
| | - Stéphanie Chanon
- 3CarMen Laboratory, INSERM 1060, INRA 1397, University of Lyon, F-69600 Oullins, France
| | - Marine Plumel
- 1Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Isabelle Chery
- 1Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Christine Durand
- 3CarMen Laboratory, INSERM 1060, INRA 1397, University of Lyon, F-69600 Oullins, France
| | - Alina L Evans
- 4Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, NO-2480 Koppang, Norway
| | - Jon M Arnemo
- 4Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, NO-2480 Koppang, Norway.,5Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Andreas Zedrosser
- 6Department of Environmental and Health Studies, University College of Southeast Norway, N-3800 Bø, Telemark Norway.,7Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, A-1180 Vienna, Austria
| | - Jon E Swenson
- 8Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway.,9Norwegian Institute for Nature Research, NO-7485 Trondheim, Norway
| | | | - Chantal Simon
- 3CarMen Laboratory, INSERM 1060, INRA 1397, University of Lyon, F-69600 Oullins, France
| | - Stephane Blanc
- 1Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Etienne Lefai
- 3CarMen Laboratory, INSERM 1060, INRA 1397, University of Lyon, F-69600 Oullins, France.,Université d'Auvergne, INRA, UNH UMR1019, F-63122 Saint-Genès Champanelle, France
| | - Fabrice Bertile
- 1Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
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Miyazaki M, Shimozuru M, Tsubota T. Skeletal muscles of hibernating black bears show minimal atrophy and phenotype shifting despite prolonged physical inactivity and starvation. PLoS One 2019; 14:e0215489. [PMID: 30998788 PMCID: PMC6472773 DOI: 10.1371/journal.pone.0215489] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/02/2019] [Indexed: 02/08/2023] Open
Abstract
Hibernating mammals experience prolonged periods of torpor and starvation during winter for up to 5–7 months. Though physical inactivity and malnutrition generally lead to profound loss of muscle mass and metabolic dysfunction in humans, hibernating bears show limited muscle atrophy and can successfully maintain locomotive function. These physiological features in bears allow us to hypothesize that hibernating bears uniquely alter the regulation of protein and energy metabolism in skeletal muscle which then contributes to “muscle atrophy resistance” against continued physical inactivity. In this study, alteration of signaling pathways governing protein and energy metabolisms was examined in skeletal muscle of the Japanese black bear (Ursus thibetanus japonicus). Sartorius muscle samples were collected from bear legs during late November (pre-hibernation) and early April (post-hibernation). Protein degradation pathways, through a ubiquitin-proteasome system (as assessed by increased expression of murf1 mRNA) and an autophagy-dependent system (as assessed by increased expression of atg7, beclin1, and map1lc3 mRNAs), were significantly activated in skeletal muscle following hibernation. In contrast, as indicated by a significant increase in S6K1 phosphorylation, an activation state of mTOR (mammalian/mechanistic target of rapamycin), which functions as a central regulator of protein synthesis, increased in post-hibernation samples. Gene expression of myostatin, a negative regulator of skeletal muscle mass, was significantly decreased post-hibernation. We also confirmed that the phenotype shifted toward slow-oxidative muscle and mitochondrial biogenesis. These observations suggest that protein and energy metabolism may be altered in skeletal muscle of hibernating bears, which then may contribute to limited loss of muscle mass and efficient energy utilization.
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Affiliation(s)
- Mitsunori Miyazaki
- Department of Physical Therapy, School of Rehabilitation Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
- * E-mail:
| | - Michito Shimozuru
- Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Toshio Tsubota
- Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
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35
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Oliver SR, Anderson KJ, Hunstiger MM, Andrews MT. Turning down the heat: Down-regulation of sarcolipin in a hibernating mammal. Neurosci Lett 2018; 696:13-19. [PMID: 30528880 DOI: 10.1016/j.neulet.2018.11.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 02/01/2023]
Abstract
Hibernation in mammals is a whole-body phenotype that involves profound reductions in oxygen consumption, metabolic reactions, core body temperature, neural activity and heart rate. An important aspect of mammalian hibernation is the ability to reverse this state of hypothermic torpor by rewarming and subsequent arousal. Brown adipose tissue (BAT) and skeletal muscle shivering have been characterized as the predominant driving forces for thermogenesis during arousal. Conversely, the thermogenic contribution of these organs needs to be minimized as hibernating mammals enter torpor. Because skeletal muscle accounts for approximately 40% of the dry mass of the typical mammalian body, we aim to broaden the spotlight to include the importance of down-regulating skeletal muscle non-shivering thermogenesis during hibernation to allow for whole-body cooling and long-term maintenance of a depressed core body temperature when the animal is in torpor. This minireview will briefly describe the current understanding of thermoregulation in hibernating mammals and present new preliminary data on the importance of skeletal muscle and the micro-peptide sarcolipin as a major thermogenic target.
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Affiliation(s)
- S Ryan Oliver
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Kyle J Anderson
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, MN 55812, USA.
| | - Moriah M Hunstiger
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Matthew T Andrews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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36
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Nespolo RF, Gaitan-Espitia JD, Quintero-Galvis JF, Fernandez FV, Silva AX, Molina C, Storey KB, Bozinovic F. A functional transcriptomic analysis in the relict marsupial Dromiciops gliroides
reveals adaptive regulation of protective functions during hibernation. Mol Ecol 2018; 27:4489-4500. [DOI: 10.1111/mec.14876] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
- Departamento de Ecología; Center of Applied Ecology and Sustainability (CAPES); Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
- Millennium Institute for Integrative Biology (iBio); Santiago Chile
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences; The University of Hong Kong; Hong Kong SAR China
- CSIRO Oceans & Atmosphere; Hobart Tasmania Australia
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Fernanda V. Fernandez
- Instituto de Fisiología; Facultad de Medicina; Universidad Austral de Chile; Valdivia Chile
| | - Andrea X. Silva
- AUSTRALomics, Vicerrectoría de Investigación, Desarrollo y Creación Artística; Universidad Austral de Chile; Valdivia Chile
| | - Cristian Molina
- AUSTRALomics, Vicerrectoría de Investigación, Desarrollo y Creación Artística; Universidad Austral de Chile; Valdivia Chile
| | - Kenneth B. Storey
- Department of Biology and Institute of Biochemistry; Carleton University; Ottawa Ontario Canada
| | - Francisco Bozinovic
- Departamento de Ecología; Center of Applied Ecology and Sustainability (CAPES); Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
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Ou J, Ball JM, Luan Y, Zhao T, Miyagishima KJ, Xu Y, Zhou H, Chen J, Merriman DK, Xie Z, Mallon BS, Li W. iPSCs from a Hibernator Provide a Platform for Studying Cold Adaptation and Its Potential Medical Applications. Cell 2018; 173:851-863.e16. [PMID: 29576452 DOI: 10.1016/j.cell.2018.03.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/12/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022]
Abstract
Hibernating mammals survive hypothermia (<10°C) without injury, a remarkable feat of cellular preservation that bears significance for potential medical applications. However, mechanisms imparting cold resistance, such as cytoskeleton stability, remain elusive. Using the first iPSC line from a hibernating mammal (13-lined ground squirrel), we uncovered cellular pathways critical for cold tolerance. Comparison between human and ground squirrel iPSC-derived neurons revealed differential mitochondrial and protein quality control responses to cold. In human iPSC-neurons, cold triggered mitochondrial stress, resulting in reactive oxygen species overproduction and lysosomal membrane permeabilization, contributing to microtubule destruction. Manipulations of these pathways endowed microtubule cold stability upon human iPSC-neurons and rat (a non-hibernator) retina, preserving its light responsiveness after prolonged cold exposure. Furthermore, these treatments significantly improved microtubule integrity in cold-stored kidneys, demonstrating the potential for prolonging shelf-life of organ transplants. Thus, ground squirrel iPSCs offer a unique platform for bringing cold-adaptive strategies from hibernators to humans in clinical applications. VIDEO ABSTRACT.
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Affiliation(s)
- Jingxing Ou
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John M Ball
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yizhao Luan
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tantai Zhao
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Ophthalmology, The Second Xiang-Ya Hospital, Central South University, Changsha 410011, China
| | - Kiyoharu J Miyagishima
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yufeng Xu
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou 310009, China
| | - Huizhi Zhou
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinguo Chen
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dana K Merriman
- Department of Biology, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Barbara S Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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38
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Faherty SL, Villanueva‐Cañas JL, Blanco MB, Albà MM, Yoder AD. Transcriptomics in the wild: Hibernation physiology in free‐ranging dwarf lemurs. Mol Ecol 2018; 27:709-722. [DOI: 10.1111/mec.14483] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
| | - José Luis Villanueva‐Cañas
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
- Evolutionary Genomics Group Research Programme on Biomedical Informatics (GRIB) Hospital del Mar Research Institute (IMIM) Universitat Pompeu Fabra (UPF) Barcelona Spain
| | | | - M. Mar Albà
- Evolutionary Genomics Group Research Programme on Biomedical Informatics (GRIB) Hospital del Mar Research Institute (IMIM) Universitat Pompeu Fabra (UPF) Barcelona Spain
- Catalan Institution for Research and Advanced Studies (ICREA) Barcelona Spain
| | - Anne D. Yoder
- Department of Biology Duke University Durham NC USA
- Duke Lemur Center Durham NC USA
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Bryan K, McGivney BA, Farries G, McGettigan PA, McGivney CL, Gough KF, MacHugh DE, Katz LM, Hill EW. Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components. BMC Genomics 2017; 18:595. [PMID: 28793853 PMCID: PMC5551008 DOI: 10.1186/s12864-017-4007-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/02/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. However, the biomolecular mechanisms underlying such responses still need to be fully elucidated. Here we performed a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses (n = 51) before and after a bout of high-intensity exercise and again after an extended period of training. We hypothesized that regular high-intensity exercise training primes the transcriptome for the demands of high-intensity exercise. RESULTS An extensive set of genes was observed to be significantly differentially regulated in response to a single bout of high-intensity exercise in the untrained cohort (3241 genes) and following multiple bouts of high-intensity exercise training over a six-month period (3405 genes). Approximately one-third of these genes (1025) and several biological processes related to energy metabolism were common to both the exercise and training responses. We then developed a novel network-based computational analysis pipeline to test the hypothesis that these transcriptional changes also influence the contextual molecular interactome and its dynamics in response to exercise and training. The contextual network analysis identified several important hub genes, including the autophagosomal-related gene GABARAPL1, and dynamic functional modules, including those enriched for mitochondrial respiratory chain complexes I and V, that were differentially regulated and had their putative interactions 're-wired' in the exercise and/or training responses. CONCLUSION Here we have generated for the first time, a comprehensive set of genes that are differentially expressed in Thoroughbred skeletal muscle in response to both exercise and training. These data indicate that consecutive bouts of high-intensity exercise result in a priming of the skeletal muscle transcriptome for the demands of the next exercise bout. Furthermore, this may also lead to an extensive 're-wiring' of the molecular interactome in both exercise and training and include key genes and functional modules related to autophagy and the mitochondrion.
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Affiliation(s)
- Kenneth Bryan
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Beatrice A. McGivney
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Gabriella Farries
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Paul A. McGettigan
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Charlotte L. McGivney
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Katie F. Gough
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
| | - David E. MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Lisa M. Katz
- UCD School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Ireland
| | - Emmeline W. Hill
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Ireland
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40
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Cutler AA, Dammer EB, Doung DM, Seyfried NT, Corbett AH, Pavlath GK. Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell 2017; 16:738-749. [PMID: 28544616 PMCID: PMC5506426 DOI: 10.1111/acel.12604] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Skeletal muscle aging is accompanied by loss of muscle mass and strength. Examining changes in myonuclear proteins with age would provide insight into molecular processes which regulate these profound changes in muscle physiology. However, muscle tissue is highly adapted for contraction and thus comprised largely of contractile proteins making the nuclear proteins difficult to identify from whole muscle samples. By developing a method to purify myonuclei from whole skeletal muscle, we were able to collect myonuclei for analysis by flow cytometry, biochemistry, and mass spectrometry. Nuclear purification dramatically increased the number and intensity of nuclear proteins detected by mass spectrometry compared to whole tissue. We exploited this increased proteomic depth to investigate age-related changes to the myonuclear proteome. Nuclear levels of 54 of 779 identified proteins (7%) changed significantly with age; these proteins were primarily involved in chromatin maintenance and RNA processing. To determine whether the changes we detected were specific to myonuclei or were common to nuclei of excitatory tissues, we compared aging in myonuclei to aging in brain nuclei. Although several of the same processes were affected by aging in both brain and muscle nuclei, the specific proteins involved in these alterations differed between the two tissues. Isolating myonuclei allowed a deeper view into the myonuclear proteome than previously possible facilitating identification of novel age-related changes in skeletal muscle. Our technique will enable future studies into a heretofore underrepresented compartment of skeletal muscle.
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Affiliation(s)
- Alicia A. Cutler
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
- Graduate Program in Biochemistry, Cell and Developmental Biology; Emory University; Atlanta GA 30322 USA
| | - Eric B. Dammer
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | - Duc M. Doung
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | | | | | - Grace K. Pavlath
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
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41
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Welinder KG, Hansen R, Overgaard MT, Brohus M, Sønderkær M, von Bergen M, Rolle-Kampczyk U, Otto W, Lindahl TL, Arinell K, Evans AL, Swenson JE, Revsbech IG, Frøbert O. Biochemical Foundations of Health and Energy Conservation in Hibernating Free-ranging Subadult Brown Bear Ursus arctos. J Biol Chem 2016; 291:22509-22523. [PMID: 27609515 DOI: 10.1074/jbc.m116.742916] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/02/2016] [Indexed: 12/12/2022] Open
Abstract
Brown bears (Ursus arctos) hibernate for 5-7 months without eating, drinking, urinating, and defecating at a metabolic rate of only 25% of the summer activity rate. Nonetheless, they emerge healthy and alert in spring. We quantified the biochemical adaptations for hibernation by comparing the proteome, metabolome, and hematological features of blood from hibernating and active free-ranging subadult brown bears with a focus on conservation of health and energy. We found that total plasma protein concentration increased during hibernation, even though the concentrations of most individual plasma proteins decreased, as did the white blood cell types. Strikingly, antimicrobial defense proteins increased in concentration. Central functions in hibernation involving the coagulation response and protease inhibition, as well as lipid transport and metabolism, were upheld by increased levels of very few key or broad specificity proteins. The changes in coagulation factor levels matched the changes in activity measurements. A dramatic 45-fold increase in sex hormone-binding globulin levels during hibernation draws, for the first time, attention to its significant but unknown role in maintaining hibernation physiology. We propose that energy for the costly protein synthesis is reduced by three mechanisms as follows: (i) dehydration, which increases protein concentration without de novo synthesis; (ii) reduced protein degradation rates due to a 6 °C reduction in body temperature and decreased protease activity; and (iii) a marked redistribution of energy resources only increasing de novo synthesis of a few key proteins. The comprehensive global data identified novel biochemical strategies for bear adaptations to the extreme condition of hibernation and have implications for our understanding of physiology in general.
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Affiliation(s)
- Karen Gjesing Welinder
- From the Department of Chemistry and Bioscience, Section of Biotechnology, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark,
| | - Rasmus Hansen
- From the Department of Chemistry and Bioscience, Section of Biotechnology, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Michael Toft Overgaard
- From the Department of Chemistry and Bioscience, Section of Biotechnology, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Malene Brohus
- From the Department of Chemistry and Bioscience, Section of Biotechnology, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Mads Sønderkær
- From the Department of Chemistry and Bioscience, Section of Biotechnology, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Martin von Bergen
- From the Department of Chemistry and Bioscience, Section of Biotechnology, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark.,the Departments of Metabolomics and.,Proteomics, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318 Leipzig, Germany
| | | | - Wolfgang Otto
- Proteomics, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318 Leipzig, Germany
| | - Tomas L Lindahl
- the Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Karin Arinell
- the Department of Cardiology, Faculty of Health, Örebro University, 701 85 Örebro, Sweden
| | - Alina L Evans
- the Department of Forestry and Wildlife Management, Hedmark University College, Campus Evenstrand, 2411 Elverum, Norway
| | - Jon E Swenson
- the Department for Ecology and Natural Resource Management, Norwegian University of Life Sciences, Postbox 5014, 1432 Ås, Norway.,the Norwegian Institute for Nature Research, Tungasletta 2, N-7485 Trondheim, Norway, and
| | - Inge G Revsbech
- the Department of Bioscience, Zoophysiology, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark
| | - Ole Frøbert
- the Department of Cardiology, Faculty of Health, Örebro University, 701 85 Örebro, Sweden
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42
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Reilly BD, Franklin CE. Prevention of muscle wasting and osteoporosis: the value of examining novel animal models. J Exp Biol 2016; 219:2582-95. [DOI: 10.1242/jeb.128348] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
ABSTRACT
Bone mass and skeletal muscle mass are controlled by factors such as genetics, diet and nutrition, growth factors and mechanical stimuli. Whereas increased mechanical loading of the musculoskeletal system stimulates an increase in the mass and strength of skeletal muscle and bone, reduced mechanical loading and disuse rapidly promote a decrease in musculoskeletal mass, strength and ultimately performance (i.e. muscle atrophy and osteoporosis). In stark contrast to artificially immobilised laboratory mammals, animals that experience natural, prolonged bouts of disuse and reduced mechanical loading, such as hibernating mammals and aestivating frogs, consistently exhibit limited or no change in musculoskeletal performance. What factors modulate skeletal muscle and bone mass, and what physiological and molecular mechanisms protect against losses of muscle and bone during dormancy and following arousal? Understanding the events that occur in different organisms that undergo natural periods of prolonged disuse and suffer negligible musculoskeletal deterioration could not only reveal novel regulatory factors but also might lead to new therapeutic options. Here, we review recent work from a diverse array of species that has revealed novel information regarding physiological and molecular mechanisms that dormant animals may use to conserve musculoskeletal mass despite prolonged inactivity. By highlighting some of the differences and similarities in musculoskeletal biology between vertebrates that experience disparate modes of dormancy, it is hoped that this Review will stimulate new insights and ideas for future studies regarding the regulation of atrophy and osteoporosis in both natural and clinical models of muscle and bone disuse.
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Affiliation(s)
- Beau D. Reilly
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig E. Franklin
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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43
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Dang K, Feng B, Gao Y, Hu N, Jiang S, Fu W, Hinghofer-Szalkay HG. Muscle protection during hibernation of Daurian ground squirrels (Spermophilus dauricus): role of atrogin-1, MuRF1, and fiber-type transition. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0242] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated the mechanism of protection from skeletal muscle atrophy in the hind limb extensor digitorum longus (EDL) muscle of hibernating Daurian ground squirrels (Spermophilus dauricus Brandt, 1843). The effects of unrestrained hibernation and 14 day hind limb unloading (HLU) on EDL were studied in three seasons (summer, autumn, and winter). Atrogin-1 and MuRF1 mRNA skeletal muscle expression, wet muscle mass, and muscle to body mass ratios were unchanged during hibernation in all three seasons. EDL mass measurements decreased following HLU and atrogin-1 and MuRF1 mRNA expression increased. In summer, atrogin-1 and MuRF1 mRNA expression increased by 85% and 75%, respectively; in autumn, by 95% and 69%, respectively; and in winter, by 91% and 65%, respectively (P < 0.05). In the HLU group, microscopic skeletal muscle changes were present, including a reduction in the percentage of type-I skeletal muscle fibers. Fat storage in Daurian ground squirrels and a shorter photoperiod during hibernation did not affect the protective mechanisms that prevented skeletal muscle atrophy. The results of this study suggest that the stable expression of atrogin-1 and MuRF1 and the transition from fast glycolytic fibers to slow oxidative fibers are associated with a lack of skeletal muscle atrophy in the hibernating Daurian ground squirrel.
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Affiliation(s)
- Kai Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi’an, 710069, People’s Republic of China
| | - Ban Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi’an, 710069, People’s Republic of China
| | - Yunfang Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi’an, 710069, People’s Republic of China
| | - Naifei Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi’an, 710069, People’s Republic of China
| | - Shanfeng Jiang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi’an, 710069, People’s Republic of China
| | - Weiwei Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi’an, 710069, People’s Republic of China
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44
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Güth R, Chaidez A, Samanta MP, Unguez GA. Properties of skeletal muscle in the teleost Sternopygus macrurus are unaffected by short-term electrical inactivity. Physiol Genomics 2016; 48:699-710. [PMID: 27449658 DOI: 10.1152/physiolgenomics.00068.2016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/18/2016] [Indexed: 11/22/2022] Open
Abstract
Skeletal muscle is distinguished from other tissues on the basis of its shape, biochemistry, and physiological function. Based on mammalian studies, fiber size, fiber types, and gene expression profiles are regulated, in part, by the electrical activity exerted by the nervous system. To address whether similar adaptations to changes in electrical activity in skeletal muscle occur in teleosts, we studied these phenotypic properties of ventral muscle in the electric fish Sternopygus macrurus following 2 and 5 days of electrical inactivation by spinal transection. Our data show that morphological and biochemical properties of skeletal muscle remained largely unchanged after these treatments. Specifically, the distribution of type I and type II muscle fibers and the cross-sectional areas of these fiber types observed in control fish remained unaltered after each spinal transection survival period. This response to electrical inactivation was generally reflected at the transcript level in real-time PCR and RNA-seq data by showing little effect on the transcript levels of genes associated with muscle fiber type differentiation and plasticity, the sarcomere complex, and pathways implicated in the regulation of muscle fiber size. Data from this first study characterizing the acute influence of neural activity on muscle mass and sarcomere gene expression in a teleost are discussed in the context of comparative studies in mammalian model systems and vertebrate species from different lineages.
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Affiliation(s)
- Robert Güth
- Department of Biology, New Mexico State University, Las Cruces, New Mexico; and
| | - Alexander Chaidez
- Department of Biology, New Mexico State University, Las Cruces, New Mexico; and
| | | | - Graciela A Unguez
- Department of Biology, New Mexico State University, Las Cruces, New Mexico; and
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45
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Dang K, Li YZ, Gong LC, Xue W, Wang HP, Goswami N, Gao YF. Stable atrogin-1 (Fbxo32) and MuRF1 (Trim63) gene expression is involved in the protective mechanism in soleus muscle of hibernating Daurian ground squirrels (Spermophilus dauricus). Biol Open 2016; 5:62-71. [PMID: 26740574 PMCID: PMC4728309 DOI: 10.1242/bio.015776] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding the mechanisms that protect against or limit muscle atrophy in hibernators during prolonged inactivity has important implications for its treatment. We examined whether external factors influence the pathways regulating protein synthesis and degradation, leading to muscle atrophy prevention in Daurian ground squirrels (Spermophilus dauricus). We investigated the effects of 14-day hindlimb-unloading (HU) in different seasons and two-month hibernation on the soleus (SOL) muscle wet mass, muscle-to-body mass ratio, fiber cross sectional area (CSA), fiber distribution and muscle ultrastructure. We also measured changes in the protein expression and activation states of Akt, mTOR and FoxO1 and the mRNA expression of atrogin-1 and MuRF1. Compared with the control groups, autumn and winter HU significantly lowered SOL muscle wet mass and muscle-to-body mass ratio, decreased type I and II fiber CSA and induced ultrastructural anomalies. However, these measured indices were unchanged between Pre-hibernation and Hibernation groups. Furthermore, phosphorylation levels of Akt and mTOR significantly decreased, while the phosphorylation level of FoxO1 and mRNA expression of atrogin-1 and MuRF1 increased after HU. During hibernation, the phosphorylation levels of Akt and mTOR significantly decreased, but the phosphorylation level of FoxO1 and mRNA expression of atrogin-1 and MuRF1 remained unchanged. Overall, our findings suggest that disuse and seasonality may not be sufficient to initiate the innate protective mechanism that prevents SOL atrophy during prolonged periods of hibernation inactivity. The stable expression of atrogin-1 and MuRF1 may facilitate to prevent SOL atrophy via controlling ubiquitination of muscle proteins during hibernation. Summary: mRNA expression of atrogin-1 and MuRF1 remains unchanged during hibernation of Daurian ground squirrels, suggesting that stable expression of these genes may facilitate the prevention of SOL atrophy via controlling ubiquitylation of muscle proteins during hibernation.
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Affiliation(s)
- Kai Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China
| | - Ya-Zhao Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China
| | - Ling-Chen Gong
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China
| | - Wei Xue
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China
| | - Hui-Ping Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China
| | - Nandu Goswami
- Gravitational Physiology and Medicine Research Unit, Institute of Physiology, Center of Physiological Medicine, Medical University Graz, Graz 8010, Austria
| | - Yun-Fang Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an 710069, China
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46
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Hindle AG, Otis JP, Epperson LE, Hornberger TA, Goodman CA, Carey HV, Martin SL. Prioritization of skeletal muscle growth for emergence from hibernation. ACTA ACUST UNITED AC 2014; 218:276-84. [PMID: 25452506 DOI: 10.1242/jeb.109512] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian hibernators provide an extreme example of naturally occurring challenges to muscle homeostasis. The annual hibernation cycle is characterized by shifts between summer euthermy with tissue anabolism and accumulation of body fat reserves, and winter heterothermy with fasting and tissue catabolism. The circannual patterns of skeletal muscle remodelling must accommodate extended inactivity during winter torpor, the motor requirements of transient winter active periods, and sustained activity following spring emergence. Muscle volume in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) calculated from MRI upper hindlimb images (n=6 squirrels, n=10 serial scans) declined from hibernation onset, reaching a nadir in early February. Paradoxically, mean muscle volume rose sharply after February despite ongoing hibernation, and continued total body mass decline until April. Correspondingly, the ratio of muscle volume to body mass was steady during winter atrophy (October-February) but increased (+70%) from February to May, which significantly outpaced changes in liver or kidney examined by the same method. Generally stable myocyte cross-sectional area and density indicated that muscle remodelling is well regulated in this hibernator, despite vastly altered seasonal fuel and activity levels. Body composition analysis by echo MRI showed lean tissue preservation throughout hibernation amid declining fat mass by the end of winter. Muscle protein synthesis was 66% depressed in early but not late winter compared with a summer fasted baseline, while no significant changes were observed in the heart, liver or intestine, providing evidence that could support a transition in skeletal muscle regulation between early and late winter, prior to spring emergence and re-feeding.
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Affiliation(s)
- Allyson G Hindle
- Cell & Developmental Biology, University of Colorado School of Medicine, Mail Stop 8108, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Jessica P Otis
- Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - L Elaine Epperson
- Cell & Developmental Biology, University of Colorado School of Medicine, Mail Stop 8108, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Troy A Hornberger
- Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Craig A Goodman
- Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Hannah V Carey
- Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Sandra L Martin
- Cell & Developmental Biology, University of Colorado School of Medicine, Mail Stop 8108, 12801 East 17th Avenue, Aurora, CO 80045, USA
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