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Reißmann M, Rajavel A, Kokov ZA, Schmitt AO. Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability. Genes (Basel) 2023; 14:1982. [PMID: 38002925 PMCID: PMC10671444 DOI: 10.3390/genes14111982] [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: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses (Equus caballus) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1, CCL5, CD40LG, FOS, IL1R2, IL20RA, and IL22RA2, on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2, GYG1, HIF1A, MOGAT1, PFKFB3, PLIN5, SIK1, and STBD1.
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Affiliation(s)
- Monika Reißmann
- Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Zaur A. Kokov
- Institute of Physics and Mathematics, Kabardino-Balkarian State University, Chernyshevsky 173, Nalchik 360004, Russia;
| | - Armin O. Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
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2
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Holtby AR, Hall TJ, McGivney BA, Han H, Murphy KJ, MacHugh DE, Katz LM, Hill EW. Integrative genomics analysis highlights functionally relevant genes for equine behaviour. Anim Genet 2023. [DOI: 10.1111/age.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/29/2023]
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3
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Influence of mTOR-regulated anabolic pathways on equine skeletal muscle health. J Equine Vet Sci 2023; 124:104281. [PMID: 36905972 DOI: 10.1016/j.jevs.2023.104281] [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: 03/01/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Skeletal muscle is a highly dynamic organ that is essential for locomotion as well as endocrine regulation in all populations of horses. However, despite the importance of adequate muscle development and maintenance, the mechanisms underlying protein anabolism in horses on different diets, exercise programs, and at different life stages remain obscure. Mechanistic target of rapamycin (mTOR) is a key component of the protein synthesis pathway and is regulated by biological factors such as insulin and amino acid availability. Providing a diet ample in vital amino acids, such as leucine and glutamine, is essential in activating sensory pathways that recruit mTOR to the lysosome and assist in the translation of important downstream targets. When the diet is well balanced, mitochondrial biogenesis and protein synthesis are activated in response to increased exercise bouts in the performing athlete. It is important to note that the mTOR kinase pathways are multi-faceted and very complex, with several binding partners and targets that lead to specific functions in protein turnover of the cell, and ultimately, the capacity to maintain or grow muscle mass. Further, these pathways are likely altered across the lifespan, with an emphasis of growth in young horses while decreases in musculature with aged horses appears to be attributable to degradation or other regulators of protein synthesis rather than alterations in the mTOR pathway. Previous work has begun to pinpoint ways in which the mTOR pathway is influenced by diet, exercise, and age; however, future research is warranted to quantify the functional outcomes related to changes in mTOR. Promisingly, this could provide direction on appropriate management techniques to support skeletal muscle growth and maximize athletic potential in differing equine populations.
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4
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Han H, McGivney BA, Allen L, Bai D, Corduff LR, Davaakhuu G, Davaasambuu J, Dorjgotov D, Hall TJ, Hemmings AJ, Holtby AR, Jambal T, Jargalsaikhan B, Jargalsaikhan U, Kadri NK, MacHugh DE, Pausch H, Readhead C, Warburton D, Dugarjaviin M, Hill EW. Common protein-coding variants influence the racing phenotype in galloping racehorse breeds. Commun Biol 2022; 5:1320. [PMID: 36513809 PMCID: PMC9748125 DOI: 10.1038/s42003-022-04206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.
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Affiliation(s)
- Haige Han
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Beatrice A. McGivney
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Lucy Allen
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Dongyi Bai
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Leanne R. Corduff
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Gantulga Davaakhuu
- grid.425564.40000 0004 0587 3863Institute of Biology, Mongolian Academy of Sciences, Peace Avenue 54B, Ulaanbaatar, 13330 Mongolia
| | - Jargalsaikhan Davaasambuu
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Dulguun Dorjgotov
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Thomas J. Hall
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Andrew J. Hemmings
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Amy R. Holtby
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Tuyatsetseg Jambal
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Badarch Jargalsaikhan
- grid.444534.60000 0000 8485 883XDepartment of Obstetrics and Gynecology, Mongolian National University of Medical Sciences, Ulaanbaatar, 14210 Mongolia
| | - Uyasakh Jargalsaikhan
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Naveen K. Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - David E. MacHugh
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland ,grid.7886.10000 0001 0768 2743UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Carol Readhead
- grid.20861.3d0000000107068890Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - David Warburton
- grid.42505.360000 0001 2156 6853The Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027 USA
| | - Manglai Dugarjaviin
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Emmeline W. Hill
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland ,grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
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5
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Valberg SJ, Velez-Irizarry D, Williams ZJ, Henry ML, Iglewski H, Herrick K, Fenger C. Enriched Pathways of Calcium Regulation, Cellular/Oxidative Stress, Inflammation, and Cell Proliferation Characterize Gluteal Muscle of Standardbred Horses between Episodes of Recurrent Exertional Rhabdomyolysis. Genes (Basel) 2022; 13:1853. [PMID: 36292738 PMCID: PMC9601720 DOI: 10.3390/genes13101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/04/2022] Open
Abstract
Certain Standardbred racehorses develop recurrent exertional rhabdomyolysis (RER-STD) for unknown reasons. We compared gluteal muscle histopathology and gene/protein expression between Standardbreds with a history of, but not currently experiencing rhabdomyolysis (N = 9), and race-trained controls (N = 7). Eight RER-STD had a few mature fibers with small internalized myonuclei, one out of nine had histologic evidence of regeneration and zero out of nine degeneration. However, RER-STD versus controls had 791/13,531 differentially expressed genes (DEG). The top three gene ontology (GO) enriched pathways for upregulated DEG (N = 433) were inflammation/immune response (62 GO terms), cell proliferation (31 GO terms), and hypoxia/oxidative stress (31 GO terms). Calcium ion regulation (39 GO terms), purine nucleotide metabolism (32 GO terms), and electron transport (29 GO terms) were the top three enriched GO pathways for down-regulated DEG (N = 305). DEG regulated RYR1 and sarcoplasmic reticulum calcium stores. Differentially expressed proteins (DEP ↑N = 50, ↓N = 12) involved the sarcomere (24% of DEP), electron transport (23%), metabolism (20%), inflammation (6%), cell/oxidative stress (7%), and other (17%). DEP included ↑superoxide dismutase, ↑catalase, and DEP/DEG included several cysteine-based antioxidants. In conclusion, gluteal muscle of RER-susceptible Standardbreds is characterized by perturbation of pathways for calcium regulation, cellular/oxidative stress, inflammation, and cellular regeneration weeks after an episode of rhabdomyolysis that could represent therapeutic targets.
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Affiliation(s)
- Stephanie J. Valberg
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Deborah Velez-Irizarry
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Zoë J. Williams
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Marisa L. Henry
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Hailey Iglewski
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Keely Herrick
- Mary Anne McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Clara Fenger
- Equine Integrated Medicine, PLC, Lexington, KY 40324, USA
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6
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Denham J, McCluskey M, Denham MM, Sellami M, Davie AJ. Epigenetic control of exercise adaptations in the equine athlete: Current evidence and future directions. Equine Vet J 2020; 53:431-450. [PMID: 32671871 DOI: 10.1111/evj.13320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/04/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Horses (Equus ferus caballus) have evolved over the past 300 years in response to man-made selection for particular athletic traits. Some of the selected traits were selected based on the size and horses' muscular power (eg Clydesdales), whereas other breeds were bred for peak running performance (eg Thoroughbred and Arabian). Although the physiological changes and some of the cellular adaptations responsible for athletic potential of horses have been identified, the molecular mechanisms are only just beginning to be comprehensively investigated. The purpose of this review was to outline and discuss the current understanding of the molecular mechanisms underpinning the athletic performance and cardiorespiratory fitness in athletic breeds of horses. A brief review of the biology of epigenetics is provided, including discussion on DNA methylation, histone modifications and small RNAs, followed by a summary and critical review of the current work on the exercise-induced epigenetic and transcriptional changes in horses. Important unanswered questions and currently unexplored areas that deserve attention are highlighted. Finally, a rationale for the analysis of epigenetic modifications in the context with exercise-related traits and ailments associated with athletic breeds of horses is outlined in order to help guide future research.
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Affiliation(s)
- Joshua Denham
- RMIT University, School of Health and Biomedical Sciences, Melbourne, VIC, Australia
| | | | | | - Maha Sellami
- Qatar University, College of Arts and Sciences (CAS), Sport Science Program (SSP), Doha, Qatar
| | - Allan J Davie
- Australian Equine Racing and Research Centre (AERR), Ballina, NSW, Australia
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7
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Klein DJ, McKeever KH, Mirek ET, Anthony TG. Metabolomic Response of Equine Skeletal Muscle to Acute Fatiguing Exercise and Training. Front Physiol 2020; 11:110. [PMID: 32132934 PMCID: PMC7040365 DOI: 10.3389/fphys.2020.00110] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
The athletic horse, despite being over 50% muscle mass, remains understudied with regard to the effects of exercise and training on skeletal muscle metabolism. To begin to address this knowledge gap, we employed an untargeted metabolomics approach to characterize the exercise-induced and fitness-related changes in the skeletal muscle of eight unconditioned Standardbred horses (four male, four female) before and after a 12-week training period. Before training, unconditioned horses showed a high degree of individual variation in the skeletal muscle metabolome, resulting in very few differences basally and at 3 and 24 h after acute fatiguing exercise. Training did not alter body composition but did improve maximal aerobic and running capacities (p < 0.05), and significantly altered the skeletal muscle metabolome (p < 0.05, q < 0.1). While sex independently influenced body composition and distance run following training (p < 0.05), sex did not affect the skeletal muscle metabolome. Exercise-induced metabolomic alterations (p < 0.05, q < 0.1) largely centered on the branched-chain amino acids (BCAA), xenobiotics, and a variety of lipid and nucleotide-related metabolites, particularly in the conditioned state. Further, training increased (p < 0.05, q < 0.1) the relative abundance of almost every identified lipid species, and this was accompanied by increased plasma BCAAs (p < 0.0005), phenylalanine (p = 0.01), and tyrosine (p < 0.02). Acute exercise in the conditioned state decreased (p < 0.05, q < 0.1) the relative abundance of almost all lipid-related species in skeletal muscle by 24 h post-exercise, whereas plasma amino acids remained unaltered. These changes occurred alongside increased muscle gene expression (p < 0.05) related to lipid uptake (Cd36) and lipid (Cpt1b) and BCAA (Bckdk) utilization. This work suggests that metabolites related to amino acid, lipid, nucleotide and xenobiotic metabolism play pivotal roles in the response of equine skeletal muscle to vigorous exercise and training. Use of these and future data sets could be used to track the impact of training and fitness on equine health and may lead to novel predictors and/or diagnostic biomarkers.
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Affiliation(s)
- Dylan J Klein
- Department of Health and Exercise Science, Rowan University, Glassboro, NJ, United States
| | - Kenneth H McKeever
- Rutgers Equine Science Center, Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Emily T Mirek
- Department of Nutritional Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Tracy G Anthony
- Department of Nutritional Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,New Jersey Institute for Food, Nutrition, and Health, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
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8
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Farries G, Bryan K, McGivney CL, McGettigan PA, Gough KF, Browne JA, MacHugh DE, Katz LM, Hill EW. Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome. Front Genet 2019; 10:1215. [PMID: 31850069 PMCID: PMC6902038 DOI: 10.3389/fgene.2019.01215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/04/2019] [Indexed: 01/10/2023] Open
Abstract
While over ten thousand genetic loci have been associated with phenotypic traits and inherited diseases in genome-wide association studies, in most cases only a relatively small proportion of the trait heritability is explained and biological mechanisms underpinning these traits have not been clearly identified. Expression quantitative trait loci (eQTL) are subsets of genomic loci shown experimentally to influence gene expression. Since gene expression is one of the primary determinants of phenotype, the identification of eQTL may reveal biologically relevant loci and provide functional links between genomic variants, gene expression and ultimately phenotype. Skeletal muscle (gluteus medius) gene expression was quantified by RNA-seq for 111 Thoroughbreds (47 male, 64 female) in race training at a single training establishment sampled at two time-points: at rest (n = 92) and four hours after high-intensity exercise (n = 77); n = 60 were sampled at both time points. Genotypes were generated from the Illumina Equine SNP70 BeadChip. Applying a False Discovery Rate (FDR) corrected P-value threshold (PFDR < 0.05), association tests identified 3,583 cis-eQTL associated with expression of 1,456 genes at rest; 4,992 cis-eQTL associated with the expression of 1,922 genes post-exercise; 1,703 trans-eQTL associated with 563 genes at rest; and 1,219 trans-eQTL associated with 425 genes post-exercise. The gene with the highest cis-eQTL association at both time-points was the endosome-associated-trafficking regulator 1 gene (ENTR1; Rest: PFDR = 3.81 × 10-27, Post-exercise: PFDR = 1.66 × 10-24), which has a potential role in the transcriptional regulation of the solute carrier family 2 member 1 glucose transporter protein (SLC2A1). Functional analysis of genes with significant eQTL revealed significant enrichment for cofactor metabolic processes. These results suggest heritable variation in genomic elements such as regulatory sequences (e.g. gene promoters, enhancers, silencers), microRNA and transcription factor genes, which are associated with metabolic function and may have roles in determining end-point muscle and athletic performance phenotypes in Thoroughbred horses. The incorporation of the eQTL identified with genome and transcriptome-wide association may reveal useful biological links between genetic variants and their impact on traits of interest, such as elite racing performance and adaptation to training.
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Affiliation(s)
- Gabriella Farries
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Kenneth Bryan
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Paul A McGettigan
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Katie F Gough
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lisa Michelle Katz
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Emmeline W Hill
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,Research and Development, Plusvital Ltd., Dublin, Ireland
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9
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Valberg SJ, Perumbakkam S, McKenzie EC, Finno CJ. Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. Physiol Genomics 2018; 50:1036-1050. [PMID: 30289745 PMCID: PMC6337024 DOI: 10.1152/physiolgenomics.00044.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log2 fold change (FC) in genes involved in sulfur compound/cysteine metabolism such as cystathionine-beta-synthase ( CBS, ↓4.51), a cysteine and neutral amino acid membrane transporter ( SLC7A10, ↓1.80 MFM), and a cationic transporter (SLC24A1, ↓1.11 MFM). In MFM vs. control at rest, 284 genes were DE with >1 log2 FC in pathways for structure morphogenesis, fiber organization, tissue development, and cell differentiation including > 1 log2 FC in cardiac alpha actin ( ACTC1 ↑2.5 MFM), cytoskeletal desmoplakin ( DSP ↑2.4 MFM), and basement membrane usherin ( USH2A ↓2.9 MFM). Proteome analysis revealed significantly lower antioxidant peroxiredoxin 6 content (PRDX6, ↓4.14 log2 FC MFM), higher fatty acid transport enzyme carnitine palmitoyl transferase (CPT1B, ↑3.49 MFM), and lower sarcomere protein tropomyosin (TPM2, ↓3.24 MFM) in MFM vs. control muscle at rest. We propose that in MFM horses, altered cysteine metabolism and a deficiency of cysteine-containing antioxidants combined with a high capacity to oxidize fatty acids and generate ROS during aerobic exercise causes chronic oxidation and aggregation of key proteins such as desmin.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan.,Department of Population Sciences, University of Minnesota , St. Paul, Minnesota
| | - Sudeep Perumbakkam
- Department of Large Animal Clinical Sciences, Michigan State University , East Lansing, Michigan
| | - Erica C McKenzie
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University , Corvallis, Oregon
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California Davis , Davis, California
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10
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Kim HA, Kim MC, Kim NY, Ryu DY, Lee HS, Kim Y. Integrated analysis of microRNA and mRNA expressions in peripheral blood leukocytes of Warmblood horses before and after exercise. J Vet Sci 2018; 19:99-106. [PMID: 28927254 PMCID: PMC5799405 DOI: 10.4142/jvs.2018.19.1.99] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/29/2017] [Accepted: 09/06/2017] [Indexed: 01/26/2023] Open
Abstract
Exercise capacity is a valuable trait in horses, and it has been used as a horse selection criterion. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully described. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA expression profiles, respectively. The expressions of 6 miRNAs, including 4 known and 2 novel miRNAs, were altered by exercise. The predicted target genes of the differentially expressed miRNAs identified by NGS were matched to the exercise-induced mRNAs determined by microarray analysis. Five genes (LOC100050849, LOC100054517, KHDRBS3, LOC100053996, and LOC100062720) from the microarray analysis were matched to the predicted target genes of the 6 miRNAs. The subset of mRNAs and miRNAs affected by exercise in peripheral blood leukocytes may be useful in elucidating the molecular mechanisms of exercise-associated physiology in horses.
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Affiliation(s)
- Hang-Ah Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Myung-Chul Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Na-Yon Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Doug-Young Ryu
- Laboratory of Environmental Health and Biomarkers, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hong-Seok Lee
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Yongbaek Kim
- Laboratory of Veterinary Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.,Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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11
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Zhang C, Ni P, Ahmad HI, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Y, Wang H, Asif AR, Xiao C, Chen J, Ma Y, Liu X, Du X, Zhao S. Detecting the Population Structure and Scanning for Signatures of Selection in Horses ( Equus caballus) From Whole-Genome Sequencing Data. Evol Bioinform Online 2018; 14:1176934318775106. [PMID: 29899660 PMCID: PMC5990873 DOI: 10.1177/1176934318775106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/14/2018] [Indexed: 12/18/2022] Open
Abstract
Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Pan Ni
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Hafiz Ishfaq Ahmad
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - M Gemingguli
- College of Animal Science, Tarim University, Alar, China
| | | | - D Gulibaheti
- College of Animal Science, Tarim University, Alar, China
| | - Yaping Fang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Haiyang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Akhtar Rasool Asif
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Changyi Xiao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jianhai Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yunlong Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiangdong Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaoyong Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
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12
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Evaluation of microRNA expression in plasma and skeletal muscle of thoroughbred racehorses in training. BMC Vet Res 2017; 13:347. [PMID: 29166903 PMCID: PMC5700565 DOI: 10.1186/s12917-017-1277-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 11/16/2017] [Indexed: 12/19/2022] Open
Abstract
Background Circulating miRNAs (ci-miRNAs) are endogenous, non-coding RNAs emerging as potential diagnostic biomarkers. Equine miRNAs have been previously identified including subsets of tissue-specific miRNAs. In order to investigate ci-miRNAs as diagnostic tools, normal patterns of expression for different scenarios including responses to exercise need to be identified. Human studies have demonstrated that many ci-miRNAs are up-regulated following exercise with changes in expression patterns in skeletal muscle. However, technical challenges such as haemolysis impact on accurate plasma ci-miRNA quantification, with haemolysis often occurring naturally in horses following moderate-to-intense exercise. The objectives of this study were to identify plasma ci-miRNA profiles and skeletal muscle miRNAs before and after exercise in Thoroughbreds (Tb), and to evaluate for the presence and effect of haemolysis on plasma ci-miRNA determination. Resting and post-exercise plasma ci-miRNA profiles and haemolysis were evaluated in twenty 3 year-old Tbs in sprint training. Resting and post-exercise skeletal muscle miRNA abundance was evaluated in a second cohort of eleven 2 year-old Tbs just entering sprint training. Haemolysis was further quantified in resting blood samples from twelve Tbs in sprint training. A human plasma panel containing 179 miRNAs was used for profiling, with haemolysis assessed spectrophotometrically. Data was analysed using a paired Student’s t-test and Pearson’s rank correlation. Results Plasma ci-miRNA data for 13/20 horses and all skeletal muscle miRNA data passed quality control. From plasma, 52/179 miRNAs were detected at both time-points. Haemolysis levels were greater than the threshold for accurate quantification of ci-miRNAs in 18/25 resting and all post-exercise plasma samples. Positive correlations (P < 0.05) between haemolysis and miRNA abundance were detected for all but 4 miRNAs, so exercise-induced changes in plasma ci-miRNA expression could not be quantified. In skeletal muscle samples, 97/179 miRNAs were detected with 5 miRNAs (miR-21-5p, let-7d-3p, let-7d-5p, miR-30b-5p, miR-30e-5p) differentially expressed (DE, P < 0.05) between time-points. Conclusions The degree of haemolysis needs to be determined prior to quantifying plasma ci-miRNA expression from horses in high-intensity exercise training. Identification of DE miRNAs in skeletal muscle indicates modification of miRNA expression may contribute to adaptive training responses in Tbs. Using a human plasma panel likely limited detection of equine-specific miRNAs.
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13
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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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Dube S, Chionuma H, Matoq A, Alshiekh-Nasany R, Abbott L, Poiesz BJ, Dube DK. Expression of various sarcomeric tropomyosin isoforms in equine striated muscles. Open Vet J 2017; 7:180-191. [PMID: 28717602 PMCID: PMC5498770 DOI: 10.4314/ovj.v7i2.17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/15/2017] [Indexed: 01/09/2023] Open
Abstract
In order to better understand the training and athletic activity of horses, we must have complete understanding of the isoform diversity of various myofibrillar protein genes like tropomyosin. Tropomyosin (TPM), a coiled-coil dimeric protein, is a component of thin filament in striated muscles. In mammals, four TPM genes (TPM1, TPM2, TPM3, and TPM4) generate a multitude of TPM isoforms via alternate splicing and/or using different promoters. Unfortunately, our knowledge of TPM isoform diversity in the horse is very limited. Hence, we undertook a comprehensive exploratory study of various TPM isoforms from horse heart and skeletal muscle. We have cloned and sequenced two sarcomeric isoforms of the TPM1 gene called TPM1α and TPM1κ, one sarcomeric isoform of the TPM2 and one of the TPM3 gene, TPM2α and TPM3α respectively. By qRT-PCR using both relative expression and copy number, we have shown that TPM1α expression compared to TPM1κ is very high in heart. On the other hand, the expression of TPM1α is higher in skeletal muscle compared to heart. Further, the expression of TPM2α and TPM3α are higher in skeletal muscle compared to heart. Using western blot analyses with CH1 monoclonal antibody we have shown the high expression levels of sarcomeric TPM proteins in cardiac and skeletal muscle. Due to the paucity of isoform specific antibodies we cannot specifically detect the expression of TPM1κ in horse striated muscle. To the best of our knowledge this is the very first report on the characterization of sarcmeric TPMs in horse striated muscle.
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Affiliation(s)
- Syamalima Dube
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
| | - Henry Chionuma
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
| | - Amr Matoq
- University of Florida, College of Medicine-Jacksonville, Suite 1130, 841 Prudential Drive, Jacksonville, FL 32207, USA
| | - Ruham Alshiekh-Nasany
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
| | - Lynn Abbott
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
| | - Bernard J Poiesz
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
| | - Dipak K Dube
- Department of Medicine, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
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15
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Ropka-Molik K, Stefaniuk-Szmukier M, Z˙ukowski K, Piórkowska K, Bugno-Poniewierska M. Exercise-induced modification of the skeletal muscle transcriptome in Arabian horses. Physiol Genomics 2017; 49:318-326. [DOI: 10.1152/physiolgenomics.00130.2016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 01/20/2023] Open
Abstract
It has been found that Arabian and Thoroughbred horses differ in muscle fiber structure and thus in physiological changes occurring in muscles during exercise. The aim of the present study was to identify the global gene expression modifications that occur in skeletal muscle following a training regime to prepare for flat racing. Whole transcriptomes of muscle (gluteus medius) were compared between three time points of tissue collection: T0 (untrained horses), T1 (horses after intense gallop phase), and T2 (horses at the end of racing season), 23 samples in total. The numerous groups of exercise-regulated differentially expressed genes (DEGs) were related to muscle cell structure and signaling and included insulin-like growth factor 1 receptor ( IGF1R), insulin receptor ( INSR), transforming growth factor beta receptors 1 and 2 ( TGFBR1, TGFBR2), vascular endothelial growth factor B ( VEGFB); epidermal growth factor ( EGF), hepatocyte growth factor ( HGF), and vascular endothelial growth factor D ( FIGF). In Arabian horses, exercise modified the expression of genes belonging to the PPAR signaling pathway (e.g., PPARA, PPARD, and PLIN2), calcium signaling pathway, and pathways associated with metabolic processes (e.g., oxidative phosphorylation, fatty acid metabolism, glycolysis/gluconeogenesis, and citrate cycle). According to detected gene expression modifications, our results suggested that in Arabian horses, exercise switches energy generation toward fatty acid utilization and enhances glycogen transport and calcium signaling. The use of the RNA-Seq approach in analyzing the skeletal muscle transcriptome allowed for the proposal of a panel of new candidate genes potentially related to body homeostasis maintenance and racing performance in Arabian horses.
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Affiliation(s)
- Katarzyna Ropka-Molik
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Cracow, Poland
| | - Monika Stefaniuk-Szmukier
- Department of Horse Breeding, Institute of Animal Science, University of Agriculture in Cracow, Poland; and
| | - Kacper Z˙ukowski
- Department of Animal Genetics and Breeding, National Research Institute of Animal Production, Cracow, Poland
| | - Katarzyna Piórkowska
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Cracow, Poland
| | - Monika Bugno-Poniewierska
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Cracow, Poland
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16
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Ropka-Molik K, Stefaniuk-Szmukier M, Żukowski K, Piórkowska K, Gurgul A, Bugno-Poniewierska M. Transcriptome profiling of Arabian horse blood during training regimens. BMC Genet 2017; 18:31. [PMID: 28381206 PMCID: PMC5382464 DOI: 10.1186/s12863-017-0499-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 03/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Arabian horses are believed to be one of the oldest and most influential horse breeds in the world. Blood is the main tissue involved in maintaining body homeostasis, and it is considered a marker of the processes taking place in the other tissues. Thus, the aim of our study was to identify the genetic basis of changes occurring in the blood of Arabian horses subjected to a training regimen and to compare the global gene expression profiles between different training periods (T1: after a slow canter phase that is considered a conditioning phase, T2: after an intense gallop phase, and T3: at the end of the racing season) and between trained and untrained horses (T0). RNA sequencing was performed on 37 samples with a 75-bp single-end run on a HiScanSQ platform (Illumina), and differentially expressed genes (DEGs) were identified based on DESeq2 (v1.11.25) software. RESULTS An increase in the number of DEGs between subsequent training periods was observed, and the highest amount of DEGs (440) was detected between untrained horses (T0) and horses at the end of the racing season (T3). The comparisons of the T2 vs. T3 transcriptomes and the T0 vs. T3 transcriptomes showed a significant gain of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in the T3 period compared to T2 and T0, respectively). Forty differentially expressed genes were detected between the T1 and T2 periods, and 296 between T2 and T3. Functional annotation showed that the most abundant genes up-regulated in exercise were involved in pathways regulating cell cycle (PI3K-Akt signalling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis, as well as immunity processes (Jak-STAT signalling pathway). CONCLUSIONS We investigated whether training causes permanent transcriptome changes in horse blood as a reflection of adaptation to conditioning and the maintenance of fitness to compete in flat races. The present study identified the overrepresented molecular pathways and genes that are essential for maintaining body homeostasis during long-term exercise in Arabian horses. Selected DEGs should be further investigated as markers that are potentially associated with racing performance in Arabian horses.
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Affiliation(s)
- Katarzyna Ropka-Molik
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
| | - Monika Stefaniuk-Szmukier
- Department of Horse Breeding, Institute of Animal Science, University of Agriculture in Cracow, Kracow, Poland
| | - Kacper Żukowski
- Department of Animal Genetics and Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Katarzyna Piórkowska
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Artur Gurgul
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Monika Bugno-Poniewierska
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
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17
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Gaona-López C, Julián-Sánchez A, Riveros-Rosas H. Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PLoS One 2016; 11:e0166851. [PMID: 27893862 PMCID: PMC5125639 DOI: 10.1371/journal.pone.0166851] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/05/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenase (ADH) activity is widely distributed in the three domains of life. Currently, there are three non-homologous NAD(P)+-dependent ADH families reported: Type I ADH comprises Zn-dependent ADHs; type II ADH comprises short-chain ADHs described first in Drosophila; and, type III ADH comprises iron-containing ADHs (FeADHs). These three families arose independently throughout evolution and possess different structures and mechanisms of reaction. While types I and II ADHs have been extensively studied, analyses about the evolution and diversity of (type III) FeADHs have not been published yet. Therefore in this work, a phylogenetic analysis of FeADHs was performed to get insights into the evolution of this protein family, as well as explore the diversity of FeADHs in eukaryotes. PRINCIPAL FINDINGS Results showed that FeADHs from eukaryotes are distributed in thirteen protein subfamilies, eight of them possessing protein sequences distributed in the three domains of life. Interestingly, none of these protein subfamilies possess protein sequences found simultaneously in animals, plants and fungi. Many FeADHs are activated by or contain Fe2+, but many others bind to a variety of metals, or even lack of metal cofactor. Animal FeADHs are found in just one protein subfamily, the hydroxyacid-oxoacid transhydrogenase (HOT) subfamily, which includes protein sequences widely distributed in fungi, but not in plants), and in several taxa from lower eukaryotes, bacteria and archaea. Fungi FeADHs are found mainly in two subfamilies: HOT and maleylacetate reductase (MAR), but some can be found also in other three different protein subfamilies. Plant FeADHs are found only in chlorophyta but not in higher plants, and are distributed in three different protein subfamilies. CONCLUSIONS/SIGNIFICANCE FeADHs are a diverse and ancient protein family that shares a common 3D scaffold with a patchy distribution in eukaryotes. The majority of sequenced FeADHs from eukaryotes are distributed in just two subfamilies, HOT and MAR (found mainly in animals and fungi). These two subfamilies comprise almost 85% of all sequenced FeADHs in eukaryotes.
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Affiliation(s)
- Carlos Gaona-López
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
- * E-mail:
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18
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Mulliniks JT, Cope ER, McFarlane ZD, Hobbs JD, Waterman RC. Drivers of grazing livestock efficiency: how physiology, metabolism, experience and adaptability influence productivity. J Anim Sci 2016. [DOI: 10.2527/jas.2015-0711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Modulation of rat monocyte/macrophage innate functions by increasing intensities of swimming exercise is associated with heat shock protein status. Mol Cell Biochem 2016; 421:111-25. [DOI: 10.1007/s11010-016-2791-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/06/2016] [Indexed: 12/16/2022]
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20
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Pereira GL, de Matteis R, Regitano LC, Chardulo LAL, Curi RA. MSTN , CKM , and DMRT3 Gene Variants in Different Lines of Quarter Horses. J Equine Vet Sci 2016. [DOI: 10.1016/j.jevs.2015.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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21
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Gim JA, Lee S, Kim DS, Jeong KS, Hong CP, Bae JH, Moon JW, Choi YS, Cho BW, Cho HG, Bhak J, Kim HS. HEpD: a database describing epigenetic differences between Thoroughbred and Jeju horses. Gene 2015; 560:83-8. [PMID: 25637569 DOI: 10.1016/j.gene.2015.01.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/19/2014] [Accepted: 01/23/2015] [Indexed: 11/19/2022]
Abstract
With the advent of next-generation sequencing technology, genome-wide maps of DNA methylation are now available. The Thoroughbred horse is bred for racing, while the Jeju horse is a traditional Korean horse bred for racing or food. The methylation profiles of equine organs may provide genomic clues underlying their athletic traits. We have developed a database to elucidate genome-wide DNA methylation patterns of the cerebrum, lung, heart, and skeletal muscle from Thoroughbred and Jeju horses. Using MeDIP-Seq, our database provides information regarding significantly enriched methylated regions beyond a threshold, methylation density of a specific region, and differentially methylated regions (DMRs) for tissues from two equine breeds. It provided methylation patterns at 784 gene regions in the equine genome. This database can potentially help researchers identify DMRs in the tissues of these horse species and investigate the differences between the Thoroughbred and Jeju horse breeds.
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Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 609-735, Republic of Korea
| | - Sugi Lee
- Department of Statistics, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Dae-Soo Kim
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Kwang-Seuk Jeong
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Institute of Environmental Technology & Industry, Pusan National University, Busan 609-735, Republic of Korea
| | - Chang Pyo Hong
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Jin-Han Bae
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, Republic of Korea
| | - Jae-Woo Moon
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Yong-Seok Choi
- Genetic Engineering Institute, Pusan National University, Busan 609-735, Republic of Korea; Department of Statistics, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Byung-Wook Cho
- Department of Animal Science, College of Life Sciences, Pusan National University, Miryang 627-702, Republic of Korea
| | - Hwan-Gue Cho
- School of Computer Science and Engineering, College of Engineering, Pusan National University, Busan 609-735, Republic of Korea
| | - Jong Bhak
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea; BioMedical Engineering, UNIST, Ulsan, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 609-735, Republic of Korea.
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22
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Hill EW, Gu J, McGivney BA, MacHugh DE. Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance. Anim Genet 2015; 41 Suppl 2:56-63. [PMID: 21070277 DOI: 10.1111/j.1365-2052.2010.02104.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Athletic performance is influenced by a complex interplay among the environment and a suite of genes, which contributes to system-wide structure and function. In a panel of elite and non-elite Thoroughbred horses (n=148), we genotyped 68 SNPs in 17 putative exercise-relevant genes chosen from a genome scan for selection. We performed a series of case-control and quantitative association tests for relationships with racecourse performance. Thirteen SNPs in nine genes were significantly (P<0.05) associated with a performance phenotype. We selected five SNPs in four genes (ACSS1, ACN9, COX4I1, PDK4) for validation in an independent sample set of elite and non-elite Thoroughbreds (n=130). Two SNPs in the PDK4 gene were validated (P<0.01) for associations with elite racing performance. When all samples were considered together (n=278), the PDK4_ 38973231 SNP was strongly associated (P<0.0005) with elite racing performance. Individuals with the A:A and A:G genotypes had a 16.2-16.6 lb advantage over G:G individuals in terms of handicap rating. Re-sequencing of the PDK4 gene and further genotyping will be required to identify the causative variant that is likely influencing exercise-induced variation in expression of the gene. Notwithstanding, this information may be employed as a marker for the selection of racehorses with the genetic potential for superior racing ability.
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Affiliation(s)
- E W Hill
- Animal Genomics Laboratory, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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Gim JA, Hong CP, Kim DS, Moon JW, Choi Y, Eo J, Kwon YJ, Lee JR, Jung YD, Bae JH, Choi BH, Ko J, Song S, Ahn K, Ha HS, Yang YM, Lee HK, Park KD, Do KT, Han K, Yi JM, Cha HJ, Ayarpadikannan S, Cho BW, Bhak J, Kim HS. Genome-wide analysis of DNA methylation before-and after exercise in the thoroughbred horse with MeDIP-Seq. Mol Cells 2015; 38:210-20. [PMID: 25666347 PMCID: PMC4363720 DOI: 10.14348/molcells.2015.2138] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 12/14/2022] Open
Abstract
Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethylated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.
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Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Chang Pyo Hong
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270,
Korea
| | - Dae-Soo Kim
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806,
Korea
| | - Jae-Woo Moon
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270,
Korea
| | - Yuri Choi
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Jungwoo Eo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Yun-Jeong Kwon
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Ja-Rang Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Yi-Deun Jung
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Jin-Han Bae
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Junsu Ko
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270,
Korea
| | - Sanghoon Song
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270,
Korea
| | - Kung Ahn
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270,
Korea
| | - Hong-Seok Ha
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Young Mok Yang
- Department of Pathology, School of Medicine, and Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701,
Korea
| | - Hak-Kyo Lee
- Department of Biotechnology, Hankyong National University, Anseong 456-749,
Korea
| | - Kyung-Do Park
- Department of Biotechnology, Hankyong National University, Anseong 456-749,
Korea
| | - Kyoung-Tag Do
- Department of Equine Sciences, Sorabol College, Gyeongju 780-711,
Korea
| | - Kyudong Han
- Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714,
Korea
| | - Joo Mi Yi
- Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS), Busan 619-953,
Korea
| | - Hee-Jae Cha
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 602-702,
Korea
| | - Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | - Byung-Wook Cho
- Department of Animal Science, College of Life Sciences, Pusan National University, Miryang 627-702,
Korea
| | - Jong Bhak
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270,
Korea
- BioMedical Engineering, UNIST, Ulsan 689-798,
Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
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Early changes in costameric and mitochondrial protein expression with unloading are muscle specific. BIOMED RESEARCH INTERNATIONAL 2014; 2014:519310. [PMID: 25313365 PMCID: PMC4182083 DOI: 10.1155/2014/519310] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/23/2014] [Indexed: 11/25/2022]
Abstract
We hypothesised that load-sensitive expression of costameric proteins, which hold the sarcomere in place and position the mitochondria, contributes to the early adaptations of antigravity muscle to unloading and would depend on muscle fibre composition and chymotrypsin activity of the proteasome. Biopsies were obtained from vastus lateralis (VL) and soleus (SOL) muscles of eight men before and after 3 days of unilateral lower limb suspension (ULLS) and subjected to fibre typing and measures for costameric (FAK and FRNK), mitochondrial (NDUFA9, SDHA, UQCRC1, UCP3, and ATP5A1), and MHCI protein and RNA content. Mean cross-sectional area (MCSA) of types I and II muscle fibres in VL and type I fibres in SOL demonstrated a trend for a reduction after ULLS (0.05 ≤ P < 0.10). FAK phosphorylation at tyrosine 397 showed a 20% reduction in VL muscle (P = 0.029). SOL muscle demonstrated a specific reduction in UCP3 content (−23%; P = 0.012). Muscle-specific effects of ULLS were identified for linear relationships between measured proteins, chymotrypsin activity and fibre MCSA. The molecular modifications in costamere turnover and energy homoeostasis identify that aspects of atrophy and fibre transformation are detectable at the protein level in weight-bearing muscles within 3 days of unloading.
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Kim H, Lee T, Park W, Lee JW, Kim J, Lee BY, Ahn H, Moon S, Cho S, Do KT, Kim HS, Lee HK, Lee CK, Kong HS, Yang YM, Park J, Kim HM, Kim BC, Hwang S, Bhak J, Burt D, Park KD, Cho BW, Kim H. Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse. DNA Res 2013; 20:287-98. [PMID: 23580538 PMCID: PMC3686434 DOI: 10.1093/dnares/dst010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The modern horse (Equus caballus) is the product of over 50 million yrs of evolution. The athletic abilities of the horse have been enhanced during the past 6000 yrs under domestication. Therefore, the horse serves as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. The structure and function of skeletal muscle show remarkable plasticity to the physical and metabolic challenges following exercise. Here, we reveal an evolutionary layer of responsiveness to exercise-stress in the skeletal muscle of the racing horse. We analysed differentially expressed genes and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. By estimating genome-wide dN/dS ratios using six mammalian genomes, and FST and iHS using re-sequencing data derived from 20 horses, we were able to peel back the evolutionary layers of adaptations to exercise-stress in the horse. We found that the oldest and thickest layer (dN/dS) consists of system-wide tissue and organ adaptations. We further find that, during the period of horse domestication, the older layer (FST) is mainly responsible for adaptations to inflammation and energy metabolism, and the most recent layer (iHS) for neurological system process, cell adhesion, and proteolysis.
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Affiliation(s)
- Hyeongmin Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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Animal models as tools to investigate antidiabetic and anti-inflammatory plants. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:142087. [PMID: 22899950 PMCID: PMC3414199 DOI: 10.1155/2012/142087] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/30/2012] [Indexed: 01/12/2023]
Abstract
Plants have been historically used for diabetes treatment and related anti-inflammatory activity throughout the world; few of them have been validated by scientific criteria. Recently, a large diversity of animal models has been developed for better understanding the pathogenesis of diabetes mellitus and its underlying inflammatory mechanism and new drugs have been introduced in the market to treat this disease. The aim of this work is to review the available animal models of diabetes and anti-inflammatory activity along with some in vitro models which have been used as tools to investigate the mechanism of action of drugs with potential antidiabetic properties and related anti-inflammatory mechanism. At present, the rigorous procedures for evaluation of conventional antidiabetic medicines have rarely been applied to test raw plant materials used as traditional treatments for diabetes; and natural products, mainly derived from plants, have been tested in chemically induced diabetes model. This paper contributes to design new strategies for the development of novel antidiabetic drugs and its related inflammatory activity in order to treat this serious condition which represents a global public health problem.
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Hill EW, Eivers SS, McGivney BA, Fonseca RG, Gu J, Smith NA, Browne JA, MacHugh DE, Katz LM. Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle. Equine Vet J 2011:576-81. [PMID: 21059063 DOI: 10.1111/j.2042-3306.2010.00206.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
REASONS FOR PERFORMING STUDY The role of molecular signalling pathways in the phenotypic adaptation of skeletal muscle to different exercise stimuli in the Thoroughbred horse has not been reported previously. OBJECTIVE To examine CKM, COX4I1, COX4I2 and PDK4 gene expression following high intensity sprint and moderate intensity treadmill exercise stimuli in skeletal muscle of Thoroughbred horses. MATERIALS AND METHODS Two groups of trained 3-year-old Thoroughbred horses participated. Group A (n = 6 females, n = 3 males) participated in an incremental step test (moderate intensity) to fatigue or HR(max) on a Sato high speed treadmill (distance = 5418.67 m ± 343.21). Group B (n = 8 females) participated in routine 'work' (sprint) on an all-weather gallop (distance = 812.83 m ± 12.53). Biopsy samples were obtained from the gluteus medius pre-exercise (T(0)), immediately post exercise (T(1)) and 4 h post exercise (T(2)). For physiological relevance venous blood samples were collected to measure plasma lactate and creatine kinase concentrations. Changes in mRNA expression were determined by quantitative real-time RT-PCR for creatine kinase muscle (CKM), cytochrome c oxidase subunit IV isoform 1 (COX4I1), cytochrome c oxidase subunit IV isoform 2 (COX4I2) and pyruvate dehydrogenase kinase, isozyme 4 (PDK4) genes. Statistical significance (α < 0.05) was determined using Student's t tests. RESULTS COX4I2 mRNA expression decreased significantly in Group A and remained unchanged in Group B between T(0) vs. T(2) (-1.7-fold, P = 0.017; -1.0-fold, P = 0.859). PDK4 mRNA expression increased significantly in Group B but not in Group A between T(0) vs. T(1) (3.8-fold, P = 0.039; 1.4-fold, P = 0.591). There were no significant changes in the expression in CKM or COX4I1 mRNA abundance in either group. CONCLUSIONS Different exercise protocols elicit variable transcriptional responses in key exercise relevant genes in equine skeletal muscle due to variation in metabolic demand.
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Affiliation(s)
- E W Hill
- Animal Genomics Laboratory, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin 4, Ireland.
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Hernández-Tobías A, Julián-Sánchez A, Piña E, Riveros-Rosas H. Natural alcohol exposure: Is ethanol the main substrate for alcohol dehydrogenases in animals? Chem Biol Interact 2011; 191:14-25. [DOI: 10.1016/j.cbi.2011.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 01/30/2023]
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BARREY E. Reviewe: Genetics and genomics in equine exercise physiology: an overview of the new applications of molecular biology as positive and negative markers of performance and health. Equine Vet J 2010:561-8. [DOI: 10.1111/j.2042-3306.2010.00299.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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30
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Schröder W, Klostermann A, Distl O. Candidate genes for physical performance in the horse. Vet J 2010; 190:39-48. [PMID: 21115378 DOI: 10.1016/j.tvjl.2010.09.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 08/12/2010] [Accepted: 09/30/2010] [Indexed: 12/22/2022]
Abstract
Intense selection for speed, endurance or pulling power in the domestic horse (Equus caballus) has resulted in a number of adaptive changes in the phenotype required for elite athletic performance. To date, studies in humans have revealed a large number of genes involved in elite athletic performance, but studies in horses are rare. The horse genome assembly and bioinformation tools for genome analyses have been used to compare human performance genes with their equine orthologues, both to retrieve pathways for these genes and to investigate their chromosomal distribution. In this review, 28 candidate genes for equine performance are presented that have polymorphisms associated with human elite athletic performance and may have impact on athletic performance in horses. A significant accumulation of candidate genes was found on horse chromosomes 4 and 12. Genes involved in pathways for focal adhesion, regulation of actin cytoskeleton, neuroactive ligand-receptor interaction, and calcium signalling were over-represented. Genome-wide association studies for athletic performance in horses may benefit from the strong conserved synteny of the chromosomal arrangement of genes in humans and horses.
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Affiliation(s)
- Wiebke Schröder
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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31
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Modulation of circulating purines and pyrimidines by physical exercise in the horse. Eur J Appl Physiol 2010; 111:549-56. [PMID: 20931219 DOI: 10.1007/s00421-010-1673-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
Abstract
This study was designed to examine the influence of sub-maximal exercise on purine and pyrimidine catabolism in horses. Ten horses were initially trained for 12 weeks at the end of which they underwent a standardized exercise test (SET); venous blood samples were taken at rest, 5 and 30 min after the SET. Six untrained healthy horses, from which a blood withdrawal was taken at rest, were used as the control group. Samples were analyzed by HPLC for the simultaneous determination of uric acid, uridine, β-pseudouridine and creatinine in plasma. Glucose and lactate were measured in blood. Trained horses had basal uridine levels significantly lower than sedentary horses. The SET caused significant increase in plasma uric acid, uridine, β-pseudouridine and creatinine. Following the SET, a significant negative correlation was found between plasma uridine and glucose, whilst a significant positive correlation was observed between plasma uric acid and creatinine. These results indicate that increase in energy demand during exercise in the horse causes not only the degradation of purine but also of pyrimidine compounds, the latter possibly exerting a control on glucose uptake as also demonstrated in human beings.
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A genome-wide SNP-association study confirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genomics 2010; 11:552. [PMID: 20932346 PMCID: PMC3091701 DOI: 10.1186/1471-2164-11-552] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/11/2010] [Indexed: 11/25/2022] Open
Abstract
Background Thoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible for variation in individual aptitude for race distance, and that muscle phenotypes in particular are important. Results A genome-wide SNP-association study for optimum racing distance was performed using the EquineSNP50 Bead Chip genotyping array in a cohort of n = 118 elite Thoroughbred racehorses divergent for race distance aptitude. In a cohort-based association test we evaluated genotypic variation at 40,977 SNPs between horses suited to short distance (≤ 8 f) and middle-long distance (> 8 f) races. The most significant SNP was located on chromosome 18: BIEC2-417495 ~690 kb from the gene encoding myostatin (MSTN) [Punadj. = 6.96 × 10-6]. Considering best race distance as a quantitative phenotype, a peak of association on chromosome 18 (chr18:65809482-67545806) comprising eight SNPs encompassing a 1.7 Mb region was observed. Again, similar to the cohort-based analysis, the most significant SNP was BIEC2-417495 (Punadj. = 1.61 × 10-9; PBonf. = 6.58 × 10-5). In a candidate gene study we have previously reported a SNP (g.66493737C>T) in MSTN associated with best race distance in Thoroughbreds; however, its functional and genome-wide relevance were uncertain. Additional re-sequencing in the flanking regions of the MSTN gene revealed four novel 3' UTR SNPs and a 227 bp SINE insertion polymorphism in the 5' UTR promoter sequence. Linkage disequilibrium was highest between g.66493737C>T and BIEC2-417495 (r2 = 0.86). Conclusions Comparative association tests consistently demonstrated the g.66493737C>T SNP as the superior variant in the prediction of distance aptitude in racehorses (g.66493737C>T, P = 1.02 × 10-10; BIEC2-417495, Punadj. = 1.61 × 10-9). Functional investigations will be required to determine whether this polymorphism affects putative transcription-factor binding and gives rise to variation in gene and protein expression. Nonetheless, this study demonstrates that the g.66493737C>T SNP provides the most powerful genetic marker for prediction of race distance aptitude in Thoroughbreds.
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Abstract
The objective of this review is to introduce equine clinicians to the rapidly evolving field of clinical genomics with a vision of improving the health and welfare of the domestic horse. For 15 years a consortium of veterinary geneticists and clinicians has worked together under the umbrella of The Horse Genome Project. This group, encompassing 22 laboratories in 12 countries, has made rapid progress, developing several iterations of linkage, physical and comparative gene maps of the horse with increasing levels of detail. In early 2006, the research was greatly facilitated when the US National Human Genome Research Institute of the National Institutes of Health added the horse to the list of mammalian species scheduled for whole genome sequencing. The genome of the domestic horse has now been sequenced and is available to researchers worldwide in publicly accessible databases. This achievement creates the potential for transformative change within the horse industry, particularly in the fields of internal medicine, sports medicine and reproduction. The genome sequence has enabled the development of new genome-wide tools and resources for studying inherited diseases of the horse. To date, researchers have identified 11 mutations causing 10 clinical syndromes in the horse. Testing is commercially available for all but one of these diseases. Future research will probably identify the genetic bases for other equine diseases, produce new diagnostic tests and generate novel therapeutics for some of these conditions. This will enable equine clinicians to play a critical role in ensuring the thoughtful and appropriate application of this knowledge as they assist clients with breeding and clinical decision-making.
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Affiliation(s)
- M M Brosnahan
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, New York, USA
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McGivney BA, McGettigan PA, Browne JA, Evans ACO, Fonseca RG, Loftus BJ, Lohan A, MacHugh DE, Murphy BA, Katz LM, Hill EW. Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training. BMC Genomics 2010; 11:398. [PMID: 20573200 PMCID: PMC2900271 DOI: 10.1186/1471-2164-11-398] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 06/23/2010] [Indexed: 11/22/2022] Open
Abstract
Background Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways. Functional groups displaying highly significant (P < 0.0001) increased expression included mitochondrion, oxidative phosphorylation and fatty acid metabolism while functional groups with decreased expression were mainly associated with structural genes and included the sarcoplasm, laminin complex and cytoskeleton. Conclusion Exercise training in Thoroughbred racehorses results in coordinate changes in the gene expression of functional groups of genes related to metabolism, oxidative phosphorylation and muscle structure.
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Affiliation(s)
- Beatrice A McGivney
- Animal Genomics Laboratory, UCD School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
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Mienaltowski MJ, Huang L, Bathke AC, Stromberg AJ, MacLeod JN. Transcriptional comparisons between equine articular repair tissue, neonatal cartilage, cultured chondrocytes and mesenchymal stromal cells. Brief Funct Genomics 2010; 9:238-50. [PMID: 20348544 DOI: 10.1093/bfgp/elq007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human and equine cell transplant strategies for cartilage lesions usually result in scar tissue that is similar to what is produced naturally during the repair process. In this study, culture-expanded de-differentiated chondrocytes and primary bone marrow stromal cells at a pre-transplantation time-point were compared along with neonatal cartilage to repair tissue. Transcriptional profiling using a 9413-probeset equine-specific cDNA microarray and targeted real-time quantitative polymerase chain reaction validation were used to characterize relationships between these cell types and repair tissue both broadly and for individual cartilage biomarkers. The greatest divergence in expression was detected for transcripts encoding matrix proteins that typically define the differentiation status of normal articular cartilage and fibrocartilage repair tissue. Expression patterns and gene ontology analyses indicated that while the repair cells were more chondrogenic than bone marrow stromal cells and de-differentiated cultured chondrocytes, steady-state levels of transcripts encoding cartilage biomarkers were substantially lower than the amounts found in neonatal articular cartilage. By characterizing gene expression differences amongst these tissues, we present important targets to monitor when developing improvements to cartilage engineering therapies.
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