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Perelmuter S, Soogoor A, Maliszewski K, Grimshaw A. Investigating the overlapping presentation of irritable bowel syndrome and vulvodynia: a scoping review of the evidence and mechanisms. Sex Med Rev 2024; 12:559-568. [PMID: 39084679 DOI: 10.1093/sxmrev/qeae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
INTRODUCTION Vulvodynia is a complex and multifactorial medical condition characterized by pain in the vulvar area without any identifiable cause. Vulvodynia is underdiagnosed, leading to increased risk of sexual dysfunction and reduced quality of life. Irritable bowel syndrome (IBS) is a gastrointestinal disorder predominantly affecting women. Vulvodynia and IBS frequently co-occur in women, with a 2- to 4-fold increased likelihood of IBS diagnosis in those with vulvodynia. These conditions may share underlying causes, highlighting the need for research to better understand their shared pathophysiology and develop effective therapeutics. OBJECTIVE The aim of this scoping review was to assess the evidence of simultaneous presentation of IBS and vulvodynia. METHODS A comprehensive search was conducted in 6 databases between inception of database and August 2023: PubMed, Web of Science, Scopus, Science Direct, Google Scholar, and Cochrane Library. Studies included primary research about IBS and vulvodynia in terms of presentation overlap, diagnosis, or treatment. Data were extracted from eligible studies, summarized, and collated. RESULTS Of the 306 unique articles identified, 33 were included in the final analysis: 20 cross-sectional studies, 4 case-control studies, 2 case reports, 4 cohort studies, 2 quasi-experimental studies, and 1 randomized trial. Common themes included a high prevalence of overlapping vulvodynia and IBS with a significant diagnostic delay in vulvodynia, mast cell involvement and visceral hypersensitization as common pathophysiology, and the need for a multimodal treatment. CONCLUSION Our review adds to the evidence that there is an association between vulvodynia and IBS. Despite this, research on the underlying molecular mechanisms of this association is scarce, and diagnostic delays persist for vulvodynia. Increasing awareness of the overlap of these conditions will improve screening for vulvodynia in the patient population with IBS, thereby improving the diagnostic delay, and understanding the pathophysiology will enable treatment strategies that address both conditions.
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Affiliation(s)
- Sara Perelmuter
- Weill Cornell Medical College, New York, NY 10021, United States
| | - Anantha Soogoor
- College of Osteopathic Medicine, William Carey University, Hattiesburg, MS 39401, United States
| | - Katelyn Maliszewski
- College of Osteopathic Medicine, Des Moines University, Des Moines, IA 50266, United States
| | - Alyssa Grimshaw
- Harvey Cushing/John Hay Whitney Medical Library, Yale University, New Haven, CT 06511, United States
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Zhou X, Lv Y, Xie H, Li Y, Liu C, Zheng M, Wu R, Zhou S, Gu X, Li J, Mi D. RNA sequencing of exosomes secreted by fibroblast and Schwann cells elucidates mechanisms underlying peripheral nerve regeneration. Neural Regen Res 2024; 19:1812-1821. [PMID: 38103248 PMCID: PMC10960293 DOI: 10.4103/1673-5374.387980] [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: 06/30/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202408000-00035/figure1/v/2023-12-16T180322Z/r/image-tiff Exosomes exhibit complex biological functions and mediate a variety of biological processes, such as promoting axonal regeneration and functional recovery after injury. Long non-coding RNAs (lncRNAs) have been reported to play a crucial role in axonal regeneration. However, the role of the lncRNA-microRNA-messenger RNA (mRNA)-competitive endogenous RNA (ceRNA) network in exosome-mediated axonal regeneration remains unclear. In this study, we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts (FC-EXOs) and Schwann cells (SC-EXOs). Differential gene expression analysis, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, and protein-protein interaction network analysis were used to explore the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs. We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs, which suggests that it may promote axonal regeneration. In addition, using the miRWalk and Starbase prediction databases, we constructed a regulatory network of ceRNAs targeting Rps5, including 27 microRNAs and five lncRNAs. The ceRNA regulatory network, which included Ftx and Miat, revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury. Our findings suggest that exosomes derived from fibroblast and Schwann cells could be used to treat injuries of peripheral nervous system.
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Affiliation(s)
- Xinyang Zhou
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Yehua Lv
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, Jiangsu Province, China
| | - Huimin Xie
- Nantong Stomatological Hospital Affiliated to Nantong University, Nantong, Jiangsu Province, China
| | - Yan Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Chang Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Mengru Zheng
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Ronghua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Songlin Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xiaosong Gu
- Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Jingjing Li
- Department of General Practice, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Daguo Mi
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, Jiangsu Province, China
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Mou K, Chan SMH, Vlahos R. Musculoskeletal crosstalk in chronic obstructive pulmonary disease and comorbidities: Emerging roles and therapeutic potentials. Pharmacol Ther 2024; 257:108635. [PMID: 38508342 DOI: 10.1016/j.pharmthera.2024.108635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/13/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a multifaceted respiratory disorder characterized by progressive airflow limitation and systemic implications. It has become increasingly apparent that COPD exerts its influence far beyond the respiratory system, extending its impact to various organ systems. Among these, the musculoskeletal system emerges as a central player in both the pathogenesis and management of COPD and its associated comorbidities. Muscle dysfunction and osteoporosis are prevalent musculoskeletal disorders in COPD patients, leading to a substantial decline in exercise capacity and overall health. These manifestations are influenced by systemic inflammation, oxidative stress, and hormonal imbalances, all hallmarks of COPD. Recent research has uncovered an intricate interplay between COPD and musculoskeletal comorbidities, suggesting that muscle and bone tissues may cross-communicate through the release of signalling molecules, known as "myokines" and "osteokines". We explored this dynamic relationship, with a particular focus on the role of the immune system in mediating the cross-communication between muscle and bone in COPD. Moreover, we delved into existing and emerging therapeutic strategies for managing musculoskeletal disorders in COPD. It underscores the development of personalized treatment approaches that target both the respiratory and musculoskeletal aspects of COPD, offering the promise of improved well-being and quality of life for individuals grappling with this complex condition. This comprehensive review underscores the significance of recognizing the profound impact of COPD on the musculoskeletal system and its comorbidities. By unravelling the intricate connections between these systems and exploring innovative treatment avenues, we can aspire to enhance the overall care and outcomes for COPD patients, ultimately offering hope for improved health and well-being.
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Affiliation(s)
- Kevin Mou
- Centre for Respiratory Science and Health, School of Health & Biomedical Sciences, RMIT University, Melbourne, VIC, Australia
| | - Stanley M H Chan
- Centre for Respiratory Science and Health, School of Health & Biomedical Sciences, RMIT University, Melbourne, VIC, Australia
| | - Ross Vlahos
- Centre for Respiratory Science and Health, School of Health & Biomedical Sciences, RMIT University, Melbourne, VIC, Australia.
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Hoolachan JM, McCallion E, Sutton ER, Çetin Ö, Pacheco-Torres P, Dimitriadi M, Sari S, Miller GJ, Okoh M, Walter LM, Claus P, Wood MJA, Tonge DP, Bowerman M. A transcriptomics-based drug repositioning approach to identify drugs with similar activities for the treatment of muscle pathologies in spinal muscular atrophy (SMA) models. Hum Mol Genet 2024; 33:400-425. [PMID: 37947217 PMCID: PMC10877467 DOI: 10.1093/hmg/ddad192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/08/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a genetic neuromuscular disorder caused by the reduction of survival of motor neuron (SMN) protein levels. Although three SMN-augmentation therapies are clinically approved that significantly slow down disease progression, they are unfortunately not cures. Thus, complementary SMN-independent therapies that can target key SMA pathologies and that can support the clinically approved SMN-dependent drugs are the forefront of therapeutic development. We have previously demonstrated that prednisolone, a synthetic glucocorticoid (GC) improved muscle health and survival in severe Smn-/-;SMN2 and intermediate Smn2B/- SMA mice. However, long-term administration of prednisolone can promote myopathy. We thus wanted to identify genes and pathways targeted by prednisolone in skeletal muscle to discover clinically approved drugs that are predicted to emulate prednisolone's activities. Using an RNA-sequencing, bioinformatics, and drug repositioning pipeline on skeletal muscle from symptomatic prednisolone-treated and untreated Smn-/-; SMN2 SMA and Smn+/-; SMN2 healthy mice, we identified molecular targets linked to prednisolone's ameliorative effects and a list of 580 drug candidates with similar predicted activities. Two of these candidates, metformin and oxandrolone, were further investigated in SMA cellular and animal models, which highlighted that these compounds do not have the same ameliorative effects on SMA phenotypes as prednisolone; however, a number of other important drug targets remain. Overall, our work further supports the usefulness of prednisolone's potential as a second-generation therapy for SMA, identifies a list of potential SMA drug treatments and highlights improvements for future transcriptomic-based drug repositioning studies in SMA.
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Affiliation(s)
- Joseph M Hoolachan
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Eve McCallion
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Emma R Sutton
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Özge Çetin
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Paloma Pacheco-Torres
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Maria Dimitriadi
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Suat Sari
- Department of Pharmaceutical Chemistry, Hacettepe University, Ankara, 06100, Turkey
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Gavin J Miller
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Centre for Glycoscience, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Magnus Okoh
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Lisa M Walter
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe, Headington Oxford, OX3 9DU, United Kingdom
| | - Daniel P Tonge
- School of Life Sciences, Huxley Building, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Melissa Bowerman
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, United Kingdom
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Pierre A, Bourel C, Favory R, Brassart B, Wallet F, Daussin FN, Normandin S, Howsam M, Romien R, Lemaire J, Grolaux G, Durand A, Frimat M, Bastide B, Amouyel P, Boulanger E, Preau S, Lancel S. Sepsis-like Energy Deficit Is Not Sufficient to Induce Early Muscle Fiber Atrophy and Mitochondrial Dysfunction in a Murine Sepsis Model. BIOLOGY 2023; 12:529. [PMID: 37106730 PMCID: PMC10136327 DOI: 10.3390/biology12040529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Sepsis-induced myopathy is characterized by muscle fiber atrophy, mitochondrial dysfunction, and worsened outcomes. Whether whole-body energy deficit participates in the early alteration of skeletal muscle metabolism has never been investigated. Three groups were studied: "Sepsis" mice, fed ad libitum with a spontaneous decrease in caloric intake (n = 17), and "Sham" mice fed ad libitum (Sham fed (SF), n = 13) or subjected to pair-feeding (Sham pair fed (SPF), n = 12). Sepsis was induced by the intraperitoneal injection of cecal slurry in resuscitated C57BL6/J mice. The feeding of the SPF mice was restricted according to the food intake of the Sepsis mice. Energy balance was evaluated by indirect calorimetry over 24 h. The tibialis anterior cross-sectional area (TA CSA), mitochondrial function (high-resolution respirometry), and mitochondrial quality control pathways (RTqPCR and Western blot) were assessed 24 h after sepsis induction. The energy balance was positive in the SF group and negative in both the SPF and Sepsis groups. The TA CSA did not differ between the SF and SPF groups, but was reduced by 17% in the Sepsis group compared with the SPF group (p < 0.05). The complex-I-linked respiration in permeabilized soleus fibers was higher in the SPF group than the SF group (p < 0.05) and lower in the Sepsis group than the SPF group (p < 0.01). Pgc1α protein expression increased 3.9-fold in the SPF mice compared with the SF mice (p < 0.05) and remained unchanged in the Sepsis mice compared with the SPF mice; the Pgc1α mRNA expression decreased in the Sepsis compared with the SPF mice (p < 0.05). Thus, the sepsis-like energy deficit did not explain the early sepsis-induced muscle fiber atrophy and mitochondrial dysfunction, but led to specific metabolic adaptations not observed in sepsis.
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Affiliation(s)
- Alexandre Pierre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Claire Bourel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Raphael Favory
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Benoit Brassart
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Frederic Wallet
- Division of Bacteriology, Biology Pathology Institute of Lille, CHU de Lille, F-59000 Lille, France
| | - Frederic N. Daussin
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d’Opale, ULR 7369-URePSSS-Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000 Lille, France
| | - Sylvain Normandin
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Michael Howsam
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
| | - Raphael Romien
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
| | - Jeremy Lemaire
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
| | - Gaelle Grolaux
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
| | - Arthur Durand
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Marie Frimat
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Nephrology, CHU de Lille, Université de Lille, F-59000 Lille, France
| | - Bruno Bastide
- Univ. Lille, Univ. Artois, Univ. Littoral Côte d’Opale, ULR 7369-URePSSS-Unité de Recherche Pluridisciplinaire Sport Santé Société, F-59000 Lille, France
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
| | - Eric Boulanger
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
| | - Sebastien Preau
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
- Division of Intensive Care, Hôpital Roger Salengro, CHU de Lille, F-59000 Lille, France
| | - Steve Lancel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, F-59000 Lille, France
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Catalani E, Zecchini S, Giovarelli M, Cherubini A, Del Quondam S, Brunetti K, Silvestri F, Roux-Biejat P, Napoli A, Casati SR, Ceci M, Romano N, Bongiorni S, Prantera G, Clementi E, Perrotta C, De Palma C, Cervia D. RACK1 is evolutionary conserved in satellite stem cell activation and adult skeletal muscle regeneration. Cell Death Dis 2022; 8:459. [PMID: 36396939 PMCID: PMC9672362 DOI: 10.1038/s41420-022-01250-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
Skeletal muscle growth and regeneration involves the activity of resident adult stem cells, namely satellite cells (SC). Despite numerous mechanisms have been described, different signals are emerging as relevant in SC homeostasis. Here we demonstrated that the Receptor for Activated C-Kinase 1 (RACK1) is important in SC function. RACK1 was expressed transiently in the skeletal muscle of post-natal mice, being abundant in the early phase of muscle growth and almost disappearing in adult mature fibers. The presence of RACK1 in interstitial SC was also detected. After acute injury in muscle of both mouse and the fruit fly Drosophila melanogaster (used as alternative in vivo model) we found that RACK1 accumulated in regenerating fibers while it declined with the progression of repair process. To note, RACK1 also localized in the active SC that populate recovering tissue. The dynamics of RACK1 levels in isolated adult SC of mice, i.e., progressively high during differentiation and low compared to proliferating conditions, and RACK1 silencing indicated that RACK1 promotes both the formation of myotubes and the accretion of nascent myotubes. In Drosophila with depleted RACK1 in all muscle cells or, specifically, in SC lineage we observed a delayed recovery of skeletal muscle after physical damage as well as the low presence of active SC in the wound area. Our results also suggest the coupling of RACK1 to muscle unfolded protein response during SC activation. Collectively, we provided the first evidence that transient levels of the evolutionarily conserved factor RACK1 are critical for adult SC activation and proper skeletal muscle regeneration, favoring the efficient progression of SC from a committed to a fully differentiated state.
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Detection of Target Genes for Drug Repurposing to Treat Skeletal Muscle Atrophy in Mice Flown in Spaceflight. Genes (Basel) 2022; 13:genes13030473. [PMID: 35328027 PMCID: PMC8953707 DOI: 10.3390/genes13030473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle atrophy is a common condition in aging, diabetes, and in long duration spaceflights due to microgravity. This article investigates multi-modal gene disease and disease drug networks via link prediction algorithms to select drugs for repurposing to treat skeletal muscle atrophy. Key target genes that cause muscle atrophy in the left and right extensor digitorum longus muscle tissue, gastrocnemius, quadriceps, and the left and right soleus muscles are detected using graph theoretic network analysis, by mining the transcriptomic datasets collected from mice flown in spaceflight made available by GeneLab. We identified the top muscle atrophy gene regulators by the Pearson correlation and Bayesian Markov blanket method. The gene disease knowledge graph was constructed using the scalable precision medicine knowledge engine. We computed node embeddings, random walk measures from the networks. Graph convolutional networks, graph neural networks, random forest, and gradient boosting methods were trained using the embeddings, network features for predicting links and ranking top gene-disease associations for skeletal muscle atrophy. Drugs were selected and a disease drug knowledge graph was constructed. Link prediction methods were applied to the disease drug networks to identify top ranked drugs for therapeutic treatment of skeletal muscle atrophy. The graph convolution network performs best in link prediction based on receiver operating characteristic curves and prediction accuracies. The key genes involved in skeletal muscle atrophy are associated with metabolic and neurodegenerative diseases. The drugs selected for repurposing using the graph convolution network method were nutrients, corticosteroids, anti-inflammatory medications, and others related to insulin.
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Miao W, Ma Z, Tang Z, Yu L, Liu S, Huang T, Wang P, Wu T, Song Z, Zhang H, Li Y, Zhou L. Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs. Front Nutr 2021; 8:742672. [PMID: 34660666 PMCID: PMC8511529 DOI: 10.3389/fnut.2021.742672] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022] Open
Abstract
Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.
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Affiliation(s)
- Weiwei Miao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zeqiang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zhanyang Tang
- Tilapia Seed Farm, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Lin Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tengda Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Peng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tian Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ziyi Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Haojie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
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9
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Fujita H, Horie M, Shimizu K, Nagamori E. Microarray profiling of gene expression in C2C12 myotubes trained by electric pulse stimulation. J Biosci Bioeng 2021; 132:417-422. [PMID: 34348874 DOI: 10.1016/j.jbiosc.2021.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
Electric pulse-stimulated C2C12 myotubes are gaining interest in the field of muscle physiology and biotechnology because electric pulse stimulation (EPS) enhances sarcomere structure development and active tension generation capability. Recently, we found that termination of EPS results in the rapid loss of active tension generation accompanied by disassembly of the sarcomere structure, which may represent an in vitro muscle atrophy model. To elucidate the molecular mechanism underlying this rapid loss of active tension generation and sarcomere structure disassembly after termination of EPS, we performed transcriptomic analysis using microarray. After termination of EPS, 74 genes were upregulated and 120 genes were downregulated after 30 min; however, atrophy-related genes were not found among these genes. To further assess the effect of EPS on gene expression, we re-applied EPS after its termination for 8 h and searched for genes whose expression was reversed. Four genes were upregulated by termination of EPS and downregulated by the re-application of EPS, whereas two genes were downregulated by termination of EPS and upregulated by the re-application of EPS. Although none of these genes were atrophy- or hypertrophy-related, the results presented in this study will contribute to the understanding of gene expression changes that mediate rapid loss of active tension generation and sarcomere structure disassembly following termination of EPS in C2C12 myotubes.
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Affiliation(s)
- Hideaki Fujita
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Masanobu Horie
- Division of Biochemical Engineering, Radioisotope Research Center, Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazunori Shimizu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Eiji Nagamori
- Department of Biomedical Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka 535-8585, Japan.
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10
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Gorza L, Sorge M, Seclì L, Brancaccio M. Master Regulators of Muscle Atrophy: Role of Costamere Components. Cells 2021; 10:cells10010061. [PMID: 33401549 PMCID: PMC7823551 DOI: 10.3390/cells10010061] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/11/2022] Open
Abstract
The loss of muscle mass and force characterizes muscle atrophy in several different conditions, which share the expression of atrogenes and the activation of their transcriptional regulators. However, attempts to antagonize muscle atrophy development in different experimental contexts by targeting contributors to the atrogene pathway showed partial effects in most cases. Other master regulators might independently contribute to muscle atrophy, as suggested by our recent evidence about the co-requirement of the muscle-specific chaperone protein melusin to inhibit unloading muscle atrophy development. Furthermore, melusin and other muscle mass regulators, such as nNOS, belong to costameres, the macromolecular complexes that connect sarcolemma to myofibrils and to the extracellular matrix, in correspondence with specific sarcomeric sites. Costameres sense a mechanical load and transduce it both as lateral force and biochemical signals. Recent evidence further broadens this classic view, by revealing the crucial participation of costameres in a sarcolemmal “signaling hub” integrating mechanical and humoral stimuli, where mechanical signals are coupled with insulin and/or insulin-like growth factor stimulation to regulate muscle mass. Therefore, this review aims to enucleate available evidence concerning the early involvement of costamere components and additional putative master regulators in the development of major types of muscle atrophy.
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Affiliation(s)
- Luisa Gorza
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy
- Correspondence:
| | - Matteo Sorge
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (M.S.); (L.S.); (M.B.)
| | - Laura Seclì
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (M.S.); (L.S.); (M.B.)
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126 Torino, Italy; (M.S.); (L.S.); (M.B.)
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11
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Hughes DC, Baehr LM, Driscoll JR, Lynch SA, Waddell DS, Bodine SC. Identification and characterization of Fbxl22, a novel skeletal muscle atrophy-promoting E3 ubiquitin ligase. Am J Physiol Cell Physiol 2020; 319:C700-C719. [PMID: 32783651 DOI: 10.1152/ajpcell.00253.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Muscle-specific E3 ubiquitin ligases have been identified in muscle atrophy-inducing conditions. The purpose of the current study was to explore the functional role of F-box and leucine-rich protein 22 (Fbxl22), and a newly identified splice variant (Fbxl22-193), in skeletal muscle homeostasis and neurogenic muscle atrophy. In mouse C2C12 muscle cells, promoter fragments of the Fbxl22 gene were cloned and fused with the secreted alkaline phosphatase reporter gene to assess the transcriptional regulation of Fbxl22. The tibialis anterior muscles of male C57/BL6 mice (12-16 wk old) were electroporated with expression plasmids containing the cDNA of two Fbxl22 splice variants and tissues collected after 7, 14, and 28 days. Gastrocnemius muscles of wild-type and muscle-specific RING finger 1 knockout (MuRF1 KO) mice were electroporated with an Fbxl22 RNAi or empty plasmid and denervated 3 days posttransfection, and tissues were collected 7 days postdenervation. The full-length gene and novel splice variant are transcriptionally induced early (after 3 days) during neurogenic muscle atrophy. In vivo overexpression of Fbxl22 isoforms in mouse skeletal muscle leads to evidence of myopathy/atrophy, suggesting that both are involved in the process of neurogenic muscle atrophy. Knockdown of Fbxl22 in the muscles of MuRF1 KO mice resulted in significant additive muscle sparing 7 days after denervation. Targeting two E3 ubiquitin ligases appears to have a strong additive effect on protecting muscle mass loss with denervation, and these findings have important implications in the development of therapeutic strategies to treat muscle atrophy.
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Affiliation(s)
- David C Hughes
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Leslie M Baehr
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Julia R Driscoll
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - Sarah A Lynch
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - David S Waddell
- Department of Biology, University of North Florida, Jacksonville, Florida
| | - Sue C Bodine
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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12
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Segalés J, Perdiguero E, Serrano AL, Sousa-Victor P, Ortet L, Jardí M, Budanov AV, Garcia-Prat L, Sandri M, Thomson DM, Karin M, Hee Lee J, Muñoz-Cánoves P. Sestrin prevents atrophy of disused and aging muscles by integrating anabolic and catabolic signals. Nat Commun 2020; 11:189. [PMID: 31929511 PMCID: PMC6955241 DOI: 10.1038/s41467-019-13832-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022] Open
Abstract
A unique property of skeletal muscle is its ability to adapt its mass to changes in activity. Inactivity, as in disuse or aging, causes atrophy, the loss of muscle mass and strength, leading to physical incapacity and poor quality of life. Here, through a combination of transcriptomics and transgenesis, we identify sestrins, a family of stress-inducible metabolic regulators, as protective factors against muscle wasting. Sestrin expression decreases during inactivity and its genetic deficiency exacerbates muscle wasting; conversely, sestrin overexpression suffices to prevent atrophy. This protection occurs through mTORC1 inhibition, which upregulates autophagy, and AKT activation, which in turn inhibits FoxO-regulated ubiquitin-proteasome-mediated proteolysis. This study reveals sestrin as a central integrator of anabolic and degradative pathways preventing muscle wasting. Since sestrin also protected muscles against aging-induced atrophy, our findings have implications for sarcopenia.
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Affiliation(s)
- Jessica Segalés
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
- Centro Nacional de Investigaciones Cardiovasculares, 28019, Madrid, Spain
| | - Eusebio Perdiguero
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
| | - Antonio L Serrano
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
| | - Pedro Sousa-Victor
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
- Instituto de Medicina Molecular (iMM), Faculdade de Medicina, Universidade de Lisboa, 1649, Lisbon, Portugal
| | - Laura Ortet
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
| | - Mercè Jardí
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
| | - Andrei V Budanov
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, D02 R590, Ireland
- Engelhardt Institute of Molecular Biology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991, Moscow, Russia
| | - Laura Garcia-Prat
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain
- Centro Nacional de Investigaciones Cardiovasculares, 28019, Madrid, Spain
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Marco Sandri
- Department of Biomedical Science, University of Padova, 35100, Padova, Italy
| | - David M Thomson
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Michael Karin
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109-2200, USA
| | - Pura Muñoz-Cánoves
- Department of Experimental & Health Sciences, University Pompeu Fabra, CIBERNED, 08003, Barcelona, Spain.
- Centro Nacional de Investigaciones Cardiovasculares, 28019, Madrid, Spain.
- ICREA, 08003, Barcelona, Spain.
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13
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Brzeszczyńska J, Meyer A, McGregor R, Schilb A, Degen S, Tadini V, Johns N, Langen R, Schols A, Glass DJ, Roubenoff R, Ross JA, Fearon KCH, Greig CA, Jacobi C. Alterations in the in vitro and in vivo regulation of muscle regeneration in healthy ageing and the influence of sarcopenia. J Cachexia Sarcopenia Muscle 2018; 9:93-105. [PMID: 29214748 PMCID: PMC5803613 DOI: 10.1002/jcsm.12252] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Sarcopenia is defined as the age-related loss of skeletal muscle mass and function. While all humans lose muscle with age, 2-5% of elderly adults develop functional consequences (disabilities). The aim of this study was to investigate muscle myogenesis in healthy elderly adults, with or without sarcopenia, compared with middle-aged controls using both in vivo and in vitro approaches to explore potential biomarker or causative molecular pathways associated with sarcopenic versus non-sarcopenic skeletal muscle phenotypes during ageing. METHODS Biomarkers of multiple molecular pathways associated with muscle regeneration were analysed using quantitative polymerase chain reaction in quadriceps muscle samples obtained from healthy elderly sarcopenic (HSE, n = 7) or non-sarcopenic (HENS, n = 21) and healthy middle-aged control (HMC, n = 22) groups. An in vitro system of myogenesis (using myoblasts from human donors aged 17-83 years) was used to mimic the environmental challenges of muscle regeneration over time. RESULTS The muscle biopsies showed evidence of satellite cell activation in HENS (Pax3, P < 0.01, Pax7, P < 0.0001) compared with HMC. Early myogenesis markers Myogenic Differentiation 1 (MyoD1) and Myogenic factor 5 (Myf5) (P < 0.0001) and the late myogenesis marker myogenin (MyoG) (P < 0.01) were increased in HENS. In addition, there was a 30-fold upregulation of TNF-α in HENS compared with HMC (P < 0.0001). The in vitro system demonstrated age-related upregulation of pro-inflammatory cytokines (2-fold upregulation of interleukin (IL)-6, IL-8 mRNA, increased secretion of tumor necrosis factor-α (TNF-α) and IL-6, all P < 0.05) associated with impaired kinetics of myotube differentiation. The HSE biopsy samples showed satellite cell activation (Pax7, P < 0.05) compared with HMC. However, no significant upregulation of the early myogenesis (MyoD and Myf5) markers was evident; only the late myogenesis marker myogenin was upregulated (P < 0.05). Higher activation of the oxidative stress pathway was found in HENS compared with the HSE group. In contrast, there was 10-fold higher upregulation of HSPA1A a stress-induced chaperone acting upon misfolded proteins in HSE compared with the HENS group. CONCLUSIONS Both pathological and adaptive processes are active in skeletal muscle during healthy ageing. Muscle regeneration pathways are activated during healthy ageing, but there is evidence of dysregulation in sarcopenia. In addition, increased cellular stress, with an impaired oxidative-stress and mis-folded protein response (HSPA1A), may be associated with the development of sarcopenia. The in vitro system of young and old myoblasts replicated some of the differences between young and old muscle.
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Affiliation(s)
- Joanna Brzeszczyńska
- Tissue Injury and Repair Group, Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.,Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, UK
| | - Angelika Meyer
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Robin McGregor
- Cardiovascular and Metabolic Disease Center, College of Medicine, Inje University, Busan, Republic of Korea
| | - Alain Schilb
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Simone Degen
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Valentina Tadini
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Neil Johns
- Tissue Injury and Repair Group, Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.,Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, UK
| | - Ramon Langen
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Annemie Schols
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - David J Glass
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ronenn Roubenoff
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James A Ross
- Tissue Injury and Repair Group, Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.,Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, UK
| | | | - Carolyn A Greig
- School of Sport, Exercise and Rehabilitation Sciences and MRC-Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Carsten Jacobi
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland and Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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14
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Brzeszczyńska J, Johns N, Schilb A, Degen S, Degen M, Langen R, Schols A, Glass DJ, Roubenoff R, Greig CA, Jacobi C, Fearon KC, Ross JA. Loss of oxidative defense and potential blockade of satellite cell maturation in the skeletal muscle of patients with cancer but not in the healthy elderly. Aging (Albany NY) 2017; 8:1690-702. [PMID: 27454226 PMCID: PMC5032690 DOI: 10.18632/aging.101006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/12/2016] [Indexed: 12/11/2022]
Abstract
Muscle wasting in old age or cancer may result from failed myofiber regeneration and/or accelerated atrophy. This study aimed to determine from transcriptomic analysis of human muscle the integrity of the cellular stress response system in relation to satellite cell differentiation or apoptosis in patients with cancer (weight-stable (CWS) or weight-losing (CWL)) or healthy elderly (HE) when compared with healthy middle-aged controls (HMA). 28 patients with cancer (CWS: 18 and CWL: 10), HE: 21 and HMA: 20 underwent biopsy of quadriceps muscle. The expression of transcription factors for muscle regeneration (Pax3, Pax7 and MyoD) was increased in CWS and HE compared with HMA (p≤0.001). In contrast, the expression of the late myogenic differentiation marker MyoG was reduced in CWS and CWL but increased in HE (p≤0.0001). Bax was significantly increased in CWS, CWL and HE (p≤0.0001). Expression of the oxidative defense genes SOD2, GCLM, and Nrf2 was decreased in CWS and CWL but increased in HE (p≤0.0001). There is evidence for blockade of satellite cell maturation, upregulation of apoptosis and reduced oxidative defense in the muscle of cancer patients. In the healthy elderly the potential for differentiation and oxidative defense is maintained.
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Affiliation(s)
- Joanna Brzeszczyńska
- Tissue Injury and Repair Group, Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, Scotland, UK
| | - Neil Johns
- Tissue Injury and Repair Group, Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, Scotland, UK
| | - Alain Schilb
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland.,Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Simone Degen
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland.,Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Martin Degen
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland.,Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ramon Langen
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Annemie Schols
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - David J Glass
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland.,Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ronenn Roubenoff
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland.,Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Carolyn A Greig
- School of Sport, Exercise and Rehabilitation Sciences and MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Carsten Jacobi
- Novartis Institutes for Biomedical Research Basel, Novartis Pharma AG, CH-4056 Basel, Switzerland.,Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Kenneth Ch Fearon
- Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, Scotland, UK
| | - James A Ross
- Tissue Injury and Repair Group, Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK.,Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, Scotland, UK
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15
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Cutler AA, Dammer EB, Doung DM, Seyfried NT, Corbett AH, Pavlath GK. Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell 2017; 16:738-749. [PMID: 28544616 PMCID: PMC5506426 DOI: 10.1111/acel.12604] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Skeletal muscle aging is accompanied by loss of muscle mass and strength. Examining changes in myonuclear proteins with age would provide insight into molecular processes which regulate these profound changes in muscle physiology. However, muscle tissue is highly adapted for contraction and thus comprised largely of contractile proteins making the nuclear proteins difficult to identify from whole muscle samples. By developing a method to purify myonuclei from whole skeletal muscle, we were able to collect myonuclei for analysis by flow cytometry, biochemistry, and mass spectrometry. Nuclear purification dramatically increased the number and intensity of nuclear proteins detected by mass spectrometry compared to whole tissue. We exploited this increased proteomic depth to investigate age-related changes to the myonuclear proteome. Nuclear levels of 54 of 779 identified proteins (7%) changed significantly with age; these proteins were primarily involved in chromatin maintenance and RNA processing. To determine whether the changes we detected were specific to myonuclei or were common to nuclei of excitatory tissues, we compared aging in myonuclei to aging in brain nuclei. Although several of the same processes were affected by aging in both brain and muscle nuclei, the specific proteins involved in these alterations differed between the two tissues. Isolating myonuclei allowed a deeper view into the myonuclear proteome than previously possible facilitating identification of novel age-related changes in skeletal muscle. Our technique will enable future studies into a heretofore underrepresented compartment of skeletal muscle.
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Affiliation(s)
- Alicia A. Cutler
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
- Graduate Program in Biochemistry, Cell and Developmental Biology; Emory University; Atlanta GA 30322 USA
| | - Eric B. Dammer
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | - Duc M. Doung
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | | | | | - Grace K. Pavlath
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
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16
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Integration of miRNA and mRNA expression profiles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia. Sci Rep 2017; 7:6998. [PMID: 28765595 PMCID: PMC5539204 DOI: 10.1038/s41598-017-07236-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/28/2017] [Indexed: 12/28/2022] Open
Abstract
Cardiac cachexia (CC) is a common complication of heart failure (HF) associated with muscle wasting and poor patient prognosis. Although different mechanisms have been proposed to explain muscle wasting during CC, its pathogenesis is still not understood. Here, we described an integrative analysis between miRNA and mRNA expression profiles of muscle wasting during CC. Global gene expression profiling identified 1,281 genes and 19 miRNAs differentially expressed in muscle wasting during CC. Several of these deregulated genes are known or putative targets of the altered miRNAs, including miR-29a-3p, miR-29b-3p, miR-210-5p, miR-214, and miR-489. Gene ontology analysis on integrative mRNA/miRNA expression profiling data revealed miRNA interactions affecting genes that regulate extra-cellular matrix (ECM) organization, proteasome protein degradation, citric acid cycle and respiratory electron transport. We further identified 11 miRNAs, including miR-29a-3p and miR-29b-3p, which target 21 transcripts encoding the collagen proteins related to ECM organization. Integrative miRNA and mRNA global expression data allowed us to identify miRNA target genes involved in skeletal muscle wasting in CC. Our functional experiments in C2C12 cells confirmed that miR-29b down-regulates collagen genes and contributes to muscle cell atrophy. Collectively, our results suggest that key ECM-associated miRNAs and their target genes may contribute to CC in HF.
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17
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Abstract
OBJECTIVE In sepsis, the disease course of critically ill patients is often complicated by muscle failure leading to ICU-acquired weakness. The myokine transforming growth factor-β1 increases during inflammation and mediates muscle atrophy in vivo. We observed that the transforming growth factor-β1 inhibitor, secreted frizzled-related protein 2, was down-regulated in skeletal muscle of ICU-acquired weakness patients. We hypothesized that secreted frizzled-related protein 2 reduction enhances transforming growth factor-β1-mediated effects and investigated the interrelationship between transforming growth factor-β1 and secreted frizzled-related protein 2 in inflammation-induced atrophy. DESIGN Observational study and prospective animal trial. SETTING Two ICUs and research laboratory. PATIENTS/SUBJECTS Twenty-six critically ill patients with Sequential Organ Failure Assessment scores greater than or equal to 8 underwent a skeletal muscle biopsy from the vastus lateralis at median day 5 in ICU. Four patients undergoing elective orthopedic surgery served as controls. To search for signaling pathways enriched in muscle of ICU-acquired weakness patients, a gene set enrichment analysis of our recently published gene expression profiles was performed. Quantitative reverse transcriptase-polymerase chain reaction, Western blot, and immunohistochemistry were used to analyze secreted frizzled-related protein 2 expression and protein content. A mouse model of inflammation-induced skeletal muscle atrophy due to polymicrobial sepsis and cultured myocytes were used for mechanistic analyses. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Gene set enrichment analysis uncovered transforming growth factor-β1 signaling activation in vastus lateralis from ICU-acquired weakness patients. Muscular secreted frizzled-related protein 2 expression was reduced after 5 days in ICU. Likewise, muscular secreted frizzled-related protein 2 expression was decreased early and continuously in mice with inflammation-induced atrophy. In muscle, secreted frizzled-related protein 2 was predominantly contained in fast twitch/type II myofibers. Secreted frizzled-related protein 2 physically interacted and colocalized with transforming growth factor-β1 through its cysteine-rich domain. Finally, secreted frizzled-related protein 2 prevented transforming growth factor-β1-induced atrophy in C2C12 myotubes. CONCLUSIONS Muscular secreted frizzled-related protein 2 is down-regulated in ICU-acquired weakness patients and mice with inflammation-induced muscle atrophy. Decreased secreted frizzled-related protein 2 possibly establishes a positive feedback loop enhancing transforming growth factor-β1-mediated atrophic effects in inflammation-induced atrophy.
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18
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GRMD cardiac and skeletal muscle metabolism gene profiles are distinct. BMC Med Genomics 2017; 10:21. [PMID: 28390424 PMCID: PMC5385041 DOI: 10.1186/s12920-017-0257-2] [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: 09/07/2016] [Accepted: 03/30/2017] [Indexed: 11/18/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, which codes for the dystrophin protein. While progress has been made in defining the molecular basis and pathogenesis of DMD, major gaps remain in understanding mechanisms that contribute to the marked delay in cardiac compared to skeletal muscle dysfunction. Methods To address this question, we analyzed cardiac and skeletal muscle tissue microarrays from golden retriever muscular dystrophy (GRMD) dogs, a genetically and clinically homologous model for DMD. A total of 15 dogs, 3 each GRMD and controls at 6 and 12 months plus 3 older (47–93 months) GRMD dogs, were assessed. Results GRMD dogs exhibited tissue- and age-specific transcriptional profiles and enriched functions in skeletal but not cardiac muscle, consistent with a “metabolic crisis” seen with DMD microarray studies. Most notably, dozens of energy production-associated molecules, including all of the TCA cycle enzymes and multiple electron transport components, were down regulated. Glycolytic and glycolysis shunt pathway-associated enzymes, such as those of the anabolic pentose phosphate pathway, were also altered, in keeping with gene expression in other forms of muscle atrophy. On the other hand, GRMD cardiac muscle genes were enriched in nucleotide metabolism and pathways that are critical for neuromuscular junction maintenance, synaptic function and conduction. Conclusions These findings suggest differential metabolic dysfunction may contribute to distinct pathological phenotypes in skeletal and cardiac muscle. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0257-2) contains supplementary material, which is available to authorized users.
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Sternopygus macrurus electric organ transcriptome and cell size exhibit insensitivity to short-term electrical inactivity. ACTA ACUST UNITED AC 2016; 110:233-244. [PMID: 27864094 DOI: 10.1016/j.jphysparis.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/03/2016] [Accepted: 11/13/2016] [Indexed: 11/22/2022]
Abstract
Electrical activity is an important regulator of cellular function and gene expression in electrically excitable cell types. In the weakly electric teleost fish Sternopygus macrurus, electrocytes, i.e., the current-producing cells of the electric organ, derive from a striated muscle lineage. Mature electrocytes are larger than muscle fibers, do not contain sarcomeres, and are driven continuously at frequencies higher than those exerted on muscle cells. Previous work showed that the removal of electrical activity by spinal cord transection (ST) for two and five weeks led to an upregulation of some sarcomeric proteins and a decrease in electrocyte size. To test whether changes in gene transcription preceded these phenotypic changes, we determined the sensitivity of electrocyte gene expression to electrical inactivity periods of two and five days after ST. Whole tissue gene expression profiles using deep RNA sequencing showed minimal alterations in the levels of myogenic transcription factor and sarcomeric transcripts after either ST period. Moreover, while analysis of differentially expressed genes showed a transient upregulation of genes associated with proteolytic mechanisms at two days and an increase in mRNA levels of cytoskeletal genes at five days after electrical silencing, electrocyte size was not affected. Electrical inactivity also resulted in the downregulation of genes that were classified into enriched clusters associated with functions of axon migration and synapse structure. Overall, these data demonstrate that unlike tissues in the myogenic lineage in other vertebrate species, regulation of gene transcription and cell size in the muscle-like electrocytes of S. macrurus is highly insensitive to short-term electrical inactivity. Moreover, together with data obtained from control and long-term ST studies, the present data suggest that neural input might influence post-transcriptional processes to affect the mature electrocyte phenotype.
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Li X, Xiao Y, Fan S, Xiao M, Wang X, Chen X, Li C, Zong G, Zhou G, Wan C. RACK1 overexpression associates with pancreatic ductal adenocarcinoma growth and poor prognosis. Exp Mol Pathol 2016; 101:176-186. [PMID: 27498047 DOI: 10.1016/j.yexmp.2016.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/24/2016] [Accepted: 08/02/2016] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The receptor for activated protein kinase C (RACK1) is a scaffold protein involved in multiple intracellular signal pathways. Previous studies have shown that RACK1 is associated with the progression of multiple cancer types, including hepatocellular carcinoma and gastric cancer. However, the role of RACK1 in human pancreatic ductal adenocarcinoma (PDAC) remains unclear. METHODS In this study, the expression of RACK1 was evaluated by Western blot analysis in 8 paired fresh PDAC tissues and immunohistochemistry on 179 paraffin-embedded slices. Then, we used Fisher exact test to analyze the correlation between RACK1 expression and clinicopathological characteristics. Starvation and re-feeding assay was used to assess cell cycle. Western blot, CCK8, flow cytometry assays, and colony formation analyses demonstrated that RACK1 played an essential role in PDAC development. Annexin-V/PI apoptotic assay and western blot showed that RACK1 was involved in regulating the apoptosis of PDAC cells. RESULTS RACK1 was highly expressed in PDAC tissues and cell lines and was significantly associated with multiple clinicopathological factors. Univariate and multivariate analyses showed that high RACK1 expression was identified to be an independent prognostic factor for PDAC patients' survival. In vitro, serum starvation-refeeding experiment suggested that RACK1 was upregulated in proliferating PDAC cells, together with the percentage of cells at the S phase, and was correlated with the expression of Cyclin D1. Moreover, Overexpression of RACK1 facilitated the proliferation and cell cycle progression of PDAC cells, while downregulation of RACK1 induced growth impairment, G1/S cell cycle arrest and apoptosis in PDAC cells. Silencing RACK1 decreased bcl-2 expression, increased cleaved caspase3 expression level and induced the apoptosis of PDAC cells. CONCLUSIONS Our results suggest that RACK1 could play an important role in the tumorigenesis of PDAC and serve as a potential therapeutical target in PDAC treatment.
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Affiliation(s)
- Xiaohong Li
- Department of General Surgey, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Ying Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China; Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, Jiangsu, China
| | - Shaoqing Fan
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Mingbing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Xiaotong Wang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Xudong Chen
- Department of Pathology, Affiliated Cancer Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Chunsun Li
- Department of Pathology, Affiliated Cancer Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Guijuan Zong
- Department of Pathology, Affiliated Cancer Hospital of Nantong University, Nantong 226001, Jiangsu, China
| | - Guoxiong Zhou
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu, China.
| | - Chunhua Wan
- Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, Jiangsu, China; Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226001, Jiangsu, China.
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21
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Ciszek BP, Khan AA, Dang H, Slade GD, Smith S, Bair E, Maixner W, Zolnoun D, Nackley AG. MicroRNA expression profiles differentiate chronic pain condition subtypes. Transl Res 2015; 166:706-720.e11. [PMID: 26166255 PMCID: PMC4656098 DOI: 10.1016/j.trsl.2015.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/21/2015] [Accepted: 06/13/2015] [Indexed: 02/07/2023]
Abstract
Chronic pain is a significant health care problem, ineffectively treated because of its unclear etiology and heterogeneous clinical presentation. Emerging evidence demonstrates that microRNAs (miRNAs) regulate the expression of pain-relevant genes, yet little is known about their role in chronic pain. Here, we evaluate the relationship among pain, psychological characteristics, plasma cytokines, and whole blood miRNAs in 22 healthy controls (HCs); 33 subjects with chronic pelvic pain (vestibulodynia, VBD); and 23 subjects with VBD and irritable bowel syndrome (VBD + IBS). VBD subjects were similar to HCs in self-reported pain, psychological profiles, and remote bodily pain. VBD + IBS subjects reported decreased health and function; and an increase in headaches, somatization, and remote bodily pain. Furthermore, VBD subjects exhibited a balance in proinflammatory and anti-inflammatory cytokines, whereas VBD + IBS subjects failed to exhibit a compensatory increase in anti-inflammatory cytokines. VBD subjects differed from controls in expression of 10 miRNAs of predicted importance for pain and estrogen signaling. VBD + IBS subjects differed from controls in expression of 11 miRNAs of predicted importance for pain, cell physiology, and insulin signaling. miRNA expression was correlated with pain-relevant phenotypes and cytokine levels. These results suggest that miRNAs represent a valuable tool for differentiating VBD subtypes (localized pain with apparent peripheral neurosensory disruption vs widespread pain with a central sensory contribution) that may require different treatment approaches.
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Affiliation(s)
- Brittney P Ciszek
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC
| | - Asma A Khan
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC
| | - Hong Dang
- Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC
| | - Gary D Slade
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC
| | - Shad Smith
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC
| | - Eric Bair
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC
| | - William Maixner
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC
| | - Denniz Zolnoun
- Pelvic Pain Center, University of North Carolina, Chapel Hill, NC
| | - Andrea G Nackley
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, NC.
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22
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Aedo JE, Maldonado J, Aballai V, Estrada JM, Bastias-Molina M, Meneses C, Gallardo-Escarate C, Silva H, Molina A, Valdés JA. mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis). BMC Genomics 2015; 16:1024. [PMID: 26626593 PMCID: PMC4667402 DOI: 10.1186/s12864-015-2232-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/19/2015] [Indexed: 01/07/2023] Open
Abstract
Background Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cortisol, each species presents specificities in the cell response and stress tolerance. Therefore, culturing new species requires a detailed knowledge of these specific responses. The red cusk-eel (Genypterus chilensis) is a new economically important marine species for the Chilean aquaculture industry. However, there is no information on the stress- and cortisol-induced mechanisms that decrease skeletal muscle growth in this teleost. Results Using Illumina RNA-seq technology, skeletal muscle sequence reads for G. chilensis were generated under control and handling stress conditions. Reads were mapped onto a reference transcriptome, resulting in the in silico identification of 785 up-regulated and 167 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of catabolic genes associated with skeletal muscle atrophy. These results were validated by RT-qPCR analysis for ten candidates genes involved in ubiquitin-mediated proteolysis, autophagy and skeletal muscle growth. Additionally, using a primary culture of fish skeletal muscle cells, the effect of cortisol was evaluated in relation to red cusk-eel skeletal muscle atrophy. Conclusions The present data demonstrated that handling stress promotes skeletal muscle atrophy in the marine teleost G. chilensis through the expression of components of the ubiquitin-proteasome and autophagy-lysosome systems. Furthermore, cortisol was a powerful inductor of skeletal muscle atrophy in fish myotubes. This study is an important step towards understanding the atrophy system in non-model teleost species and provides novel insights on the cellular and molecular mechanisms that control skeletal muscle growth in early vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2232-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge E Aedo
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Jonathan Maldonado
- Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, Universidad de Chile, Facultad de Ciencias Agronómicas, Av. Santa Rosa 11315, La Pintana, 8820808, Santiago, Chile
| | - Víctor Aballai
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Juan M Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Macarena Bastias-Molina
- Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Cristian Gallardo-Escarate
- Laboratory of Biotechnology and Aquatic Genomics, Universidad de Concepción, Concepción, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), P.O. Box 160-C, Concepción, Chile
| | - Herman Silva
- Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, Universidad de Chile, Facultad de Ciencias Agronómicas, Av. Santa Rosa 11315, La Pintana, 8820808, Santiago, Chile
| | - Alfredo Molina
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), P.O. Box 160-C, Concepción, Chile.,Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan A Valdés
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. .,Interdisciplinary Center for Aquaculture Research (INCAR), P.O. Box 160-C, Concepción, Chile. .,Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile.
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23
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Lynch CJ, Kimball SR, Xu Y, Salzberg AC, Kawasawa YI. Global deletion of BCATm increases expression of skeletal muscle genes associated with protein turnover. Physiol Genomics 2015; 47:569-80. [PMID: 26351290 DOI: 10.1152/physiolgenomics.00055.2015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/04/2015] [Indexed: 01/04/2023] Open
Abstract
Consumption of a protein-containing meal by a fasted animal promotes protein accretion in skeletal muscle, in part through leucine stimulation of protein synthesis and indirectly through repression of protein degradation mediated by its metabolite, α-ketoisocaproate. Mice lacking the mitochondrial branched-chain aminotransferase (BCATm/Bcat2), which interconverts leucine and α-ketoisocaproate, exhibit elevated protein turnover. Here, the transcriptomes of gastrocnemius muscle from BCATm knockout (KO) and wild-type mice were compared by next-generation RNA sequencing (RNA-Seq) to identify potential adaptations associated with their persistently altered nutrient signaling. Statistically significant changes in the abundance of 1,486/∼39,010 genes were identified. Bioinformatics analysis of the RNA-Seq data indicated that pathways involved in protein synthesis [eukaryotic initiation factor (eIF)-2, mammalian target of rapamycin, eIF4, and p70S6K pathways including 40S and 60S ribosomal proteins], protein breakdown (e.g., ubiquitin mediated), and muscle degeneration (apoptosis, atrophy, myopathy, and cell death) were upregulated. Also in agreement with our previous observations, the abundance of mRNAs associated with reduced body size, glycemia, plasma insulin, and lipid signaling pathways was altered in BCATm KO mice. Consistently, genes encoding anaerobic and/or oxidative metabolism of carbohydrate, fatty acids, and branched chain amino acids were modestly but systematically reduced. Although there was no indication that muscle fiber type was different between KO and wild-type mice, a difference in the abundance of mRNAs associated with a muscular dystrophy phenotype was observed, consistent with the published exercise intolerance of these mice. The results suggest transcriptional adaptations occur in BCATm KO mice that along with altered nutrient signaling may contribute to their previously reported protein turnover, metabolic and exercise phenotypes.
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Affiliation(s)
- Christopher J Lynch
- Department of Cellular and Molecular Physiology, College of Medicine, Penn State University, Hershey, Pennsylvania;
| | - Scot R Kimball
- Department of Cellular and Molecular Physiology, College of Medicine, Penn State University, Hershey, Pennsylvania
| | - Yuping Xu
- Department of Cellular and Molecular Physiology, College of Medicine, Penn State University, Hershey, Pennsylvania
| | - Anna C Salzberg
- The Institute for Personalized Medicine, College of Medicine, Penn State University, Hershey, Pennsylvania
| | - Yuka Imamura Kawasawa
- The Institute for Personalized Medicine, College of Medicine, Penn State University, Hershey, Pennsylvania; Department of Pharmacology, College of Medicine, Penn State University, Hershey, Pennsylvania; and Department of Biochemistry and Molecular Biology, College of Medicine, Penn State University, Hershey, Pennsylvania
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24
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Rea IM, Dellet M, Mills KI. Living long and ageing well: is epigenomics the missing link between nature and nurture? Biogerontology 2015; 17:33-54. [PMID: 26133292 DOI: 10.1007/s10522-015-9589-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 06/22/2015] [Indexed: 12/12/2022]
Abstract
Human longevity is a complex trait and increasingly we understand that both genes and lifestyle interact in the longevity phenotype. Non-genetic factors, including diet, physical activity, health habits, and psychosocial factors contribute approximately 50% of the variability in human lifespan with another 25% explained by genetic differences. Family clusters of nonagenarian and centenarian siblings, who show both exceptional age-span and health-span, are likely to have inherited facilitatory gene groups, but also have nine decades of life experiences and behaviours which have interacted with their genetic profiles. Identification of their shared genes is just one small step in the link from genes to their physical and psychological profiles. Behavioural genomics is beginning to demonstrate links to biological mechanisms through regulation of gene expression, which directs the proteome and influences the personal phenotype. Epigenetics has been considered the missing link between nature and nurture. Although there is much that remains to be discovered, this article will discuss some of genetic and environmental factors which appear important in good quality longevity and link known epigenetic mechanisms to themes identified by nonagenarians themselves related to their longevity. Here we suggest that exceptional 90-year old siblings have adopted a range of behaviours and life-styles which have contributed to their ageing-well-phenotype and which link with important public health messages.
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Affiliation(s)
- Irene Maeve Rea
- School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland, UK. .,School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK.
| | - Margaret Dellet
- School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland, UK.,Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast , Belfast, Northern Ireland, UK
| | - Ken I Mills
- School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland, UK.,Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, Northern Ireland, UK
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25
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Broos S, Van Leemputte M, Deldicque L, Thomis MA. History-dependent force, angular velocity and muscular endurance in ACTN3 genotypes. Eur J Appl Physiol 2015; 115:1637-43. [DOI: 10.1007/s00421-015-3144-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/24/2015] [Indexed: 10/23/2022]
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26
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Rabinovich RA, Drost E, Manning JR, Dunbar DR, Díaz-Ramos M, Lakhdar R, Bastos R, MacNee W. Genome-wide mRNA expression profiling in vastus lateralis of COPD patients with low and normal fat free mass index and healthy controls. Respir Res 2015; 16:1. [PMID: 25567521 PMCID: PMC4333166 DOI: 10.1186/s12931-014-0139-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 10/24/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) has significant systemic effects beyond the lungs amongst which muscle wasting is a prominent contributor to exercise limitation and an independent predictor of morbidity and mortality. The molecular mechanisms leading to skeletal muscle dysfunction/wasting are not fully understood and are likely to be multi-factorial. The need to develop therapeutic strategies aimed at improving skeletal muscle dysfunction/wasting requires a better understanding of the molecular mechanisms responsible for these abnormalities. Microarrays are powerful tools that allow the investigation of the expression of thousands of genes, virtually the whole genome, simultaneously. We aim at identifying genes and molecular pathways involved in skeletal muscle wasting in COPD. METHODS We assessed and compared the vastus lateralis transcriptome of COPD patients with low fat free mass index (FFMI) as a surrogate of muscle mass (COPDL) (FEV1 30 ± 3.6%pred, FFMI 15 ± 0.2 Kg.m(-2)) with patients with COPD and normal FFMI (COPDN) (FEV1 44 ± 5.8%pred, FFMI 19 ± 0.5 Kg.m(-2)) and a group of age and sex matched healthy controls (C) (FEV1 95 ± 3.9%pred, FFMI 20 ± 0.8 Kg.m(-2)) using Agilent Human Whole Genome 4x44K microarrays. The altered expression of several of these genes was confirmed by real time TaqMan PCR. Protein levels of P21 were assessed by immunoblotting. RESULTS A subset of 42 genes was differentially expressed in COPDL in comparison to both COPDN and C (PFP < 0.05; -1.5 ≥ FC ≥ 1.5). The altered expression of several of these genes was confirmed by real time TaqMan PCR and correlated with different functional and structural muscle parameters. Five of these genes (CDKN1A, GADD45A, PMP22, BEX2, CGREF1, CYR61), were associated with cell cycle arrest and growth regulation and had been previously identified in studies relating muscle wasting and ageing. Protein levels of CDKN1A, a recognized marker of premature ageing/cell cycle arrest, were also found to be increased in COPDL. CONCLUSIONS This study provides evidence of differentially expressed genes in peripheral muscle in COPD patients corresponding to relevant biological processes associated with skeletal muscle wasting and provides potential targets for future therapeutic interventions to prevent loss of muscle function and mass in COPD.
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Affiliation(s)
- Roberto A Rabinovich
- ELEGI Colt Laboratory, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, Scotland, EH16 4TJ, UK.
| | - Ellen Drost
- ELEGI Colt Laboratory, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, Scotland, EH16 4TJ, UK.
| | - Jonathan R Manning
- Centre for Cardiovascular Science, University of Edinburgh, Scotland, UK.
| | - Donald R Dunbar
- Centre for Cardiovascular Science, University of Edinburgh, Scotland, UK.
| | - MaCarmen Díaz-Ramos
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
| | - Ramzi Lakhdar
- ELEGI Colt Laboratory, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, Scotland, EH16 4TJ, UK.
| | - Ricardo Bastos
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Ciber de Enfermedades Respiratorias (CIBERES), Barcelona, Spain.
| | - William MacNee
- ELEGI Colt Laboratory, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, Scotland, EH16 4TJ, UK.
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27
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Nakao R, Yamamoto S, Yasumoto Y, Kadota K, Oishi K. Impact of denervation-induced muscle atrophy on housekeeping gene expression in mice. Muscle Nerve 2014; 51:276-81. [DOI: 10.1002/mus.24310] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2014] [Indexed: 01/30/2023]
Affiliation(s)
- Reiko Nakao
- Biological Clock Research Group, Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; Central 6, 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
| | - Saori Yamamoto
- Biological Clock Research Group, Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; Central 6, 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
| | - Yuki Yasumoto
- Biological Clock Research Group, Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; Central 6, 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
- Department of Applied Biological Science, Graduate School of Science and Technology; Tokyo University of Science; Chiba Japan
| | - Koji Kadota
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences; University of Tokyo; Tokyo Japan
| | - Katsutaka Oishi
- Biological Clock Research Group, Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; Central 6, 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
- Department of Applied Biological Science, Graduate School of Science and Technology; Tokyo University of Science; Chiba Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences; University of Tokyo; Kashiwa Chiba Japan
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28
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Fedorov VB, Goropashnaya AV, Stewart NC, Tøien Ø, Chang C, Wang H, Yan J, Showe LC, Showe MK, Barnes BM. Comparative functional genomics of adaptation to muscular disuse in hibernating mammals. Mol Ecol 2014; 23:5524-37. [PMID: 25314618 PMCID: PMC4245363 DOI: 10.1111/mec.12963] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/24/2014] [Accepted: 10/03/2014] [Indexed: 01/04/2023]
Abstract
Hibernation is an energy-saving adaptation that involves a profound suppression of physical activity that can continue for 6-8 months in highly seasonal environments. While immobility and disuse generate muscle loss in most mammalian species, in contrast, hibernating bears and ground squirrels demonstrate limited muscle atrophy over the prolonged periods of physical inactivity during winter, suggesting that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. To identify common transcriptional programmes that underlie molecular mechanisms preventing muscle loss, we conducted a large-scale gene expression screen in hind limb muscles comparing hibernating and summer-active black bears and arctic ground squirrels using custom 9600 probe cDNA microarrays. A molecular pathway analysis showed an elevated proportion of overexpressed genes involved in all stages of protein biosynthesis and ribosome biogenesis in muscle of both species during torpor of hibernation that suggests induction of translation at different hibernation states. The induction of protein biosynthesis probably contributes to attenuation of disuse muscle atrophy through the prolonged periods of immobility of hibernation. The lack of directional changes in genes of protein catabolic pathways does not support the importance of metabolic suppression for preserving muscle mass during winter. Coordinated reduction in multiple genes involved in oxidation-reduction and glucose metabolism detected in both species is consistent with metabolic suppression and lower energy demand in skeletal muscle during inactivity of hibernation.
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Affiliation(s)
- Vadim B. Fedorov
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Anna V. Goropashnaya
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Nathan C. Stewart
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Øivind Tøien
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Celia Chang
- Systems and Computational Biology Center, the Wistar Institute, Philadelphia, PA 19104, USA
| | - Haifang Wang
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Louise C. Showe
- Systems and Computational Biology Center, the Wistar Institute, Philadelphia, PA 19104, USA
| | - Michael K. Showe
- Systems and Computational Biology Center, the Wistar Institute, Philadelphia, PA 19104, USA
| | - Brian M. Barnes
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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Bollinger LM, Witczak CA, Houmard JA, Brault JJ. SMAD3 augments FoxO3-induced MuRF-1 promoter activity in a DNA-binding-dependent manner. Am J Physiol Cell Physiol 2014; 307:C278-87. [PMID: 24920680 DOI: 10.1152/ajpcell.00391.2013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Muscle-specific RING finger-1 (MuRF-1), a ubiquitin ligase and key regulator of proteasome-dependent protein degradation, is highly expressed during skeletal muscle atrophy. The transcription factor forkhead box O3 (FoxO3) induces MuRF-1 expression, but the direct role of other major atrophy-related transcription factors, such as SMAD3, is largely unknown. The goal of this study was to determine whether SMAD3 individually regulates, or with FoxO3 coordinately regulates, MuRF-1 expression. In cultured myotubes or human embryonic kidney cells, MuRF-1 mRNA content and promoter activity were increased by FoxO3 but not by SMAD3 overexpression. However, FoxO3 and SMAD3 coexpression synergistically increased MuRF-1 mRNA and promoter activity. Mutation of the SMAD-binding element (SBE) in the proximal MuRF-1 promoter or overexpression of a SMAD3 DNA-binding mutant attenuated FoxO3-dependent MuRF-1 promoter activation, showing that SMAD binding to DNA is required for optimal activation of FoxO3-induced transcription of MuRF-1. Using chromatin immunoprecipitation, SMAD3 DNA binding increased FoxO3 abundance and SBE mutation reduced FoxO3 abundance on the MuRF-1 promoter. Furthermore, SMAD3 overexpression dose-dependently increased FoxO3 protein content, and coexpression of FoxO3 and SMAD3 synergistically increased FoxO-dependent gene transcription [assessed with a FoxO response element (FRE)-driven reporter]. Collectively, these results show that SMAD3 regulates transcription of MuRF-1 by increasing FoxO3 binding at a conserved FRE-SBE motif within the proximal promoter region, and by increasing FoxO3 protein content and transcriptional activity. These data are the first to indicate that two major transcription factors regulating protein degradation, FoxO3 and SMAD3, converge to coordinately and directly regulate transcription of MuRF-1.
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Affiliation(s)
- Lance M Bollinger
- Department of Kinesiology, Human Performance Laboratory, College of Health and Human Performance, East Carolina University, Greenville, North Carolina; Department of Biochemistry and Molecular Biology, Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina; and East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina
| | - Carol A Witczak
- Department of Kinesiology, Human Performance Laboratory, College of Health and Human Performance, East Carolina University, Greenville, North Carolina; Department of Biochemistry and Molecular Biology, Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina; and East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina
| | - Joseph A Houmard
- Department of Kinesiology, Human Performance Laboratory, College of Health and Human Performance, East Carolina University, Greenville, North Carolina; East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina
| | - Jeffrey J Brault
- Department of Kinesiology, Human Performance Laboratory, College of Health and Human Performance, East Carolina University, Greenville, North Carolina; Department of Biochemistry and Molecular Biology, Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina; and East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina
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Režen T, Kovanda A, Eiken O, Mekjavic IB, Rogelj B. Expression changes in human skeletal muscle miRNAs following 10 days of bed rest in young healthy males. Acta Physiol (Oxf) 2014; 210:655-66. [PMID: 24410893 DOI: 10.1111/apha.12228] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/20/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022]
Abstract
AIM Studies in humans show global changes in mRNA and protein expression occur in human skeletal muscle during bed rest. As microRNAs are important regulators of expression, we analysed the global microRNA expression changes in human muscle following 10 days of sustained bed rest, with the rationale that miRNAs play key roles in atrophy of skeletal muscle. METHODS We analysed expression of miRNA and selected target proteins before and after 10 days of bed rest in biopsies obtained from the vastus lateralis muscle of 6 healthy males. RESULTS Fifteen of 152 miRNAs detected in human muscle tissue were differentially expressed, and all of them with exception of two were downregulated. The downregulated miRNAs include the following: miR-206, a myomir involved in function and maintenance of skeletal muscle; miR-23a, involved in insulin response and atrophy defence; and several members of the let-7 family involved in cell cycle, cell differentiation and glucose homeostasis. Predicted gene targets of these miRNAs are members of the MAPK, TNF receptor, ALK1, TGF-beta receptor and SMAD signalling pathways. All of these pathways were previously indicated to be involved in skeletal muscle response to physical inactivity. We also measured protein expression of selected miRNA targets and observed a decrease in HDAC4. CONCLUSION Our data demonstrate that miRNAs in postural muscles are affected by sustained inactivity and unloading, as induced by prolonged bed rest, and hence are potentially involved in regulation of skeletal muscle adjustments to inactivity. We also propose new miRNAs involved in regulation of biological processes in adult human muscle.
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Affiliation(s)
- T. Režen
- Biomedical Research Institute BRIS; Ljubljana Slovenia
| | - A. Kovanda
- Biomedical Research Institute BRIS; Ljubljana Slovenia
- Department of Biotechnology; Jozef Stefan Institute; Ljubljana Slovenia
| | - O. Eiken
- Department of Environmental Physiology; Swedish Aerospace Physiology Centre; Royal Institute of Technology; Stockholm Sweden
| | - I. B. Mekjavic
- Department of Automation, Biocybernetics and Robotics; Jozef Stefan Institute; Ljubljana Slovenia
| | - B. Rogelj
- Biomedical Research Institute BRIS; Ljubljana Slovenia
- Department of Biotechnology; Jozef Stefan Institute; Ljubljana Slovenia
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LIN YANG, CUI MANHUA, TENG HONG, WANG FENGWEN, YU WEI, XU TIANMIN. Silencing the receptor of activated C-kinase 1 (RACK1) suppresses tumorigenicity in epithelial ovarian cancer in vitro and in vivo. Int J Oncol 2014; 44:1252-8. [DOI: 10.3892/ijo.2014.2274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/18/2013] [Indexed: 11/05/2022] Open
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Garton F, Seto J, Quinlan K, Yang N, Houweling P, North K. α-Actinin-3 deficiency alters muscle adaptation in response to denervation and immobilization. Hum Mol Genet 2013; 23:1879-93. [DOI: 10.1093/hmg/ddt580] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Suetta C, Frandsen U, Jensen L, Jensen MM, Jespersen JG, Hvid LG, Bayer M, Petersson SJ, Schrøder HD, Andersen JL, Heinemeier KM, Aagaard P, Schjerling P, Kjaer M. Aging affects the transcriptional regulation of human skeletal muscle disuse atrophy. PLoS One 2012; 7:e51238. [PMID: 23284670 PMCID: PMC3526599 DOI: 10.1371/journal.pone.0051238] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 11/05/2012] [Indexed: 12/24/2022] Open
Abstract
Important insights concerning the molecular basis of skeletal muscle disuse-atrophy and aging related muscle loss have been obtained in cell culture and animal models, but these regulatory signaling pathways have not previously been studied in aging human muscle. In the present study, muscle atrophy was induced by immobilization in healthy old and young individuals to study the time-course and transcriptional factors underlying human skeletal muscle atrophy. The results reveal that irrespectively of age, mRNA expression levels of MuRF-1 and Atrogin-1 increased in the very initial phase (2–4 days) of human disuse-muscle atrophy along with a marked reduction in PGC-1α and PGC-1β (1–4 days) and a ∼10% decrease in myofiber size (4 days). Further, an age-specific decrease in Akt and S6 phosphorylation was observed in young muscle within the first days (1–4 days) of immobilization. In contrast, Akt phosphorylation was unchanged in old muscle after 2 days and increased after 4 days of immobilization. Further, an age-specific down-regulation of MuRF-1 and Atrogin-1 expression levels was observed following 2 weeks of immobilization, along with a slowing atrophy response in aged skeletal muscle. Neither the immediate loss of muscle mass, nor the subsequent age-differentiated signaling responses could be explained by changes in inflammatory mediators, apoptosis markers or autophagy indicators. Collectively, these findings indicate that the time-course and regulation of human skeletal muscle atrophy is age dependent, leading to an attenuated loss in aging skeletal muscle when exposed to longer periods of immobility-induced disuse.
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MESH Headings
- Adult
- Aged
- Aging/genetics
- Aging/metabolism
- Aging/pathology
- Aging/physiology
- Apoptosis/genetics
- Autophagy/genetics
- Cytokines/metabolism
- Forkhead Transcription Factors/genetics
- Heat-Shock Proteins/genetics
- Humans
- Insulin-Like Growth Factor I/metabolism
- Male
- Middle Aged
- Muscle Contraction/genetics
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle Proteins/genetics
- Muscle Strength/genetics
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscle, Skeletal/physiopathology
- Muscular Disorders, Atrophic/genetics
- Muscular Disorders, Atrophic/metabolism
- Muscular Disorders, Atrophic/pathology
- Muscular Disorders, Atrophic/physiopathology
- NF-kappa B/metabolism
- Organ Size
- Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha
- Proto-Oncogene Proteins c-akt/metabolism
- Signal Transduction/genetics
- Transcription Factors/genetics
- Transcription, Genetic/genetics
- Transcriptome
- Tripartite Motif Proteins
- Ubiquitin-Protein Ligases/genetics
- Young Adult
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Affiliation(s)
- Charlotte Suetta
- Institute of Sports Medicine and Center for Healthy Aging, University of Copenhagen, Bispebjerg Hospital, Copenhagen, Denmark.
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Genomic and proteomic profiling reveals reduced mitochondrial function and disruption of the neuromuscular junction driving rat sarcopenia. Mol Cell Biol 2012; 33:194-212. [PMID: 23109432 DOI: 10.1128/mcb.01036-12] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Molecular mechanisms underlying sarcopenia, the age-related loss of skeletal muscle mass and function, remain unclear. To identify molecular changes that correlated best with sarcopenia and might contribute to its pathogenesis, we determined global gene expression profiles in muscles of rats aged 6, 12, 18, 21, 24, and 27 months. These rats exhibit sarcopenia beginning at 21 months. Correlation of the gene expression versus muscle mass or age changes, and functional annotation analysis identified gene signatures of sarcopenia distinct from gene signatures of aging. Specifically, mitochondrial energy metabolism (e.g., tricarboxylic acid cycle and oxidative phosphorylation) pathway genes were the most downregulated and most significantly correlated with sarcopenia. Also, perturbed were genes/pathways associated with neuromuscular junction patency (providing molecular evidence of sarcopenia-related functional denervation and neuromuscular junction remodeling), protein degradation, and inflammation. Proteomic analysis of samples at 6, 18, and 27 months confirmed the depletion of mitochondrial energy metabolism proteins and neuromuscular junction proteins. Together, these findings suggest that therapeutic approaches that simultaneously stimulate mitochondrogenesis and reduce muscle proteolysis and inflammation have potential for treating sarcopenia.
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Pillon NJ, Arane K, Bilan PJ, Chiu TT, Klip A. Muscle cells challenged with saturated fatty acids mount an autonomous inflammatory response that activates macrophages. Cell Commun Signal 2012; 10:30. [PMID: 23078640 PMCID: PMC3507850 DOI: 10.1186/1478-811x-10-30] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/16/2012] [Indexed: 12/11/2022] Open
Abstract
Obesity is associated with chronic low-grade inflammation. Within adipose tissue of mice fed a high fat diet, resident and infiltrating macrophages assume a pro-inflammatory phenotype characterized by the production of cytokines which in turn impact on the surrounding tissue. However, inflammation is not restricted to adipose tissue and high fat-feeding is responsible for a significant increase in pro-inflammatory cytokine expression in muscle. Although skeletal muscle is the major disposer of dietary glucose and a major determinant of glycemia, the origin and consequence of muscle inflammation in the development of insulin resistance are poorly understood. We used a cell culture approach to investigate the vectorial crosstalk between muscle cells and macrophages upon exposure to physiological, low levels of saturated and unsaturated fatty acids. Inflammatory pathway activation and cytokine expression were analyzed in L6 muscle cells expressing myc-tagged GLUT4 (L6GLUT4myc) exposed to 0.2 mM palmitate or palmitoleate. Conditioned media thereof, free of fatty acids, were then tested for their ability to activate RAW264.7 macrophages. Palmitate -but not palmitoleate- induced IL-6, TNFα and CCL2 expression in muscle cells, through activation of the NF-κB pathway. Palmitate (0.2 mM) alone did not induce insulin resistance in muscle cells, yet conditioned media from palmitate-challenged muscle cells selectively activated macrophages towards a pro-inflammatory phenotype. These results demonstrate that low concentrations of palmitate activate autonomous inflammation in muscle cells to release factors that turn macrophages pro-inflammatory. We hypothesize that saturated fat-induced, low-grade muscle cell inflammation may trigger resident skeletal muscle macrophage polarization, possibly contributing to insulin resistance in vivo.
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Affiliation(s)
- Nicolas J Pillon
- Program in Cell Biology, The Hospital for Sick Children,Toronto, Ontario, M5G 1X8, Canada.
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Abstract
We propose that the well-documented therapeutic actions of repeated physical activities over human lifespan are mediated by the rapidly turning over proto-oncogenic Myc (myelocytomatosis) network of transcription factors. This transcription factor network is unique in utilizing promoter and epigenomic (acetylation/deacetylation, methylation/demethylation) mechanisms for controlling genes that include those encoding intermediary metabolism (the primary source of acetyl groups), mitochondrial functions and biogenesis, and coupling their expression with regulation of cell growth and proliferation. We further propose that remote functioning of the network occurs because there are two arms of this network, which consists of driver cells (e.g., working myocytes) that metabolize carbohydrates, fats, proteins, and oxygen and produce redox-modulating metabolites such as H₂O₂, NAD⁺, and lactate. The exercise-induced products represent autocrine, paracrine, or endocrine signals for target recipient cells (e.g., aortic endothelium, hepatocytes, and pancreatic β-cells) in which the metabolic signals are coupled with genomic networks and interorgan signaling is activated. And finally, we propose that lactate, the major metabolite released from working muscles and transported into recipient cells, links the two arms of the signaling pathway. Recently discovered contributions of the Myc network in stem cell development and maintenance further suggest that regular physical activity may prevent age-related diseases such as cardiovascular pathologies, cancers, diabetes, and neurological functions through prevention of stem cell dysfunctions and depletion with aging. Hence, regular physical activities may attenuate the various deleterious effects of the Myc network on health, the wild side of the Myc-network, through modulating transcription of genes associated with glucose and energy metabolism and maintain a healthy human status.
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Affiliation(s)
- Kishorchandra Gohil
- Exercise Physiology Laboratory, Dept. of Integrative Biology, University of California, Berkeley, CA 94720, USA
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37
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Shi S, Deng YZ, Zhao JS, Ji XD, Shi J, Feng YX, Li G, Li JJ, Zhu D, Koeffler HP, Zhao Y, Xie D. RACK1 promotes non-small-cell lung cancer tumorigenicity through activating sonic hedgehog signaling pathway. J Biol Chem 2012; 287:7845-58. [PMID: 22262830 DOI: 10.1074/jbc.m111.315416] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) is a deadly disease due to lack of effective diagnosis biomarker and therapeutic target. Much effort has been made in defining gene defects in NSCLC, but its full molecular pathogenesis remains unexplored. Here, we found RACK1 (receptor of activated kinase 1) was elevated in most NSCLC, and its expression level correlated with key pathological characteristics including tumor differentiation, stage, and metastasis. In addition, RACK1 activated sonic hedgehog signaling pathway by interacting with and activating Smoothened to mediate Gli1-dependent transcription in NSCLC cells. And silencing RACK1 dramatically inhibited in vivo tumor growth and metastasis by blocking the sonic hedgehog signaling pathway. These results suggest that RACK1 represents a new promising diagnosis biomarker and therapeutic target for NSCLC.
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Affiliation(s)
- Shuo Shi
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, Shanghai 200031, China
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Llano-Diez M, Gustafson AM, Olsson C, Goransson H, Larsson L. Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model. BMC Genomics 2011; 12:602. [PMID: 22165895 PMCID: PMC3266306 DOI: 10.1186/1471-2164-12-602] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 12/13/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Acute quadriplegic myopathy (AQM) or critical illness myopathy (CIM) is frequently observed in intensive care unit (ICU) patients. To elucidate duration-dependent effects of the ICU intervention on molecular and functional networks that control the muscle wasting and weakness associated with AQM, a gene expression profile was analyzed at time points varying from 6 hours to 14 days in a unique experimental rat model mimicking ICU conditions, i.e., post-synaptically paralyzed, mechanically ventilated and extensively monitored animals. RESULTS During the observation period, 1583 genes were significantly up- or down-regulated by factors of two or greater. A significant temporal gene expression pattern was constructed at short (6 h-4 days), intermediate (5-8 days) and long (9-14 days) durations. A striking early and maintained up-regulation (6 h-14d) of muscle atrogenes (muscle ring-finger 1/tripartite motif-containing 63 and F-box protein 32/atrogin-1) was observed, followed by an up-regulation of the proteolytic systems at intermediate and long durations (5-14d). Oxidative stress response genes and genes that take part in amino acid catabolism, cell cycle arrest, apoptosis, muscle development, and protein synthesis together with myogenic factors were significantly up-regulated from 5 to 14 days. At 9-14 d, genes involved in immune response and the caspase cascade were up-regulated. At 5-14d, genes related to contractile (myosin heavy chain and myosin binding protein C), regulatory (troponin, tropomyosin), developmental, caveolin-3, extracellular matrix, glycolysis/gluconeogenesis, cytoskeleton/sarcomere regulation and mitochondrial proteins were down-regulated. An activation of genes related to muscle growth and new muscle fiber formation (increase of myogenic factors and JunB and down-regulation of myostatin) and up-regulation of genes that code protein synthesis and translation factors were found from 5 to 14 days. CONCLUSIONS Novel temporal patterns of gene expression have been uncovered, suggesting a unique, coordinated and highly complex mechanism underlying the muscle wasting associated with AQM in ICU patients and providing new target genes and avenues for intervention studies.
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Affiliation(s)
- Monica Llano-Diez
- Department of Clinical Neurophysiology, Uppsala University, Uppsala, Sweden
| | | | - Carl Olsson
- Department of Clinical Neurophysiology, Uppsala University, Uppsala, Sweden
| | - Hanna Goransson
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Lars Larsson
- Department of Clinical Neurophysiology, Uppsala University, Uppsala, Sweden
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Zhou YW, Munoz J, Jiang D, Jarrett HW. Laminin-α1 LG4-5 domain binding to dystroglycan mediates muscle cell survival, growth, and the AP-1 and NF-κB transcription factors but also has adverse effects. Am J Physiol Cell Physiol 2011; 302:C902-14. [PMID: 22159078 DOI: 10.1152/ajpcell.00118.2011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In our previous studies, we showed laminin binds α-dystroglycan in the dystrophin glycoprotein complex and initiates cell signaling pathways. Here, differentiated C2C12 myocytes serve as a model of skeletal muscle. C2C12 cells have a biphasic response to the laminin-α(1) laminin globular (LG) 4-5 domains (1E3) dependent on the concentration used; at low concentrations of 1E3 (<1 μg/ml), myoblast proliferation is increased while higher concentrations (>1 μg/ml) cause apoptosis in myoblasts and differentiated myotubes. This alters the activation of the transcription factors activator protein-1 (AP-1) and NF-κB via laminin-dystrophin glycoprotein complex (DGC)-src-grb2-sos1-Rac1-Pak1-c-jun N-terminal kinase (JNK)p46 and laminin-DGC-Gβγ-phosphatidylinositol 3-kinase (PI3K)-Akt pathways, respectively. A specific antibody against Ser(63) phosphorylated c-jun completely blocks or supershifts the AP-1-DNA binding resulting from laminin binding but only partially blocks or supershifts the AP-1-DNA binding resulting from 1E3. This suggests that AP-1 contains phosphorylated c-jun in the presence of hololaminin but contains a different composition in the presence of 1E3. Nuclear NF-κB was only upregulated by a low concentration of 1E3 and is then diminished by a higher concentration; it also has a biphasic response. Nuclear localization of NF-κB is affected by PI3K/Akt signaling, and DGC associated PI3K activity also shows a biphasic response to 1E3. Furthermore, our data suggest that activation of c-jun N-terminal kinase participates in the cell survival pathway and suggest that NF-κB is involved in both survival and cell death. A model is presented which incorporates these observations.
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Affiliation(s)
- Yan Wen Zhou
- Department of Chemistry, University of Texas, San Antonio, USA
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Adams DR, Ron D, Kiely PA. RACK1, A multifaceted scaffolding protein: Structure and function. Cell Commun Signal 2011; 9:22. [PMID: 21978545 PMCID: PMC3195729 DOI: 10.1186/1478-811x-9-22] [Citation(s) in RCA: 333] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/06/2011] [Indexed: 12/17/2022] Open
Abstract
The Receptor for Activated C Kinase 1 (RACK1) is a member of the tryptophan-aspartate repeat (WD-repeat) family of proteins and shares significant homology to the β subunit of G-proteins (Gβ). RACK1 adopts a seven-bladed β-propeller structure which facilitates protein binding. RACK1 has a significant role to play in shuttling proteins around the cell, anchoring proteins at particular locations and in stabilising protein activity. It interacts with the ribosomal machinery, with several cell surface receptors and with proteins in the nucleus. As a result, RACK1 is a key mediator of various pathways and contributes to numerous aspects of cellular function. Here, we discuss RACK1 gene and structure and its role in specific signaling pathways, and address how posttranslational modifications facilitate subcellular location and translocation of RACK1. This review condenses several recent studies suggesting a role for RACK1 in physiological processes such as development, cell migration, central nervous system (CN) function and circadian rhythm as well as reviewing the role of RACK1 in disease.
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Affiliation(s)
- David R Adams
- Department of Life Sciences, and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland.
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41
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Parasitic infections and myositis. Parasitol Res 2011; 110:1-18. [PMID: 21881948 DOI: 10.1007/s00436-011-2609-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 08/04/2011] [Indexed: 12/20/2022]
Abstract
Infectious myositis may be caused by a wide variety of bacterial, fungal, viral, and parasitic agents. Parasitic myositis is most commonly a result of trichinosis, cystericercosis, or toxoplasmosis, but other parasites may be involved. A parasitic cause of myositis is suggested by history of residence or travel to endemic area and presence of eosinophilia. The diagnosis of parasitic myositis is suggested by the clinical picture and radiologic imaging, and the etiologic agent is confirmed by parasitologic, serologic, and molecular methods, together with histopathologic examination of tissue biopsies. Therapy is based on the clinical presentation and the underlying pathogen. Drug resistance should be put into consideration in different geographic areas, and it can be avoided through the proper use of anti-parasitic drugs.
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Sylvius N, Bonne G, Straatman K, Reddy T, Gant TW, Shackleton S. MicroRNA expression profiling in patients with lamin A/C‐associated muscular dystrophy. FASEB J 2011; 25:3966-78. [DOI: 10.1096/fj.11-182915] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nicolas Sylvius
- Department of BiochemistryUniversity of Leicester Leicester UK
| | - Gise'le Bonne
- Institut National de la Santé et de la Recherche Médicale, U974 Paris France
- Université Pierre et Marie Curie‐Paris 6, UM 76Centre National de la Recherche Scientifique, UMR7215, Institut de Myologie, IFR14 Paris France
- Assistance Publique‐Hôpitaux de Paris, Groupe Hospitalier Pitié‐Salpêtrie're, U.F. Cardiogénétique et MyogénétiqueService de Biochimie Métabolique Paris France
| | - Kees Straatman
- Centre for Core Biotechnology ServicesUniversity of Leicester Leicester UK
| | - Thimma Reddy
- Department of BiochemistryUniversity of Leicester Leicester UK
| | | | - Sue Shackleton
- Department of BiochemistryUniversity of Leicester Leicester UK
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Martini P, Risso D, Sales G, Romualdi C, Lanfranchi G, Cagnin S. Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. BMC Bioinformatics 2011; 12:92. [PMID: 21481242 PMCID: PMC3094239 DOI: 10.1186/1471-2105-12-92] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 04/11/2011] [Indexed: 01/21/2023] Open
Abstract
Background In the last decades, microarray technology has spread, leading to a dramatic increase of publicly available datasets. The first statistical tools developed were focused on the identification of significant differentially expressed genes. Later, researchers moved toward the systematic integration of gene expression profiles with additional biological information, such as chromosomal location, ontological annotations or sequence features. The analysis of gene expression linked to physical location of genes on chromosomes allows the identification of transcriptionally imbalanced regions, while, Gene Set Analysis focuses on the detection of coordinated changes in transcriptional levels among sets of biologically related genes. In this field, meta-analysis offers the possibility to compare different studies, addressing the same biological question to fully exploit public gene expression datasets. Results We describe STEPath, a method that starts from gene expression profiles and integrates the analysis of imbalanced region as an a priori step before performing gene set analysis. The application of STEPath in individual studies produced gene set scores weighted by chromosomal activation. As a final step, we propose a way to compare these scores across different studies (meta-analysis) on related biological issues. One complication with meta-analysis is batch effects, which occur because molecular measurements are affected by laboratory conditions, reagent lots and personnel differences. Major problems occur when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. We evaluated the power of combining chromosome mapping and gene set enrichment analysis, performing the analysis on a dataset of leukaemia (example of individual study) and on a dataset of skeletal muscle diseases (meta-analysis approach). In leukaemia, we identified the Hox gene set, a gene set closely related to the pathology that other algorithms of gene set analysis do not identify, while the meta-analysis approach on muscular disease discriminates between related pathologies and correlates similar ones from different studies. Conclusions STEPath is a new method that integrates gene expression profiles, genomic co-expressed regions and the information about the biological function of genes. The usage of the STEPath-computed gene set scores overcomes batch effects in the meta-analysis approaches allowing the direct comparison of different pathologies and different studies on a gene set activation level.
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Affiliation(s)
- Paolo Martini
- CRIBI Biotechnology Centre, Department of Biology, University of Padova, via U, Bassi 58/B, 35121 Padova, Italy
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Baron D, Dubois E, Bihouée A, Teusan R, Steenman M, Jourdon P, Magot A, Péréon Y, Veitia R, Savagner F, Ramstein G, Houlgatte R. Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. BMC Genomics 2011; 12:113. [PMID: 21324190 PMCID: PMC3049149 DOI: 10.1186/1471-2164-12-113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 02/16/2011] [Indexed: 12/12/2022] Open
Abstract
Background DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and combine data across multiple studies. Meta-analysis of transcriptome data is a valuable method to achieve it. It enables to highlight conserved gene signatures between multiple independent studies. However, using it is made difficult by the diversity of the available data: different microarray platforms, different gene nomenclature, different species studied, etc. Description We have developed a system tool dedicated to muscle transcriptome data. This system comprises a collection of microarray data as well as a query tool. This latter allows the user to extract similar clusters of co-expressed genes from the database, using an input gene list. Common and relevant gene signatures can thus be searched more easily. The dedicated database consists in a large compendium of public data (more than 500 data sets) related to muscle (skeletal and heart). These studies included seven different animal species from invertebrates (Drosophila melanogaster, Caenorhabditis elegans) and vertebrates (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus). After a renormalization step, clusters of co-expressed genes were identified in each dataset. The lists of co-expressed genes were annotated using a unified re-annotation procedure. These gene lists were compared to find significant overlaps between studies. Conclusions Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified. Focusing on a specific pathology (Duchenne Muscular Dystrophy) we validated results across independent studies and revealed robust biomarkers and new pathways of interest. The meta-analyses performed with MADMuscle show the usefulness of this approach. Our method can be applied to all public transcriptome data.
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Long KK, Montano M, Pavlath GK. Sca-1 is negatively regulated by TGF-beta1 in myogenic cells. FASEB J 2010; 25:1156-65. [PMID: 21156809 DOI: 10.1096/fj.10-170308] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sca-1 (stem cell antigen-1) is a member of the Ly-6 family of proteins and regulates cell proliferation, differentiation, and self-renewal in multiple tissues. In skeletal muscle, Sca-1 inhibits both proliferation and differentiation of myogenic cells. Sca-1 expression is dynamically regulated during muscle regeneration, and mice lacking Sca-1 display increased fibrosis following muscle injury. Here, we show that Sca-1 expression is negatively regulated by TGF-β1 and that this inhibition is dependent on Smad3. We demonstrate that levels of TGF-β1 in skeletal muscle rapidly increase on injury and that the majority of this TGFβ1 is produced by infiltrating macrophages. Sca-1 is expressed in multiple cell types, and we demonstrate that TGF-β1 represses Sca-1 expression in T cells and other immune cell populations derived from the spleen, indicating that regulation by TGF-β1 is a general feature of Sca-1 expression in multiple cell types. Elucidation of the mechanisms by which Sca-1 expression is regulated may aid in the understanding of muscle homeostasis, potentially identifying novel therapeutic targets for muscle diseases.
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Affiliation(s)
- Kimberly K Long
- Department of Infectious Diseases, Boston Medical Center, Boston, Massachusetts, USA
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Trollet C, Anvar SY, Venema A, Hargreaves IP, Foster K, Vignaud A, Ferry A, Negroni E, Hourde C, Baraibar MA, 't Hoen PAC, Davies JE, Rubinsztein DC, Heales SJ, Mouly V, van der Maarel SM, Butler-Browne G, Raz V, Dickson G. Molecular and phenotypic characterization of a mouse model of oculopharyngeal muscular dystrophy reveals severe muscular atrophy restricted to fast glycolytic fibres. Hum Mol Genet 2010; 19:2191-207. [PMID: 20207626 DOI: 10.1093/hmg/ddq098] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by ptosis, dysphagia and proximal limb weakness. Autosomal-dominant OPMD is caused by a short (GCG)(8-13) expansions within the first exon of the poly(A)-binding protein nuclear 1 gene (PABPN1), leading to an expanded polyalanine tract in the mutated protein. Expanded PABPN1 forms insoluble aggregates in the nuclei of skeletal muscle fibres. In order to gain insight into the different physiological processes affected in OPMD muscles, we have used a transgenic mouse model of OPMD (A17.1) and performed transcriptomic studies combined with a detailed phenotypic characterization of this model at three time points. The transcriptomic analysis revealed a massive gene deregulation in the A17.1 mice, among which we identified a significant deregulation of pathways associated with muscle atrophy. Using a mathematical model for progression, we have identified that one-third of the progressive genes were also associated with muscle atrophy. Functional and histological analysis of the skeletal muscle of this mouse model confirmed a severe and progressive muscular atrophy associated with a reduction in muscle strength. Moreover, muscle atrophy in the A17.1 mice was restricted to fast glycolytic fibres, containing a large number of intranuclear inclusions (INIs). The soleus muscle and, in particular, oxidative fibres were spared, even though they contained INIs albeit to a lesser degree. These results demonstrate a fibre-type specificity of muscle atrophy in this OPMD model. This study improves our understanding of the biological pathways modified in OPMD to identify potential biomarkers and new therapeutic targets.
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Cavalieri D, Calura E, Romualdi C, Marchi E, Radonjic M, Van Ommen B, Müller M. Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis. BMC Genomics 2009; 10:596. [PMID: 20003344 PMCID: PMC2801700 DOI: 10.1186/1471-2164-10-596] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 12/11/2009] [Indexed: 12/28/2022] Open
Abstract
Background The application of high-throughput genomic tools in nutrition research is a widespread practice. However, it is becoming increasingly clear that the outcome of individual expression studies is insufficient for the comprehensive understanding of such a complex field. Currently, the availability of the large amounts of expression data in public repositories has opened up new challenges on microarray data analyses. We have focused on PPARα, a ligand-activated transcription factor functioning as fatty acid sensor controlling the gene expression regulation of a large set of genes in various metabolic organs such as liver, small intestine or heart. The function of PPARα is strictly connected to the function of its target genes and, although many of these have already been identified, major elements of its physiological function remain to be uncovered. To further investigate the function of PPARα, we have applied a cross-species meta-analysis approach to integrate sixteen microarray datasets studying high fat diet and PPARα signal perturbations in different organisms. Results We identified 164 genes (MDEGs) that were differentially expressed in a constant way in response to a high fat diet or to perturbations in PPARs signalling. In particular, we found five genes in yeast which were highly conserved and homologous of PPARα targets in mammals, potential candidates to be used as models for the equivalent mammalian genes. Moreover, a screening of the MDEGs for all known transcription factor binding sites and the comparison with a human genome-wide screening of Peroxisome Proliferating Response Elements (PPRE), enabled us to identify, 20 new potential candidate genes that show, both binding site, both change in expression in the condition studied. Lastly, we found a non random localization of the differentially expressed genes in the genome. Conclusion The results presented are potentially of great interest to resume the currently available expression data, exploiting the power of in silico analysis filtered by evolutionary conservation. The analysis enabled us to indicate potential gene candidates that could fill in the gaps with regards to the signalling of PPARα and, moreover, the non-random localization of the differentially expressed genes in the genome, suggest that epigenetic mechanisms are of importance in the regulation of the transcription operated by PPARα.
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Affiliation(s)
- Duccio Cavalieri
- Department of Pharmacology, University of Firenze, Firenze, Italy.
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Silva-Almeida M, Carvalho LOP, Abreu-Silva AL, d'Escoffier LN, Calabrese KS. Leishsmania (Leishmania) amazonensis infection: Muscular involvement in BALB/c and C3H.HeN mice. Exp Parasitol 2009; 124:315-8. [PMID: 19944691 DOI: 10.1016/j.exppara.2009.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 11/10/2009] [Accepted: 11/17/2009] [Indexed: 01/04/2023]
Abstract
Recent studies have provided some insights into Leishsmania (Leishmania) amazonensis muscular infection in dogs, although, muscular disease due to leishmaniasis has been poorly documented. The aim of our study was to evaluate involvement of Leishmania in muscular infection of two distinct mouse strains (BALB/c and C3H.He), with different genetic backgrounds. BALB/c mice, susceptible to Leishmania infection, showed, at the beginning of infection, a great number of infected macrophages among muscle fibers; however, in C3H.He resistant mice, muscle fibers were less damaged than in BALB/c mice, but some parasitized macrophages could be seen among them. A follow up of the infection showed an intense inflammatory infiltrate mainly composed of infected macrophages in BALB/c muscles and the presence of amastigotes within muscle fibers; while C3H.He mice exhibited a moderate inflammatory infiltrate among skeletal muscle fibers and an absence of amastigotes. Total destruction of muscles was observed in BALB/c mice in the late phase of infection (day 90) while C3H.He mice showed a process of muscle repair. We concluded that: (1) the muscles of BALB/c mice were more affected by leishmaniasis than those of C3/H.He mice; (2) Leishmania amastigotes are capable of infecting muscular fibers, as observed in BALB/c mice; (3) as inflammatory infiltrate is less intense in C3H.He mice these animals are capable of restoring muscular fibers.
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Affiliation(s)
- M Silva-Almeida
- Laboratório de Imunomodulação e Protozoologia do Instituto Oswaldo Cruz/FIOCRUZ, Pavilhão Carlos Chagas, 3 degrees andar, Av. Brasil, 4365, Manguinhos, CEP 20045-900, Rio de Janeiro, Brazil
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Salem M, Kenney PB, Rexroad CE, Yao J. Proteomic signature of muscle atrophy in rainbow trout. J Proteomics 2009; 73:778-89. [PMID: 19903543 DOI: 10.1016/j.jprot.2009.10.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/13/2009] [Accepted: 10/31/2009] [Indexed: 02/06/2023]
Abstract
Muscle deterioration arises as a physiological response to elevated energetic demands of fish during sexual maturation and spawning. Previously, we used this model to characterize the transcriptomic mechanisms associated with fish muscle degradation and identified potential biological markers of muscle growth and quality. However, transcriptional measurements do not necessarily reflect changes in active mature proteins. Here we report the characterization of proteomic profile in degenerating muscle of rainbow trout in relation to the female reproductive cycle using a LC/MS-based label-free protein quantification method. A total of 146 significantly changed proteins in atrophying muscles (FDR <5%) was identified. Proteins were clustered according to their gene ontology identifiers. Muscle atrophy was associated with decreased abundance in proteins of anaerobic respiration, protein biosynthesis, monooxygenases, follistatins, and myogenin, as well as growth hormone, interleukin-1 and estrogen receptors. In contrast, proteins of MAPK/ERK kinase, glutamine synthetase, transcription factors, Stat3, JunB, Id2, and NFkappaB inhibitor, were greater in atrophying muscle. These changes are discussed in light of the mammalian muscle atrophy paradigm and proposed fish-specific mechanisms of muscle degradation. These data will help identify genes associated with muscle degeneration and superior flesh quality in rainbow trout, facilitating identification of genetic markers for muscle growth and quality.
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Affiliation(s)
- Mohamed Salem
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, United States
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Baqai FP, Gridley DS, Slater JM, Luo-Owen X, Stodieck LS, Ferguson V, Chapes SK, Pecaut MJ. Effects of spaceflight on innate immune function and antioxidant gene expression. J Appl Physiol (1985) 2009; 106:1935-42. [PMID: 19342437 DOI: 10.1152/japplphysiol.91361.2008] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Spaceflight conditions have a significant impact on a number of physiological functions due to psychological stress, radiation, and reduced gravity. To explore the effect of the flight environment on immunity, C57BL/6NTac mice were flown on a 13-day space shuttle mission (STS-118). In response to flight, animals had a reduction in liver, spleen, and thymus masses compared with ground (GRD) controls (P < 0.005). Splenic lymphocyte, monocyte/macrophage, and granulocyte counts were significantly reduced in the flight (FLT) mice (P < 0.05). Although spontaneous blastogenesis of splenocytes in FLT mice was increased, response to lipopolysaccharide (LPS), a B-cell mitogen derived from Escherichia coli, was decreased compared with GRD mice (P < 0.05). Secretion of IL-6 and IL-10, but not TNF-alpha, by LPS-stimulated splenocytes was increased in FLT mice (P < 0.05). Finally, many of the genes responsible for scavenging reactive oxygen species were upregulated after flight. These data indicate that exposure to the spaceflight environment can increase anti-inflammatory mechanisms and change the ex vivo response to LPS, a bacterial product associated with septic shock and a prominent Th1 response.
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Affiliation(s)
- Farnaz P Baqai
- Department of Radiation Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
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