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Gao Y, Feng C, Ma J, Yan Q. Protein arginine methyltransferases (PRMTs): Orchestrators of cancer pathogenesis, immunotherapy dynamics, and drug resistance. Biochem Pharmacol 2024; 221:116048. [PMID: 38346542 DOI: 10.1016/j.bcp.2024.116048] [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: 11/27/2023] [Revised: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Protein Arginine Methyltransferases (PRMTs) are a family of enzymes regulating protein arginine methylation, which is a post-translational modification crucial for various cellular processes. Recent studies have highlighted the mechanistic role of PRMTs in cancer pathogenesis, immunotherapy, and drug resistance. PRMTs are involved in diverse oncogenic processes, including cell proliferation, apoptosis, and metastasis. They exert their effects by methylation of histones, transcription factors, and other regulatory proteins, resulting in altered gene expression patterns. PRMT-mediated histone methylation can lead to aberrant chromatin remodeling and epigenetic changes that drive oncogenesis. Additionally, PRMTs can directly interact with key signaling pathways involved in cancer progression, such as the PI3K/Akt and MAPK pathways, thereby modulating cell survival and proliferation. In the context of cancer immunotherapy, PRMTs have emerged as critical regulators of immune responses. They modulate immune checkpoint molecules, including programmed cell death protein 1 (PD-1), through arginine methylation. Drug resistance is a significant challenge in cancer treatment, and PRMTs have been implicated in this phenomenon. PRMTs can contribute to drug resistance through multiple mechanisms, including the epigenetic regulation of drug efflux pumps, altered DNA damage repair, and modulation of cell survival pathways. In conclusion, PRMTs play critical roles in cancer pathogenesis, immunotherapy, and drug resistance. In this overview, we have endeavored to illuminate the mechanistic intricacies of PRMT-mediated processes. Shedding light on these aspects will offer valuable insights into the fundamental biology of cancer and establish PRMTs as promising therapeutic targets.
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Affiliation(s)
- Yihang Gao
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China
| | - Chongchong Feng
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China.
| | - Jingru Ma
- Department of Laboratory Medicine, the Second Hospital of Jilin University, Changchun 130000, China
| | - Qingzhu Yan
- Department of Ultrasound Medicine, the Second Hospital of Jilin University, Changchun 130000, China
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2
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Chen T, Liu J, Li S, Wang P, Shang G. The role of protein arginine N-methyltransferases in inflammation. Semin Cell Dev Biol 2024; 154:208-214. [PMID: 36075843 DOI: 10.1016/j.semcdb.2022.08.005] [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: 08/13/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
Protein arginine methyltransferases (PRMTs) promote the methylation of numerous proteins at their arginine residues. An increasing number of publications have suggested that dysregulation of PRMTs participates in various human diseases, such as cardiovascular diseases, cancer, diabetes and neurodegenerative disorders. Inflammation is one normal response to infection or injury by immune system, which can keep body homeostasis. Emerging data reveal that inflammation is associated with the development of numerous diseases. Moreover, accumulated evidence proves that PRMTs have been characterized to regulate inflammation in various diseases. In this review article, we delineate the function and molecular mechanism of PRMTs in regulation of inflammation in current literature. Moreover, we discuss that targeting PRMTs by its inhibitors and compounds could have therapeutic potential.
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Affiliation(s)
- Ting Chen
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jinxin Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Shizhe Li
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Peter Wang
- Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Anhui 233030, China.
| | - Guanning Shang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
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3
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Kim KH, Oprescu SN, Snyder MM, Kim A, Jia Z, Yue F, Kuang S. PRMT5 mediates FoxO1 methylation and subcellular localization to regulate lipophagy in myogenic progenitors. Cell Rep 2023; 42:113329. [PMID: 37883229 PMCID: PMC10727913 DOI: 10.1016/j.celrep.2023.113329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/29/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
Development is regulated by various factors, including protein methylation status. While PRMT5 is well known for its roles in oncogenesis by mediating symmetric di-methylation of arginine, its role in normal development remains elusive. Using Myod1Cre to drive Prmt5 knockout in embryonic myoblasts (Prmt5MKO), we dissected the role of PRMT5 in myogenesis. The Prmt5MKO mice are born normally but exhibit progressive muscle atrophy and premature death. Prmt5MKO inhibits proliferation and promotes premature differentiation of embryonic myoblasts, reducing the number and regenerative function of satellite cells in postnatal mice. Mechanistically, PRMT5 methylates and destabilizes FoxO1. Prmt5MKO increases the total FoxO1 level and promotes its cytoplasmic accumulation, leading to activation of autophagy and depletion of lipid droplets (LDs). Systemic inhibition of autophagy in Prmt5MKO mice restores LDs in myoblasts and moderately improves muscle regeneration. Together, PRMT5 is essential for muscle development and regeneration at least partially through mediating FoxO1 methylation and LD turnover.
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Affiliation(s)
- Kun Ho Kim
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Stephanie N Oprescu
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Madigan M Snyder
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Aran Kim
- Department of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Zhihao Jia
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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Angelopoulou E, Pyrgelis ES, Ahire C, Suman P, Mishra A, Piperi C. Functional Implications of Protein Arginine Methyltransferases (PRMTs) in Neurodegenerative Diseases. BIOLOGY 2023; 12:1257. [PMID: 37759656 PMCID: PMC10525691 DOI: 10.3390/biology12091257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
During the aging of the global population, the prevalence of neurodegenerative diseases will be continuously growing. Although each disorder is characterized by disease-specific protein accumulations, several common pathophysiological mechanisms encompassing both genetic and environmental factors have been detected. Among them, protein arginine methyltransferases (PRMTs), which catalyze the methylation of arginine of various substrates, have been revealed to regulate several cellular mechanisms, including neuronal cell survival and excitability, axonal transport, synaptic maturation, and myelination. Emerging evidence highlights their critical involvement in the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS) spectrum, Huntington's disease (HD), spinal muscular atrophy (SMA) and spinal and bulbar muscular atrophy (SBMA). Underlying mechanisms include the regulation of gene transcription and RNA splicing, as well as their implication in various signaling pathways related to oxidative stress responses, apoptosis, neuroinflammation, vacuole degeneration, abnormal protein accumulation and neurotransmission. The targeting of PRMTs is a therapeutic approach initially developed against various forms of cancer but currently presents a novel potential strategy for neurodegenerative diseases. In this review, we discuss the accumulating evidence on the role of PRMTs in the pathophysiology of neurodegenerative diseases, enlightening their pathogenesis and stimulating future research.
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Affiliation(s)
- Efthalia Angelopoulou
- 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (E.A.); (E.-S.P.)
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Efstratios-Stylianos Pyrgelis
- 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, 11528 Athens, Greece; (E.A.); (E.-S.P.)
| | - Chetana Ahire
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, Kamrup 781101, Assam, India; (C.A.); (P.S.)
| | - Prachi Suman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, Kamrup 781101, Assam, India; (C.A.); (P.S.)
| | - Awanish Mishra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Guwahati, Changsari, Kamrup 781101, Assam, India; (C.A.); (P.S.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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So HK, Kim H, Lee J, You CL, Yun CE, Jeong HJ, Jin EJ, Jo Y, Ryu D, Bae GU, Kang JS. Protein Arginine Methyltransferase 1 Ablation in Motor Neurons Causes Mitochondrial Dysfunction Leading to Age-related Motor Neuron Degeneration with Muscle Loss. RESEARCH (WASHINGTON, D.C.) 2023; 6:0158. [PMID: 37342629 PMCID: PMC10278992 DOI: 10.34133/research.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023]
Abstract
Neuromuscular dysfunction is tightly associated with muscle wasting that occurs with age or due to degenerative diseases. However, the molecular mechanisms underlying neuromuscular dysfunction are currently unclear. Recent studies have proposed important roles of Protein arginine methyltransferase 1 (Prmt1) in muscle stem cell function and muscle maintenance. In the current study, we set out to determine the role of Prmt1 in neuromuscular function by generating mice with motor neuron-specific ablation of Prmt1 (mnKO) using Hb9-Cre. mnKO exhibited age-related motor neuron degeneration and neuromuscular dysfunction leading to premature muscle loss and lethality. Prmt1 deficiency also impaired motor function recovery and muscle reinnervation after sciatic nerve injury. The transcriptome analysis of aged mnKO lumbar spinal cords revealed alterations in genes related to inflammation, cell death, oxidative stress, and mitochondria. Consistently, mnKO lumbar spinal cords of sciatic nerve injury model or aged mice exhibited elevated cellular stress response in motor neurons. Furthermore, Prmt1 inhibition in motor neurons elicited mitochondrial dysfunction. Our findings demonstrate that Prmt1 ablation in motor neurons causes age-related motor neuron degeneration attributing to muscle loss. Thus, Prmt1 is a potential target for the prevention or intervention of sarcopenia and neuromuscular dysfunction related to aging.
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Affiliation(s)
- Hyun-Kyung So
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hyebeen Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jinwoo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Research Institute of Aging-Related Diseases, AniMusCure, Inc., Suwon, Korea
| | - Chang-Lim You
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Chae-Eun Yun
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hyeon-Ju Jeong
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Eun-Ju Jin
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Yunju Jo
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Gyu-Un Bae
- Drug Information Research Institute, Muscle Physiome Research Center, College of Pharmacy, Sookmyung Women’s University, Seoul, Korea
| | - Jong-Sun Kang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
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Zhong Q, Zheng K, Li W, An K, Liu Y, Xiao X, Hai S, Dong B, Li S, An Z, Dai L. Post-translational regulation of muscle growth, muscle aging and sarcopenia. J Cachexia Sarcopenia Muscle 2023. [PMID: 37127279 DOI: 10.1002/jcsm.13241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/07/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023] Open
Abstract
Skeletal muscle makes up 30-40% of the total body mass. It is of great significance in maintaining digestion, inhaling and exhaling, sustaining body posture, exercising, protecting joints and many other aspects. Moreover, muscle is also an important metabolic organ that helps to maintain the balance of sugar and fat. Defective skeletal muscle function not only limits the daily activities of the elderly but also increases the risk of disability, hospitalization and death, placing a huge burden on society and the healthcare system. Sarcopenia is a progressive decline in muscle mass, muscle strength and muscle function with age caused by environmental and genetic factors, such as the abnormal regulation of protein post-translational modifications (PTMs). To date, many studies have shown that numerous PTMs, such as phosphorylation, acetylation, ubiquitination, SUMOylation, glycosylation, glycation, methylation, S-nitrosylation, carbonylation and S-glutathionylation, are involved in the regulation of muscle health and diseases. This article systematically summarizes the post-translational regulation of muscle growth and muscle atrophy and helps to understand the pathophysiology of muscle aging and develop effective strategies for diagnosing, preventing and treating sarcopenia.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kun Zheng
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Wanmeng Li
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kang An
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xina Xiao
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Hai
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Biao Dong
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shuangqing Li
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhenmei An
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- Department of Endocrinology and Metabolism, General Practice Ward/International Medical Center Ward, General Practice Medical Center and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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Papanikolaou NA, Nikolaidis M, Amoutzias GD, Fouza A, Papaioannou M, Pandey A, Papavassiliou AG. The Dynamic and Crucial Role of the Arginine Methylproteome in Myoblast Cell Differentiation. Int J Mol Sci 2023; 24:2124. [PMID: 36768448 PMCID: PMC9916730 DOI: 10.3390/ijms24032124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
Protein arginine methylation is an extensive and functionally significant post-translational modification. However, little is known about its role in differentiation at the systems level. Using stable isotope labeling by amino acids in cell culture (SILAC) proteomics of whole proteome analysis in proliferating or five-day differentiated mouse C2C12 myoblasts, followed by high-resolution mass spectrometry, biochemical assays, and specific immunoprecipitation of mono- or dimethylated arginine peptides, we identified several protein families that were differentially methylated on arginine. Our study is the first to reveal global changes in the arginine mono- or dimethylation of proteins in proliferating myoblasts and differentiated myocytes and to identify enriched protein domains and novel short linear motifs (SLiMs). Our data may be crucial for dissecting the links between differentiation and cancer growth.
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Affiliation(s)
- Nikolaos A. Papanikolaou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larisa, Greece
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larisa, Greece
| | - Ariadni Fouza
- Fifth Surgical Department, Ippokrateio General Hospital, School of Medicine, Aristotle University of Thessaloniki, 54643 Thessaloniki, Macedonia, Greece
| | - Maria Papaioannou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Boesch J, Pierrel E, Lambert C, Doelemeyer A, Kreider J, Accart N, Summermatter S. Chemokine-like receptor 1 plays a critical role in modulating the regenerative and contractile properties of muscle tissue. Front Physiol 2022; 13:1044488. [PMID: 36467705 PMCID: PMC9713634 DOI: 10.3389/fphys.2022.1044488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/04/2022] [Indexed: 10/28/2023] Open
Abstract
Musculoskeletal diseases are a leading contributor to mobility disability worldwide. Since the majority of patients with musculoskeletal diseases present with associated muscle weakness, treatment approaches typically comprise an element of resistance training to restore physical strength. The health-promoting effects of resistance exercise are mediated via complex, multifarious mechanisms including modulation of systemic and local inflammation. Here we investigated whether targeted inhibition of the chemerin pathway, which largely controls inflammatory processes via chemokine-like receptor 1 (CMKLR1), can improve skeletal muscle function. Using genetically modified mice, we demonstrate that blockade of CMKLR1 transiently increases maximal strength during growth, but lastingly decreases strength endurance. In-depth analyses of the underlying long-term adaptations revealed microscopic alterations in the number of Pax7-positive satellite cells, as well as molecular changes in genes governing myogenesis and calcium handling. Taken together, these data provide evidence of a critical role for CMKLR1 in regulating skeletal muscle function by modulating the regenerative and contractile properties of muscle tissue. CMKLR1 antagonists are increasingly viewed as therapeutic modalities for a variety of diseases (e.g., psoriasis, metabolic disorders, and multiple sclerosis). Our findings thus have implications for the development of novel drug substances that aim at targeting the chemerin pathway for musculoskeletal or other diseases.
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Affiliation(s)
| | | | | | | | | | | | - Serge Summermatter
- Musculoskeletal Diseases, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
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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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