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Tebbenkamp AT, Huggett SB, Lombardi V, Zampedri L, AlQahtani A, Kokkinis A, Malaspina A, Rinaldi C, Grunseich C, Fratta P, Viglietta V. Protein biomarker signature in patients with spinal and bulbar muscular atrophy. JCI Insight 2024; 9:e176383. [PMID: 38973610 DOI: 10.1172/jci.insight.176383] [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] [Indexed: 07/09/2024] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is a slowly progressing disease with limited sensitive biomarkers that support clinical research. We analyzed plasma and serum samples from patients with SBMA and matched healthy controls in multiple cohorts, identifying 40 highly reproducible SBMA-associated proteins out of nearly 3,000 measured. These proteins were robustly enriched in gene sets of skeletal muscle expression and processes related to mitochondria and calcium signaling. Many proteins outperformed currently used clinical laboratory tests (e.g., creatine kinase [CK]) in distinguishing patients from controls and in their correlations with clinical and functional traits in patients. Two of the 40 proteins, Ectodysplasin A2 receptor (EDA2R) and Repulsive guidance molecule A (RGMA), were found to be associated with decreased survival and body weight in a mouse model of SBMA. In summary, we identified what we believe to be a robust and novel set of fluid protein biomarkers in SBMA that are linked with relevant disease features in patients and in a mouse model of disease. Changes in these SBMA-associated proteins could be used as an early predictor of treatment effects in clinical trials.
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Affiliation(s)
| | | | | | - Luca Zampedri
- University College London (UCL), London, United Kingdom
| | - Abdullah AlQahtani
- Neurogenetics Branch, National Institute of Neurological Disease and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela Kokkinis
- Neurogenetics Branch, National Institute of Neurological Disease and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Carlo Rinaldi
- Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, United Kingdom
| | - Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disease and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Pietro Fratta
- University College London (UCL), London, United Kingdom
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2
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Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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3
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Smith IC, Chakraborty S, Bourque PR, Sampaio ML, Melkus G, Lochmüller H, Woulfe J, Parks RJ, Brais B, Warman-Chardon J. Emerging and established biomarkers of oculopharyngeal muscular dystrophy. Neuromuscul Disord 2023; 33:824-834. [PMID: 37926637 DOI: 10.1016/j.nmd.2023.09.010] [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: 07/28/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is a rare, primarily autosomal dominant, late onset muscular dystrophy commonly presenting with ptosis, dysphagia, and subsequent weakness of proximal muscles. Although OPMD diagnosis can be confirmed with high confidence by genetic testing, the slow progression of OPMD poses a significant challenge to clinical monitoring and a barrier to assessing the efficacy of treatments during clinical trials. Accordingly, there is a pressing need for more sensitive measures of OPMD progression, particularly those which do not require a muscle biopsy. This review provides an overview of progress in OPMD biomarkers from clinical assessment, quantitative imaging, histological assessments, and genomics, as well as hypothesis-generating "omics" approaches. The ongoing search for biomarkers relevant to OPMD progression needs an integrative, longitudinal approach combining validated and experimental approaches which may include clinical, imaging, demographic, and biochemical assessment methods. A multi-omics approach to biochemical biomarker discovery could help provide context for differences found between individuals with varying levels of disease activity and provide insight into pathomechanisms and prognosis of OPMD.
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Affiliation(s)
- Ian C Smith
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | | | - Pierre R Bourque
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada
| | - Marcos L Sampaio
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Department of Medical Imaging, The Ottawa Hospital, Ottawa, Ontario K1Y 4E9, Canada; Department of Radiology, Radiation Oncology and Medical Physics, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Gerd Melkus
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Department of Medical Imaging, The Ottawa Hospital, Ottawa, Ontario K1Y 4E9, Canada; Department of Physics, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Hanns Lochmüller
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - John Woulfe
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada
| | - Robin J Parks
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada
| | - Bernard Brais
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Jodi Warman-Chardon
- The Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada; Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Department of Medicine, The Ottawa Hospital/University of Ottawa, Ottawa, ON K1H 8L6, Canada; Eric Poulin Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1Y 4E9, Canada; Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada; Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada.
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4
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
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5
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Nguyen CDL, Jimenez-Moreno AC, Merker M, Bowers CJ, Nikolenko N, Hentschel A, Müntefering T, Isham A, Ruck T, Vorgerd M, Dobelmann V, Gourdon G, Schara-Schmidt U, Gangfuss A, Schröder C, Sickmann A, Gross C, Gorman G, Stenzel W, Kollipara L, Hathazi D, Spendiff S, Gagnon C, Preusse C, Duchesne E, Lochmüller H, Roos A. Periostin as a blood biomarker of muscle cell fibrosis, cardiomyopathy and disease severity in myotonic dystrophy type 1. J Neurol 2023; 270:3138-3158. [PMID: 36892629 DOI: 10.1007/s00415-023-11633-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 03/10/2023]
Abstract
BACKGROUND AND PURPOSE Myotonic dystrophy type 1 (DM1) is the most common form of adult-onset muscular dystrophy and is caused by an repeat expansion [r(CUG)exp] located in the 3' untranslated region of the DMPK gene. Symptoms include skeletal and cardiac muscle dysfunction and fibrosis. In DM1, there is a lack of established biomarkers in routine clinical practice. Thus, we aimed to identify a blood biomarker with relevance for DM1-pathophysiology and clinical presentation. METHODS We collected fibroblasts from 11, skeletal muscles from 27, and blood samples from 158 DM1 patients. Moreover, serum, cardiac, and skeletal muscle samples from DMSXL mice were included. We employed proteomics, immunostaining, qPCR and ELISA. Periostin level were correlated with CMRI-data available for some patients. RESULTS Our studies identified Periostin, a modulator of fibrosis, as a novel biomarker candidate for DM1: proteomic profiling of human fibroblasts and murine skeletal muscles showed significant dysregulation of Periostin. Immunostaining on skeletal and cardiac muscles from DM1 patients and DMSXL mice showed an extracellular increase of Periostin, indicating fibrosis. qPCR studies indicated increased POSTN expression in fibroblasts and muscle. Quantification of Periostin in blood samples from DMSXL mice and two large validation cohorts of DM1 patients showed decreased levels in animals and diseased individuals correlating with repeat expansion and disease severity and presence of cardiac symptoms identified by MRI. Analyses of longitudinal blood samples revealed no correlation with disease progression. CONCLUSIONS Periostin might serve as a novel stratification biomarker for DM1 correlating with disease severity, presence of cardiac malfunction and fibrosis.
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Affiliation(s)
- Chi D L Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | | | - Monika Merker
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | | | | | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Thomas Müntefering
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - Angus Isham
- Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Tobias Ruck
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - Matthias Vorgerd
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, 44789, Bochum, Germany
| | - Vera Dobelmann
- Department of Neurology, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - Genevieve Gourdon
- Institut National de la Santé et de la Recherche Médicale UMR 1163, Paris, France.,Laboratory CTGDM, Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Ulrike Schara-Schmidt
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
| | - Andrea Gangfuss
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany
| | - Charlotte Schröder
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Claudia Gross
- Institute of Clinical Genetics and Tumor Genetics Bonn, Maximilianstraße 28D, 53111, Bonn, Germany
| | - Grainne Gorman
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Denisa Hathazi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sally Spendiff
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Cynthia Gagnon
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.,School of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada
| | - Corinna Preusse
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elise Duchesne
- Department of Health Sciences, Université du Québec à Chicoutimi, Québec, Canada
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.,Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Centro Nacional de Análisis Genómico, Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Andreas Roos
- Department of Neurology, University Hospital Bergmannsheil, Heimer Institute for Muscle Research, 44789, Bochum, Germany. .,Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45147, Essen, Germany. .,Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada.
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6
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Proteomic profiling of impaired excitation-contraction coupling and abnormal calcium handling in muscular dystrophy. Proteomics 2022; 22:e2200003. [PMID: 35902360 PMCID: PMC10078611 DOI: 10.1002/pmic.202200003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/06/2022]
Abstract
The X-linked inherited neuromuscular disorder Duchenne muscular dystrophy is characterised by primary abnormalities in the membrane cytoskeletal component dystrophin. The almost complete absence of the Dp427-M isoform of dystrophin in skeletal muscles renders contractile fibres more susceptible to progressive degeneration and a leaky sarcolemma membrane. This in turn results in abnormal calcium homeostasis, enhanced proteolysis and impaired excitation-contraction coupling. Biochemical and mass spectrometry-based proteomic studies of both patient biopsy specimens and genetic animal models of dystrophinopathy have demonstrated significant changes in the concentration and/or physiological function of essential calcium-regulatory proteins in dystrophin-lacking voluntary muscles. Abnormalities include dystrophinopathy-associated changes in voltage sensing receptors, calcium release channels, calcium pumps and calcium binding proteins. This review article provides an overview of the importance of the sarcolemmal dystrophin-glycoprotein complex and the wider dystrophin complexome in skeletal muscle and its linkage to depolarisation-induced calcium-release mechanisms and the excitation-contraction-relaxation cycle. Besides chronic inflammation, fat substitution and reactive myofibrosis, a major pathobiochemical hallmark of X-linked muscular dystrophy is represented by the chronic influx of calcium ions through the damaged plasmalemma in conjunction with abnormal intracellular calcium fluxes and buffering. Impaired calcium handling proteins should therefore be included in an improved biomarker signature of Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
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7
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Gargan S, Dowling P, Zweyer M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic Identification of Markers of Membrane Repair, Regeneration and Fibrosis in the Aged and Dystrophic Diaphragm. Life (Basel) 2022; 12:1679. [PMID: 36362832 PMCID: PMC9696191 DOI: 10.3390/life12111679] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 07/30/2023] Open
Abstract
Deficiency in the membrane cytoskeletal protein dystrophin is the underlying cause of the progressive muscle wasting disease named Duchenne muscular dystrophy. In order to detect novel disease marker candidates and confirm the complexity of the pathobiochemical signature of dystrophinopathy, mass spectrometric screening approaches represent ideal tools for comprehensive biomarker discovery studies. In this report, we describe the comparative proteomic analysis of young versus aged diaphragm muscles from wild type versus the dystrophic mdx-4cv mouse model of X-linked muscular dystrophy. The survey confirmed the drastic reduction of the dystrophin-glycoprotein complex in the mdx-4cv diaphragm muscle and concomitant age-dependent changes in key markers of muscular dystrophy, including proteins involved in cytoskeletal organization, metabolite transportation, the cellular stress response and excitation-contraction coupling. Importantly, proteomic markers of the regulation of membrane repair, tissue regeneration and reactive myofibrosis were detected by mass spectrometry and changes in key proteins were confirmed by immunoblotting. Potential disease marker candidates include various isoforms of annexin, the matricellular protein periostin and a large number of collagens. Alterations in these proteoforms can be useful to evaluate adaptive, compensatory and pathobiochemical changes in the intracellular cytoskeleton, myofiber membrane integrity and the extracellular matrix in dystrophin-deficient skeletal muscle tissues.
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Affiliation(s)
- Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Ireland
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children’s Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, D09 E432 Dublin, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, D09 E432 Dublin, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Ireland
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8
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Nimer RM, Sumaily KM, Almuslat A, Jabar MA, Sabi EM, Al-Muhaizea MA, Rahman AMA. Dystrophin Protein Quantification as a Duchenne Muscular Dystrophy Diagnostic Biomarker in Dried Blood Spots Using Multiple Reaction Monitoring Tandem Mass Spectrometry: A Preliminary Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123662. [PMID: 35744792 PMCID: PMC9231037 DOI: 10.3390/molecules27123662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022]
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder characterized by progressive muscle loss, leading to difficulties in movement. Mutations in the DMD gene that code for the protein dystrophin are responsible for the development of DMD disorder, where the synthesis of this protein is completely halted. Therefore, circulating dystrophin protein could be a promising biomarker of DMD disease. Current methods for diagnosing DMD have sensitivity, specificity, and reproducibility limitations. Herein, a quantitative liquid chromatography-tandem spectrometry (LC-MS/MS) technique in multiple reaction monitoring (MRM) mode was designed and validated for accurate dystrophin protein measurement in a dried blood spot (DBS). The method was successfully validated on the basis of international guidelines regarding calibration curves, precision, and accuracy. In addition, patients and healthy controls were used to test the amount of dystrophin protein circulating in DBS samples as a potential biomarker for DMD disorders. DMD patients were found to have considerably lower levels than controls. To the best of our knowledge, this is the first study to report dystrophin levels in DBS through LC-MS/MS as a diagnostic marker for DMD to the proposed MRM method, providing a highly specific and sensitive approach to dystrophin quantification in a DBS that can be applied in DMD screening.
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Affiliation(s)
- Refat M. Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Correspondence: (R.M.N.); (A.M.A.R.)
| | - Khalid M. Sumaily
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (K.M.S.); (E.M.S.)
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh 11461, Saudi Arabia
| | - Arwa Almuslat
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Mai Abdel Jabar
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
| | - Essa M. Sabi
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (K.M.S.); (E.M.S.)
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh 11461, Saudi Arabia
| | - Mohammad A. Al-Muhaizea
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Anas M. Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Correspondence: (R.M.N.); (A.M.A.R.)
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9
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Gangfuß A, Schara-Schmidt U, Roos A. [Genomics and proteomics in the research of neuromuscular diseases]. DER NERVENARZT 2021; 93:114-121. [PMID: 34622318 DOI: 10.1007/s00115-021-01201-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Neurological diseases affect 3-5% of children and, apart from cardiovascular diseases and cancer, represent the most prominent cause of morbidity and mortality in adults and particularly in the aged population of western Europe. Neuromuscular disorders are a subgroup of neurological diseases and often have a genetic origin, which leads to familial clustering. Despite the enormous progress in the analysis of the genome, such as by sequence analysis of coding regions of deoxyribonucleic acid or even the entire deoxyribonucleic acid sequence, in approximately 50% of the patients suffering from rare forms of neurological diseases the genetic cause remains unsolved. The reasons for this limited detection rate are presented in this article. If a treatment concept is available, under certain conditions this can have an impact on the adequate and early treatment of these patients. Considering neuromuscular disorders as a paradigm, this article reports on the advantages of the inclusion of next generation sequencing analysis-based DNA investigations as an omics technology (genomics) and the advantage of the integration with protein analyses (proteomics). A special focus is on the combination of genomics and proteomics in the sense of a proteogenomic approach in the diagnostics and research of these diseases. Along this line, this article presents a proteogenomic approach in the context of a multidisciplinary project aiming towards improved diagnostic work-up and future treatment of patients with neuromuscular diseases; "NMD-GPS: gene and protein signatures as a global positioning system in patients suffering from neuromuscular diseases".
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Affiliation(s)
- Andrea Gangfuß
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland
| | - Ulrike Schara-Schmidt
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland
| | - Andreas Roos
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland. .,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Kanada.
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10
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Ohlendieck K, Swandulla D. Complexity of skeletal muscle degeneration: multi-systems pathophysiology and organ crosstalk in dystrophinopathy. Pflugers Arch 2021; 473:1813-1839. [PMID: 34553265 PMCID: PMC8599371 DOI: 10.1007/s00424-021-02623-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Duchenne muscular dystrophy is a highly progressive muscle wasting disorder due to primary abnormalities in one of the largest genes in the human genome, the DMD gene, which encodes various tissue-specific isoforms of the protein dystrophin. Although dystrophinopathies are classified as primary neuromuscular disorders, the body-wide abnormalities that are associated with this disorder and the occurrence of organ crosstalk suggest that a multi-systems pathophysiological view should be taken for a better overall understanding of the complex aetiology of X-linked muscular dystrophy. This article reviews the molecular and cellular effects of deficiency in dystrophin isoforms in relation to voluntary striated muscles, the cardio-respiratory system, the kidney, the liver, the gastrointestinal tract, the nervous system and the immune system. Based on the establishment of comprehensive biomarker signatures of X-linked muscular dystrophy using large-scale screening of both patient specimens and genetic animal models, this article also discusses the potential usefulness of novel disease markers for more inclusive approaches to differential diagnosis, prognosis and therapy monitoring that also take into account multi-systems aspects of dystrophinopathy. Current therapeutic approaches to combat muscular dystrophy are summarised.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Co. Kildare, Maynooth, W23F2H6, Ireland.
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Co. Kildare, Maynooth, W23F2H6, Ireland.
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, 53115, Bonn, Germany.
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11
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Multiomic Approaches to Uncover the Complexities of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2021; 22:ijms22168954. [PMID: 34445659 PMCID: PMC8396646 DOI: 10.3390/ijms22168954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Despite major progress in treating skeletal muscle disease associated with dystrophinopathies, cardiomyopathy is emerging as a major cause of death in people carrying dystrophin gene mutations that remain without a targeted cure even with new treatment directions and advances in modelling abilities. The reasons for the stunted progress in ameliorating dystrophin-associated cardiomyopathy (DAC) can be explained by the difficulties in detecting pathophysiological mechanisms which can also be efficiently targeted within the heart in the widest patient population. New perspectives are clearly required to effectively address the unanswered questions concerning the identification of authentic and effectual readouts of DAC occurrence and severity. A potential way forward to achieve further therapy breakthroughs lies in combining multiomic analysis with advanced preclinical precision models. This review presents the fundamental discoveries made using relevant models of DAC and how omics approaches have been incorporated to date.
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12
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Mass Spectrometric Profiling of Extraocular Muscle and Proteomic Adaptations in the mdx-4cv Model of Duchenne Muscular Dystrophy. Life (Basel) 2021; 11:life11070595. [PMID: 34206383 PMCID: PMC8304255 DOI: 10.3390/life11070595] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/16/2022] Open
Abstract
Extraocular muscles (EOMs) represent a specialized type of contractile tissue with unique cellular, physiological, and biochemical properties. In Duchenne muscular dystrophy, EOMs stay functionally unaffected in the course of disease progression. Therefore, it was of interest to determine their proteomic profile in dystrophinopathy. The proteomic survey of wild type mice and the dystrophic mdx-4cv model revealed a broad spectrum of sarcomere-associated proteoforms, including components of the thick filament, thin filament, M-band and Z-disk, as well as a variety of muscle-specific markers. Interestingly, the mass spectrometric analysis revealed unusual expression levels of contractile proteins, especially isoforms of myosin heavy chain. As compared to diaphragm muscle, both proteomics and immunoblotting established isoform MyHC14 as a new potential marker in wild type EOMs, in addition to the previously identified isoforms MyHC13 and MyHC15. Comparative proteomics was employed to establish alterations in the protein expression profile between normal EOMs and dystrophin-lacking EOMs. The analysis of mdx-4cv EOMs identified elevated levels of glycolytic enzymes and molecular chaperones, as well as decreases in mitochondrial enzymes. These findings suggest a process of adaptation in dystrophin-deficient EOMs via a bioenergetic shift to more glycolytic metabolism, as well as an efficient cellular stress response in EOMs in dystrophinopathy.
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13
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Tobias IS, Galpin AJ. Moving human muscle physiology research forward: an evaluation of fiber type-specific protein research methodologies. Am J Physiol Cell Physiol 2020; 319:C858-C876. [DOI: 10.1152/ajpcell.00107.2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human skeletal muscle is a heterogeneous tissue composed of multiple fiber types that express unique contractile and metabolic properties. While analysis of mixed fiber samples predominates and holds value, increasing attention has been directed toward studying proteins segregated by fiber type, a methodological distinction termed “fiber type-specific.” Fiber type-specific protein studies have the advantage of uncovering key molecular effects that are often missed in mixed fiber homogenate studies but also require greater time and resource-intensive methods, particularly when applied to human muscle. This review summarizes and compares current methods used for fiber type-specific protein analysis, highlighting their advantages and disadvantages for human muscle studies, in addition to recent advances in these techniques. These methods can be grouped into three categories based on the initial processing of the tissue: 1) muscle-specific fiber homogenates, 2) cross sections of fiber bundles, and 3) isolated single fibers, with various subtechniques for performing fiber type identification and protein quantification. The relative implementation for each unique methodological approach is analyzed from 83 fiber type-specific studies of proteins in live human muscle found in the literature to date. These studies have investigated several proteins involved in a wide range of cellular functions that are important to muscle tissue. The second half of this review summarizes key findings from this ensemble of fiber type-specific human protein studies. We highlight examples of where this analytical approach has helped to improve understanding of important physiological topics such as insulin sensitivity, muscle hypertrophy, muscle fatigue, and adaptation to different exercise programs.
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Affiliation(s)
- Irene S. Tobias
- Biochemistry and Molecular Exercise Physiology Laboratory, Center for Sport Performance, California State University, Fullerton, California
| | - Andrew J. Galpin
- Biochemistry and Molecular Exercise Physiology Laboratory, Center for Sport Performance, California State University, Fullerton, California
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14
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Koutsoulidou A, Phylactou LA. Circulating Biomarkers in Muscular Dystrophies: Disease and Therapy Monitoring. Mol Ther Methods Clin Dev 2020; 18:230-239. [PMID: 32637452 PMCID: PMC7327849 DOI: 10.1016/j.omtm.2020.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Muscular dystrophies are a group of inherited disorders that primarily affect the muscle tissues. Across the muscular dystrophies, symptoms commonly compromise the quality of life in all areas of functioning. It is well noted that muscular dystrophies need reliable and measurable biomarkers that will monitor the progress of the disease and evaluate the potential therapeutic approaches. In this review, we analyze the current findings regarding the development of blood-based circulating biomarkers for different types of muscular dystrophies. We emphasize those muscular dystrophies that gained particular interest for the development of biomarkers, including Duchenne muscular dystrophy, Becker muscular dystrophy, myotonic dystrophy types 1 and 2, Ullrich congenital muscular dystrophy, congenital muscular dystrophy type 1A, Facioscapulohumeral muscular dystrophy, and limb-girdle muscular dystrophy types 2A, 2B, 2C, and 2D, recently renamed as limb-girdle muscular dystrophy R1 calpain3-related, R2 dysferlin-related, R5 γ-sarcoglycan-related, and R3 α-sarcoglycan-related. This review highlights the up-to-date progress in the development of biomarkers at the level of proteins, lipids, and metabolites, as well as microRNAs (miRNAs) that currently are the main potential biomarker candidates in muscular dystrophies.
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Affiliation(s)
- Andrie Koutsoulidou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus.,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus.,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
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15
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Proteomic profiling of fatty acid binding proteins in muscular dystrophy. Expert Rev Proteomics 2020; 17:137-148. [PMID: 32067530 DOI: 10.1080/14789450.2020.1732214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Duchenne muscular dystrophy is a neuromuscular disorder, which is caused by abnormalities in the DMD gene that encodes the membrane cytoskeletal protein dystrophin. Besides progressive skeletal muscle wasting, dystrophinopathy also affects non-skeletal muscle tissues, including cells in the cardio-respiratory system, the central nervous system, the liver and the kidney.Areas covered: This review summarizes the proteomic characterization of a key class of lipid chaperones, the large family of fatty acid binding proteins, and their potential role in muscular dystrophy. Recent proteomic surveys using animal models and patient specimens are reviewed. Pathobiochemical changes in specific proteoforms of fatty acid binding protein in the multi-system pathology of dystrophinopathy are discussed.Expert opinion: The mass spectrometric identification of distinct changes in fatty acid binding proteins in muscle, heart, liver, kidney and serum demonstrates that considerable alterations occur in key steps of metabolite transport and fat metabolism in muscular dystrophy. These new findings might be helpful to further develop a comprehensive biomarker signature of metabolic changes in X-linked muscular dystrophy, which should improve (i) our understanding of complex pathobiochemical changes due to dystrophin deficiency, (ii) the identification of novel therapeutic targets, and (iii) the design of differential diagnostic, prognostic and therapy-monitoring approaches.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
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16
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Bao K, Li X, Kajikawa T, Toshiharu A, Selevsek N, Grossmann J, Hajishengallis G, Bostanci N. Pressure Cycling Technology Assisted Mass Spectrometric Quantification of Gingival Tissue Reveals Proteome Dynamics during the Initiation and Progression of Inflammatory Periodontal Disease. Proteomics 2020; 20:e1900253. [PMID: 31881116 DOI: 10.1002/pmic.201900253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/04/2019] [Indexed: 12/13/2022]
Abstract
Understanding the progression of periodontal tissue destruction is at the forefront of periodontal research. The authors aimed to capture the dynamics of gingival tissue proteome during the initiation and progression of experimental (ligature-induced) periodontitis in mice. Pressure cycling technology (PCT), a recently developed platform that uses ultra-high pressure to disrupt tissues, is utilized to achieve efficient and reproducible protein extraction from ultra-small amounts of gingival tissues in combination with liquid chromatography-tandem mass spectrometry (MS). The MS data are processed using Progenesis QI and the regulated proteins are subjected to METACORE, STRING, and WebGestalt for functional enrichment analysis. A total of 1614 proteins with ≥2 peptides are quantified with an estimated protein false discovery rate of 0.06%. Unsupervised clustering analysis shows that the gingival tissue protein abundance is mainly dependent on the periodontitis progression stage. Gene ontology enrichment analysis reveals an overrepresentation in innate immune regulation (e.g., neutrophil-mediated immunity and antimicrobial peptides), signal transduction (e.g., integrin signaling), and homeostasis processes (e.g., platelet activation and aggregation). In conclusion, a PCT-assisted label-free quantitative proteomics workflow that allowed cataloging the deepest gingival tissue proteome on a rapid timescale and provided novel mechanistic insights into host perturbation during periodontitis progression is applied.
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Affiliation(s)
- Kai Bao
- Section of Peridontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Kartolinska Insitutet, Alfred Nobels alle 8, 14104, Huddinge, Sweden
| | - Xiaofei Li
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, PA, 19104, Philadelphia, USA
| | - Tetsuhiro Kajikawa
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, PA, 19104, Philadelphia, USA
| | - Abe Toshiharu
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, PA, 19104, Philadelphia, USA
| | - Nathalie Selevsek
- Swiss Integrative Center for Human Health, Passage du Cardinal 13 B, CH-1700, Fribourg, Switzerland
| | - Jonas Grossmann
- Function Genomic Centre, ETH Zurich and University of Zurich, 8092, Zurich, Switzerland
| | - George Hajishengallis
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, PA, 19104, Philadelphia, USA
| | - Nagihan Bostanci
- Section of Peridontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Kartolinska Insitutet, Alfred Nobels alle 8, 14104, Huddinge, Sweden
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17
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Dowling P, Zweyer M, Raucamp M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic and cell biological profiling of the renal phenotype of the mdx-4cv mouse model of Duchenne muscular dystrophy. Eur J Cell Biol 2019; 99:151059. [PMID: 31776009 DOI: 10.1016/j.ejcb.2019.151059] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 02/08/2023] Open
Abstract
The X-linked inherited muscle wasting disease Duchenne muscular dystrophy, which is caused by primary abnormalities in the membrane cytoskeletal protein dystrophin, is a multi-system disorder. Highly progressive forms of dystrophinopathy are associated with a complex secondary pathophysiology, including renal dysfunction. It was therefore of interest to carry out a systematic survey of potential proteome-wide changes in the kidney of the established mdx-4cv mouse model of dystrophinopathy. Of 5878 mass spectrometrically identified kidney proteins, 82 versus 142 proteins were shown to be decreased or increased, respectively, in association with muscular dystrophy. The most decreased versus increased protein species are the ACSM3 isoform of mitochondrial acyl-coenzyme A synthetase and the FABP1 isoform of fatty acid binding protein, respectively. Both proteomic findings were verified by immunofluorescence microscopy and immunoblot analysis. Interestingly, haematoxylin/eosin staining indicated diffuse whitish deposits in the mdx-4cv kidney, and an increased intensity of Sudan Black labelling of kidney cells revealed ectopic fat deposition. Although the proteomic results and cell biological findings do not demonstrate a direct functional link between increased FABP1 and fat accumulation, the results suggest that the up-regulation of FABP1 may be related to abnormal fat metabolism. This makes FABP1 potentially a novel pathobiochemical indicator for studying kidney abnormalities in the mdx-4cv model of dystrophinopathy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth W23F2H6, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth W23F2H6, Co. Kildare, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D53115 Bonn, Germany
| | - Maren Raucamp
- Institute of Physiology II, University of Bonn, D53115 Bonn, Germany
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth W23F2H6, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth W23F2H6, Co. Kildare, Ireland.
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18
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Dowling P, Murphy S, Zweyer M, Raucamp M, Swandulla D, Ohlendieck K. Emerging proteomic biomarkers of X-linked muscular dystrophy. Expert Rev Mol Diagn 2019; 19:739-755. [PMID: 31359811 DOI: 10.1080/14737159.2019.1648214] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Progressive skeletal muscle wasting is the manifesting symptom of Duchenne muscular dystrophy, an X-linked inherited disorder triggered by primary abnormalities in the DMD gene. The almost complete loss of dystrophin isoform Dp427 causes a multi-system pathology that features in addition to skeletal muscle weakness also late-onset cardio-respiratory deficiencies, impaired metabolism and abnormalities in the central nervous system. Areas covered: This review focuses on the mass spectrometry-based proteomic characterization of X-linked muscular dystrophy with special emphasis on the identification of novel biomarker candidates in skeletal muscle tissues, as well as non-muscle tissues and various biofluids. Individual sections focus on molecular and cellular aspects of the pathogenic changes in dystrophinopathy, proteomic workflows used in biomarker research, the proteomics of the dystrophin-glycoprotein complex and the potential usefulness of newly identified protein markers involved in fibre degeneration, fibrosis and inflammation. Expert opinion: The systematic application of large-scale proteomic surveys has identified a distinct cohort of both tissue- and biofluid-associated protein species with considerable potential for improving diagnostic, prognostic and therapy-monitoring procedures. Novel proteomic markers include components involved in fibre contraction, cellular signalling, ion homeostasis, cellular stress response, energy metabolism and the immune response, as well as maintenance of the cytoskeletal and extracellular matrix.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland , Kildare , Ireland.,Human Health Research Institute, Maynooth University , Kildare , Ireland
| | - Sandra Murphy
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne , UK
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn , Bonn , Germany
| | - Maren Raucamp
- Institute of Physiology II, University of Bonn , Bonn , Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland , Kildare , Ireland.,Human Health Research Institute, Maynooth University , Kildare , Ireland
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19
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Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
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20
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Murphy S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Proteomic profiling of giant skeletal muscle proteins. Expert Rev Proteomics 2019; 16:241-256. [DOI: 10.1080/14789450.2019.1575205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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21
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Murphy S, Zweyer M, Henry M, Meleady P, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic profiling of liver tissue from the mdx- 4cv mouse model of Duchenne muscular dystrophy. Clin Proteomics 2018; 15:34. [PMID: 30386187 PMCID: PMC6205794 DOI: 10.1186/s12014-018-9212-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022] Open
Abstract
Background Duchenne muscular dystrophy is a highly complex multi-system disease caused by primary abnormalities in the membrane cytoskeletal protein dystrophin. Besides progressive skeletal muscle degeneration, this neuromuscular disorder is also associated with pathophysiological perturbations in many other organs including the liver. To determine potential proteome-wide alterations in liver tissue, we have used a comparative and mass spectrometry-based approach to study the dystrophic mdx-4cv mouse model of dystrophinopathy. Methods The comparative proteomic profiling of mdx-4cv versus wild type liver extracts was carried out with an Orbitrap Fusion Tribrid mass spectrometer. The distribution of identified liver proteins within protein families and potential protein interaction patterns were analysed by systems bioinformatics. Key findings on fatty acid binding proteins were confirmed by immunoblot analysis and immunofluorescence microscopy. Results The proteomic analysis revealed changes in a variety of protein families, affecting especially fatty acid, carbohydrate and amino acid metabolism, biotransformation, the cellular stress response and ion handling in the mdx-4cv liver. Drastically increased protein species were identified as fatty acid binding protein FABP5, ferritin and calumenin. Decreased liver proteins included phosphoglycerate kinase, apolipoprotein and perilipin. The drastic change in FABP5 was independently verified by immunoblotting and immunofluorescence microscopy. Conclusions The proteomic results presented here indicate that the intricate and multifaceted pathogenesis of the mdx-4cv model of dystrophinopathy is associated with secondary alterations in the liver affecting especially fatty acid transportation. Since FABP5 levels were also shown to be elevated in serum from dystrophic mice, this protein might be a useful indicator for monitoring liver changes in X-linked muscular dystrophy.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- 2Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Michael Henry
- 3National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- 3National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Rustam R Mundegar
- 2Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Dieter Swandulla
- 2Institute of Physiology II, University of Bonn, 53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Chemical crosslinking analysis of β-dystroglycan in dystrophin-deficient skeletal muscle. HRB Open Res 2018; 1:17. [PMID: 35528858 PMCID: PMC9039762 DOI: 10.12688/hrbopenres.12846.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
Background: In Duchenne muscular dystrophy, primary abnormalities in the membrane cytoskeletal protein dystrophin trigger the loss of sarcolemmal linkage between the extracellular matrix component laminin-211 and the intracellular cortical actin membrane cytoskeleton. The disintegration of the dystrophin-associated glycoprotein complex renders the plasma membrane of contractile fibres more susceptible to micro-rupturing, which is associated with abnormal calcium handling and impaired cellular signalling in dystrophinopathy. Methods: The oligomerisation pattern of β-dystroglycan, an integral membrane protein belonging to the core dystrophin complex, was studied using immunoprecipitation and chemical crosslinking analysis. A homo-bifunctional and non-cleavable agent with water-soluble and amine-reactive properties was employed to study protein oligomerisation in normal versus dystrophin-deficient skeletal muscles. Crosslinker-induced protein oligomerisation was determined by a combination of gel-shift analysis and immunoblotting. Results: Although proteomics was successfully applied for the identification of dystroglycan as a key component of the dystrophin-associated glycoprotein complex in the muscle membrane fraction, mass spectrometric analysis did not efficiently recognize this relatively low-abundance protein after immunoprecipitation or chemical crosslinking. As an alternative approach, comparative immunoblotting was used to evaluate the effects of chemical crosslinking. Antibody decoration of the crosslinked microsomal protein fraction from wild type versus the
mdx-4cv mouse model of dystrophinopathy revealed oligomers that contain β-dystroglycan. The protein exhibited a comparable reduction in gel electrophoretic mobility in both normal and dystrophic samples. The membrane repair proteins dysferlin and myoferlin, which are essential components of fibre regeneration, as well as the caveolae-associated protein cavin-1, were also shown to exist in high-molecular mass complexes. Conclusions: The muscular dystrophy-related reduction in the concentration of β-dystroglycan, which forms in conjunction with its extracellular binding partner α-dystroglycan a critical plasmalemmal receptor for laminin-211, does not appear to alter its oligomeric status. Thus, independent of direct interactions with dystrophin, this sarcolemmal glycoprotein appears to exist in a supramolecular assembly in muscle.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, Bonn, D‑53115, Germany
| | | | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, Bonn, D‑53115, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland
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Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Chemical crosslinking analysis of β-dystroglycan in dystrophin-deficient skeletal muscle. HRB Open Res 2018; 1:17. [PMID: 35528858 PMCID: PMC9039762 DOI: 10.12688/hrbopenres.12846.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 07/30/2023] Open
Abstract
Background: In Duchenne muscular dystrophy, primary abnormalities in the membrane cytoskeletal protein dystrophin trigger the loss of sarcolemmal linkage between the extracellular matrix component laminin-211 and the intracellular cortical actin membrane cytoskeleton. The disintegration of the dystrophin-associated glycoprotein complex renders the plasma membrane of contractile fibres more susceptible to micro-rupturing, which is associated with abnormal calcium handling and impaired cellular signalling in dystrophinopathy. Methods: The oligomerisation pattern of β-dystroglycan, an integral membrane protein belonging to the core dystrophin complex, was studied using immunoprecipitation and chemical crosslinking analysis. A homo-bifunctional and non-cleavable agent with water-soluble and amine-reactive properties was employed to study protein oligomerisation in normal versus dystrophin-deficient skeletal muscles. Crosslinker-induced protein oligomerisation was determined by a combination of gel-shift analysis and immunoblotting. Results: Although proteomics was successfully applied for the identification of dystroglycan as a key component of the dystrophin-associated glycoprotein complex in the muscle membrane fraction, mass spectrometric analysis did not efficiently recognize this relatively low-abundance protein after immunoprecipitation or chemical crosslinking. As an alternative approach, comparative immunoblotting was used to evaluate the effects of chemical crosslinking. Antibody decoration of the crosslinked microsomal protein fraction from wild type versus the mdx-4cv mouse model of dystrophinopathy revealed oligomers that contain β-dystroglycan. The protein exhibited a comparable reduction in gel electrophoretic mobility in both normal and dystrophic samples. The membrane repair proteins dysferlin and myoferlin, which are essential components of fibre regeneration, as well as the caveolae-associated protein cavin-1, were also shown to exist in high-molecular mass complexes. Conclusions: The muscular dystrophy-related reduction in the concentration of β-dystroglycan, which forms in conjunction with its extracellular binding partner α-dystroglycan a critical plasmalemmal receptor for laminin-211, does not appear to alter its oligomeric status. Thus, independent of direct interactions with dystrophin, this sarcolemmal glycoprotein appears to exist in a supramolecular assembly in muscle.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, Bonn, D‑53115, Germany
| | | | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, Bonn, D‑53115, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland
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Beekman C, Janson AA, Baghat A, van Deutekom JC, Datson NA. Use of capillary Western immunoassay (Wes) for quantification of dystrophin levels in skeletal muscle of healthy controls and individuals with Becker and Duchenne muscular dystrophy. PLoS One 2018; 13:e0195850. [PMID: 29641567 PMCID: PMC5895072 DOI: 10.1371/journal.pone.0195850] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/31/2018] [Indexed: 01/14/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a neuromuscular disease characterized by progressive weakness of the skeletal and cardiac muscles. This X-linked disorder is caused by open reading frame disrupting mutations in the DMD gene, resulting in strong reduction or complete absence of dystrophin protein. In order to use dystrophin as a supportive or even surrogate biomarker in clinical studies on investigational drugs aiming at correcting the primary cause of the disease, the ability to reliably quantify dystrophin expression in muscle biopsies of DMD patients pre- and post-treatment is essential. Here we demonstrate the application of the ProteinSimple capillary immunoassay (Wes) method, a gel- and blot-free method requiring less sample, antibody and time to run than conventional Western blot assay. We optimized dystrophin quantification by Wes using 2 different antibodies and found it to be highly sensitive, reproducible and quantitative over a large dynamic range. Using a healthy control muscle sample as a reference and α-actinin as a protein loading/muscle content control, a panel of skeletal muscle samples consisting of 31 healthy controls, 25 Becker Muscle dystrophy (BMD) and 17 DMD samples was subjected to Wes analysis. In healthy controls dystrophin levels varied 3 to 5-fold between the highest and lowest muscle samples, with the reference sample representing the average of all 31 samples. In BMD muscle samples dystrophin levels ranged from 10% to 90%, with an average of 33% of the healthy muscle average, while for the DMD samples the average dystrophin level was 1.3%, ranging from 0.7% to 7% of the healthy muscle average. In conclusion, Wes is a suitable, efficient and reliable method for quantification of dystrophin expression as a biomarker in DMD clinical drug development.
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Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic serum biomarkers for neuromuscular diseases. Expert Rev Proteomics 2018; 15:277-291. [DOI: 10.1080/14789450.2018.1429923] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn, Germany
| | | | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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