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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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Golding AE, Li W, Blank PS, Cologna SM, Zimmerberg J. Relative quantification of progressive changes in healthy and dysferlin-deficient mouse skeletal muscle proteomes. Muscle Nerve 2023; 68:805-816. [PMID: 37706611 DOI: 10.1002/mus.27975] [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: 11/09/2022] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023]
Abstract
INTRODUCTION/AIMS Individuals with dysferlinopathies, a group of genetic muscle diseases, experience delay in the onset of muscle weakness. The cause of this delay and subsequent muscle wasting are unknown, and there are currently no clinical interventions to limit or prevent muscle weakness. To better understand molecular drivers of dysferlinopathies, age-dependent changes in the proteomic profile of skeletal muscle (SM) in wild-type (WT) and dysferlin-deficient mice were identified. METHODS Quadriceps were isolated from 6-, 18-, 42-, and 77-wk-old C57BL/6 (WT, Dysf+/+ ) and BLAJ (Dysf-/- ) mice (n = 3, 2 male/1 female or 1 male/2 female, 24 total). Whole-muscle proteomes were characterized using liquid chromatography-mass spectrometry with relative quantification using TMT10plex isobaric labeling. Principle component analysis was utilized to detect age-dependent proteomic differences over the lifespan of, and between, WT and dysferlin-deficient SM. The biological relevance of proteins with significant variation was established using Ingenuity Pathway Analysis. RESULTS Over 3200 proteins were identified between 6-, 18-, 42-, and 77-wk-old mice. In total, 46 proteins varied in aging WT SM (p < .01), while 365 varied in dysferlin-deficient SM. However, 569 proteins varied between aged-matched WT and dysferlin-deficient SM. Proteins with significant variation in expression across all comparisons followed distinct temporal trends. DISCUSSION Proteins involved in sarcolemma repair and regeneration underwent significant changes in SM over the lifespan of WT mice, while those associated with immune infiltration and inflammation were overly represented over the lifespan of dysferlin-deficient mice. The proteins identified herein are likely to contribute to our overall understanding of SM aging and dysferlinopathy disease progression.
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Affiliation(s)
- Adriana E Golding
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Section on Intracellular Protein Trafficking, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Wenping Li
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois, USA
| | - Paul S Blank
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois, USA
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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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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Dubreil L, Damane N, Fleurisson R, Charrier M, Pichon J, Leroux I, Schleder C, Ledevin M, Larcher T, Jamme F, Puentes J, Rouger K. Specific and label-free endogenous signature of dystrophic muscle by Synchrotron deep ultraviolet radiation. Sci Rep 2023; 13:10808. [PMID: 37402811 PMCID: PMC10319894 DOI: 10.1038/s41598-023-37762-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
Dystrophic muscle is characterized by necrosis/regeneration cycles, inflammation, and fibro-adipogenic development. Conventional histological stainings provide essential topographical data of this remodeling but may be limited to discriminate closely related pathophysiological contexts. They fail to mention microarchitecture changes linked to the nature and spatial distribution of tissue compartment components. We investigated whether label-free tissue autofluorescence revealed by Synchrotron deep ultraviolet (DUV) radiation could serve as an additional tool for monitoring dystrophic muscle remodeling. Using widefield microscopy with specific emission fluorescence filters and microspectroscopy defined by high spectral resolution, we analyzed samples from healthy dogs and two groups of dystrophic dogs: naïve (severely affected) and MuStem cell-transplanted (clinically stabilized) animals. Multivariate statistical analysis and machine learning approaches demonstrated that autofluorescence emitted at 420-480 nm by the Biceps femoris muscle effectively discriminates between healthy, dystrophic, and transplanted dog samples. Microspectroscopy showed that dystrophic dog muscle displays higher and lower autofluorescence due to collagen cross-linking and NADH respectively than that of healthy and transplanted dogs, defining biomarkers to evaluate the impact of cell transplantation. Our findings demonstrate that DUV radiation is a sensitive, label-free method to assess the histopathological status of dystrophic muscle using small amounts of tissue, with potential applications in regenerative medicine.
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Affiliation(s)
| | - Noreddine Damane
- Oniris, INRAE, PAnTher, 44300, Nantes, France
- IMT Atlantique, Lab-STICC, UMR CNRS 6285, 29238, Brest, France
| | | | | | | | | | | | | | | | - Frédéric Jamme
- Synchrotron SOLEIL, BP48, L'Orme Des Merisiers, 91120, Gif-Sur-Yvette, France
| | - John Puentes
- IMT Atlantique, Lab-STICC, UMR CNRS 6285, 29238, Brest, France
| | - Karl Rouger
- Oniris, INRAE, PAnTher, 44300, Nantes, France.
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Dowling P, Swandulla D, Ohlendieck K. Biochemical and proteomic insights into sarcoplasmic reticulum Ca 2+-ATPase complexes in skeletal muscles. Expert Rev Proteomics 2023; 20:125-142. [PMID: 37668143 DOI: 10.1080/14789450.2023.2255743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
INTRODUCTION Skeletal muscles contain large numbers of high-molecular-mass protein complexes in elaborate membrane systems. Integral membrane proteins are involved in diverse cellular functions including the regulation of ion handling, membrane homeostasis, energy metabolism and force transmission. AREAS COVERED The proteomic profiling of membrane proteins and large protein assemblies in skeletal muscles are outlined in this article. This includes a critical overview of the main biochemical separation techniques and the mass spectrometric approaches taken to study membrane proteins. As an illustrative example of an analytically challenging large protein complex, the proteomic detection and characterization of the Ca2+-ATPase of the sarcoplasmic reticulum is discussed. The biological role of this large protein complex during normal muscle functioning, in the context of fiber type diversity and in relation to mechanisms of physiological adaptations and pathophysiological abnormalities is evaluated from a proteomics perspective. EXPERT OPINION Mass spectrometry-based muscle proteomics has decisively advanced the field of basic and applied myology. Although it is technically challenging to study membrane proteins, innovations in protein separation methodology in combination with sensitive mass spectrometry and improved systems bioinformatics has allowed the detailed proteomic detection and characterization of skeletal muscle membrane protein complexes, such as Ca2+-pump proteins of the sarcoplasmic reticulum.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth Kildare, Ireland
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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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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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Mangiaterra S, Vincenzetti S, Rossi G, Marchegiani A, Gavazza A, Petit T, Sagratini G, Ricciutelli M, Cerquetella M. Evaluation of the Fecal Proteome in Healthy and Diseased Cheetahs (Acinonyx jubatus) Suffering from Gastrointestinal Disorders. Animals (Basel) 2022; 12:ani12182392. [PMID: 36139251 PMCID: PMC9494964 DOI: 10.3390/ani12182392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Fecal proteomics allows for the identification of proteins and peptides present in stools and is useful in finding possible new biomarkers for diagnosing and/or monitoring gastrointestinal (GI) disorders. In the present study, we investigated the fecal proteome in healthy and diseased cheetahs (Acinonyx jubatus). Captive individuals of this species frequently show gastrointestinal disorders characterized by recurrent episodes of diarrhea, rare episodes of vomiting and weight loss, associated with Helicobacter spp. infection. Fecal proteomic evaluation has been performed by two-dimensional electrophoresis followed by liquid chromatography-tandem mass spectrometry. In healthy cheetahs, the results showed the presence of the following proteins: collagen alpha-1 (II) chain, transthyretin, IgG Fc-binding protein, titin, dystonin, isopentenyl-diphosphate Delta-isomerase 1, sodium/potassium-transporting ATPase subunit alpha-1 and protein disulfide-isomerase A6. The presence of albumin isoforms was found only in diseased cheetahs. The present paper reports the study of the fecal proteome in the cheetah, evidences some differences between healthy and diseased patients and confirms, once again, the potential of fecal proteomics for the study of the GI environment, with promising developments regarding the identification of new diagnostic/monitoring markers.
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Affiliation(s)
- Sara Mangiaterra
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
- Correspondence:
| | - Silvia Vincenzetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Giacomo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Andrea Marchegiani
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Alessandra Gavazza
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | | | - Gianni Sagratini
- School of Pharmacy, University of Camerino, Via Sant’Agostino, 1, 32032 Camerino, MC, Italy
| | - Massimo Ricciutelli
- School of Pharmacy, University of Camerino, Via Sant’Agostino, 1, 32032 Camerino, MC, Italy
| | - Matteo Cerquetella
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
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Ravuri HG, Noor Z, Mills PC, Satake N, Sadowski P. Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. Proteomes 2022; 10:9. [PMID: 35324581 PMCID: PMC8953371 DOI: 10.3390/proteomes10010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/22/2022] [Indexed: 12/30/2022] Open
Abstract
Mass spectrometry-based plasma proteomics offers a major advance for biomarker discovery in the veterinary field, which has traditionally been limited to quantification of a small number of proteins using biochemical assays. The development of foundational data and tools related to sequential window acquisition of all theoretical mass spectra (SWATH)-mass spectrometry has allowed for quantitative profiling of a significant number of plasma proteins in humans and several animal species. Enabling SWATH in dogs enhances human biomedical research as a model species, and significantly improves diagnostic and disease monitoring capability. In this study, a comprehensive peptide spectral library specific to canine plasma proteome was developed and evaluated using SWATH for protein quantification in non-depleted dog plasma. Specifically, plasma samples were subjected to various orthogonal fractionation and digestion techniques, and peptide fragmentation data corresponding to over 420 proteins was collected. Subsequently, a SWATH-based assay was introduced that leveraged the developed resource and that enabled reproducible quantification of 400 proteins in non-depleted plasma samples corresponding to various disease conditions. The ability to profile the abundance of such a significant number of plasma proteins using a single method in dogs has the potential to accelerate biomarker discovery studies in this species.
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Affiliation(s)
- Halley Gora Ravuri
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Zainab Noor
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia;
| | - Paul C. Mills
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Nana Satake
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia; (H.G.R.); (P.C.M.)
| | - Pawel Sadowski
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Dowling P, Gargan S, Zweyer M, Sabir H, Swandulla D, Ohlendieck K. Proteomic profiling of carbonic anhydrase CA3 in skeletal muscle. Expert Rev Proteomics 2021; 18:1073-1086. [PMID: 34890519 DOI: 10.1080/14789450.2021.2017776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Carbonic anhydrase (CA) is a key enzyme that mediates the reversible hydration of carbon dioxide. Skeletal muscles contain high levels of the cytosolic isoform CA3. This enzyme has antioxidative function and plays a crucial role in the maintenance of intracellular pH homeostasis. AREAS COVERED Since elevated levels of serum CA3, often in combination with other muscle-specific proteins, are routinely used as a marker of general muscle damage, it was of interest to examine recent analyses of this enzyme carried out by modern proteomics. This review summarizes the mass spectrometry-based identification and evaluation of CA3 in normal, adapting, dystrophic, and aging skeletal muscle tissues. EXPERT OPINION The mass spectrometric characterization of CA3 confirmed this enzyme as a highly useful marker of both physiological and pathophysiological alterations in skeletal muscles. Cytosolic CA3 is clearly enriched in slow-twitching type I fibers, which makes it an ideal marker for studying fiber type shifting and muscle adaptations. Importantly, neuromuscular diseases feature distinct alterations in CA3 in skeletal muscle tissues versus biofluids, such as serum. Characteristic changes of CA3 in age-related muscle wasting and dystrophinopathy established this enzyme as a suitable biomarker candidate for differential diagnosis and monitoring of disease progression and therapeutic impact.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Margit Zweyer
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Hemmen Sabir
- 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, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
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11
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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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12
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van Westering TLE, Johansson HJ, Hanson B, Coenen-Stass AML, Lomonosova Y, Tanihata J, Motohashi N, Yokota T, Takeda S, Lehtiö J, Wood MJA, El Andaloussi S, Aoki Y, Roberts TC. Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy. Mol Cell Proteomics 2020; 19:2047-2068. [PMID: 32994316 PMCID: PMC7710136 DOI: 10.1074/mcp.ra120.002345] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/23/2022] Open
Abstract
The absence of the dystrophin protein in Duchenne muscular dystrophy (DMD) results in myofiber fragility and a plethora of downstream secondary pathologies. Although a variety of experimental therapies are in development, achieving effective treatments for DMD remains exceptionally challenging, not least because the pathological consequences of dystrophin loss are incompletely understood. Here we have performed proteome profiling in tibialis anterior muscles from two murine DMD models (mdx and mdx52) at three ages (8, 16, and 80 weeks of age), all n = 3. High-resolution isoelectric focusing liquid chromatography-tandem MS (HiRIEF-LC-MS/MS) was used to quantify the expression of 4974 proteins across all 27 samples. The two dystrophic models were found to be highly similar, whereas multiple proteins were differentially expressed relative to WT (C57BL/6) controls at each age. Furthermore, 1795 proteins were differentially expressed when samples were pooled across ages and dystrophic strains. These included numerous proteins associated with the extracellular matrix and muscle function that have not been reported previously. Pathway analysis revealed multiple perturbed pathways and predicted upstream regulators, which together are indicative of cross-talk between inflammatory, metabolic, and muscle growth pathways (e.g. TNF, INFγ, NF-κB, SIRT1, AMPK, PGC-1α, PPARs, ILK, and AKT/PI3K). Upregulation of CAV3, MVP and PAK1 protein expression was validated in dystrophic muscle by Western blot. Furthermore, MVP was upregulated during, but not required for, the differentiation of C2C12 myoblasts suggesting that this protein may affect muscle regeneration. This study provides novel insights into mutation-independent proteomic signatures characteristic of the dystrophic phenotype and its progression with aging.
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Affiliation(s)
| | - Henrik J Johansson
- Department of Oncology/Pathology, Cancer Proteomics Mass Spectrometry, SciLifeLab Stockholm, Karolinska Institutet, Stockholm, Sweden
| | - Britt Hanson
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Yulia Lomonosova
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Jun Tanihata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Norio Motohashi
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Toshifumi Yokota
- Department of Medical, Genetics, School of Human Development Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Janne Lehtiö
- Department of Oncology/Pathology, Cancer Proteomics Mass Spectrometry, SciLifeLab Stockholm, Karolinska Institutet, Stockholm, Sweden
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK; MDUK Oxford Neuromuscular Centre, Oxford, UK
| | | | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan.
| | - Thomas C Roberts
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK; Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden.
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13
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Al-Khalili Szigyarto C. Duchenne Muscular Dystrophy: recent advances in protein biomarkers and the clinical application. Expert Rev Proteomics 2020; 17:365-375. [PMID: 32713262 DOI: 10.1080/14789450.2020.1773806] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Early biomarker discovery studies have praised the value of their emerging results, predicting an unprecedented impact on health care. Biomarkers are expected to provide tests with increased specificity and sensitivity compared to existing measures, improve the decision-making process, and accelerate the development of therapies. For rare disorders, like Duchenne Muscular Dystrophy (DMD) such biomarkers can assist the development of therapies, therefore also helping to find a cure for the disease. AREA COVERED State-of-the-art technologies have been used to identify blood biomarkers for DMD and efforts have been coordinated to develop and promote translation of biomarkers for clinical practice. Biomarker translation to clinical practice is however, adjoined by challenges related to the complexity of the disease, involving numerous biological processes, and the limited sample resources. This review highlights the current progress on the development of biomarkers, describing the proteomics technologies used, the most promising findings and the challenges encountered. EXPERT OPINION Strategies for effective use of samples combined with orthogonal proteomics methods for protein quantification are essential for translating biomarkers to the patient's bed side. Progress is achieved only if strong evidence is provided that the biomarker constitutes a reliable indicator of the patient's health status for a specific context of use.
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Affiliation(s)
- Cristina Al-Khalili Szigyarto
- Science for Life Laboratory, KTH - Royal Institute of Technology , Solna, Sweden.,School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology , Stockholm, Sweden
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14
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Capitanio D, Moriggi M, Torretta E, Barbacini P, De Palma S, Viganò A, Lochmüller H, Muntoni F, Ferlini A, Mora M, Gelfi C. Comparative proteomic analyses of Duchenne muscular dystrophy and Becker muscular dystrophy muscles: changes contributing to preserve muscle function in Becker muscular dystrophy patients. J Cachexia Sarcopenia Muscle 2020; 11:547-563. [PMID: 31991054 PMCID: PMC7113522 DOI: 10.1002/jcsm.12527] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 11/08/2019] [Accepted: 11/24/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are characterized by muscle wasting leading to loss of ambulation in the first or third decade, respectively. In DMD, the lack of dystrophin hampers connections between intracellular cytoskeleton and cell membrane leading to repeated cycles of necrosis and regeneration associated with inflammation and loss of muscle ordered structure. BMD has a similar muscle phenotype but milder. Here, we address the question whether proteins at variance in BMD compared with DMD contribute to the milder phenotype in BMD, thus identifying a specific signature to be targeted for DMD treatment. METHODS Proteins extracted from skeletal muscle from DMD/BMD patients and young healthy subjects were either reduced and solubilized prior two-dimensional difference in gel electrophoresis/mass spectrometry differential analysis or tryptic digested prior label-free liquid chromatography with tandem mass spectrometry. Statistical analyses of proteins and peptides were performed by DeCyder and Perseus software and protein validation and verification by immunoblotting. RESULTS Proteomic results indicate minor changes in the extracellular matrix (ECM) protein composition in BMD muscles with retention of mechanotransduction signalling, reduced changes in cytoskeletal and contractile proteins. Conversely, in DMD patients, increased levels of several ECM cytoskeletal and contractile proteins were observed whereas some proteins of fast fibres and of Z-disc decreased. Detyrosinated alpha-tubulin was unchanged in BMD and increased in DMD although neuronal nitric oxide synthase was unchanged in BMD and greatly reduced in DMD. Metabolically, the tissue is characterized by a decrement of anaerobic metabolism both in DMD and BMD compared with controls, with increased levels of the glycogen metabolic pathway in BMD. Oxidative metabolism is severely compromised in DMD with impairment of malate shuttle; conversely, it is active in BMD supporting the tricarboxylic acid cycle and respiratory chain. Adipogenesis characterizes DMD, whereas proteins involved in fatty acids beta-oxidation are increased in BMD. Proteins involved in protein/amino acid metabolism, cell development, calcium handling, endoplasmic reticulum/sarcoplasmic reticulum stress response, and inflammation/immune response were increased in DMD. Both disorders are characterized by the impairment of N-linked protein glycosylation in the endoplasmic reticulum. Authophagy was decreased in DMD whereas it was retained in BMD. CONCLUSIONS The mechanosensing and metabolic disruption are central nodes of DMD/BMD phenotypes. The ECM proteome composition and the metabolic rewiring in BMD lead to preservation of energy levels supporting autophagy and cell renewal, thus promoting the retention of muscle function. Conversely, DMD patients are characterized by extracellular and cytoskeletal protein dysregulation and by metabolic restriction at the level of α-ketoglutarate leading to shortage of glutamate-derived molecules that over time triggers lipogenesis and lipotoxicity.
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Affiliation(s)
- Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Manuela Moriggi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Enrica Torretta
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Pietro Barbacini
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Sara De Palma
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Agnese Viganò
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.,Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London, Institute of Child Health, London, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Alessandra Ferlini
- Dubowitz Neuromuscular Centre, University College London, Institute of Child Health, London, UK.,Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
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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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Disease-specific and glucocorticoid-responsive serum biomarkers for Duchenne Muscular Dystrophy. Sci Rep 2019; 9:12167. [PMID: 31434957 PMCID: PMC6704115 DOI: 10.1038/s41598-019-48548-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Extensive biomarker discoveries for DMD have occurred in the past 7 years, and a vast array of these biomarkers were confirmed in independent cohorts and across different laboratories. In these previous studies, glucocorticoids and age were two major confounding variables. In this new study, using SomaScan technology and focusing on a subset of young DMD patients who were not yet treated with glucocorticoids, we identified 108 elevated and 70 decreased proteins in DMD relative to age matched healthy controls (p value < 0.05 after adjusting for multiple testing). The majority of the elevated proteins were muscle centric followed by cell adhesion, extracellular matrix proteins and a few pro-inflammatory proteins. The majority of decreased proteins were of cell adhesion, however, some had to do with cell differentiation and growth factors. Subsequent treatment of this group of DMD patients with glucocorticoids affected two major groups of pharmacodynamic biomarkers. The first group consisted of 80 serum proteins that were not associated with DMD and either decreased or increased following treatment with glucocorticoids, and therefore were reflective of a broader effect of glucocorticoids. The second group consisted of 17 serum proteins that were associated with DMD and these tended to normalize under treatment, thus reflecting physiologic effects of glucocorticoid treatment in DMD. In summary, we have identified a variety of circulating protein biomarkers that reflect the complex nature of DMD pathogenesis and response to glucocorticoids.
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17
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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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18
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Fecal Proteomic Analysis in Healthy Dogs and in Dogs Suffering from Food Responsive Diarrhea. ScientificWorldJournal 2019; 2019:2742401. [PMID: 30718980 PMCID: PMC6335819 DOI: 10.1155/2019/2742401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
Different laboratory markers are routinely used in the diagnosis and management of gastrointestinal (GI) disease in dogs. In the present study, starting from feces from both healthy dogs and dogs suffering from food responsive diarrhea (FRD), we tried to find proteins differently expressed in the two groups of dogs, by using a proteomic approach. Interestingly, we found that the immunoglobulin J-chain isoform 1 (species: Canis lupus familiaris) was identified only in diseased dogs (not in healthy). J-chain combines especially IgA monomers to IgA dimers and plays a crucial role for their secretions into mucosal interface. Being the first study of that kind in the dog, it is only possible to hypothesize that their presence could be likely due to an increased activation of the immune system or to a mucosal damage or both in FRD patients. Similarly, it is still impossible to assess whether this protein could be used as diagnostic/prognostic marker of GI disease; however, this study represents a promising first step toward fecal proteomics in canine GI disorders.
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19
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Bilić P, Kuleš J, Galan A, Gomes de Pontes L, Guillemin N, Horvatić A, Festa Sabes A, Mrljak V, Eckersall PD. Proteomics in Veterinary Medicine and Animal Science: Neglected Scientific Opportunities with Immediate Impact. Proteomics 2018; 18:e1800047. [DOI: 10.1002/pmic.201800047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/24/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Petra Bilić
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
| | - Josipa Kuleš
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
| | - Asier Galan
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
| | - Leticia Gomes de Pontes
- Botucatu Medical School; Sao Paulo State University (UNESP); Avenida José Barbosa de Barros, 1780; Botucatu 18610-307 Brazil
| | - Nicolas Guillemin
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
| | - Anita Horvatić
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
| | - Amanda Festa Sabes
- Department of Clinical and Veterinary Surgery; Faculty of Agrarian and Veterinary Sciences; Via de Acesso Paulo Donato Castellane s/n. 14884-900 Jaboticabal São Paulo Brazil
| | - Vladimir Mrljak
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
| | - Peter David Eckersall
- VetMedZg Proteomics Laboratory; Faculty of Veterinary Medicine; University of Zagreb; Heinzelova 55 10000 Zagreb Croatia
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medicine; Veterinary Medicine and Life Sciences; University of Glasgow; Glasgow G61 1QH UK
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20
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Catarinella G, Latella L. Bet on autophagy in the race against muscular dystrophies. Muscle Nerve 2018; 58:332-334. [PMID: 29742807 DOI: 10.1002/mus.26164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Giorgia Catarinella
- Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Lucia Latella
- Epigenetics and Regenerative Medicine, IRCCS Fondazione Santa Lucia, Rome, Italy.,Institute of Translational Pharmacology, National Research Council of Italy, Via Fosso del Cavaliere 100 Rome, Italy
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21
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Murphy S, Zweyer M, Henry M, Meleady P, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic analysis of the sarcolemma-enriched fraction from dystrophic mdx-4cv skeletal muscle. J Proteomics 2018; 191:212-227. [PMID: 29408692 DOI: 10.1016/j.jprot.2018.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/12/2018] [Accepted: 01/28/2018] [Indexed: 02/07/2023]
Abstract
The highly progressive neuromuscular disorder dystrophinopathy is triggered by primary abnormalities in the Dmd gene, which causes cytoskeletal instability and loss of sarcolemmal integrity. Comparative organellar proteomics was employed to identify sarcolemma-associated proteins with an altered concentration in dystrophic muscle tissue from the mdx-4cv mouse model of dystrophinopathy. A lectin agglutination method was used to prepare a sarcolemma-enriched fraction and resulted in the identification of 190 significantly changed protein species. Proteomics established differential expression patterns for key components of the muscle plasma membrane, cytoskeletal network, extracellular matrix, metabolic pathways, cellular stress response, protein synthesis, immune response and neuromuscular junction. The deficiency in dystrophin and drastic reduction in dystrophin-associated proteins appears to trigger (i) enhanced membrane repair involving myoferlin, dysferlin and annexins, (ii) increased protein synthesis and the compensatory up-regulation of cytoskeletal proteins, (iii) the decrease in the scaffolding protein periaxin and myelin PO involved in myelination of motor neurons, (iv) complex changes in bioenergetic pathways, (v) elevated levels of molecular chaperones to prevent proteotoxic effects, (vi) increased collagen deposition causing reactive myofibrosis, (vii) disturbed ion homeostasis at the sarcolemma and associated membrane systems, and (viii) a robust inflammatory response by the innate immune system in response to chronic muscle damage. SIGNIFICANCE: Duchenne muscular dystrophy is a devastating muscle wasting disease and represents the most frequently inherited neuromuscular disorder in humans. Genetic abnormalities in the Dmd gene cause a loss of sarcolemmal integrity and highly progressive muscle fibre degeneration. Changes in the neuromuscular system are associated with necrosis, fibrosis and inflammation. In order to evaluate secondary changes in the sarcolemma membrane system due to the lack of the membrane cytoskeletal protein dystrophin, comparative organellar proteomics was used to study the mdx-4cv mouse model of dystrophinopathy. Mass spectrometric analyses identified a variety of altered components of the extracellular matrix-sarcolemma-cytoskeleton axis in dystrophic muscles. This included proteins involved in membrane repair, cytoskeletal restoration, calcium homeostasis, cellular signalling, stress response, neuromuscular transmission and reactive myofibrosis, as well as immune cell infiltration. These pathobiochemical alterations agree with the idea of highly complex secondary changes in X-linked muscular dystrophy and support the concept that micro-rupturing of the dystrophin-deficient plasma membrane is at the core of muscle wasting pathology.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 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
| | - Rustam R Mundegar
- 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, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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22
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Abstract
Duchenne muscular dystrophy is a highly progressive neuromuscular disorder caused by primary abnormalities in the Dmd gene encoding the membrane cytoskeletal protein dystrophin. Dystrophinopathies are multi-systems disorders that are characterized by severe skeletal muscle wasting, with loss of independent ambulation in the early teenage years, followed by cardio-respiratory complications and premature death. Nonprogressive cognitive impairments are estimated to affect approximately one-third of dystrophic children. To identify the molecular mechanisms behind the impaired brain function in dystrophinopathy, liquid chromatography-based mass spectrometry offers an unbiased and technology-driven approach. In this chapter, we give a detailed description of a label-free mass spectrometric method to investigate proteome-wide changes in the dystrophin-deficient brain from a genetic mouse model of Duchenne muscular dystrophy.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Callan Building, North Campus, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland Maynooth, Callan Building, North Campus, Maynooth, Co. Kildare, Ireland.
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23
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Pambianco S, Giovarelli M, Perrotta C, Zecchini S, Cervia D, Di Renzo I, Moscheni C, Ripolone M, Violano R, Moggio M, Bassi MT, Puri PL, Latella L, Clementi E, De Palma C. Reversal of Defective Mitochondrial Biogenesis in Limb-Girdle Muscular Dystrophy 2D by Independent Modulation of Histone and PGC-1α Acetylation. Cell Rep 2017; 17:3010-3023. [PMID: 27974213 DOI: 10.1016/j.celrep.2016.11.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 06/10/2016] [Accepted: 11/11/2016] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial dysfunction occurs in many muscle degenerative disorders. Here, we demonstrate that mitochondrial biogenesis was impaired in limb-girdle muscular dystrophy (LGMD) 2D patients and mice and was associated with impaired OxPhos capacity. Two distinct approaches that modulated histones or peroxisome proliferator-activated receptor-gamma coactivator 1 α (PGC-1α) acetylation exerted equivalent functional effects by targeting different mitochondrial pathways (mitochondrial biogenesis or fatty acid oxidation[FAO]). The histone deacetylase inhibitor Trichostatin A (TSA) changed chromatin assembly at the PGC-1α promoter, restored mitochondrial biogenesis, and enhanced muscle oxidative capacity. Conversely, nitric oxide (NO) triggered post translation modifications of PGC-1α and induced FAO, recovering the bioenergetics impairment of muscles but shunting the defective mitochondrial biogenesis. In conclusion, a transcriptional blockade of mitochondrial biogenesis occurred in LGMD-2D and could be recovered by TSA changing chromatin conformation, or it could be overcome by NO activating a mitochondrial salvage pathway.
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Affiliation(s)
- Sarah Pambianco
- Department of Biomedical and Clinical Sciences "Luigi Sacco," Università degli Studi di Milano, 20157 Milano, Italy
| | - Matteo Giovarelli
- Department of Biomedical and Clinical Sciences "Luigi Sacco," Università degli Studi di Milano, 20157 Milano, Italy
| | - Cristiana Perrotta
- Department of Biomedical and Clinical Sciences "Luigi Sacco," Università degli Studi di Milano, 20157 Milano, Italy
| | - Silvia Zecchini
- Department of Biomedical and Clinical Sciences, Unit of Clinical Pharmacology, University Hospital "Luigi Sacco"-ASST Fatebenefratelli Sacco, National Research Council-Institute of Neuroscience, Università degli Studi di Milano, 20157 Milano, Italy
| | - Davide Cervia
- Department of Biomedical and Clinical Sciences "Luigi Sacco," Università degli Studi di Milano, 20157 Milano, Italy; Department for Innovation in Biological, Agro-food and Forest systems, Università degli Studi della Tuscia, 01100 Viterbo, Italy
| | - Ilaria Di Renzo
- Department of Biomedical and Clinical Sciences "Luigi Sacco," Università degli Studi di Milano, 20157 Milano, Italy
| | - Claudia Moscheni
- Department of Biomedical and Clinical Sciences "Luigi Sacco," Università degli Studi di Milano, 20157 Milano, Italy
| | - Michela Ripolone
- Neuromuscular Unit, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, 20122 Milano, Italy
| | - Raffaella Violano
- Neuromuscular Unit, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, 20122 Milano, Italy
| | - Maurizio Moggio
- Neuromuscular Unit, Dino Ferrari Centre, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, 20122 Milano, Italy
| | | | - Pier Lorenzo Puri
- Epigenetics and Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, 00142 Roma, Italy; Sanford Children's Health Research Center, Sanford Prebys Burnham Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lucia Latella
- Epigenetics and Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, 00142 Roma, Italy; National Research Council-Institute of Translational Pharmacology, 00179 Roma, Italy
| | - Emilio Clementi
- Department of Biomedical and Clinical Sciences, Unit of Clinical Pharmacology, University Hospital "Luigi Sacco"-ASST Fatebenefratelli Sacco, National Research Council-Institute of Neuroscience, Università degli Studi di Milano, 20157 Milano, Italy; IRCCS Eugenio Medea, 23842 Bosisio Parini, Italy.
| | - Clara De Palma
- Department of Biomedical and Clinical Sciences, Unit of Clinical Pharmacology, University Hospital "Luigi Sacco"-ASST Fatebenefratelli Sacco, National Research Council-Institute of Neuroscience, Università degli Studi di Milano, 20157 Milano, Italy.
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24
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Lardenois A, Jagot S, Lagarrigue M, Guével B, Ledevin M, Larcher T, Dubreil L, Pineau C, Rouger K, Guével L. Quantitative proteome profiling of dystrophic dog skeletal muscle reveals a stabilized muscular architecture and protection against oxidative stress after systemic delivery of MuStem cells. Proteomics 2017; 16:2028-42. [PMID: 27246553 DOI: 10.1002/pmic.201600002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/02/2016] [Accepted: 05/30/2016] [Indexed: 12/23/2022]
Abstract
Proteomic profiling plays a decisive role in the elucidation of molecular signatures representative of a specific clinical context. MuStem cell based therapy represents a promising approach for clinical applications to cure Duchenne muscular dystrophy (DMD). To expand our previous studies collected in the clinically relevant DMD animal model, we decided to investigate the skeletal muscle proteome 4 months after systemic delivery of allogenic MuStem cells. Quantitative proteomics with isotope-coded protein labeling was used to compile quantitative changes in the protein expression profiles of muscle in transplanted Golden Retriever muscular dystrophy (GRMD) dogs as compared to Golden Retriever muscular dystrophy dogs. A total of 492 proteins were quantified, including 25 that were overrepresented and 46 that were underrepresented after MuStem cell transplantation. Interestingly, this study demonstrates that somatic stem cell therapy impacts on the structural integrity of the muscle fascicle by acting on fibers and its connections with the extracellular matrix. We also show that cell infusion promotes protective mechanisms against oxidative stress and favors the initial phase of muscle repair. This study allows us to identify putative candidates for tissue markers that might be of great value in objectively exploring the clinical benefits resulting from our cell-based therapy for DMD. All MS data have been deposited in the ProteomeXchange with identifier PXD001768 (http://proteomecentral.proteomexchange.org/dataset/PXD001768).
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Affiliation(s)
- Aurélie Lardenois
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Sabrina Jagot
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France.,Université de Nantes, Nantes, France
| | - Mélanie Lagarrigue
- Protim, Irset Inserm UMR 1085, Campus de Beaulieu, Rennes, France.,Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Blandine Guével
- Protim, Irset Inserm UMR 1085, Campus de Beaulieu, Rennes, France.,Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Mireille Ledevin
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Thibaut Larcher
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Laurence Dubreil
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Charles Pineau
- Protim, Irset Inserm UMR 1085, Campus de Beaulieu, Rennes, France.,Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Karl Rouger
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Laëtitia Guével
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France.,Université de Nantes, Nantes, France
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25
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Murphy S, Brinkmeier H, Krautwald M, Henry M, Meleady P, Ohlendieck K. Proteomic profiling of the dystrophin complex and membrane fraction from dystrophic mdx muscle reveals decreases in the cytolinker desmoglein and increases in the extracellular matrix stabilizers biglycan and fibronectin. J Muscle Res Cell Motil 2017; 38:251-268. [DOI: 10.1007/s10974-017-9478-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/05/2017] [Indexed: 01/14/2023]
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26
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Nio Y, Tanaka M, Hirozane Y, Muraki Y, Okawara M, Hazama M, Matsuo T. Phosphodiesterase 4 inhibitor and phosphodiesterase 5 inhibitor combination therapy has antifibrotic and anti‐inflammatory effects in mdx mice with Duchenne muscular dystrophy. FASEB J 2017; 31:5307-5320. [DOI: 10.1096/fj.201700249r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/25/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yasunori Nio
- Extra Value Generation and General Medicine Drug Discovery UnitTakeda Pharmaceutical Company Limited Fujisawa Japan
| | - Masayuki Tanaka
- Inflammation Drug Discovery UnitTakeda Pharmaceutical Company Limited Fujisawa Japan
| | - Yoshihiko Hirozane
- Biomolecular Research LaboratoriesPharmaceutical Research DivisionTakeda Pharmaceutical Company Limited Fujisawa Japan
| | - Yo Muraki
- Extra Value Generation and General Medicine Drug Discovery UnitTakeda Pharmaceutical Company Limited Fujisawa Japan
| | - Mitsugi Okawara
- Extra Value Generation and General Medicine Drug Discovery UnitTakeda Pharmaceutical Company Limited Fujisawa Japan
| | - Masatoshi Hazama
- Extra Value Generation and General Medicine Drug Discovery UnitTakeda Pharmaceutical Company Limited Fujisawa Japan
| | - Takanori Matsuo
- Extra Value Generation and General Medicine Drug Discovery UnitTakeda Pharmaceutical Company Limited Fujisawa Japan
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27
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Carr SJ, Zahedi RP, Lochmüller H, Roos A. Mass spectrometry-based protein analysis to unravel the tissue pathophysiology in Duchenne muscular dystrophy. Proteomics Clin Appl 2017. [DOI: 10.1002/prca.201700071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stephanie J. Carr
- John Walton Muscular Dystrophy Research Centre; Institute of Genetic Medicine; Newcastle University; Newcastle upon Tyne UK
| | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften, ISAS e.V.; Dortmund Germany
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre; Institute of Genetic Medicine; Newcastle University; Newcastle upon Tyne UK
| | - Andreas Roos
- John Walton Muscular Dystrophy Research Centre; Institute of Genetic Medicine; Newcastle University; Newcastle upon Tyne UK
- Leibniz-Institut für Analytische Wissenschaften, ISAS e.V.; Dortmund Germany
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28
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Fröhlich T, Kemter E, Flenkenthaler F, Klymiuk N, Otte KA, Blutke A, Krause S, Walter MC, Wanke R, Wolf E, Arnold GJ. Progressive muscle proteome changes in a clinically relevant pig model of Duchenne muscular dystrophy. Sci Rep 2016; 6:33362. [PMID: 27634466 PMCID: PMC5025886 DOI: 10.1038/srep33362] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 08/24/2016] [Indexed: 01/16/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by genetic deficiency of dystrophin and characterized by massive structural and functional changes of skeletal muscle tissue, leading to terminal muscle failure. We recently generated a novel genetically engineered pig model reflecting pathological hallmarks of human DMD better than the widely used mdx mouse. To get insight into the hierarchy of molecular derangements during DMD progression, we performed a proteome analysis of biceps femoris muscle samples from 2-day-old and 3-month-old DMD and wild-type (WT) pigs. The extent of proteome changes in DMD vs. WT muscle increased markedly with age, reflecting progression of the pathological changes. In 3-month-old DMD muscle, proteins related to muscle repair such as vimentin, nestin, desmin and tenascin C were found to be increased, whereas a large number of respiratory chain proteins were decreased in abundance in DMD muscle, indicating serious disturbances in aerobic energy production and a reduction of functional muscle tissue. The combination of proteome data for fiber type specific myosin heavy chain proteins and immunohistochemistry showed preferential degeneration of fast-twitch fiber types in DMD muscle. The stage-specific proteome changes detected in this large animal model of clinically severe muscular dystrophy provide novel molecular readouts for future treatment trials.
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Affiliation(s)
- Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Florian Flenkenthaler
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Nikolai Klymiuk
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Kathrin A Otte
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Andreas Blutke
- Institute of Veterinary Pathology, Centre for Clinical Veterinary Medicine, LMU Munich, Veterinärstr. 13, D-80539 Munich, Germany
| | - Sabine Krause
- Friedrich-Baur-Institute, Department of Neurology, LMU Munich, Ziemssenstr. 1, D-80336 Munich, Germany
| | - Maggie C Walter
- Friedrich-Baur-Institute, Department of Neurology, LMU Munich, Ziemssenstr. 1, D-80336 Munich, Germany
| | - Rüdiger Wanke
- Institute of Veterinary Pathology, Centre for Clinical Veterinary Medicine, LMU Munich, Veterinärstr. 13, D-80539 Munich, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany.,Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
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29
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Dowling P, Murphy S, Ohlendieck K. Proteomic profiling of muscle fibre type shifting in neuromuscular diseases. Expert Rev Proteomics 2016; 13:783-99. [DOI: 10.1080/14789450.2016.1209416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Fuller HR, Graham LC, Llavero Hurtado M, Wishart TM. Understanding the molecular consequences of inherited muscular dystrophies: advancements through proteomic experimentation. Expert Rev Proteomics 2016; 13:659-71. [PMID: 27329572 DOI: 10.1080/14789450.2016.1202768] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/14/2016] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Proteomic techniques offer insights into the molecular perturbations occurring in muscular-dystrophies (MD). Revisiting published datasets can highlight conserved downstream molecular alterations, which may be worth re-assessing to determine whether their experimental manipulation is capable of modulating disease severity. AREAS COVERED Here, we review the MD literature, highlighting conserved molecular insights warranting mechanistic investigation for therapeutic potential. We also describe a workflow currently proving effective for efficient identification of biomarkers & therapeutic targets in other neurodegenerative conditions, upon which future MD proteomic investigations could be modelled. Expert commentary: Studying disease models can be useful for identifying biomarkers and model specific degenerative cascades, but rarely offer translatable mechanistic insights into disease pathology. Conversely, direct analysis of human samples undergoing degeneration presents challenges derived from complex chronic degenerative molecular processes. This requires a carefully planed & reproducible experimental paradigm accounting for patient selection through to grouping by disease severity and ending with proteomic data filtering and processing.
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Affiliation(s)
- Heidi R Fuller
- a Wolfson Centre for Inherited Neuromuscular Disease , RJAH Orthopaedic Hospital , Oswestry , UK
- b Institute for Science and Technology in Medicine , Keele University , Staffordshire , UK
| | - Laura C Graham
- c Euan MacDonald Centre for Motor Neurone Disease Research , University of Edinburgh , Edinburgh , UK
- d Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Edinburgh , UK
| | - Maica Llavero Hurtado
- c Euan MacDonald Centre for Motor Neurone Disease Research , University of Edinburgh , Edinburgh , UK
- d Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Edinburgh , UK
| | - Thomas M Wishart
- c Euan MacDonald Centre for Motor Neurone Disease Research , University of Edinburgh , Edinburgh , UK
- d Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Studies , University of Edinburgh , Edinburgh , UK
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31
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Arecco N, Clarke CJ, Jones FK, Simpson DM, Mason D, Beynon RJ, Pisconti A. Elastase levels and activity are increased in dystrophic muscle and impair myoblast cell survival, proliferation and differentiation. Sci Rep 2016; 6:24708. [PMID: 27241590 PMCID: PMC4886533 DOI: 10.1038/srep24708] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/04/2016] [Indexed: 01/31/2023] Open
Abstract
In Duchenne muscular dystrophy, progressive loss of muscle tissue is accompanied by fibrosis, chronic inflammation and reduced muscle regenerative capacity. Although much is known about the development of fibrosis and chronic inflammation in muscular dystrophy, less is known about how they are mechanistically linked to loss of muscle regenerative capacity. We have developed a proteomics method to discover dystrophy-associated changes in the muscle progenitor cell niche, which identified serine proteases, and especially neutrophil elastase, as candidates. We show that elastase activity is increased in dystrophic (mdx4cv) muscle and impairs myoblast survival in culture. While the effect of elastase on C2C12 cell survival correlates with the kinetics of elastase-mediated degradation of the substrate to which the cells adhere, the effect of elastase on satellite cell-derived primary myoblast growth and differentiation is substrate-independent and even more dramatic than the effect on C2C12 cells, suggesting a detrimental role for elastase on myogenesis in vivo. Additionally, elastase impairs differentiation of both primary and C2C12 myoblasts into myotubes. Our findings evidence the importance of neutrophil-mediated inflammation in muscular dystrophy and indicate elastase-mediated regulation of myoblast behaviour as a potential mechanism underlying loss of regenerative capacity in dystrophic muscle.
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Affiliation(s)
- N Arecco
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - C J Clarke
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - F K Jones
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - D M Simpson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.,Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - D Mason
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.,Centre for Cell Imaging, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - R J Beynon
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.,Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - A Pisconti
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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32
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Robriquet F, Babarit C, Larcher T, Dubreil L, Ledevin M, Goubin H, Rouger K, Guével L. Identification in GRMD dog muscle of critical miRNAs involved in pathophysiology and effects associated with MuStem cell transplantation. BMC Musculoskelet Disord 2016; 17:209. [PMID: 27170302 PMCID: PMC4865027 DOI: 10.1186/s12891-016-1060-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/03/2016] [Indexed: 11/10/2022] Open
Abstract
Background Duchenne muscular dystrophy (DMD) is an X-linked muscle disease that leads to fibre necrosis and progressive paralysis. At present, DMD remains a lethal disease without any effective treatment, requiring a better understanding of the pathophysiological processes and comprehensive assessment of the newly identified therapeutic strategies. MicroRNAs including members of the muscle-specific myomiR family have been identified as being deregulated in muscle of DMD patients and in mdx mice used as a model for DMD. In recent years, the Golden Retriever muscular dystrophy (GRMD) dog has appeared as the crucial animal model for objectively assessing the potential of new innovative approaches. Here, we first aim at establishing the muscle expression pattern of five selected miRNAs in this clinically relevant model to determine if they are similarly affected compared with other DMD contexts. Second, we attempt to show whether these miRNAs could be impacted by the systemic delivery of a promising stem cell candidate (referred to as MuStem cells) to implement our knowledge on its mode of action and/or identify markers associated with cell therapy efficacy. Methods A comparative study of miRNAs expression levels and cellular localization was performed on 9-month-old healthy dogs, as well as on three sub-sets of GRMD dog (without immunosuppression or cell transplantation, with continuous immunosuppressive regimen and with MuStem cell transplantation under immunosuppression), using RT-qPCR and in situ hybridization. Results We find that miR-222 expression is markedly up-regulated in GRMD dog muscle compared to healthy dog, while miR-486 tends to be down-expressed. Intriguingly, the expression of miR-1, miR-133a and miR-206 does not change. In situ hybridization exploration reveals, for the first time, that miR-486 and miR-206 are mainly localized in newly regenerated fibres in GRMD dog muscle. In addition, we show that cyclosporine-based immunosuppression, classically used in allogeneic cell transplantation, exclusively impacts the miR-206 expression. Finally, we demonstrate that intra-arterial administration of MuStem cells results in up-regulation of miR-133a and miR-222 concomitantly with a down-expression of two sarcomeric proteins corresponding to miR-222 targets. Conclusion We point out a differential muscle expression of miR-222 and miR-486 associated with the pathophysiology of the clinically relevant GRMD dog model with a tissue localization focused on regenerated fibres. We also establish a modified expression of miR-133a and miR-222 subsequent to MuStem cell infusion. Electronic supplementary material The online version of this article (doi:10.1186/s12891-016-1060-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florence Robriquet
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France.,Université de Nantes, F-44322, Nantes, France
| | - Candice Babarit
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France
| | - Thibaut Larcher
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France
| | - Laurence Dubreil
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France
| | - Mireille Ledevin
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France
| | - Hélicia Goubin
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France
| | - Karl Rouger
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France
| | - Laëtitia Guével
- INRA UMR 703 PAnTher "Physiopathologie Animale et bioThérapie du muscle et du système nerveux", Oniris, Atlanpôle - La Chantrerie, Route du Gachet C.S. 40706, F-44307, Nantes Cedex 03, France. .,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307, Nantes, France. .,Université de Nantes, F-44322, Nantes, France.
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33
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CanisOme — The protein signatures of Canis lupus familiaris diseases. J Proteomics 2016; 136:193-201. [DOI: 10.1016/j.jprot.2016.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/19/2015] [Accepted: 01/08/2016] [Indexed: 12/19/2022]
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34
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Murphy S, Ohlendieck K. The biochemical and mass spectrometric profiling of the dystrophin complexome from skeletal muscle. Comput Struct Biotechnol J 2015; 14:20-7. [PMID: 26793286 PMCID: PMC4688399 DOI: 10.1016/j.csbj.2015.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 12/12/2022] Open
Abstract
The development of advanced mass spectrometric methodology has decisively enhanced the analytical capabilities for studies into the composition and dynamics of multi-subunit protein complexes and their associated components. Large-scale complexome profiling is an approach that combines the systematic isolation and enrichment of protein assemblies with sophisticated mass spectrometry-based identification methods. In skeletal muscles, the membrane cytoskeletal protein dystrophin of 427 kDa forms tight interactions with a variety of sarcolemmal, cytosolic and extracellular proteins, which in turn associate with key components of the extracellular matrix and the intracellular cytoskeleton. A major function of this enormous assembly of proteins, including dystroglycans, sarcoglycans, syntrophins, dystrobrevins, sarcospan, laminin and cortical actin, is postulated to stabilize muscle fibres during the physical tensions of continuous excitation-contraction-relaxation cycles. This article reviews the evidence from recent proteomic studies that have focused on the characterization of the dystrophin-glycoprotein complex and its central role in the establishment of the cytoskeleton-sarcolemma-matrisome axis. Proteomic findings suggest a close linkage of the core dystrophin complex with a variety of protein species, including tubulin, vimentin, desmin, annexin, proteoglycans and collagens. Since the almost complete absence of dystrophin is the underlying cause for X-linked muscular dystrophy, a more detailed understanding of the composition, structure and plasticity of the dystrophin complexome may have considerable biomedical implications.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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35
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Chan JCY, Zhou L, Chan ECY. The Isotope-Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications. ACTA ACUST UNITED AC 2015; 82:23.2.1-23.2.19. [PMID: 26521713 DOI: 10.1002/0471140864.ps2302s82] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The isotope-coded affinity tag (ICAT) technique has been applied to measure pairwise changes in protein expression through differential stable isotopic labeling of proteins or peptides followed by identification and quantification using a mass spectrometer. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). Due to the cysteine-specificity of the ICAT reagents, the ICAT technique has also been applied to perform relative quantitation of cysteine redox modifications such as oxidation and nitrosylation. This unit describes both protein quantitation and profiling of cysteine redox modifications using the ICAT technique.
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Affiliation(s)
| | - Lei Zhou
- Singapore Eye Research Institute, Singapore
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36
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Roberts TC, Johansson HJ, McClorey G, Godfrey C, Blomberg KEM, Coursindel T, Gait MJ, Smith CIE, Lehtiö J, El Andaloussi S, Wood MJA. Multi-level omics analysis in a murine model of dystrophin loss and therapeutic restoration. Hum Mol Genet 2015; 24:6756-68. [PMID: 26385637 PMCID: PMC4634378 DOI: 10.1093/hmg/ddv381] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/11/2015] [Indexed: 01/16/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a classical monogenic disorder, a model disease for genomic studies and a priority candidate for regenerative medicine and gene therapy. Although the genetic cause of DMD is well known, the molecular pathogenesis of disease and the response to therapy are incompletely understood. Here, we describe analyses of protein, mRNA and microRNA expression in the tibialis anterior of the mdx mouse model of DMD. Notably, 3272 proteins were quantifiable and 525 identified as differentially expressed in mdx muscle (P < 0.01). Therapeutic restoration of dystrophin by exon skipping induced widespread shifts in protein and mRNA expression towards wild-type expression levels, whereas the miRNome was largely unaffected. Comparison analyses between datasets showed that protein and mRNA ratios were only weakly correlated (r = 0.405), and identified a multitude of differentially affected cellular pathways, upstream regulators and predicted miRNA-target interactions. This study provides fundamental new insights into gene expression and regulation in dystrophic muscle.
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Affiliation(s)
- Thomas C Roberts
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK, Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Henrik J Johansson
- Department of Oncology/Pathology, Cancer Proteomics Mass Spectrometry, SciLifeLab Stockholm, Karolinska Institutet, Stockholm SE-171 21, Sweden
| | - Graham McClorey
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - K Emelie M Blomberg
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge SE-141 86, Sweden and
| | - Thibault Coursindel
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Michael J Gait
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - C I Edvard Smith
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge SE-141 86, Sweden and
| | - Janne Lehtiö
- Department of Oncology/Pathology, Cancer Proteomics Mass Spectrometry, SciLifeLab Stockholm, Karolinska Institutet, Stockholm SE-171 21, Sweden
| | - Samir El Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK, Department of Laboratory Medicine, Karolinska Institutet, Huddinge SE-141 86, Sweden and
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK,
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Murphy S, Zweyer M, Mundegar RR, Henry M, Meleady P, Swandulla D, Ohlendieck K. Concurrent Label-Free Mass Spectrometric Analysis of Dystrophin Isoform Dp427 and the Myofibrosis Marker Collagen in Crude Extracts from mdx-4cv Skeletal Muscles. Proteomes 2015; 3:298-327. [PMID: 28248273 PMCID: PMC5217383 DOI: 10.3390/proteomes3030298] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/18/2015] [Accepted: 09/03/2015] [Indexed: 01/06/2023] Open
Abstract
The full-length dystrophin protein isoform of 427 kDa (Dp427), the absence of which represents the principal abnormality in X-linked muscular dystrophy, is difficult to identify and characterize by routine proteomic screening approaches of crude tissue extracts. This is probably related to its large molecular size, its close association with the sarcolemmal membrane, and its existence within a heterogeneous glycoprotein complex. Here, we used a careful extraction procedure to isolate the total protein repertoire from normal versus dystrophic mdx-4cv skeletal muscles, in conjunction with label-free mass spectrometry, and successfully identified Dp427 by proteomic means. In contrast to a considerable number of previous comparative studies of the total skeletal muscle proteome, using whole tissue proteomics we show here for the first time that the reduced expression of this membrane cytoskeletal protein is the most significant alteration in dystrophinopathy. This agrees with the pathobiochemical concept that the almost complete absence of dystrophin is the main defect in Duchenne muscular dystrophy and that the mdx-4cv mouse model of dystrophinopathy exhibits only very few revertant fibers. Significant increases in collagens and associated fibrotic marker proteins, such as fibronectin, biglycan, asporin, decorin, prolargin, mimecan, and lumican were identified in dystrophin-deficient muscles. The up-regulation of collagen in mdx-4cv muscles was confirmed by immunofluorescence microscopy and immunoblotting. Thus, this is the first mass spectrometric study of crude tissue extracts that puts the proteomic identification of dystrophin in its proper pathophysiological context.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Co. Kildare, Ireland.
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Rustam R Mundegar
- Department of Physiology II, University of Bonn, Bonn D-53115, 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
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Co. Kildare, Ireland.
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Holland A, Murphy S, Dowling P, Ohlendieck K. Pathoproteomic profiling of the skeletal muscle matrisome in dystrophinopathy associated myofibrosis. Proteomics 2015; 16:345-66. [PMID: 26256116 DOI: 10.1002/pmic.201500158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/12/2015] [Accepted: 07/24/2015] [Indexed: 12/14/2022]
Abstract
The gradual accumulation of collagen and associated proteins of the extracellular matrix is a crucial myopathological parameter of many neuromuscular disorders. Progressive tissue damage and fibrosis play a key pathobiochemical role in the dysregulation of contractile functions and often correlates with poor motor outcome in muscular dystrophies. Following a brief introduction into the role of the extracellular matrix in skeletal muscles, we review here the proteomic profiling of myofibrosis and its intrinsic role in X-linked muscular dystrophy. Although Duchenne muscular dystrophy is primarily a disease of the membrane cytoskeleton, one of its most striking histopathological features is a hyperactive connective tissue and tissue scarring. We outline the identification of novel factors involved in the modulation of the extracellular matrix in muscular dystrophy, such as matricellular proteins. The establishment of novel proteomic markers will be helpful in improving the diagnosis, prognosis, and therapy monitoring in relation to fibrotic substitution of contractile tissue. In the future, the prevention of fibrosis will be crucial for providing optimum conditions to apply novel pharmacological treatments, as well as establish cell-based approaches or gene therapeutic interventions. The elimination of secondary abnormalities in the matrisome promises to reduce tissue scarring and the loss of skeletal muscle elasticity.
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Affiliation(s)
- Ashling Holland
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Abstract
Duchenne muscular dystrophy is the most common form of muscular dystrophy. Genetic and biochemical research over the years has characterized the cause, pathophysiology and development of the disease providing several potential therapeutic targets and/or biomarkers. High throughput - omic technologies have provided a comprehensive understanding of the changes occurring in dystrophic muscles. Murine and canine animal models have been a valuable source to profile muscles and body fluids, thus providing candidate biomarkers that can be evaluated in patients. This review will illustrate known circulating biomarkers that could track disease progression and response to therapy in patients affected by Duchenne muscular dystrophy. We present an overview of the transcriptomic, proteomic, metabolomics and lipidomic biomarkers described in literature. We show how studies in muscle tissue have led to the identification of serum and urine biomarkers and we highlight the importance of evaluating biomarkers as possible surrogate endpoints to facilitate regulatory processes for new medicinal products.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Institute of Human Genetics, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, UK
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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40
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Holland A, Henry M, Meleady P, Winkler CK, Krautwald M, Brinkmeier H, Ohlendieck K. Comparative Label-Free Mass Spectrometric Analysis of Mildly versus Severely Affected mdx Mouse Skeletal Muscles Identifies Annexin, Lamin, and Vimentin as Universal Dystrophic Markers. Molecules 2015; 20:11317-44. [PMID: 26102067 PMCID: PMC6272583 DOI: 10.3390/molecules200611317] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/10/2015] [Accepted: 06/12/2015] [Indexed: 11/16/2022] Open
Abstract
The primary deficiency in the membrane cytoskeletal protein dystrophin results in complex changes in dystrophic muscles. In order to compare the degree of secondary alterations in differently affected subtypes of skeletal muscles, we have conducted a global analysis of proteome-wide changes in various dystrophin-deficient muscles. In contrast to the highly degenerative mdx diaphragm muscle, which showed considerable alterations in 35 distinct proteins, the spectrum of mildly to moderately dystrophic skeletal muscles, including interosseus, flexor digitorum brevis, soleus, and extensor digitorum longus muscle, exhibited a smaller number of changed proteins. Compensatory mechanisms and/or cellular variances may be responsible for differing secondary changes in individual mdx muscles. Label-free mass spectrometry established altered expression levels for diaphragm proteins associated with contraction, energy metabolism, the cytoskeleton, the extracellular matrix and the cellular stress response. Comparative immunoblotting verified the differences in the degree of secondary changes in dystrophin-deficient muscles and showed that the up-regulation of molecular chaperones, the compensatory increase in proteins of the intermediate filaments, the fibrosis-related increase in collagen levels and the pathophysiological decrease in calcium binding proteins is more pronounced in mdx diaphragm as compared to the less severely affected mdx leg muscles. Annexin, lamin, and vimentin were identified as universal dystrophic markers.
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Affiliation(s)
- Ashling Holland
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - 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.
| | - Claudia K Winkler
- Institute of Pathophysiology, University Medicine Greifswald, D-17495 Karlsburg, Germany.
| | - Mirjam Krautwald
- Institute of Pathophysiology, University Medicine Greifswald, D-17495 Karlsburg, Germany.
| | - Heinrich Brinkmeier
- Institute of Pathophysiology, University Medicine Greifswald, D-17495 Karlsburg, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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41
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Murphy S, Henry M, Meleady P, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Simultaneous Pathoproteomic Evaluation of the Dystrophin-Glycoprotein Complex and Secondary Changes in the mdx-4cv Mouse Model of Duchenne Muscular Dystrophy. BIOLOGY 2015; 4:397-423. [PMID: 26067837 PMCID: PMC4498307 DOI: 10.3390/biology4020397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022]
Abstract
In skeletal muscle, the dystrophin-glycoprotein complex forms a membrane-associated assembly of relatively low abundance, making its detailed proteomic characterization in normal versus dystrophic tissues technically challenging. To overcome this analytical problem, we have enriched the muscle membrane fraction by a minimal differential centrifugation step followed by the comprehensive label-free mass spectrometric analysis of microsomal membrane preparations. This organelle proteomic approach successfully identified dystrophin and its binding partners in normal versus dystrophic hind limb muscles. The introduction of a simple pre-fractionation step enabled the simultaneous proteomic comparison of the reduction in the dystrophin-glycoprotein complex and secondary changes in the mdx-4cv mouse model of dystrophinopathy in a single analytical run. The proteomic screening of the microsomal fraction from dystrophic hind limb muscle identified the full-length dystrophin isoform Dp427 as the most drastically reduced protein in dystrophinopathy, demonstrating the remarkable analytical power of comparative muscle proteomics. Secondary pathoproteomic expression patterns were established for 281 proteins, including dystrophin-associated proteins and components involved in metabolism, signalling, contraction, ion-regulation, protein folding, the extracellular matrix and the cytoskeleton. Key findings were verified by immunoblotting. Increased levels of the sarcolemmal Na+/K+-ATPase in dystrophic leg muscles were also confirmed by immunofluorescence microscopy. Thus, the reduction of sample complexity in organelle-focused proteomics can be advantageous for the profiling of supramolecular protein complexes in highly intricate systems, such as skeletal muscle tissue.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - 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.
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Rustam R Mundegar
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Dieter Swandulla
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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Robriquet F, Lardenois A, Babarit C, Larcher T, Dubreil L, Leroux I, Zuber C, Ledevin M, Deschamps JY, Fromes Y, Cherel Y, Guevel L, Rouger K. Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation. PLoS One 2015; 10:e0123336. [PMID: 25955839 PMCID: PMC4425432 DOI: 10.1371/journal.pone.0123336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/02/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Several adult stem cell populations exhibit myogenic regenerative potential, thus representing attractive candidates for therapeutic approaches of neuromuscular diseases such as Duchenne Muscular Dystrophy (DMD). We have recently shown that systemic delivery of MuStem cells, skeletal muscle-resident stem cells isolated in healthy dog, generates the remodelling of muscle tissue and gives rise to striking clinical benefits in Golden Retriever Muscular Dystrophy (GRMD) dog. This global effect, which is observed in the clinically relevant DMD animal model, leads us to question here the molecular pathways that are impacted by MuStem cell transplantation. To address this issue, we compare the global gene expression profile between healthy, GRMD and MuStem cell treated GRMD dog muscle, four months after allogenic MuStem cell transplantation. RESULTS In the dystrophic context of the GRMD dog, disease-related deregulation is observed in the case of 282 genes related to various processes such as inflammatory response, regeneration, calcium ion binding, extracellular matrix organization, metabolism and apoptosis regulation. Importantly, we reveal the impact of MuStem cell transplantation on several molecular and cellular pathways based on a selection of 31 genes displaying signals specifically modulated by the treatment. Concomitant with a diffuse dystrophin expression, a histological remodelling and a stabilization of GRMD dog clinical status, we show that cell delivery is associated with an up-regulation of genes reflecting a sustained enhancement of muscle regeneration. We also identify a decreased mRNA expression of a set of genes having metabolic functions associated with lipid homeostasis and energy. Interestingly, ubiquitin-mediated protein degradation is highly enhanced in GRMD dog muscle after systemic delivery of MuStem cells. CONCLUSIONS Overall, our results provide the first high-throughput characterization of GRMD dog muscle and throw new light on the complex molecular/cellular effects associated with muscle repair and the clinical efficacy of MuStem cell-based therapy.
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Affiliation(s)
- Florence Robriquet
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
- Université de Nantes, Nantes, France
| | - Aurélie Lardenois
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Candice Babarit
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Thibaut Larcher
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Laurence Dubreil
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Isabelle Leroux
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Céline Zuber
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Mireille Ledevin
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Jack-Yves Deschamps
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Yves Fromes
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
- Laboratoire RMN AIM-CEA, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Yan Cherel
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Laetitia Guevel
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
- Université de Nantes, Nantes, France
- * E-mail:
| | - Karl Rouger
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
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Holland A, Dowling P, Meleady P, Henry M, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Label-free mass spectrometric analysis of the mdx-4cv diaphragm identifies the matricellular protein periostin as a potential factor involved in dystrophinopathy-related fibrosis. Proteomics 2015; 15:2318-31. [PMID: 25737063 DOI: 10.1002/pmic.201400471] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/19/2014] [Accepted: 02/26/2015] [Indexed: 01/17/2023]
Abstract
Proteomic profiling plays a decisive role in the identification of novel biomarkers of muscular dystrophy and the elucidation of new pathobiochemical mechanisms that underlie progressive muscle wasting. Building on the findings of recent comparative analyses of tissue samples and body fluids from dystrophic animals and patients afflicted with Duchenne muscular dystrophy, we have used here label-free MS to study the severely dystrophic diaphragm from the not extensively characterized mdx-4cv mouse. This animal model of progressive muscle wasting exhibits less dystrophin-positive revertant fibers than the conventional mdx mouse, making it ideal for the future monitoring of experimental therapies. The pathoproteomic signature of the mdx-4cv diaphragm included a significant increase in the fibrosis marker collagen and related extracellular matrix proteins (asporin, decorin, dermatopontin, prolargin) and cytoskeletal proteins (desmin, filamin, obscurin, plectin, spectrin, tubulin, vimentin, vinculin), as well as decreases in proteins of ion homeostasis (parvalbumin) and the contractile apparatus (myosin-binding protein). Importantly, one of the most substantially increased proteins was identified as periostin, a matricellular component and apparent marker of fibrosis and tissue damage. Immunoblotting confirmed a considerable increase of periostin in the dystrophin-deficient diaphragm from both mdx and mdx-4cv mice, suggesting an involvement of this matricellular protein in dystrophinopathy-related fibrosis.
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Affiliation(s)
- Ashling Holland
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, County Kildare, Ireland
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, County Kildare, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn, Germany
| | | | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, County Kildare, Ireland
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44
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Santacatterina F, Chamorro M, de Arenas CN, Navarro C, Martín MA, Cuezva JM, Sánchez-Aragó M. Quantitative analysis of proteins of metabolism by reverse phase protein microarrays identifies potential biomarkers of rare neuromuscular diseases. J Transl Med 2015; 13:65. [PMID: 25880557 PMCID: PMC4342896 DOI: 10.1186/s12967-015-0424-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/30/2015] [Indexed: 11/16/2022] Open
Abstract
Background Muscle diseases have been associated with changes in the expression of proteins involved in energy metabolism. To this aim we have developed a number of monoclonal antibodies against proteins of energy metabolism. Methods Herein, we have used Reverse Phase Protein Microarrays (RPMA), a high throughput technique, to investigate quantitative changes in protein expression with the aim of identifying potential biomarkers in rare neuromuscular diseases. A cohort of 73 muscle biopsies that included samples from patients diagnosed of Duchenne (DMD), Becker (BMD), symptomatic forms of DMD and BMD in female carriers (Xp21 Carriers), Limb Girdle Muscular Dystrophy Type 2C (LGMD2C), neuronal ceroid lipofuscinosis (NCL), glycogenosis type V (Mc Ardle disease), isolated mitochondrial complex I deficiency, intensive care unit myopathy and control donors were investigated. The nineteen proteins of energy metabolism studied included members of the mitochondrial oxidation of pyruvate, the tricarboxylic acid cycle, β-oxidation of fatty acids, electron transport and oxidative phosphorylation, glycogen metabolism, glycolysis and oxidative stress using highly specific antibodies. Results The results indicate that the phenotype of energy metabolism offers potential biomarkers that could be implemented to refine the understanding of the biological principles of rare diseases and, eventually, the management of these patients. Conclusions We suggest that some biomarkers of energy metabolism could be translated into the clinics to contribute to the improvement of the clinical handling of patients affected by rare diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0424-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fulvio Santacatterina
- Departamento de Biología Molecular, Centro de Biología Molecular, c/ Nicolás Cabrera 1, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain.
| | - Margarita Chamorro
- Departamento de Biología Molecular, Centro de Biología Molecular, c/ Nicolás Cabrera 1, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain.
| | - Cristina Núñez de Arenas
- Departamento de Biología Molecular, Centro de Biología Molecular, c/ Nicolás Cabrera 1, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain.
| | - Carmen Navarro
- Instituto de Investigación Biomédico de Vigo (IBIV), Hospital Universitario de Vigo, Meixoeiro, 36200, Vigo, Spain.
| | - Miguel A Martín
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain. .,Laboratorio de Enfermedades Mitocondriales y Neuromusculares, Hospital Universitario 12 de Octubre, 28041, Madrid, Spain.
| | - José M Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular, c/ Nicolás Cabrera 1, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain.
| | - María Sánchez-Aragó
- Departamento de Biología Molecular, Centro de Biología Molecular, c/ Nicolás Cabrera 1, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain.
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45
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Ayoglu B, Chaouch A, Lochmüller H, Politano L, Bertini E, Spitali P, Hiller M, Niks EH, Gualandi F, Pontén F, Bushby K, Aartsma-Rus A, Schwartz E, Le Priol Y, Straub V, Uhlén M, Cirak S, 't Hoen PAC, Muntoni F, Ferlini A, Schwenk JM, Nilsson P, Al-Khalili Szigyarto C. Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies. EMBO Mol Med 2015; 6:918-36. [PMID: 24920607 PMCID: PMC4119355 DOI: 10.15252/emmm.201303724] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Despite the recent progress in the broad-scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA). Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies.
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Affiliation(s)
- Burcu Ayoglu
- Affinity Proteomics, SciLifeLab, School of Biotechnology KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Amina Chaouch
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Luisa Politano
- Cardiomiology and Medical Genetics, Department of Experimental Medicine, Second University of Naples, Naples, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesú Children's Hospital, Rome, Italy
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Monika Hiller
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric H Niks
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fredrik Pontén
- SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kate Bushby
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Annemieke Aartsma-Rus
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Volker Straub
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Mathias Uhlén
- Affinity Proteomics, SciLifeLab, School of Biotechnology KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sebahattin Cirak
- Research Center for Genetic Medicine, Childrens National Medical Center, Washington, DC, USA
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, UCL Institute of Child Health, London, UK
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology KTH-Royal Institute of Technology, Stockholm, Sweden
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46
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Kornegay JN, Spurney CF, Nghiem PP, Brinkmeyer-Langford CL, Hoffman EP, Nagaraju K. Pharmacologic management of Duchenne muscular dystrophy: target identification and preclinical trials. ILAR J 2015; 55:119-49. [PMID: 24936034 DOI: 10.1093/ilar/ilu011] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked human disorder in which absence of the protein dystrophin causes degeneration of skeletal and cardiac muscle. For the sake of treatment development, over and above definitive genetic and cell-based therapies, there is considerable interest in drugs that target downstream disease mechanisms. Drug candidates have typically been chosen based on the nature of pathologic lesions and presumed underlying mechanisms and then tested in animal models. Mammalian dystrophinopathies have been characterized in mice (mdx mouse) and dogs (golden retriever muscular dystrophy [GRMD]). Despite promising results in the mdx mouse, some therapies have not shown efficacy in DMD. Although the GRMD model offers a higher hurdle for translation, dogs have primarily been used to test genetic and cellular therapies where there is greater risk. Failed translation of animal studies to DMD raises questions about the propriety of methods and models used to identify drug targets and test efficacy of pharmacologic intervention. The mdx mouse and GRMD dog are genetically homologous to DMD but not necessarily analogous. Subcellular species differences are undoubtedly magnified at the whole-body level in clinical trials. This problem is compounded by disparate cultures in clinical trials and preclinical studies, pointing to a need for greater rigor and transparency in animal experiments. Molecular assays such as mRNA arrays and genome-wide association studies allow identification of genetic drug targets more closely tied to disease pathogenesis. Genes in which polymorphisms have been directly linked to DMD disease progression, as with osteopontin, are particularly attractive targets.
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47
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ROS and RNS signaling in skeletal muscle: critical signals and therapeutic targets. ANNUAL REVIEW OF NURSING RESEARCH 2014; 31:367-87. [PMID: 24894146 DOI: 10.1891/0739-6686.31.367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The health of skeletal muscle is promoted by optimal nutrition and activity/exercise through the activation of molecular signaling pathways. Reactive oxygen species (ROS) or reactive nitrogen species (RNS) have been shown to modulate numerous biochemical processes including glucose uptake, gene expression, calcium signaling, and contractility. In pathological conditions, ROS/RNS signaling excess or dysfunction contributes to contractile dysfunction and myopathy in skeletal muscle. Here we provide a brief review of ROS/RNS chemistry and discuss concepts of ROS/RNS signaling and its role in physiological and pathophysiological processes within striated muscle.
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48
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Brinkmeier H, Ohlendieck K. Chaperoning heat shock proteins: Proteomic analysis and relevance for normal and dystrophin-deficient muscle. Proteomics Clin Appl 2014; 8:875-95. [DOI: 10.1002/prca.201400015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/24/2014] [Accepted: 05/28/2014] [Indexed: 12/15/2022]
Affiliation(s)
| | - Kay Ohlendieck
- Department of Biology; National University of Ireland; Maynooth Co. Kildare Ireland
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49
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de Oliveira BM, Matsumura CY, Fontes-Oliveira CC, Gawlik KI, Acosta H, Wernhoff P, Durbeej M. Quantitative proteomic analysis reveals metabolic alterations, calcium dysregulation, and increased expression of extracellular matrix proteins in laminin α2 chain-deficient muscle. Mol Cell Proteomics 2014; 13:3001-13. [PMID: 24994560 DOI: 10.1074/mcp.m113.032276] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Congenital muscular dystrophy with laminin α2 chain deficiency (MDC1A) is one of the most severe forms of muscular disease and is characterized by severe muscle weakness and delayed motor milestones. The genetic basis of MDC1A is well known, yet the secondary mechanisms ultimately leading to muscle degeneration and subsequent connective tissue infiltration are not fully understood. In order to obtain new insights into the molecular mechanisms underlying MDC1A, we performed a comparative proteomic analysis of affected muscles (diaphragm and gastrocnemius) from laminin α2 chain-deficient dy(3K)/dy(3K) mice, using multidimensional protein identification technology combined with tandem mass tags. Out of the approximately 700 identified proteins, 113 and 101 proteins, respectively, were differentially expressed in the diseased gastrocnemius and diaphragm muscles compared with normal muscles. A large portion of these proteins are involved in different metabolic processes, bind calcium, or are expressed in the extracellular matrix. Our findings suggest that metabolic alterations and calcium dysregulation could be novel mechanisms that underlie MDC1A and might be targets that should be explored for therapy. Also, detailed knowledge of the composition of fibrotic tissue, rich in extracellular matrix proteins, in laminin α2 chain-deficient muscle might help in the design of future anti-fibrotic treatments. All MS data have been deposited in the ProteomeXchange with identifier PXD000978 (http://proteomecentral.proteomexchange.org/dataset/PXD000978).
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Affiliation(s)
- Bruno Menezes de Oliveira
- From the §Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, BMC B12, 221 84 Lund, Sweden
| | - Cintia Y Matsumura
- From the §Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, BMC B12, 221 84 Lund, Sweden; ¶Departament of Functional and Structural Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Cibely C Fontes-Oliveira
- From the §Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, BMC B12, 221 84 Lund, Sweden
| | - Kinga I Gawlik
- From the §Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, BMC B12, 221 84 Lund, Sweden
| | - Helena Acosta
- ‖Stem Cell Center, Lund University, BMC B12, 221 84 Lund, Sweden
| | - Patrik Wernhoff
- From the §Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, BMC B12, 221 84 Lund, Sweden
| | - Madeleine Durbeej
- From the §Department of Experimental Medical Science, Unit of Muscle Biology, Lund University, BMC B12, 221 84 Lund, Sweden;
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50
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Hollinger K, Shanely RA, Quindry JC, Selsby JT. Long-term quercetin dietary enrichment decreases muscle injury in mdx mice. Clin Nutr 2014; 34:515-22. [PMID: 24998094 DOI: 10.1016/j.clnu.2014.06.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/07/2014] [Accepted: 06/10/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND & AIMS Duchenne muscular dystrophy results from a mutation in the dystrophin gene, which leads to a dystrophin-deficiency. Dystrophic muscle is marked by progressive muscle injury and loss of muscle fibers. Activation of the PGC-1α pathway has been previously shown to decrease disease-related muscle damage. Oral administration of the flavonol, quercetin, appears to be an effective and safe method to activate the PGC-1α pathway. The aim of this investigation was to determine the extent to which long term dietary quercetin enrichment would decrease muscle injury in dystrophic skeletal muscle. We hypothesized that a quercetin enriched diet would rescue dystrophic muscle from further decline and increase utrophin abundance. METHODS Beginning at three-months of age and continuing to nine-months of age mdx mice (n = 10/group) were assigned to either to mdx-control receiving standard chow or to mdx-quercetin receiving a 0.2% quercetin-enriched diet. At nine-months of age mice were sacrificed and costal diaphragms collected. One hemidiaphragm was used for histological analysis and the second hemidiaphragm was used to determine gene expression via RT-qPCR. RESULTS The diaphragm from the mdx-quercetin group had 24% (p ≤ 0.05) more muscle fibers/area and 34% (p ≤ 0.05) fewer centrally nucleated fibers compared to the mdx-control group. Further, there were 44% (p ≤ 0.05) fewer infiltrating immune cells/area, a corresponding 31% (p ≤ 0.05) reduction in TNF gene expression, and a near 50% reduction in fibrosis. The quercetin-enriched diet increased expression of genes associated with oxidative metabolism but did not increase utrophin protein abundance. CONCLUSIONS Long-term quercetin supplementation decreased disease-related muscle injury in dystrophic skeletal muscle; however the role of PGC-1α pathway activation as a mediator of this response is unclear.
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Affiliation(s)
- Katrin Hollinger
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - R Andrew Shanely
- Human Performance Laboratory, Appalachian State University, North Carolina Research Campus, Kannapolis, NC 28081, USA; Appalachian State University, College of Health Sciences, Boone, NC, USA
| | - John C Quindry
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | - Joshua T Selsby
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
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