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Parente AD, Bolland DE, Huisinga KL, Provost JJ. Physiology of malate dehydrogenase and how dysregulation leads to disease. Essays Biochem 2024:EBC20230085. [PMID: 38962852 DOI: 10.1042/ebc20230085] [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: 03/03/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
Malate dehydrogenase (MDH) is pivotal in mammalian tissue metabolism, participating in various pathways beyond its classical roles and highlighting its adaptability to cellular demands. This enzyme is involved in maintaining redox balance, lipid synthesis, and glutamine metabolism and supports rapidly proliferating cells' energetic and biosynthetic needs. The involvement of MDH in glutamine metabolism underlines its significance in cell physiology. In contrast, its contribution to lipid metabolism highlights its role in essential biosynthetic processes necessary for cell maintenance and proliferation. The enzyme's regulatory mechanisms, such as post-translational modifications, underscore its complexity and importance in metabolic regulation, positioning MDH as a potential target in metabolic dysregulation. Furthermore, the association of MDH with various pathologies, including cancer and neurological disorders, suggests its involvement in disease progression. The overexpression of MDH isoforms MDH1 and MDH2 in cancers like breast, prostate, and pancreatic ductal adenocarcinoma, alongside structural modifications, implies their critical role in the metabolic adaptation of tumor cells. Additionally, mutations in MDH2 linked to pheochromocytomas, paragangliomas, and other metabolic diseases emphasize MDH's role in metabolic homeostasis. This review spotlights MDH's potential as a biomarker and therapeutic target, advocating for further research into its multifunctional roles and regulatory mechanisms in health and disease.
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Affiliation(s)
- Amy D Parente
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA, U.S.A
| | - Danielle E Bolland
- Department of Biology, University of Minnesota Morris, Morris, MN 56267, U.S.A
| | - Kathryn L Huisinga
- Department of Chemistry and Biochemistry, Malone University, Canton, OH 44709, U.S.A
| | - Joseph J Provost
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, U.S.A
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Seo D, Lee CM, Apio C, Heo G, Timsina J, Kohlfeld P, Boada M, Orellana A, Fernandez MV, Ruiz A, Morris JC, Schindler SE, Park T, Cruchaga C, Sung YJ. Sex and aging signatures of proteomics in human cerebrospinal fluid identify distinct clusters linked to neurodegeneration. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.18.24309102. [PMID: 38947020 PMCID: PMC11213043 DOI: 10.1101/2024.06.18.24309102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Sex and age are major risk factors for chronic diseases. Recent studies examining age-related molecular changes in plasma provided insights into age-related disease biology. Cerebrospinal fluid (CSF) proteomics can provide additional insights into brain aging and neurodegeneration. By comprehensively examining 7,006 aptamers targeting 6,139 proteins in CSF obtained from 660 healthy individuals aged from 43 to 91 years old, we subsequently identified significant sex and aging effects on 5,097 aptamers in CSF. Many of these effects on CSF proteins had different magnitude or even opposite direction as those on plasma proteins, indicating distinctive CSF-specific signatures. Network analysis of these CSF proteins revealed not only modules associated with healthy aging but also modules showing sex differences. Through subsequent analyses, several modules were highlighted for their proteins implicated in specific diseases. Module 2 and 6 were enriched for many aging diseases including those in the circulatory systems, immune mechanisms, and neurodegeneration. Together, our findings fill a gap of current aging research and provide mechanistic understanding of proteomic changes in CSF during a healthy lifespan and insights for brain aging and diseases.
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Boehler JF, Brown KJ, Ricotti V, Morris CA. N-terminal titin fragment: a non-invasive, pharmacodynamic biomarker for microdystrophin efficacy. Skelet Muscle 2024; 14:2. [PMID: 38229112 PMCID: PMC10790446 DOI: 10.1186/s13395-023-00334-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Multiple clinical trials to assess the efficacy of AAV-directed gene transfer in participants with Duchenne muscular dystrophy (DMD) are ongoing. The success of these trials currently relies on standard functional outcome measures that may exhibit variability within and between participants, rendering their use as sole measures of drug efficacy challenging. Given this, supportive objective biomarkers may be useful in enhancing observed clinical results. Creatine kinase (CK) is traditionally used as a diagnostic biomarker of DMD, but its potential as a robust pharmacodynamic (PD) biomarker is difficult due to the wide variability seen within the same participant over time. Thus, there is a need for the discovery and validation of novel PD biomarkers to further support and bolster traditional outcome measures of efficacy in DMD. METHOD Potential PD biomarkers in DMD participant urine were examined using a proteomic approach on the Somalogic platform. Findings were confirmed in both mdx mice and Golden Retriever muscular dystrophy (GRMD) dog plasma samples. RESULTS Changes in the N-terminal fragment of titin, a well-known, previously characterized biomarker of DMD, were correlated with the expression of microdystrophin protein in mice, dogs, and humans. Further, titin levels were sensitive to lower levels of expressed microdystrophin when compared to CK. CONCLUSION The measurement of objective PD biomarkers such as titin may provide additional confidence in the assessment of the mechanism of action and efficacy in gene therapy clinical trials of DMD. TRIAL REGISTRATION ClinicalTrials.gov NCT03368742.
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Affiliation(s)
- Jessica F Boehler
- Solid Biosciences, 500 Rutherford Avenue 3rd Floor, Boston, MA, 02129, USA.
| | - Kristy J Brown
- Rejuvenate Bio, 11425 Sorrento Valley Road, San Diego, CA, 92121, USA
| | - Valeria Ricotti
- National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre/University College London Great Ormond Street Institute of Child Health, London, UK
| | - Carl A Morris
- PHDL Consulting LLC, 43 Sylvanus Wood Lane, Woburn, MA, 01801, USA
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Jung U, Kim M, Dowker-Key P, Noë S, Bettaieb A, Shepherd E, Voy B. Hypoxia promotes proliferation and inhibits myogenesis in broiler satellite cells. Poult Sci 2024; 103:103203. [PMID: 37980759 PMCID: PMC10685027 DOI: 10.1016/j.psj.2023.103203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/07/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023] Open
Abstract
Breast muscle myopathies in broilers compromise meat quality and continue to plague the poultry industry. Broiler breast muscle myopathies are characterized by impaired satellite cell (SC)-mediated repair, and localized tissue hypoxia and dysregulation of oxygen homeostasis have been implicated as contributing factors. The present study was designed to test the hypothesis that hypoxia disrupts the ability of SC to differentiate and form myotubes, both of which are key components of myofiber repair, and to determine the extent to which effects are reversed by restoration of oxygen tension. Primary SC were isolated from pectoralis major of young (5 d) Cobb 700 chicks and maintained in growth conditions or induced to differentiate under normoxic (20% O2) or hypoxic (1% O2) conditions for up to 48 h. Hypoxia enhanced SC proliferation while inhibiting myogenic potential, with decreased fusion index and suppressed myotube formation. Reoxygenation after hypoxia partially reversed effects on both proliferation and myogenesis. Western blotting showed that hypoxia diminished myogenin expression, activated AMPK, upregulated proliferation markers, and increased molecular signaling of cellular stress. Hypoxia also promoted accumulation of lipid droplets in myotubes. Targeted RNAseq identified numerous differentially expressed genes across differentiation under hypoxia, including several genes that have been associated with myopathies in vivo. Altogether, these data demonstrate localized hypoxia may influence SC behavior in ways that disrupt muscle repair and promote the formation of myopathies in broilers.
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Affiliation(s)
- Usuk Jung
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Minjeong Kim
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Presley Dowker-Key
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, USA
| | - Simon Noë
- Research Group for Neurorehabilitation (eNRGy), Department of Rehabilitation Sciences, KU Leuven, 3001 Leuven, Belgium
| | - Ahmed Bettaieb
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, USA
| | - Elizabeth Shepherd
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Brynn Voy
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA.
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McDonald C, Camino E, Escandon R, Finkel RS, Fischer R, Flanigan K, Furlong P, Juhasz R, Martin AS, Villa C, Sweeney HL. Draft Guidance for Industry Duchenne Muscular Dystrophy, Becker Muscular Dystrophy, and Related Dystrophinopathies - Developing Potential Treatments for the Entire Spectrum of Disease. J Neuromuscul Dis 2024; 11:499-523. [PMID: 38363616 DOI: 10.3233/jnd-230219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Background Duchenne muscular dystrophy (DMD) and related dystrophinopathies are neuromuscular conditions with great unmet medical needs that require the development of effective medical treatments. Objective To aid sponsors in clinical development of drugs and therapeutic biological products for treating DMD across the disease spectrum by integrating advancements, patient registries, natural history studies, and more into a comprehensive guidance. Methods This guidance emerged from collaboration between the FDA, the Duchenne community, and industry stakeholders. It entailed a structured approach, involving multiple committees and boards. From its inception in 2014, the guidance underwent revisions incorporating insights from gene therapy studies, cardiac function research, and innovative clinical trial designs. Results The guidance provides a deeper understanding of DMD and its variants, focusing on patient engagement, diagnostic criteria, natural history, biomarkers, and clinical trials. It underscores patient-focused drug development, the significance of dystrophin as a biomarker, and the pivotal role of magnetic resonance imaging in assessing disease progression. Additionally, the guidance addresses cardiomyopathy's prominence in DMD and the burgeoning field of gene therapy. Conclusions The updated guidance offers a comprehensive understanding of DMD, emphasizing patient-centric approaches, innovative trial designs, and the importance of biomarkers. The focus on cardiomyopathy and gene therapy signifies the evolving realm of DMD research. It acts as a crucial roadmap for sponsors, potentially leading to improved treatments for DMD.
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Affiliation(s)
| | - Eric Camino
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Rafael Escandon
- DGBI Consulting, LLC, Bainbridge Island, Washington, DC, USA
| | | | - Ryan Fischer
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Kevin Flanigan
- Center for Experimental Neurotherapeutics, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pat Furlong
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Rose Juhasz
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Ann S Martin
- Parent Project Muscular Dystrophy, Washington, DC, USA
| | - Chet Villa
- Trinity Health Michigan, Grand Rapids, MI, USA
| | - H Lee Sweeney
- Cincinnati Children's Hospital Medical Center within the UC Department of Pediatrics, Cincinnati, OH, USA
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Wang W, Zhang T, Du L, Li K, Zhang L, Li H, Gao X, Xu L, Li J, Gao H. Transcriptomic analysis reveals diverse expression patterns underlying the fiber diameter of oxidative and glycolytic skeletal muscles in steers. Meat Sci 2024; 207:109350. [PMID: 37844514 DOI: 10.1016/j.meatsci.2023.109350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/18/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023]
Abstract
Skeletal muscles consist of heterogeneous fibers with various contractile and metabolic properties that affect meat quality. The size of muscle fibers contributes to muscle mass and myopathy. Thus, improved understanding of the expression patterns underlying fiber size might open possibilities to change them using genetic methods. The aim of this study was to reveal transcriptomic landscapes of one oxidative (Psoas major) and three glycolytic (Longissimus lumborum, Triceps brachii, and Semimembranosus) muscles. Principal component analysis (PCA) showed significant differences in gene expression among the four muscles. Specifically, 2777 differentially expressed genes (DEGs) were detected between six pairwise comparisons of the four muscles. Weighted gene co-expression network analysis (WGCNA) identified six modules, which were significantly associated with muscle fiber diameter. We also identified 23 candidate genes, and enrichment analysis showed that biosynthesis of amino acids (bta01230), sarcomere (GO:0030017), and regulation of actin cytoskeleton (bta04810) overlapped in DEGs and WGCNA. Nineteen of these genes (e.g., EEF1A2, FARSB, and PINK1) have been reported to promote or inhibit muscle growth and development. Our findings contribute to the understanding of fiber size differences among oxidative and glycolytic muscles, which may provide a basis for breeding to improve meat yield.
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Affiliation(s)
- Wenxiang Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lili Du
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Keanning Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Haipeng Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Wijekoon N, Gonawala L, Ratnayake P, Dissanayaka P, Gunarathne I, Amaratunga D, Liyanage R, Senanayaka S, Wijesekara S, Gunasekara HH, Vanarsa K, Castillo J, Hathout Y, Dalal A, Steinbusch HW, Hoffman E, Mohan C, de Silva KRD. Integrated genomic, proteomic and cognitive assessment in Duchenne Muscular Dystrophy suggest astrocyte centric pathology. Heliyon 2023; 9:e18530. [PMID: 37593636 PMCID: PMC10432191 DOI: 10.1016/j.heliyon.2023.e18530] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction Documented Duchenne Muscular Dystrophy (DMD) biomarkers are confined to Caucasians and are poor indicators of cognitive difficulties and neuropsychological alterations. Materials and methods This study correlates serum protein signatures with cognitive performance in DMD patients of South Asian origin. Study included 25 DMD patients aged 6-16 years. Cognitive profiles were assessed by Wechsler Intelligence Scale for Children. Serum proteome profiling of 1317 proteins was performed in eight DMD patients and eight age-matched healthy volunteers. Results Among the several novel observations we report, better cognitive performance in DMD was associated with increased serum levels of MMP9 and FN1 but decreased Siglec-3, C4b, and C3b. Worse cognitive performance was associated with increased serum levels of LDH-H1 and PDGF-BB but reduced GDF-11, MMP12, TPSB2, and G1B. Secondly, better cognitive performance in Processing Speed (PSI) and Perceptual Reasoning (PRI) domains was associated with intact Dp116, Dp140, and Dp71 dystrophin isoforms while better performance in Verbal Comprehension (VCI) and Working Memory (WMI) domains was associated with intact Dp116 and Dp140 isoforms. Finally, functional pathways shared with Alzheimer's Disease (AD) point towards an astrocyte-centric model for DMD. Conclusion Astrocytic dysfunction leading to synaptic dysfunction reported previously in AD may be a common pathogenic mechanism underlying both AD and DMD, linking protein alterations to cognitive impairment. This new insight may pave the path towards novel therapeutic approaches targeting reactive astrocytes.
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | | | - Pulasthi Dissanayaka
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | - Isuru Gunarathne
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Saraji Wijesekara
- Department of Pediatrics, University of Sri Jayewardenepura, 10250, Sri Lanka
- Colombo South Teaching Hospital, 10350, Sri Lanka
| | | | - Kamala Vanarsa
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - Jessica Castillo
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, India
| | - Harry W.M. Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Eric Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - K. Ranil D. de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka
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Johansson C, Hunt H, Signorelli M, Edfors F, Hober A, Svensson AS, Tegel H, Forstström B, Aartsma-Rus A, Niks E, Spitali P, Uhlén M, Szigyarto CAK. Orthogonal proteomics methods warrant the development of Duchenne muscular dystrophy biomarkers. Clin Proteomics 2023; 20:23. [PMID: 37308827 DOI: 10.1186/s12014-023-09412-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Molecular components in blood, such as proteins, are used as biomarkers to detect or predict disease states, guide clinical interventions and aid in the development of therapies. While multiplexing proteomics methods promote discovery of such biomarkers, their translation to clinical use is difficult due to the lack of substantial evidence regarding their reliability as quantifiable indicators of disease state or outcome. To overcome this challenge, a novel orthogonal strategy was developed and used to assess the reliability of biomarkers and analytically corroborate already identified serum biomarkers for Duchenne muscular dystrophy (DMD). DMD is a monogenic incurable disease characterized by progressive muscle damage that currently lacks reliable and specific disease monitoring tools. METHODS Two technological platforms are used to detect and quantify the biomarkers in 72 longitudinally collected serum samples from DMD patients at 3 to 5 timepoints. Quantification of the biomarkers is achieved by detection of the same biomarker fragment either through interaction with validated antibodies in immuno-assays or through quantification of peptides by Parallel Reaction Monitoring Mass Spectrometry assay (PRM-MS). RESULTS Five, out of ten biomarkers previously identified by affinity-based proteomics methods, were confirmed to be associated with DMD using the mass spectrometry-based method. Two biomarkers, carbonic anhydrase III and lactate dehydrogenase B, were quantified with two independent methods, sandwich immunoassays and PRM-MS, with Pearson correlations of 0.92 and 0.946 respectively. The median concentrations of CA3 and LDHB in DMD patients was elevated in comparison to those in healthy individuals by 35- and 3-fold, respectively. Levels of CA3 vary between 10.26 and 0.36 ng/ml in DMD patients whereas those of LDHB vary between 15.1 and 0.8 ng/ml. CONCLUSIONS These results demonstrate that orthogonal assays can be used to assess the analytical reliability of biomarker quantification assays, providing a means to facilitate the translation of biomarkers to clinical practice. This strategy also warrants the development of the most relevant biomarkers, markers that can be reliably quantified with different proteomics methods.
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Affiliation(s)
- Camilla Johansson
- Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Helian Hunt
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mirko Signorelli
- Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anne-Sophie Svensson
- Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forstström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik Niks
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden
| | - Cristina Al-Khalili Szigyarto
- Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.
- Science for Life Laboratory, KTH - Royal Institute of Technology, Solna, Sweden.
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Signorelli M, Tsonaka R, Aartsma-Rus A, Spitali P. Multiomic characterization of disease progression in mice lacking dystrophin. PLoS One 2023; 18:e0283869. [PMID: 37000843 PMCID: PMC10065259 DOI: 10.1371/journal.pone.0283869] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by genetic mutations leading to lack of dystrophin in skeletal muscle. A better understanding of how objective biomarkers for DMD vary across subjects and over time is needed to model disease progression and response to therapy more effectively, both in pre-clinical and clinical research. We present an in-depth characterization of disease progression in 3 murine models of DMD by multiomic analysis of longitudinal trajectories between 6 and 30 weeks of age. Integration of RNA-seq, mass spectrometry-based metabolomic and lipidomic data obtained in muscle and blood samples by Multi-Omics Factor Analysis (MOFA) led to the identification of 8 latent factors that explained 78.8% of the variance in the multiomic dataset. Latent factors could discriminate dystrophic and healthy mice, as well as different time-points. MOFA enabled to connect the gene expression signature in dystrophic muscles, characterized by pro-fibrotic and energy metabolism alterations, to inflammation and lipid signatures in blood. Our results show that omic observations in blood can be directly related to skeletal muscle pathology in dystrophic muscle.
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Affiliation(s)
- Mirko Signorelli
- Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Roula Tsonaka
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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10
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van de Velde NM, Koeks Z, Signorelli M, Verwey N, Overzier M, Bakker JA, Sajeev G, Signorovitch J, Ricotti V, Verschuuren J, Brown K, Spitali P, Niks EH. Longitudinal Assessment of Creatine Kinase, Creatine/Creatinine ratio, and Myostatin as Monitoring Biomarkers in Becker Muscular Dystrophy. Neurology 2023; 100:e975-e984. [PMID: 36849458 PMCID: PMC9990441 DOI: 10.1212/wnl.0000000000201609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 10/11/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND OBJECTIVES The slow and variable disease progression of Becker muscular dystrophy (BMD) urges the development of biomarkers to facilitate clinical trials. We explored changes in 3 muscle-enriched biomarkers in serum of patients with BMD over 4-year time and studied associations with disease severity, disease progression, and dystrophin levels in BMD. METHODS We quantitatively measured creatine kinase (CK) using the International Federation of Clinical Chemistry reference method, creatine/creatinineratio (Cr/Crn) using liquid chromatography-tandem mass spectrometry, and myostatin with ELISA in serum and assessed functional performance using the North Star Ambulatory Assessment (NSAA), 10-meter run velocity (TMRv), 6-Minute Walking Test (6MWT), and forced vital capacity in a 4-year prospective natural history study. Dystrophin levels were quantified in the tibialis anterior muscle using capillary Western immunoassay. The correlation between biomarkers, age, functional performance, mean annual change, and prediction of concurrent functional performance was analyzed using linear mixed models. RESULTS Thirty-four patients with 106 visits were included. Eight patients were nonambulant at baseline. Cr/Crn and myostatin were highly patient specific (intraclass correlation coefficient for both = 0.960). Cr/Crn was strongly negatively correlated, whereas myostatin was strongly positively correlated with the NSAA, TMRv, and 6MWT (Cr/Crn rho = -0.869 to -0.801 and myostatin rho = 0.792 to 0.842, all p < 0.001). CK showed a negative association with age (p = 0.0002) but was not associated with patients' performance. Cr/Crn and myostatin correlated moderately with the average annual change of the 6MWT (rho = -0.532 and 0.555, p = 0.02). Dystrophin levels did not correlate with the selected biomarkers nor with performance. Cr/Crn, myostatin, and age could explain up to 75% of the variance of concurrent functional performance of the NSAA, TMRv, and 6MWT. DISCUSSION Both Cr/Crn and myostatin could potentially serve as monitoring biomarkers in BMD, as higher Cr/Crn and lower myostatin were associated with lower motor performance and predictive of concurrent functional performance when combined with age. Future studies are needed to more precisely determine the context of use of these biomarkers.
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Affiliation(s)
- Nienke M van de Velde
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Zaïda Koeks
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Mirko Signorelli
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Nisha Verwey
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Maurice Overzier
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Jaap A Bakker
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Gautam Sajeev
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - James Signorovitch
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Valeria Ricotti
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Jan Verschuuren
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Kristy Brown
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Pietro Spitali
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom
| | - Erik H Niks
- From the Departments of Neurology (N.M.V., Z.K., J.V., E.H.N.), Biomedical Data Sciences (M.S.), Human Genetics (N.V., M.O., P.S.), and Clinical Chemistry and Laboratory Medicine (J.A.B.), Leiden University Medical Center, the Netherlands; Duchenne Center Netherlands (N.M.V., J.V., P.S., E.H.N.); European Reference Network for Rare Neuromuscular Diseases [ERN EURO-NMD] (N.M.V., Z.K., N.V., M.O., J.V., P.S., E.H.N.); Mathematical Institute (M.S.), Leiden University, the Netherlands; Analysis Group Inc (G.S., J.S.), Boston, MA; Solid Biosciences Inc (V.R., K.B.), Cambridge, MA; and NIHR Great Ormond Street Hospital Biomedical Research Centre (V.R.), Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, United Kingdom.
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11
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Fortunato F, Ferlini A. Biomarkers in Duchenne Muscular Dystrophy: Current Status and Future Directions. J Neuromuscul Dis 2023; 10:987-1002. [PMID: 37545256 PMCID: PMC10657716 DOI: 10.3233/jnd-221666] [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] [Accepted: 07/13/2023] [Indexed: 08/08/2023]
Abstract
Duchenne muscular dystrophy is a severe, X-linked disease characterized by decreased muscle mass and function in children. Genetic and biochemical research over the years has led to the characterization of the cause and the pathophysiology of the disease. Moreover, the elucidation of genetic mechanisms underlining Duchenne muscular dystrophy has allowed for the design of innovative personalized therapies.The identification of specific, accurate, and sensitive biomarkers is becoming crucial for evaluating muscle disease progression and response to therapies, disease monitoring, and the acceleration of drug development and related regulatory processes.This review illustrated the up-to-date progress in the development of candidate biomarkers in DMD at the level of proteins, metabolites, micro-RNAs (miRNAs) and genetic modifiers also highlighting the complexity of translating research results to clinical practice.We highlighted the challenges encountered in translating biomarkers into the clinical context and the existing bottlenecks hampering the adoption of biomarkers as surrogate endpoints. These challenges could be overcome by national and international collaborative efforts, multicenter data sharing, definition of public biobanks and patients' registries, and creation of large cohorts of patients. Novel statistical tools/ models suitable to analyze small patient numbers are also required.Finally, collaborations with pharmaceutical companies would greatly benefit biomarker discovery and their translation in clinical trials.
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Affiliation(s)
- Fernanda Fortunato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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12
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Weber FJ, Latshang TD, Blum MR, Kohler M, Wertli MM. Prognostic factors, disease course, and treatment efficacy in Duchenne muscular dystrophy: A systematic review and meta-analysis. Muscle Nerve 2022; 66:462-470. [PMID: 35860996 PMCID: PMC9804574 DOI: 10.1002/mus.27682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/10/2022] [Accepted: 07/17/2022] [Indexed: 01/05/2023]
Abstract
INTRODUCTION/AIMS Prognostic factors in Duchenne muscular dystrophy (DMD) predict the disease course and may help individualize patient care. The aim was to summarize the evidence on prognostic factors that may support treatment decisions. METHODS We searched six databases for prospective studies that each included ≥50 DMD patients with a minimum follow-up of 1 y. Primary outcomes were age at loss of ambulation (LoA), pulmonary function (forced vital capacity percent of predicted, FVC%p), and heart failure. RESULTS Out of 5074 references, 59 studies were analyzed. Corticosteroid use was associated with a delayed LoA (pooled effect hazard ratio [HR] 0.42, 95% confidence interval [CI] 0.23-0.75, I2 94%), better pulmonary function tests (higher peak FVC%, prolonged time with FVC%p > 50%, and reduced need for assisted ventilation) and delayed cardiomyopathy. Longer corticosteroid treatment was associated with later LoA (>1 y compared to <1 y; pooled HR: 0.50, 95% CI 0.27-0.90) and early treatment start (aged <5 y) may be associated with early cardiomyopathy and higher fracture risk. Genotype appeared to be an independent driver of LoA in some studies. Higher baseline physical function tests (e.g., 6-minute walk test) were associated with delayed LoA. Left ventricular dysfunction and FVC <1 L increased and the use of angiotensin-converting enzyme (ACE) inhibitors reduced the risk of heart failure and death. Fusion surgery in scoliosis may potentially preserve pulmonary function. DISCUSSION Prognostic factors that may inform clinical decisions include age at corticosteroid treatment initiation and treatment duration, ACE-inhibitor use, baseline physical function tests, pulmonary function, and cardiac dysfunction.
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Affiliation(s)
- Fabio J Weber
- Sleep Disorders Center and Pulmonary Division, University Hospital Zurich, Zurich, Switzerland
| | - Tsogyal D Latshang
- Sleep Disorders Center and Pulmonary Division, University Hospital Zurich, Zurich, Switzerland.,Sleep Disorders Center and Pulmonary Division, Kantonsspital Graubuenden, Chur, Switzerland
| | - Manuel R Blum
- Department of General Internal Medicine, University Hospital Bern, University of Bern, Bern, Switzerland.,Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Malcolm Kohler
- Sleep Disorders Center and Pulmonary Division, University Hospital Zurich, Zurich, Switzerland.,Zurich Center for Interdisciplinary Sleep Research, University of Zurich, Zurich, Switzerland
| | - Maria M Wertli
- Department of General Internal Medicine, University Hospital Bern, University of Bern, Bern, Switzerland.,Department of Internal Medicine, Cantonal Hospital Baden, Baden, Switzerland
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13
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Signorelli M, Spitali P, Szigyarto CAK, Tsonaka R. Penalized regression calibration: A method for the prediction of survival outcomes using complex longitudinal and high-dimensional data. Stat Med 2021; 40:6178-6196. [PMID: 34464990 PMCID: PMC9293191 DOI: 10.1002/sim.9178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
Longitudinal and high‐dimensional measurements have become increasingly common in biomedical research. However, methods to predict survival outcomes using covariates that are both longitudinal and high‐dimensional are currently missing. In this article, we propose penalized regression calibration (PRC), a method that can be employed to predict survival in such situations. PRC comprises three modeling steps: First, the trajectories described by the longitudinal predictors are flexibly modeled through the specification of multivariate mixed effects models. Second, subject‐specific summaries of the longitudinal trajectories are derived from the fitted mixed models. Third, the time to event outcome is predicted using the subject‐specific summaries as covariates in a penalized Cox model. To ensure a proper internal validation of the fitted PRC models, we furthermore develop a cluster bootstrap optimism correction procedure that allows to correct for the optimistic bias of apparent measures of predictiveness. PRC and the CBOCP are implemented in the R package pencal, available from CRAN. After studying the behavior of PRC via simulations, we conclude by illustrating an application of PRC to data from an observational study that involved patients affected by Duchenne muscular dystrophy, where the goal is predict time to loss of ambulation using longitudinal blood biomarkers.
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Affiliation(s)
- Mirko Signorelli
- Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Roula Tsonaka
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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14
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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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15
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Dang UJ, Ziemba M, Clemens PR, Hathout Y, Conklin LS, Hoffman EP. Serum biomarkers associated with baseline clinical severity in young steroid-naïve Duchenne muscular dystrophy boys. Hum Mol Genet 2021; 29:2481-2495. [PMID: 32592467 PMCID: PMC7471506 DOI: 10.1093/hmg/ddaa132] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/28/2020] [Accepted: 06/20/2020] [Indexed: 12/13/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by loss of dystrophin in muscle, and while all patients share the primary gene and biochemical defect, there is considerable patient–patient variability in clinical symptoms. We sought to develop multivariate models of serum protein biomarkers that explained observed variation, using functional outcome measures as proxies for severity. Serum samples from 39 steroid-naïve DMD boys 4 to <7 years enrolled into a clinical trial of vamorolone were studied (NCT02760264). Four assessments of gross motor function were carried out for each participant over a 6-week interval, and their mean was used as response for biomarker models. Weighted correlation network analysis was used for unsupervised clustering of 1305 proteins quantified using SOMAscan® aptamer profiling to define highly representative and connected proteins. Multivariate models of biomarkers were obtained for time to stand performance (strength phenotype; 17 proteins) and 6 min walk performance (endurance phenotype; 17 proteins) including some shared proteins. Identified proteins were tested with associations of mRNA expression with histological severity of muscle from dystrophinopathy patients (n = 28) and normal controls (n = 6). Strong associations predictive of both clinical and histological severity were found for ERBB4 (reductions in both blood and muscle with increasing severity), SOD1 (reductions in muscle and increases in blood with increasing severity) and CNTF (decreased levels in blood and muscle with increasing severity). We show that performance of DMD boys was effectively modeled with serum proteins, proximal strength associated with growth and remodeling pathways and muscle endurance centered on TGFβ and fibrosis pathways in muscle.
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Affiliation(s)
- Utkarsh J Dang
- Department of Health Outcomes and Administrative Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | - Michael Ziemba
- Department of Biomedical Engineering, Watson School of Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | - Paula R Clemens
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Department of Veteran Affairs Medical Center, Pittsburgh, PA 15213, USA
| | - Yetrib Hathout
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | | | | | - Eric P Hoffman
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University-SUNY, Binghamton, NY 13902, USA.,ReveraGen BioPharma, Rockville, MD 20850, USA
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16
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Validation of Chemokine Biomarkers in Duchenne Muscular Dystrophy. Life (Basel) 2021; 11:life11080827. [PMID: 34440571 PMCID: PMC8401931 DOI: 10.3390/life11080827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 02/06/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a progressive muscle disease involving complex skeletal muscle pathogenesis. The pathogenesis is triggered by sarcolemma instability due to the lack of dystrophin protein expression, leading to Ca2+ influx, muscle fiber apoptosis, inflammation, muscle necrosis, and fibrosis. Our lab recently used two high-throughput multiplexing techniques (e.g., SomaScan® aptamer assay and tandem mass tag-(TMT) approach) and identified a series of serum protein biomarkers tied to different pathobiochemical pathways. In this study, we focused on validating the circulating levels of three proinflammatory chemokines (CCL2, CXCL10, and CCL18) that are believed to be involved in an early stage of muscle pathogenesis. We used highly specific and reproducible MSD ELISA assays and examined the association of these chemokines with DMD pathogenesis, age, disease severity, and response to glucocorticoid treatment. As expected, we confirmed that these three chemokines were significantly elevated in serum and muscle samples of DMD patients relative to age-matched healthy controls (p-value < 0.05, CCL18 was not significantly altered in muscle samples). These three chemokines were not significantly elevated in Becker muscular dystrophy (BMD) patients, a milder form of dystrophinopathy, when compared in a one-way ANOVA to a control group but remained significantly elevated in the age-matched DMD group (p < 0.05). CCL2 and CCL18 but not CXCL10 declined with age in DMD patients, whereas all three chemokines remained unchanged with age in BMD and controls. Only CCL2 showed significant association with time to climb four steps in the DMD group (r = 0.48, p = 0.038) and neared significant association with patients' reported outcome in the BMD group (r = 0.39, p = 0.058). Furthermore, CCL2 was found to be elevated in a serum of the mdx mouse model of DMD, relative to wild-type mouse model. This study suggests that CCL2 might be a suitable candidate biomarker for follow-up studies to demonstrate its physiological significance and clinical utility in DMD.
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17
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Ryu JM, Na HH, Park JS, Ahn BS, Kim KC. Identification of Cleaved Haptoglobin in the Serum of Bee Venom-Hypersensitive Patients. J Acupunct Meridian Stud 2021; 14:102-109. [DOI: 10.51507/j.jams.2021.14.3.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/20/2021] [Accepted: 05/10/2021] [Indexed: 01/10/2023] Open
Affiliation(s)
- Jae-Min Ryu
- Department of Biological Sciences, College of Natural Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Han-Heom Na
- Department of Biological Sciences, College of Natural Sciences, Kangwon National University, Chuncheon, Republic of Korea
| | - Jin-Sung Park
- Korean Pharmacopuncture Institute, Seoul, Republic of Korea
| | - Byung-Soo Ahn
- Korean Pharmacopuncture Institute, Seoul, Republic of Korea
- AJ Research Institute for Integrative Medicine, Seoul, Republic of Korea
| | - Keun-Cheol Kim
- Department of Biological Sciences, College of Natural Sciences, Kangwon National University, Chuncheon, Republic of Korea
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18
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Alonso-Jiménez A, Fernández-Simón E, Natera-de Benito D, Ortez C, García C, Montiel E, Belmonte I, Pedrosa I, Segovia S, Piñol-Jurado P, Carrasco-Rozas A, Suárez-Calvet X, Jimenez-Mallebrera C, Nascimento A, Llauger J, Nuñez-Peralta C, Montesinos P, Alonso-Pérez J, Gallardo E, Illa I, Díaz-Manera J. Platelet Derived Growth Factor-AA Correlates With Muscle Function Tests and Quantitative Muscle Magnetic Resonance in Dystrophinopathies. Front Neurol 2021; 12:659922. [PMID: 34177765 PMCID: PMC8226260 DOI: 10.3389/fneur.2021.659922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Introduction: Duchenne (DMD) and Becker (BMD) muscular dystrophy are X-linked muscular disorders produced by mutations in the DMD gene which encodes the protein dystrophin. Both diseases are characterized by progressive involvement of skeletal, cardiac, and respiratory muscles. As new treatment strategies become available, reliable biomarkers and outcome measures that can monitor disease progression are needed for clinical trials. Methods: We collected clinical and functional data and blood samples from 19 DMD patients, 13 BMD patients, and 66 healthy controls (8 pediatric and 58 adult controls), and blood samples from 15 patients with dysferlinopathy (DYSF) and studied the serum concentration of 4 growth factors involved in the process of muscle fibrosis. We correlated the serum concentration of these growth factors with several muscle function tests, spirometry results and fat fraction identified by quantitative Dixon muscle MRI. Results: We found significant differences in the serum concentration of Platelet Derived Growth Factor-AA (PDGF-AA) between DMD patients and pediatric controls, in Connective Tissue Growth Factor (CTGF) between BMD patients and adult controls, and in and Transforming Growth Factor- β1 (TGF-β1) between BMD and DYSF patients. PDGF-AA showed a good correlation with several muscle function tests for both DMD and BMD patients and with thigh fat fraction in BMD patients. Moreover, PDGF-AA levels were increased in muscle biopsies of patients with DMD and BMD as was demonstrated by immunohistochemistry and Real-Time PCR studies. Conclusion: Our study suggests that PDGF-AA should be further investigated in a larger cohort of DMD and BMD patients because it might be a good biomarker candidate to monitor the progression of these diseases.
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Affiliation(s)
- Alicia Alonso-Jiménez
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Neurology Department, Neuromuscular Reference Center, University Hospital of Antwerp, Antwerp, Belgium
| | - Esther Fernández-Simón
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,John Walton Muscular Dystrophy Research Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carme García
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Montiel
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Izaskun Belmonte
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irene Pedrosa
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sonia Segovia
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Patricia Piñol-Jurado
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,John Walton Muscular Dystrophy Research Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ana Carrasco-Rozas
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Xavier Suárez-Calvet
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Cecilia Jimenez-Mallebrera
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.,Departamento de Genética, Microbiología y Estadística, Universidad de Barcelona, Barcelona, Spain
| | - Andrés Nascimento
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jaume Llauger
- Radiology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Claudia Nuñez-Peralta
- Radiology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Jorge Alonso-Pérez
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Eduard Gallardo
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Isabel Illa
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Jordi Díaz-Manera
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,John Walton Muscular Dystrophy Research Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
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19
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Signorelli M, Ebrahimpoor M, Veth O, Hettne K, Verwey N, García‐Rodríguez R, Tanganyika‐deWinter CL, Lopez Hernandez LB, Escobar Cedillo R, Gómez Díaz B, Magnusson OT, Mei H, Tsonaka R, Aartsma‐Rus A, Spitali P. Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients. EMBO Mol Med 2021; 13:e13328. [PMID: 33751844 PMCID: PMC8033515 DOI: 10.15252/emmm.202013328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
DMD is a rare disorder characterized by progressive muscle degeneration and premature death. Therapy development is delayed by difficulties to monitor efficacy non-invasively in clinical trials. In this study, we used RNA-sequencing to describe the pathophysiological changes in skeletal muscle of 3 dystrophic mouse models. We show how dystrophic changes in muscle are reflected in blood by analyzing paired muscle and blood samples. Analysis of repeated blood measurements followed the dystrophic signature at five equally spaced time points over a period of seven months. Treatment with two antisense drugs harboring different levels of dystrophin recovery identified genes associated with safety and efficacy. Evaluation of the blood gene expression in a cohort of DMD patients enabled the comparison between preclinical models and patients, and the identification of genes associated with physical performance, treatment with corticosteroids and body measures. The presented results provide evidence that blood RNA-sequencing can serve as a tool to evaluate disease progression in dystrophic mice and patients, as well as to monitor response to (dystrophin-restoring) therapies in preclinical drug development and in clinical trials.
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Affiliation(s)
- Mirko Signorelli
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenThe Netherlands
| | - Mitra Ebrahimpoor
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenThe Netherlands
| | - Olga Veth
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Kristina Hettne
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Nisha Verwey
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | | | | | - Luz B Lopez Hernandez
- Departamento de Medicina GenómicaUniversidad Autónoma de GuadalajaraGuadalajaraMexico
- Centro Médico Nacional "20 de Noviembre", ISSSTECiudad de MéxicoMexico
| | | | - Benjamín Gómez Díaz
- Sociedad Mexicana de la Distrofia Muscular A.C INR‐LGIICiudad de MéxicoMexico
| | | | - Hailiang Mei
- Sequencing Analysis Support CoreLeiden University Medical CenterLeidenThe Netherlands
| | - Roula Tsonaka
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenThe Netherlands
| | | | - Pietro Spitali
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
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20
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Fortunato F, Ferlini A. Clinical application of molecular biomarkers in Duchenne muscular dystrophy: challenges and perspectives. Expert Opin Orphan Drugs 2021. [DOI: 10.1080/21678707.2021.1903872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Fernanda Fortunato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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21
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Dabaj I, Ferey J, Marguet F, Gilard V, Basset C, Bahri Y, Brehin AC, Vanhulle C, Leturcq F, Marret S, Laquerrière A, Schmitz-Afonso I, Afonso C, Bekri S, Tebani A. Muscle metabolic remodelling patterns in Duchenne muscular dystrophy revealed by ultra-high-resolution mass spectrometry imaging. Sci Rep 2021; 11:1906. [PMID: 33479270 PMCID: PMC7819988 DOI: 10.1038/s41598-021-81090-1] [Citation(s) in RCA: 16] [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: 09/14/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a common and severe X-linked myopathy, characterized by muscle degeneration due to altered or absent dystrophin. DMD has no effective cure, and the underlying molecular mechanisms remain incompletely understood. The aim of this study is to investigate the metabolic changes in DMD using mass spectrometry-based imaging. Nine human muscle biopsies from DMD patients and nine muscle biopsies from control individuals were subjected to untargeted MSI using matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry. Both univariate and pattern recognition techniques have been used for data analysis. This study revealed significant changes in 34 keys metabolites. Seven metabolites were decreased in the Duchenne biopsies compared to control biopsies including adenosine triphosphate, and glycerophosphocholine. The other 27 metabolites were increased in the Duchenne biopsies, including sphingomyelin, phosphatidylcholines, phosphatidic acids and phosphatidylserines. Most of these dysregulated metabolites are tightly related to energy and phospholipid metabolism. This study revealed a deep metabolic remodelling in phospholipids and energy metabolism in DMD. This systems-based approach enabled exploring the metabolism in DMD in an unprecedented holistic and unbiased manner with hypothesis-free strategies.
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Affiliation(s)
- Ivana Dabaj
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031, Rouen, France
- Normandie Univ, UNIROUEN, CHU Rouen, INSERM U1245, 76000, Rouen, France
| | - Justine Ferey
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031, Rouen, Cedex, France
| | - Florent Marguet
- Normandie Univ, UNIROUEN, CHU Rouen, INSERM U1245, 76000, Rouen, France
- Department of Pathology, Rouen University Hospital, Rouen, France
| | - Vianney Gilard
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031, Rouen, Cedex, France
- Department of Neurosurgery, Rouen University Hospital, Rouen, France
| | - Carole Basset
- Department of Pathology, Rouen University Hospital, Rouen, France
| | - Youssef Bahri
- Normandie Univ, COBRA UMR 6014 Et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, 1 Rue TesnieÌre, 76821, Mont-Saint-Aignan Cedex, France
| | - Anne-Claire Brehin
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, 76000, Rouen, France
| | - Catherine Vanhulle
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031, Rouen, France
| | - France Leturcq
- APHP, Laboratoire de Génétique Et Biologie Moléculaire, HUPC Cochin, Paris, France
| | - Stéphane Marret
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031, Rouen, France
- Normandie Univ, UNIROUEN, CHU Rouen, INSERM U1245, 76000, Rouen, France
| | - Annie Laquerrière
- Normandie Univ, UNIROUEN, CHU Rouen, INSERM U1245, 76000, Rouen, France
- Department of Pathology, Rouen University Hospital, Rouen, France
| | - Isabelle Schmitz-Afonso
- Normandie Univ, COBRA UMR 6014 Et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, 1 Rue TesnieÌre, 76821, Mont-Saint-Aignan Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA UMR 6014 Et FR 3038 Univ Rouen; INSA Rouen; CNRS IRCOF, 1 Rue TesnieÌre, 76821, Mont-Saint-Aignan Cedex, France
| | - Soumeya Bekri
- Normandie Univ, UNIROUEN, CHU Rouen, INSERM U1245, 76000, Rouen, France.
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031, Rouen, Cedex, France.
| | - Abdellah Tebani
- Department of Metabolic Biochemistry, Rouen University Hospital, 76031, Rouen, Cedex, France
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22
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Quattrocelli M, Zelikovich AS, Salamone IM, Fischer JA, McNally EM. Mechanisms and Clinical Applications of Glucocorticoid Steroids in Muscular Dystrophy. J Neuromuscul Dis 2021; 8:39-52. [PMID: 33104035 PMCID: PMC7902991 DOI: 10.3233/jnd-200556] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glucocorticoid steroids are widely used as immunomodulatory agents in acute and chronic conditions. Glucocorticoid steroids such as prednisone and deflazacort are recommended for treating Duchenne Muscular Dystrophy where their use prolongs ambulation and life expectancy. Despite this benefit, glucocorticoid use in Duchenne Muscular Dystrophy is also associated with significant adverse consequences including adrenal suppression, growth impairment, poor bone health and metabolic syndrome. For other forms of muscular dystrophy like the limb girdle dystrophies, glucocorticoids are not typically used. Here we review the experimental evidence supporting multiple mechanisms of glucocorticoid action in dystrophic muscle including their role in dampening inflammation and myofiber injury. We also discuss alternative dosing strategies as well as novel steroid agents that are in development and testing, with the goal to reduce adverse consequences of prolonged glucocorticoid exposure while maximizing beneficial outcomes.
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Affiliation(s)
- Mattia Quattrocelli
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Molecular Cardiovascular Biology Division, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aaron S Zelikovich
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Isabella M Salamone
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julie A Fischer
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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23
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Alayi T, Tawalbeh SM, Ogundele M, Smith HR, Samsel AM, Barbieri ML, Hathout Y. Tandem Mass Tag-Based Serum Proteome Profiling for Biomarker Discovery in Young Duchenne Muscular Dystrophy Boys. ACS OMEGA 2020; 5:26504-26517. [PMID: 33110978 PMCID: PMC7581259 DOI: 10.1021/acsomega.0c03206] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Blood-accessible molecular biomarkers are becoming highly attractive tools to assess disease progression and response to therapies in Duchenne muscular dystrophy (DMD) especially in very young patients for whom other outcome measures remain subjective and challenging. In this study, we have standardized a highly specific and reproducible multiplexing mass spectrometry method using the tandem mass tag (TMT) strategy in combination with depletion of abundant proteins from serum and high-pH reversed-phase peptide fractionation. Differential proteome profiling of 4 year-old DMD boys (n = 9) and age-matched healthy controls (n = 9) identified 38 elevated and 50 decreased serum proteins (adjusted P < 0.05, FDR <0.05) in the DMD group relative to the healthy control group. As expected, we confirmed previously reported biomarkers but also identified novel biomarkers. These included novel muscle injury-associated biomarkers such as telethonin, smoothelin-like protein 1, cofilin-1, and plectin, additional muscle-specific enzymes such as UTP-glucose-1-phosphate uridylyltransferase, aspartate aminotransferase, pyruvate kinase PKM, lactotransferrin, tissue alpha-l-fucosidase, pantetheinase, and ficolin-1, and some pro-inflammatory and cell adhesion-associated biomarkers such as leukosialin, macrophage receptor MARCO, vitronectin, galectin-3-binding protein, and ProSAAS. The workflow including serum depletion, sample processing, and mass spectrometry analysis was found to be reproducible and stable over time with CV < 20%. Furthermore, the method was found to be superior in terms of specificity compared to other multiplexing affinity-based methods. These findings demonstrate the specificity and reliability of TMT-based mass spectrometry methods in detection and identification of serum biomarkers in presymptomatic young DMD patients.
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Affiliation(s)
- Tchilabalo
D. Alayi
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
| | - Shefa M. Tawalbeh
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
- Department
of Biomedical Engineering, Binghamton University−SUNY, 4400 Vestal Pkwy E, Binghamton, New York 13902, United States
| | - Michael Ogundele
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
- Department
of Biomedical Engineering, Binghamton University−SUNY, 4400 Vestal Pkwy E, Binghamton, New York 13902, United States
| | - Holly R. Smith
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
- Department
of Biochemistry, Binghamton University−SUNY, 4400 Vestal Pkwy E, Binghamton, New York 13902, United States
| | - Alison M. Samsel
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
| | - Marissa L. Barbieri
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
| | - Yetrib Hathout
- Department
of Pharmaceutical Science, School of Pharmacy and Pharmaceutical Sciences, Binghamton University−SUNY, Johnson City, New York 13790, United States
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24
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Koutsoulidou A, Phylactou LA. Circulating Biomarkers in Muscular Dystrophies: Disease and Therapy Monitoring. Mol Ther Methods Clin Dev 2020; 18:230-239. [PMID: 32637452 PMCID: PMC7327849 DOI: 10.1016/j.omtm.2020.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Muscular dystrophies are a group of inherited disorders that primarily affect the muscle tissues. Across the muscular dystrophies, symptoms commonly compromise the quality of life in all areas of functioning. It is well noted that muscular dystrophies need reliable and measurable biomarkers that will monitor the progress of the disease and evaluate the potential therapeutic approaches. In this review, we analyze the current findings regarding the development of blood-based circulating biomarkers for different types of muscular dystrophies. We emphasize those muscular dystrophies that gained particular interest for the development of biomarkers, including Duchenne muscular dystrophy, Becker muscular dystrophy, myotonic dystrophy types 1 and 2, Ullrich congenital muscular dystrophy, congenital muscular dystrophy type 1A, Facioscapulohumeral muscular dystrophy, and limb-girdle muscular dystrophy types 2A, 2B, 2C, and 2D, recently renamed as limb-girdle muscular dystrophy R1 calpain3-related, R2 dysferlin-related, R5 γ-sarcoglycan-related, and R3 α-sarcoglycan-related. This review highlights the up-to-date progress in the development of biomarkers at the level of proteins, lipids, and metabolites, as well as microRNAs (miRNAs) that currently are the main potential biomarker candidates in muscular dystrophies.
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Affiliation(s)
- Andrie Koutsoulidou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus.,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus.,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
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25
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Signorelli M, Ayoglu B, Johansson C, Lochmüller H, Straub V, Muntoni F, Niks E, Tsonaka R, Persson A, Aartsma-Rus A, Nilsson P, Al-Khalili Szigyarto C, Spitali P. Longitudinal serum biomarker screening identifies malate dehydrogenase 2 as candidate prognostic biomarker for Duchenne muscular dystrophy. J Cachexia Sarcopenia Muscle 2020; 11:505-517. [PMID: 31881125 PMCID: PMC7113516 DOI: 10.1002/jcsm.12517] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/13/2019] [Accepted: 10/17/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is a fatal disease for which no cure is available. Clinical trials have shown to be largely underpowered due to inter-individual variability and noisy outcome measures. The availability of biomarkers able to anticipate clinical benefit is highly needed to improve clinical trial design and facilitate drug development. METHODS In this study, we aimed to appraise the value of protein biomarkers to predict prognosis and monitor disease progression or treatment outcome in patients affected by DMD. We collected clinical data and 303 blood samples from 157 DMD patients in three clinical centres; 78 patients contributed multiple blood samples over time, with a median follow-up time of 2 years. We employed linear mixed models to identify biomarkers that are associated with disease progression, wheelchair dependency, and treatment with corticosteroids and performed survival analysis to find biomarkers whose levels are associated with time to loss of ambulation. RESULTS Our analysis led to the identification of 21 proteins whose levels significantly decrease with age and nine proteins whose levels significantly increase. Seven of these proteins are also differentially expressed in non-ambulant patients, and three proteins are differentially expressed in patients treated with glucocorticosteroids. Treatment with corticosteroids was found to partly counteract the effect of disease progression on two biomarkers, namely, malate dehydrogenase 2 (MDH2, P = 0.0003) and ankyrin repeat domain 2 (P = 0.0005); however, patients treated with corticosteroids experienced a further reduction on collagen 1 serum levels (P = 0.0003), especially following administration of deflazacort. A time to event analysis allowed to further support the use of MDH2 as a prognostic biomarker as it was associated with an increased risk of wheelchair dependence (P = 0.0003). The obtained data support the prospective evaluation of the identified biomarkers in natural history and clinical trials as exploratory biomarkers. CONCLUSIONS We identified a number of serum biomarkers associated with disease progression, loss of ambulation, and treatment with corticosteroids. The identified biomarkers are promising candidate prognostic and surrogate biomarkers, which may support drug developers if confirmed in prospective studies. The serum levels of MDH2 are of particular interest, as they correlate with disease stage and response to treatment with corticosteroids, and are also associated with the risk of wheelchair dependency and pulmonary function.
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Affiliation(s)
- Mirko Signorelli
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Burcu Ayoglu
- Department of Protein Sciences, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Camilla Johansson
- Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - 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, 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
| | - Volker Straub
- MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, UCL Institute of Child Health, London, UK
| | - Erik Niks
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roula Tsonaka
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Anja Persson
- Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annemieke Aartsma-Rus
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Nilsson
- Division of Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cristina Al-Khalili Szigyarto
- Department of Protein Sciences, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Protein Science, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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26
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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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