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Wong JPH, Blazev R, Ng YK, Goodman CA, Montgomery MK, Watt KI, Carl CS, Watt MJ, Voldstedlund CT, Richter EA, Crouch PJ, Steyn FJ, Ngo ST, Parker BL. Characterization of the skeletal muscle arginine methylome in health and disease reveals remodeling in amyotrophic lateral sclerosis. FASEB J 2024; 38:e23647. [PMID: 38787599 DOI: 10.1096/fj.202400045r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Arginine methylation is a protein posttranslational modification important for the development of skeletal muscle mass and function. Despite this, our understanding of the regulation of arginine methylation under settings of health and disease remains largely undefined. Here, we investigated the regulation of arginine methylation in skeletal muscles in response to exercise and hypertrophic growth, and in diseases involving metabolic dysfunction and atrophy. We report a limited regulation of arginine methylation under physiological settings that promote muscle health, such as during growth and acute exercise, nor in disease models of insulin resistance. In contrast, we saw a significant remodeling of asymmetric dimethylation in models of atrophy characterized by the loss of innervation, including in muscle biopsies from patients with myotrophic lateral sclerosis (ALS). Mass spectrometry-based quantification of the proteome and asymmetric arginine dimethylome of skeletal muscle from individuals with ALS revealed the largest compendium of protein changes with the identification of 793 regulated proteins, and novel site-specific changes in asymmetric dimethyl arginine (aDMA) of key sarcomeric and cytoskeletal proteins. Finally, we show that in vivo overexpression of PRMT1 and aDMA resulted in increased fatigue resistance and functional recovery in mice. Our study provides evidence for asymmetric dimethylation as a regulator of muscle pathophysiology and presents a valuable proteomics resource and rationale for numerous methylated and nonmethylated proteins, including PRMT1, to be pursued for therapeutic development in ALS.
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Affiliation(s)
- Julian P H Wong
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yaan-Kit Ng
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Craig A Goodman
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Magdalene K Montgomery
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin I Watt
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Victoria, Australia
- The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Christian S Carl
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Watt
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christian T Voldstedlund
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Erik A Richter
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Peter J Crouch
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Shyuan T Ngo
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin L Parker
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
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2
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King PH. Skeletal muscle as a molecular and cellular biomarker of disease progression in amyotrophic lateral sclerosis: a narrative review. Neural Regen Res 2024; 19:747-753. [PMID: 37843208 PMCID: PMC10664124 DOI: 10.4103/1673-5374.382226] [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: 05/07/2023] [Revised: 06/27/2023] [Accepted: 07/19/2023] [Indexed: 10/17/2023] Open
Abstract
Amyotrophic lateral sclerosis is a fatal multisystemic neurodegenerative disease with motor neurons being a primary target. Although progressive weakness is a hallmark feature of amyotrophic lateral sclerosis, there is considerable heterogeneity, including clinical presentation, progression, and the underlying triggers for disease initiation. Based on longitudinal studies with families harboring amyotrophic lateral sclerosis-associated gene mutations, it has become apparent that overt disease is preceded by a prodromal phase, possibly in years, where compensatory mechanisms delay symptom onset. Since 85-90% of amyotrophic lateral sclerosis is sporadic, there is a strong need for identifying biomarkers that can detect this prodromal phase as motor neurons have limited capacity for regeneration. Current Food and Drug Administration-approved therapies work by slowing the degenerative process and are most effective early in the disease. Skeletal muscle, including the neuromuscular junction, manifests abnormalities at the earliest stages of the disease, before motor neuron loss, making it a promising source for identifying biomarkers of the prodromal phase. The accessibility of muscle through biopsy provides a lens into the distal motor system at earlier stages and in real time. The advent of "omics" technology has led to the identification of numerous dysregulated molecules in amyotrophic lateral sclerosis muscle, ranging from coding and non-coding RNAs to proteins and metabolites. This technology has opened the door for identifying biomarkers of disease activity and providing insight into disease mechanisms. A major challenge is correlating the myriad of dysregulated molecules with clinical or histological progression and understanding their relevance to presymptomatic phases of disease. There are two major goals of this review. The first is to summarize some of the biomarkers identified in human amyotrophic lateral sclerosis muscle that have a clinicopathological correlation with disease activity, evidence of a similar dysregulation in the SOD1G93A mouse during presymptomatic stages, and evidence of progressive change during disease progression. The second goal is to review the molecular pathways these biomarkers reflect and their potential role in mitigating or promoting disease progression, and as such, their potential as therapeutic targets in amyotrophic lateral sclerosis.
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Affiliation(s)
- Peter H. King
- Department of Neurology and Center for Neurodegeneration and Experimental Therapeutics, The University of Alabama at Birmingham, Birmingham, AL, USA; Birmingham Veterans Affairs Medical Center, Birmingham, AL, USA
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3
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Lee A, Henderson R, Arachchige BJ, Robertson T, McCombe PA. Proteomic investigation of ALS motor cortex identifies known and novel pathogenetic mechanisms. J Neurol Sci 2023; 452:120753. [PMID: 37542825 DOI: 10.1016/j.jns.2023.120753] [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: 03/28/2023] [Revised: 06/30/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
The key pathological feature in ALS is death of motor neurones from the brain and spinal cord, but the molecular mechanisms underlying this degeneration remain unknown. Quantifying the motor cortex proteome in autopsy brain and comparing tissues from ALS cases and non-ALS controls is critical to understanding these mechanisms. We used Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) to characterize the proteomes of the motor cortex from ALS cases (n = 8) and control subjects (n = 8). A total of 1427 proteins were identified at a critical local false discovery rate < 5%; 187 of these exhibited significant expression differences between ALS cases and controls. Of these, 91 proteins were significantly upregulated and 96 proteins were significantly downregulated. Bioinformatics analysis revealed that these proteins are involved in molecular transport, protein trafficking, free radical scavenging, lipid metabolism, cell death and survival, nucleic acid metabolism, inflammatory response or amino acid metabolism and carbohydrate metabolism. Differentially expressed proteins were subjected to pathway analysis. This revealed abnormalities in pathways involving mitochondrial function, sirtuin signaling, oxidative phosphorylation, glycolysis, phagosome maturation, SNARE signaling, redox regulation and several others. Core analysis revealed mitochondrial dysfunction to be the top canonical pathway. The top-enriched networks involved JNK activation and inhibition of AKT signaling, suggesting that disruption of these signaling pathways could lead to demise of motor neurons in the ALS motor cortex.
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Affiliation(s)
- Aven Lee
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Robert Henderson
- Department of Neurology, Royal Brisbane & Women's Hospital (RBWH), Brisbane, QLD 4029, Australia
| | - Buddhika Jayakody Arachchige
- Mass Spectrometry Facility, Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Thomas Robertson
- Pathology, Royal Brisbane & Women's Hospital, Brisbane, QLD 4029, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Pamela Ann McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; Wesley Medical Research, The Wesley Hospital, Auchenflower, QLD 4066, Australia.
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4
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Thompson AG, Oeckl P, Feneberg E, Bowser R, Otto M, Fischer R, Kessler B, Turner MR. Advancing mechanistic understanding and biomarker development in amyotrophic lateral sclerosis. Expert Rev Proteomics 2021; 18:977-994. [PMID: 34758687 DOI: 10.1080/14789450.2021.2004890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Proteomic analysis has contributed significantly to the study of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). It has helped to define the pathological change common to nearly all cases, namely intracellular aggregates of phosphorylated TDP-43, shifting the focus of pathogenesis in ALS toward RNA biology. Proteomics has also uniquely underpinned the delineation of disease mechanisms in model systems and has been central to recent advances in human ALS biomarker development. AREAS COVERED The contribution of proteomics to understanding the cellular pathological changes, disease mechanisms, and biomarker development in ALS are covered. EXPERT OPINION Proteomics has delivered unique insights into the pathogenesis of ALS and advanced the goal of objective measurements of disease activity to improve therapeutic trials. Further developments in sensitivity and quantification are expected, with application to the presymptomatic phase of human disease offering the hope of prevention strategies.
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Affiliation(s)
| | - Patrick Oeckl
- Department of Neurology, University of Ulm, Ulm, Germany.,German Center for Neurodegenerative Diseases (Dzne e.V.), Ulm, Germany
| | - Emily Feneberg
- Department of Neurology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Robert Bowser
- Departments of Neurology and Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany.,Department of Neurology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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5
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Bergquist J. Leveraging the power of mass spectrometry to unravel complex brain pathologies. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2019; 14 Pt B:63-65. [PMID: 34977358 PMCID: PMC8686759 DOI: 10.1016/j.clinms.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jonas Bergquist
- Analytical Chemistry and Neurochemistry, Department of Chemistry - BMC, Uppsala University, Box 599, SE-75124 Uppsala, Sweden
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6
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Hedl TJ, San Gil R, Cheng F, Rayner SL, Davidson JM, De Luca A, Villalva MD, Ecroyd H, Walker AK, Lee A. Proteomics Approaches for Biomarker and Drug Target Discovery in ALS and FTD. Front Neurosci 2019; 13:548. [PMID: 31244593 PMCID: PMC6579929 DOI: 10.3389/fnins.2019.00548] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are increasing in prevalence but lack targeted therapeutics. Although the pathological mechanisms behind these diseases remain unclear, both ALS and FTD are characterized pathologically by aberrant protein aggregation and inclusion formation within neurons, which correlates with neurodegeneration. Notably, aggregation of several key proteins, including TAR DNA binding protein of 43 kDa (TDP-43), superoxide dismutase 1 (SOD1), and tau, have been implicated in these diseases. Proteomics methods are being increasingly applied to better understand disease-related mechanisms and to identify biomarkers of disease, using model systems as well as human samples. Proteomics-based approaches offer unbiased, high-throughput, and quantitative results with numerous applications for investigating proteins of interest. Here, we review recent advances in the understanding of ALS and FTD pathophysiology obtained using proteomics approaches, and we assess technical and experimental limitations. We compare findings from various mass spectrometry (MS) approaches including quantitative proteomics methods such as stable isotope labeling by amino acids in cell culture (SILAC) and tandem mass tagging (TMT) to approaches such as label-free quantitation (LFQ) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) in studies of ALS and FTD. Similarly, we describe disease-related protein-protein interaction (PPI) studies using approaches including immunoprecipitation mass spectrometry (IP-MS) and proximity-dependent biotin identification (BioID) and discuss future application of new techniques including proximity-dependent ascorbic acid peroxidase labeling (APEX), and biotinylation by antibody recognition (BAR). Furthermore, we explore the use of MS to detect post-translational modifications (PTMs), such as ubiquitination and phosphorylation, of disease-relevant proteins in ALS and FTD. We also discuss upstream technologies that enable enrichment of proteins of interest, highlighting the contributions of new techniques to isolate disease-relevant protein inclusions including flow cytometric analysis of inclusions and trafficking (FloIT). These recently developed approaches, as well as related advances yet to be applied to studies of these neurodegenerative diseases, offer numerous opportunities for discovery of potential therapeutic targets and biomarkers for ALS and FTD.
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Affiliation(s)
- Thomas J Hedl
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Flora Cheng
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Jennilee M Davidson
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Alana De Luca
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Maria D Villalva
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Heath Ecroyd
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia.,Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
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7
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Pharaoh G, Sataranatarajan K, Street K, Hill S, Gregston J, Ahn B, Kinter C, Kinter M, Van Remmen H. Metabolic and Stress Response Changes Precede Disease Onset in the Spinal Cord of Mutant SOD1 ALS Mice. Front Neurosci 2019; 13:487. [PMID: 31213966 PMCID: PMC6554287 DOI: 10.3389/fnins.2019.00487] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/29/2019] [Indexed: 12/11/2022] Open
Abstract
Many Amyotrophic Lateral Sclerosis (ALS) patients experience hypermetabolism, or an increase in measured vs. calculated metabolic rate. The cause of hypermetabolism and the effects on neuronal metabolism in ALS are currently unknown, but the efficacy of dietary interventions shows promise for metabolism as an ALS therapeutic target. The goal of this study is to measure changes in metabolic pathways as a function of disease progression in spinal cords of the SOD1G93A mouse model of ALS. We conducted a comprehensive assessment of protein expression for metabolic pathways, antioxidants, chaperones, and proteases in lumbar spinal cord from male SOD1G93A mice at pre-onset, onset, and end-stages of the disease using targeted proteomic analysis. These results reveal that protein content of metabolic proteins including proteins involved in glycolysis, β-oxidation, and mitochondrial metabolism is altered in SOD1G93A mouse spinal cord well before disease onset. The changes in mitochondrial metabolism proteins are associated with decreased maximal respiration and glycolytic flux in SOD1G93A dermal fibroblasts and increased hydrogen peroxide and lipid hydroperoxide production in mitochondria from sciatic nerve and gastrocnemius muscle fibers at end stage of disease. Consistent with redox dysregulation, expression of the glutathione antioxidant system is decreased, and peroxiredoxins and catalase expression are increased. In addition, stress response proteases and chaperones, including those involved in the mitochondrial unfolded protein response (UPRmt), are induced before disease onset. In summary, we report that metabolic and stress response changes occur in SOD1G93A lumbar spinal cord before motor symptom onset, and are primarily caused by SOD1G93A expression and do not vary greatly as a function of disease course.
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Affiliation(s)
- Gavin Pharaoh
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Physiology, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | | | - Kaitlyn Street
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Shauna Hill
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Jake Gregston
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Bumsoo Ahn
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Caroline Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Michael Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Holly Van Remmen
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Physiology, University of Oklahoma Health Science Center, Oklahoma City, OK, United States.,Oklahoma City VA Medical Center, Oklahoma City, OK, United States
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8
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Vijayakumar UG, Milla V, Cynthia Stafford MY, Bjourson AJ, Duddy W, Duguez SMR. A Systematic Review of Suggested Molecular Strata, Biomarkers and Their Tissue Sources in ALS. Front Neurol 2019; 10:400. [PMID: 31139131 PMCID: PMC6527847 DOI: 10.3389/fneur.2019.00400] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is an incurable neurodegenerative condition, characterized by the loss of upper and lower motor neurons. It affects 1-1.8/100,000 individuals worldwide, and the number of cases is projected to increase as the population ages. Thus, there is an urgent need to identify both therapeutic targets and disease-specific biomarkers-biomarkers that would be useful to diagnose and stratify patients into different sub-groups for therapeutic strategies, as well as biomarkers to follow the efficacy of any treatment tested during clinical trials. There is a lack of knowledge about pathogenesis and many hypotheses. Numerous "omics" studies have been conducted on ALS in the past decade to identify a disease-signature in tissues and circulating biomarkers. The first goal of the present review was to group the molecular pathways that have been implicated in monogenic forms of ALS, to enable the description of patient strata corresponding to each pathway grouping. This strategy allowed us to suggest 14 strata, each potentially targetable by different pharmacological strategies. The second goal of this review was to identify diagnostic/prognostic biomarker candidates consistently observed across the literature. For this purpose, we explore previous biomarker-relevant "omics" studies of ALS and summarize their findings, focusing on potential circulating biomarker candidates. We systematically review 118 papers on biomarkers published during the last decade. Several candidate markers were consistently shared across the results of different studies in either cerebrospinal fluid (CSF) or blood (leukocyte or serum/plasma). Although these candidates still need to be validated in a systematic manner, we suggest the use of combinations of biomarkers that would likely reflect the "health status" of different tissues, including motor neuron health (e.g., pNFH and NF-L, cystatin C, Transthyretin), inflammation status (e.g., MCP-1, miR451), muscle health (miR-338-3p, miR-206) and metabolism (homocysteine, glutamate, cholesterol). In light of these studies and because ALS is increasingly perceived as a multi-system disease, the identification of a panel of biomarkers that accurately reflect features of pathology is a priority, not only for diagnostic purposes but also for prognostic or predictive applications.
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Affiliation(s)
| | | | | | | | | | - Stephanie Marie-Rose Duguez
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
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9
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Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis. Sci Rep 2019; 9:4478. [PMID: 30872628 PMCID: PMC6418138 DOI: 10.1038/s41598-019-40632-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.
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10
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Iridoy MO, Zubiri I, Zelaya MV, Martinez L, Ausín K, Lachen-Montes M, Santamaría E, Fernandez-Irigoyen J, Jericó I. Neuroanatomical Quantitative Proteomics Reveals Common Pathogenic Biological Routes between Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD). Int J Mol Sci 2018; 20:E4. [PMID: 30577465 PMCID: PMC6337647 DOI: 10.3390/ijms20010004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/10/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative disorders with an overlap in clinical presentation and neuropathology. Common and differential mechanisms leading to protein expression changes and neurodegeneration in ALS and FTD were studied trough a deep neuroproteome mapping of the spinal cord. (2) Methods: A liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of the spinal cord from ALS-TAR DNA-binding protein 43 (TDP-43) subjects, ubiquitin-positive frontotemporal lobar degeneration (FTLD-U) subjects and controls without neurodegenerative disease was performed. (3) Results: 281 differentially expressed proteins were detected among ALS versus controls, while 52 proteins were dysregulated among FTLD-U versus controls. Thirty-three differential proteins were shared between both syndromes. The resulting data was subjected to network-driven proteomics analysis, revealing mitochondrial dysfunction and metabolic impairment, both for ALS and FTLD-U that could be validated through the confirmation of expression levels changes of the Prohibitin (PHB) complex. (4) Conclusions: ALS-TDP-43 and FTLD-U share molecular and functional alterations, although part of the proteostatic impairment is region- and disease-specific. We have confirmed the involvement of specific proteins previously associated with ALS (Galectin 2 (LGALS3), Transthyretin (TTR), Protein S100-A6 (S100A6), and Protein S100-A11 (S100A11)) and have shown the involvement of proteins not previously described in the ALS context (Methanethiol oxidase (SELENBP1), Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN-1), Calcyclin-binding protein (CACYBP) and Rho-associated protein kinase 2 (ROCK2)).
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Affiliation(s)
- Marina Oaia Iridoy
- Department of Neurology ComplejoHospitalario de Navarra (CHN), IdiSNA (Navarra Institute for Health Research), Irunlarrea 3, 31008 Pamplona, Spain.
| | - Irene Zubiri
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
| | - María Victoria Zelaya
- Pathological Anatomyservice Complejo Hospitalario de Navarra (CHN), IdiSNA (Navarra Institute for Health Research), Irunlarrea 3, 31008 Pamplona, Spain.
| | - Leyre Martinez
- Department of Neurology ComplejoHospitalario de Navarra (CHN), IdiSNA (Navarra Institute for Health Research), Irunlarrea 3, 31008 Pamplona, Spain.
| | - Karina Ausín
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
| | - Mercedes Lachen-Montes
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
| | - Enrique Santamaría
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
| | - Joaquín Fernandez-Irigoyen
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Irunlarrea 3, 31008 Pamplona, Spain.
| | - Ivonne Jericó
- Department of Neurology ComplejoHospitalario de Navarra (CHN), IdiSNA (Navarra Institute for Health Research), Irunlarrea 3, 31008 Pamplona, Spain.
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11
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Šoltić D, Bowerman M, Stock J, Shorrock HK, Gillingwater TH, Fuller HR. Multi-Study Proteomic and Bioinformatic Identification of Molecular Overlap between Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA). Brain Sci 2018; 8:brainsci8120212. [PMID: 30518112 PMCID: PMC6315439 DOI: 10.3390/brainsci8120212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 12/24/2022] Open
Abstract
Unravelling the complex molecular pathways responsible for motor neuron degeneration in amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) remains a persistent challenge. Interest is growing in the potential molecular similarities between these two diseases, with the hope of better understanding disease pathology for the guidance of therapeutic development. The aim of this study was to conduct a comparative analysis of published proteomic studies of ALS and SMA, seeking commonly dysregulated molecules to be prioritized as future therapeutic targets. Fifteen proteins were found to be differentially expressed in two or more proteomic studies of both ALS and SMA, and bioinformatics analysis identified over-representation of proteins known to associate in vesicles and molecular pathways, including metabolism of proteins and vesicle-mediated transport—both of which converge on endoplasmic reticulum (ER)-Golgi trafficking processes. Calreticulin, a calcium-binding chaperone found in the ER, was associated with both pathways and we independently confirm that its expression was decreased in spinal cords from SMA and increased in spinal cords from ALS mice. Together, these findings offer significant insights into potential common targets that may help to guide the development of new therapies for both diseases.
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Affiliation(s)
- Darija Šoltić
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Melissa Bowerman
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Joanne Stock
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
| | - Hannah K. Shorrock
- Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh EH8 9AG, UK; (H.K.S.); (T.H.G.)
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Thomas H. Gillingwater
- Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh EH8 9AG, UK; (H.K.S.); (T.H.G.)
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Heidi R. Fuller
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK; (D.S.); (M.B.)
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10 7AG, UK
- Correspondence: ; Tel.: +44-169-140-4693; Fax: +44-169-140-4065
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12
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Murphy KT, Hossain MI, Swiderski K, Chee A, Naim T, Trieu J, Haynes V, Read SJ, Stapleton DI, Judge SM, Trevino JG, Judge AR, Lynch GS. Mas Receptor Activation Slows Tumor Growth and Attenuates Muscle Wasting in Cancer. Cancer Res 2018; 79:706-719. [PMID: 30420474 DOI: 10.1158/0008-5472.can-18-1207] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/27/2018] [Accepted: 11/07/2018] [Indexed: 01/06/2023]
Abstract
Cancer cachexia is a multifactorial syndrome characterized by a progressive loss of skeletal muscle mass associated with significant functional impairment. Cachexia robs patients of their strength and capacity to perform daily tasks and live independently. Effective treatments are needed urgently. Here, we investigated the therapeutic potential of activating the "alternative" axis of the renin-angiotensin system, involving ACE2, angiotensin-(1-7), and the mitochondrial assembly receptor (MasR), for treating cancer cachexia. Plasmid overexpression of the MasR or pharmacologic angiotensin-(1-7)/MasR activation did not affect healthy muscle fiber size in vitro or in vivo but attenuated atrophy induced by coculture with cancer cells in vitro. In mice with cancer cachexia, the MasR agonist AVE 0991 slowed tumor development, reduced weight loss, improved locomotor activity, and attenuated muscle wasting, with the majority of these effects dependent on the orexigenic and not antitumor properties of AVE 0991. Proteomic profiling and IHC revealed that mechanisms underlying AVE 0991 effects on skeletal muscle involved miR-23a-regulated preservation of the fast, glycolytic fibers. MasR activation is a novel regulator of muscle phenotype, and AVE 0991 has orexigenic, anticachectic, and antitumorigenic effects, identifying it as a promising adjunct therapy for cancer and other serious muscle wasting conditions. SIGNIFICANCE: These findings demonstrate that MasR activation has multiple benefits of being orexigenic, anticachectic, and antitumorigenic, revealing it as a potential adjunct therapy for cancer.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/4/706/F1.large.jpg.See related commentary by Rupert et al., p. 699.
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Affiliation(s)
- Kate T Murphy
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia.
| | - Mohammed I Hossain
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Kristy Swiderski
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Annabel Chee
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Timur Naim
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Jennifer Trieu
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Vanessa Haynes
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Suzannah J Read
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - David I Stapleton
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Sarah M Judge
- Department of Physical Therapy, University of Florida Health Science Center, Gainesville, Florida
| | - Jose G Trevino
- Department of Surgery, College of Medicine, University of Florida Health Science Center, Gainesville, Florida
| | - Andrew R Judge
- Department of Physical Therapy, University of Florida Health Science Center, Gainesville, Florida
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Victoria, Australia
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13
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Szelechowski M, Amoedo N, Obre E, Léger C, Allard L, Bonneu M, Claverol S, Lacombe D, Oliet S, Chevallier S, Le Masson G, Rossignol R. Metabolic Reprogramming in Amyotrophic Lateral Sclerosis. Sci Rep 2018; 8:3953. [PMID: 29500423 PMCID: PMC5834494 DOI: 10.1038/s41598-018-22318-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/21/2018] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction in the spinal cord is a hallmark of amyotrophic lateral sclerosis (ALS), but the neurometabolic alterations during early stages of the disease remain unknown. Here, we investigated the bioenergetic and proteomic changes in ALS mouse motor neurons and patients' skin fibroblasts. We first observed that SODG93A mice presymptomatic motor neurons display alterations in the coupling efficiency of oxidative phosphorylation, along with fragmentation of the mitochondrial network. The proteome of presymptomatic ALS mice motor neurons also revealed a peculiar metabolic signature with upregulation of most energy-transducing enzymes, including the fatty acid oxidation (FAO) and the ketogenic components HADHA and ACAT2, respectively. Accordingly, FAO inhibition altered cell viability specifically in ALS mice motor neurons, while uncoupling protein 2 (UCP2) inhibition recovered cellular ATP levels and mitochondrial network morphology. These findings suggest a novel hypothesis of ALS bioenergetics linking FAO and UCP2. Lastly, we provide a unique set of data comparing the molecular alterations found in human ALS patients' skin fibroblasts and SODG93A mouse motor neurons, revealing conserved changes in protein translation, folding and assembly, tRNA aminoacylation and cell adhesion processes.
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Affiliation(s)
- M Szelechowski
- INSERM U1215, Neurocentre Magendie, 33077, Bordeaux, cedex, France
- Bordeaux University, 33000, Bordeaux, France
| | - N Amoedo
- Bordeaux University, 33000, Bordeaux, France
- INSERM U1211, MRGM, 33000, Bordeaux, France
| | - E Obre
- CELLOMET, Center of Functional Genomics (CGFB), 146 Rue Léo Saignat, 33000, Bordeaux, France
| | - C Léger
- INSERM U1215, Neurocentre Magendie, 33077, Bordeaux, cedex, France
- Bordeaux University, 33000, Bordeaux, France
| | - L Allard
- INSERM U1215, Neurocentre Magendie, 33077, Bordeaux, cedex, France
- Bordeaux University, 33000, Bordeaux, France
| | - M Bonneu
- Bordeaux University, 33000, Bordeaux, France
- Center of Functional Genomics (CGFB), Proteomic Facility, Bordeaux University, 33000, Bordeaux, France
| | - S Claverol
- Bordeaux University, 33000, Bordeaux, France
- Center of Functional Genomics (CGFB), Proteomic Facility, Bordeaux University, 33000, Bordeaux, France
| | - D Lacombe
- Bordeaux University, 33000, Bordeaux, France
- INSERM U1211, MRGM, 33000, Bordeaux, France
| | - S Oliet
- INSERM U1215, Neurocentre Magendie, 33077, Bordeaux, cedex, France
- Bordeaux University, 33000, Bordeaux, France
| | - S Chevallier
- INSERM U1215, Neurocentre Magendie, 33077, Bordeaux, cedex, France
- Bordeaux University, 33000, Bordeaux, France
| | - G Le Masson
- INSERM U1215, Neurocentre Magendie, 33077, Bordeaux, cedex, France.
- Bordeaux University, 33000, Bordeaux, France.
| | - R Rossignol
- Bordeaux University, 33000, Bordeaux, France.
- INSERM U1211, MRGM, 33000, Bordeaux, France.
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14
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Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic serum biomarkers for neuromuscular diseases. Expert Rev Proteomics 2018; 15:277-291. [DOI: 10.1080/14789450.2018.1429923] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn, Germany
| | | | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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15
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Capitanio D, Moriggi M, Gelfi C. Mapping the human skeletal muscle proteome: progress and potential. Expert Rev Proteomics 2017; 14:825-839. [PMID: 28780899 DOI: 10.1080/14789450.2017.1364996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies. Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies. Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.
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Affiliation(s)
- Daniele Capitanio
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Manuela Moriggi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Cecilia Gelfi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
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16
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Gonzalez-Freire M, Semba RD, Ubaida-Mohien C, Fabbri E, Scalzo P, Højlund K, Dufresne C, Lyashkov A, Ferrucci L. The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. J Cachexia Sarcopenia Muscle 2017; 8:5-18. [PMID: 27897395 PMCID: PMC5326819 DOI: 10.1002/jcsm.12121] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle is a large organ that accounts for up to half the total mass of the human body. A progressive decline in muscle mass and strength occurs with ageing and in some individuals configures the syndrome of 'sarcopenia', a condition that impairs mobility, challenges autonomy, and is a risk factor for mortality. The mechanisms leading to sarcopenia as well as myopathies are still little understood. The Human Skeletal Muscle Proteome Project was initiated with the aim to characterize muscle proteins and how they change with ageing and disease. We conducted an extensive review of the literature and analysed publically available protein databases. A systematic search of peer-reviewed studies was performed using PubMed. Search terms included 'human', 'skeletal muscle', 'proteome', 'proteomic(s)', and 'mass spectrometry', 'liquid chromatography-mass spectrometry (LC-MS/MS)'. A catalogue of 5431 non-redundant muscle proteins identified by mass spectrometry-based proteomics from 38 peer-reviewed scientific publications from 2002 to November 2015 was created. We also developed a nosology system for the classification of muscle proteins based on localization and function. Such inventory of proteins should serve as a useful background reference for future research on changes in muscle proteome assessed by quantitative mass spectrometry-based proteomic approaches that occur with ageing and diseases. This classification and compilation of the human skeletal muscle proteome can be used for the identification and quantification of proteins in skeletal muscle to discover new mechanisms for sarcopenia and specific muscle diseases that can be targeted for the prevention and treatment.
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Affiliation(s)
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Elisa Fabbri
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Paul Scalzo
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Alexey Lyashkov
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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17
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Engelen-Lee J, Blokhuis AM, Spliet WGM, Pasterkamp RJ, Aronica E, Demmers JAA, Broekhuizen R, Nardo G, Bovenschen N, Van Den Berg LH. Proteomic profiling of the spinal cord in ALS: decreased ATP5D levels suggest synaptic dysfunction in ALS pathogenesis. Amyotroph Lateral Scler Frontotemporal Degener 2016; 18:210-220. [DOI: 10.1080/21678421.2016.1245757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jooyeon Engelen-Lee
- Department of Neurology, Academic Medical Centre, Amsterdam, The Netherlands,
| | - Anna M. Blokhuis
- Department of Translational Neuroscience, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands,
| | - Wim G. M. Spliet
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands,
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands,
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medical Centre, Amsterdam, The Netherlands,
| | - Jeroen A. A. Demmers
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, The Netherlands,
| | - Roel Broekhuizen
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands,
| | - Giovanni Nardo
- Department of Molecular Biochemistry and Pharmacology, Mario Negri Institute for Pharmacological Research, Milano, Italy,
| | - Niels Bovenschen
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands,
- Laboratory of Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands, and
| | - Leonard H. Van Den Berg
- Department of Neurology and Neurosurgery, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, The Netherlands
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18
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Dowling P, Murphy S, Ohlendieck K. Proteomic profiling of muscle fibre type shifting in neuromuscular diseases. Expert Rev Proteomics 2016; 13:783-99. [DOI: 10.1080/14789450.2016.1209416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Sargsyan E, Artemenko K, Manukyan L, Bergquist J, Bergsten P. Oleate protects beta-cells from the toxic effect of palmitate by activating pro-survival pathways of the ER stress response. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1151-1160. [PMID: 27344025 DOI: 10.1016/j.bbalip.2016.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 06/11/2016] [Accepted: 06/20/2016] [Indexed: 12/20/2022]
Abstract
Long-term exposure of beta cells to saturated fatty acids impairs insulin secretion and increases apoptosis. In contrast, unsaturated fatty acids protect beta-cells from the long-term negative effects of saturated fatty acids. We aimed to identify the mechanisms underlying this protective action of unsaturated fatty acids. To address the aim, insulin-secreting MIN6 cells were exposed to palmitate in the absence or presence of oleate and analyzed by using nano-LC MS/MS based proteomic approach. Important findings were validated by using alternative approaches. Proteomic analysis identified 34 proteins differentially expressed in the presence of palmitate compared to control samples. These proteins play a role in insulin processing, mitochondrial function, metabolism of biomolecules, calcium homeostasis, exocytosis, receptor signaling, ER protein folding, antioxidant activity and anti-apoptotic function. When oleate was also present during culture, expression of 15 proteins was different from the expression in the presence of palmitate alone. Most of the proteins affected by oleate are targets of the ER stress response and play a pro-survival role in beta cells such as protein folding and antioxidative defence. We conclude that restoration of pro-survival pathways of the ER stress response is a major mechanism underlying the protective effect of unsaturated fatty acids in beta-cells treated with saturated fatty acids.
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Affiliation(s)
- Ernest Sargsyan
- Department of Medical Cell Biology, Uppsala University, Box 571, 75123 Uppsala, Sweden.
| | | | - Levon Manukyan
- Department of Medical Cell Biology, Uppsala University, Box 571, 75123 Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry, Uppsala University, Uppsala, Sweden; SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Peter Bergsten
- Department of Medical Cell Biology, Uppsala University, Box 571, 75123 Uppsala, Sweden
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20
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Blasco H, Vourc'h P, Pradat PF, Gordon PH, Andres CR, Corcia P. Further development of biomarkers in amyotrophic lateral sclerosis. Expert Rev Mol Diagn 2016; 16:853-68. [PMID: 27275785 DOI: 10.1080/14737159.2016.1199277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Amyotrophic lateral sclerosis (ALS) is an idiopathic neurodegenerative disease usually fatal in less than three years. Even if standard guidelines are available to diagnose ALS, the mean diagnosis delay is more than one year. In this context, biomarker discovery is a priority. Research has to focus on new diagnostic tools, based on combined explorations. AREAS COVERED In this review, we specifically focus on biology and imaging markers. We detail the innovative field of 'omics' approach and imaging and explain their limits to be useful in routine practice. We describe the most relevant biomarkers and suggest some perspectives for biomarker research. Expert commentary: The successive failures of clinical trials in ALS underline the need for new strategy based on innovative tools to stratify patients and to evaluate their responses to treatment. Biomarker data may be useful to improve the designs of clinical trials. Biomarkers are also needed to better investigate disease pathophysiology, to identify new therapeutic targets, and to improve the performance of clinical assessments for diagnosis and prognosis in the clinical setting. A consensus on the best management of neuroimaging and 'omics' methods is necessary and a systematic independent validation of findings may add robustness to future studies.
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Affiliation(s)
- H Blasco
- a UMR INSERM U930 , Université François-Rabelais de Tours , Tours , France.,b Laboratoire de Biochimie et de Biologie Moléculaire , Hôpital Bretonneau, CHRU de Tours , Tours , France
| | - P Vourc'h
- a UMR INSERM U930 , Université François-Rabelais de Tours , Tours , France.,b Laboratoire de Biochimie et de Biologie Moléculaire , Hôpital Bretonneau, CHRU de Tours , Tours , France
| | - P F Pradat
- c Département des Maladies du Système Nerveux, Assistance Publique-Hôpitaux de Paris , Hôpital de la Salpêtrière , Paris , France.,d Sorbonne Universités, UPMC Université Paris 06, CNRS, INSERM , Laboratoire d'Imagerie Biomédicale , Paris , France
| | - P H Gordon
- e Neurology Unit, Northern Navajo Medical Center , Shiprock , NM , USA
| | - C R Andres
- a UMR INSERM U930 , Université François-Rabelais de Tours , Tours , France.,b Laboratoire de Biochimie et de Biologie Moléculaire , Hôpital Bretonneau, CHRU de Tours , Tours , France
| | - P Corcia
- a UMR INSERM U930 , Université François-Rabelais de Tours , Tours , France.,b Laboratoire de Biochimie et de Biologie Moléculaire , Hôpital Bretonneau, CHRU de Tours , Tours , France.,f Centre SLA , Service de Neurologie et Neurophysiologie Clinique, CHRU de Tours , Tours , France
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21
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A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients. PLoS One 2016; 11:e0149821. [PMID: 26914813 PMCID: PMC4767403 DOI: 10.1371/journal.pone.0149821] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 02/04/2016] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to develop and apply a novel multiplex panel of solid-phase proximity ligation assays (SP-PLA) requiring only 20 μL of samples, as a tool for discovering protein biomarkers for neurological disease and treatment thereof in cerebrospinal fluid (CSF). We applied the SP-PLA to samples from two sets of patients with poorly understood nervous system pathologies amyotrophic lateral sclerosis (ALS) and neuropathic pain, where patients were treated with spinal cord stimulation (SCS). Forty-seven inflammatory and neurotrophic proteins were measured in samples from 20 ALS patients and 15 neuropathic pain patients, and compared to normal concentrations in CSF from control individuals. Nineteen of the 47 proteins were detectable in more than 95% of the 72 controls. None of the 21 proteins detectable in CSF from neuropathic pain patients were significantly altered by SCS. The levels of the three proteins, follistatin, interleukin-1 alpha, and kallikrein-5 were all significantly reduced in the ALS group compared to age-matched controls. These results demonstrate the utility of purpose designed multiplex SP-PLA panels in CSF biomarker research for understanding neuropathological and neurotherapeutic mechanisms. The protein changes found in the CSF of ALS patients may be of diagnostic interest.
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22
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Caballero-Hernandez D, Toscano MG, Cejudo-Guillen M, Garcia-Martin ML, Lopez S, Franco JM, Quintana FJ, Roodveldt C, Pozo D. The ‘Omics’ of Amyotrophic Lateral Sclerosis. Trends Mol Med 2016; 22:53-67. [DOI: 10.1016/j.molmed.2015.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 10/29/2015] [Accepted: 11/08/2015] [Indexed: 12/11/2022]
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23
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Schild M, Ruhs A, Beiter T, Zügel M, Hudemann J, Reimer A, Krumholz-Wagner I, Wagner C, Keller J, Eder K, Krüger K, Krüger M, Braun T, Nieß A, Steinacker J, Mooren FC. Basal and exercise induced label-free quantitative protein profiling of m. vastus lateralis in trained and untrained individuals. J Proteomics 2015; 122:119-32. [PMID: 25857276 DOI: 10.1016/j.jprot.2015.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/13/2015] [Accepted: 03/28/2015] [Indexed: 12/26/2022]
Abstract
UNLABELLED Morphological and metabolic adaptations of the human skeletal muscle to exercise are crucial to improve performance and prevent chronic diseases and metabolic disorders. In this study we investigated human skeletal muscle protein composition in endurance trained (ET) versus untrained individuals (UT) and its modulation by an acute bout of endurance exercise. Participants were recruited based on their VO2max and subjected to a bicycle exercise test. M. vastus lateralis biopsies were taken before and three hours after exercise. Muscle lysates were analyzed using off-gel LC-MS/MS. Relative protein abundances were compared between ET and UT at rest and after exercise. Comparing UT and ET, we identified 92 significantly changed proteins under resting conditions. Specifically, fiber-type-specific and proteins of the oxidative phosphorylation and tricarboxylic acid cycle were increased in ET. In response to acute exercise, 71 proteins in ET and 44 in UT were altered. Here, a decrease of proteins involved in energy metabolism accompanied with alterations of heat shock and proteasomal proteins could be observed. In summary, long-term endurance training increased the basal level of structural and mitochondrial proteins in skeletal muscle. In contrast, acute exercise resulted in a depletion of proteins related to substrate utilization, especially in trained athletes. BIOLOGICAL SIGNIFICANCE The investigation of the human skeletal muscle proteome in response to exercise may provide novel insights into the process of muscular plasticity. It is of importance in the development of exercise-based strategies in the prevention and therapy of many chronic inflammatory and degenerative diseases which are often accompanied by muscular deconditioning. Up to date, proteomic investigations of the human muscle proteome in adaptation to exercise are mainly focused on untrained individuals and often restricted to animal studies. In the present study we compare the protein composition in endurance trained athletes and untrained individuals in the resting muscle and its modulation in response to acute exercise. To our knowledge, we present the first comprehensive analysis of skeletal muscle proteome alterations in response to acute and long-term exercise intervention.
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Affiliation(s)
- Marius Schild
- Department of Sports Medicine, Justus-Liebig University Giessen, Kugelberg 62, 35394 Giessen, Germany
| | - Aaron Ruhs
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Thomas Beiter
- Department of Sports Medicine, University Hospital of Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Martina Zügel
- Division of Sport and Rehabilitation Medicine, University Hospital Ulm, Parkstr. 11, 89075 Ulm, Germany
| | - Jens Hudemann
- Department of Sports Medicine, University Hospital of Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Anna Reimer
- Department of Sports Medicine, Justus-Liebig University Giessen, Kugelberg 62, 35394 Giessen, Germany
| | - Ilke Krumholz-Wagner
- Department of Sports Medicine, Justus-Liebig University Giessen, Kugelberg 62, 35394 Giessen, Germany
| | - Carola Wagner
- Division of Sport and Rehabilitation Medicine, University Hospital Ulm, Parkstr. 11, 89075 Ulm, Germany
| | - Janine Keller
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Klaus Eder
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Karsten Krüger
- Department of Sports Medicine, Justus-Liebig University Giessen, Kugelberg 62, 35394 Giessen, Germany
| | - Marcus Krüger
- CECAD Research Center, Institute of Genetics, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Andreas Nieß
- Department of Sports Medicine, University Hospital of Tuebingen, Otfried-Müller-Str. 10, 72076 Tuebingen, Germany
| | - Jürgen Steinacker
- Division of Sport and Rehabilitation Medicine, University Hospital Ulm, Parkstr. 11, 89075 Ulm, Germany
| | - Frank C Mooren
- Department of Sports Medicine, Justus-Liebig University Giessen, Kugelberg 62, 35394 Giessen, Germany.
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24
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Shevchenko G, Konzer A, Musunuri S, Bergquist J. Neuroproteomics tools in clinical practice. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:705-17. [PMID: 25680928 DOI: 10.1016/j.bbapap.2015.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/30/2015] [Indexed: 12/13/2022]
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by neuronal impairment that leads to disease-specific changes in the neuronal proteins. The early diagnosis of these disorders is difficult, thus, the need for identifying, developing and using valid clinically applicable biomarkers that meet the criteria of precision, specificity and repeatability is very vital. The application of rapidly emerging technology such as mass spectrometry (MS) in proteomics has opened new avenues to accelerate biomarker discovery, both for diagnostic as well as for prognostic purposes. This review summarizes the most recent advances in the mass spectrometry-based neuroproteomics and analyses the current and future directions in the biomarker discovery for the neurodegenerative diseases. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Ganna Shevchenko
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Anne Konzer
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Sravani Musunuri
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden.
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25
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Musunuri S, Kultima K, Richard BC, Ingelsson M, Lannfelt L, Bergquist J, Shevchenko G. Micellar extraction possesses a new advantage for the analysis of Alzheimer's disease brain proteome. Anal Bioanal Chem 2014; 407:1041-57. [PMID: 25416231 DOI: 10.1007/s00216-014-8320-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 12/11/2022]
Abstract
Integral membrane proteins (MPs), such as transporters, receptors, and ion channels, are of great interest because of their participation in various vital cellular functions including cell-cell interactions, ion transport, and signal transduction. However, studies of MPs are complicated because of their hydrophobic nature, heterogeneity, and low abundance. Cloud-point extraction (CPE) with the non-ionic surfactant Triton X-114 was performed to simultaneously extract and phase separate hydrophobic and hydrophilic proteins from Alzheimer's disease (AD) and unaffected control brain tissue. Quantitative proteomics analysis of temporal neocortex samples of AD patients and controls was performed using a shotgun approach based on stable isotope dimethyl labeling (DML) quantification technique followed by nanoLC-MS/MS analysis. A total of 1096 unique proteins were identified and quantified, with 40.3 % (211/524) predicted as integral MPs with at least one transmembrane domain (TMD) found in the detergent phase, and 10 % (80/798) in the detergent-depleted phase. Among these, 62 proteins were shown to be significantly altered (p-value <0.05), in AD versus control samples. In the detergent fraction, we found 10 hydrophobic transmembrane proteins containing up to 14 putative TMDs that were significantly up- or down-regulated in AD compared with control brains. Changes in four of these proteins, alpha-enolase (ENOA), lysosome-associated membrane glycoprotein 1 (LAMP1), 14-3-3 protein gamma (1433G), and sarcoplasmic/endoplasmic reticulum calcium ATPase2 (AT2A2) were validated by immunoblotting. Our results emphasize that separating hydrophobic MPs in CPE contributes to an increased understanding of the underlying molecular mechanisms in AD. Such knowledge can become useful for the development of novel disease biomarkers.
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Affiliation(s)
- Sravani Musunuri
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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