1
|
Dowling P, Gargan S, Zweyer M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins of organelles, cellular signaling, bioenergetic metabolism and molecular chaperoning. Eur J Transl Myol 2024. [PMID: 38787292 DOI: 10.4081/ejtm.2024.12565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
During the natural aging process, frailty is often associated with abnormal muscular performance. Although inter-individual differences exit, in most elderly the tissue mass and physiological functionality of voluntary muscles drastically decreases. In order to study age-related contractile decline, animal model research is of central importance in the field of biogerontology. Here we have analyzed wild type mouse muscle to establish a proteomic map of crude tissue extracts. Proteomics is an advanced and large-scale biochemical method that attempts to identify all accessible proteins in a given biological sample. It is a technology-driven approach that uses mass spectrometry for the characterization of individual protein species. Total protein extracts were used in this study in order to minimize the potential introduction of artefacts due to excess subcellular fractionation procedures. In this report, the proteomic survey of aged muscles has focused on organellar marker proteins, as well as proteins that are involved in cellular signaling, the regulation of ion homeostasis, bioenergetic metabolism and molecular chaperoning. Hence, this study has establish a proteomic reference map of a highly suitable model system for future aging research.
Collapse
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.
| | - 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.
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases, Bonn.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - 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.
| |
Collapse
|
2
|
Dowling P, Gargan S, Zweyer M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins located in the sarcomere, cytoskeleton and the extracellular matrix. Eur J Transl Myol 2024. [PMID: 38787300 DOI: 10.4081/ejtm.2024.12564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
Sarcopenia of old age is characterized by the progressive loss of skeletal muscle mass and concomitant decrease in contractile strength. Age-related skeletal muscle dysfunctions play a key pathophysiological role in the frailty syndrome and can result in a drastically diminished quality of life in the elderly. Here we have used mass spectrometric analysis of the mouse hindlimb musculature to establish the muscle protein constellation at advanced age of a widely used sarcopenic animal model. Proteomic results were further analyzed by systems bioinformatics of voluntary muscles. In this report, the proteomic survey of aged muscles has focused on the expression patterns of proteins involved in the contraction-relaxation cycle, membrane cytoskeletal maintenance and the formation of the extracellular matrix. This includes proteomic markers of the fast versus slow phenotypes of myosin-containing thick filaments and actin-containing thin filaments, as well as proteins that are associated with the non-sarcomeric cytoskeleton and various matrisomal layers. The bioanalytical usefulness of the newly established reference map was demonstrated by the comparative screening of normal versus dystrophic muscles of old age, and findings were verified by immunoblot analysis.
Collapse
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.
| | - 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.
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases, Bonn.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - 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.
| |
Collapse
|
3
|
Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| |
Collapse
|
4
|
Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| |
Collapse
|
5
|
Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| |
Collapse
|
6
|
Dowling P, Swandulla D, Ohlendieck K. Biochemical and proteomic insights into sarcoplasmic reticulum Ca 2+-ATPase complexes in skeletal muscles. Expert Rev Proteomics 2023; 20:125-142. [PMID: 37668143 DOI: 10.1080/14789450.2023.2255743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
INTRODUCTION Skeletal muscles contain large numbers of high-molecular-mass protein complexes in elaborate membrane systems. Integral membrane proteins are involved in diverse cellular functions including the regulation of ion handling, membrane homeostasis, energy metabolism and force transmission. AREAS COVERED The proteomic profiling of membrane proteins and large protein assemblies in skeletal muscles are outlined in this article. This includes a critical overview of the main biochemical separation techniques and the mass spectrometric approaches taken to study membrane proteins. As an illustrative example of an analytically challenging large protein complex, the proteomic detection and characterization of the Ca2+-ATPase of the sarcoplasmic reticulum is discussed. The biological role of this large protein complex during normal muscle functioning, in the context of fiber type diversity and in relation to mechanisms of physiological adaptations and pathophysiological abnormalities is evaluated from a proteomics perspective. EXPERT OPINION Mass spectrometry-based muscle proteomics has decisively advanced the field of basic and applied myology. Although it is technically challenging to study membrane proteins, innovations in protein separation methodology in combination with sensitive mass spectrometry and improved systems bioinformatics has allowed the detailed proteomic detection and characterization of skeletal muscle membrane protein complexes, such as Ca2+-pump proteins of the sarcoplasmic reticulum.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth Kildare, Ireland
| |
Collapse
|
7
|
Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
| |
Collapse
|
8
|
Dowling P, Gargan S, Swandulla D, Ohlendieck K. Identification of Subproteomic Markers for Skeletal Muscle Profiling. Methods Mol Biol 2023; 2596:291-302. [PMID: 36378446 DOI: 10.1007/978-1-0716-2831-7_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The biochemical and cell biological profiling of contractile fiber types and subcellular structures plays a central role in basic and applied myology. Mass spectrometry-based proteomics presents an ideal approach for the systematic identification of proteomic and subproteomic markers. These representative components of fast versus slow muscle fibers and their subcellular fractions are highly useful for in-depth surveys of skeletal muscle adaptations to physiological challenges, as well as the improvement of diagnostic, prognostic, and therapy-monitoring methodologies in muscle pathology. This chapter outlines the identification of subproteomic markers for skeletal muscle profiling based on bottom-up and top-down approaches, including fluorescence two-dimensional difference gel electrophoresis (2D-DIGE).
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
9
|
Dowling P, Gargan S, Swandulla D, Ohlendieck K. Proteomic profiling of impaired excitation-contraction coupling and abnormal calcium handling in muscular dystrophy. Proteomics 2022; 22:e2200003. [PMID: 35902360 PMCID: PMC10078611 DOI: 10.1002/pmic.202200003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/06/2022]
Abstract
The X-linked inherited neuromuscular disorder Duchenne muscular dystrophy is characterised by primary abnormalities in the membrane cytoskeletal component dystrophin. The almost complete absence of the Dp427-M isoform of dystrophin in skeletal muscles renders contractile fibres more susceptible to progressive degeneration and a leaky sarcolemma membrane. This in turn results in abnormal calcium homeostasis, enhanced proteolysis and impaired excitation-contraction coupling. Biochemical and mass spectrometry-based proteomic studies of both patient biopsy specimens and genetic animal models of dystrophinopathy have demonstrated significant changes in the concentration and/or physiological function of essential calcium-regulatory proteins in dystrophin-lacking voluntary muscles. Abnormalities include dystrophinopathy-associated changes in voltage sensing receptors, calcium release channels, calcium pumps and calcium binding proteins. This review article provides an overview of the importance of the sarcolemmal dystrophin-glycoprotein complex and the wider dystrophin complexome in skeletal muscle and its linkage to depolarisation-induced calcium-release mechanisms and the excitation-contraction-relaxation cycle. Besides chronic inflammation, fat substitution and reactive myofibrosis, a major pathobiochemical hallmark of X-linked muscular dystrophy is represented by the chronic influx of calcium ions through the damaged plasmalemma in conjunction with abnormal intracellular calcium fluxes and buffering. Impaired calcium handling proteins should therefore be included in an improved biomarker signature of Duchenne muscular dystrophy.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| |
Collapse
|
10
|
Sohail MU, Mashood F, Oberbach A, Chennakkandathil S, Schmidt F. The role of pathogens in diabetes pathogenesis and the potential of immunoproteomics as a diagnostic and prognostic tool. Front Microbiol 2022; 13:1042362. [DOI: 10.3389/fmicb.2022.1042362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/15/2022] Open
Abstract
Diabetes mellitus (DM) is a group of metabolic diseases marked by hyperglycemia, which increases the risk of systemic infections. DM patients are at greater risk of hospitalization and mortality from bacterial, viral, and fungal infections. Poor glycemic control can result in skin, blood, bone, urinary, gastrointestinal, and respiratory tract infections and recurrent infections. Therefore, the evidence that infections play a critical role in DM progression and the hazard ratio for a person with DM dying from any infection is higher. Early diagnosis and better glycemic control can help prevent infections and improve treatment outcomes. Perhaps, half (49.7%) of the people living with DM are undiagnosed, resulting in a higher frequency of infections induced by the hyperglycemic milieu that favors immune dysfunction. Novel diagnostic and therapeutic markers for glycemic control and infection prevention are desirable. High-throughput blood-based immunoassays that screen infections and hyperglycemia are required to guide timely interventions and efficiently monitor treatment responses. The present review aims to collect information on the most common infections associated with DM, their origin, pathogenesis, and the potential of immunoproteomics assays in the early diagnosis of the infections. While infections are common in DM, their role in glycemic control and disease pathogenesis is poorly described. Nevertheless, more research is required to identify novel diagnostic and prognostic markers to understand DM pathogenesis and management of infections. Precise monitoring of diabetic infections by immunoproteomics may provide novel insights into disease pathogenesis and healthy prognosis.
Collapse
|
11
|
Potential Satellite Cell-Linked Biomarkers in Aging Skeletal Muscle Tissue: Proteomics and Proteogenomics to Monitor Sarcopenia. Proteomes 2022; 10:proteomes10030029. [PMID: 35997441 PMCID: PMC9396989 DOI: 10.3390/proteomes10030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/28/2022] [Accepted: 08/10/2022] [Indexed: 12/21/2022] Open
Abstract
Sarcopenia (Sp) is the loss of skeletal muscle mass associated with aging which causes an involution of muscle function and strength. Satellite cells (Sc) are myogenic stem cells, which are activated by injury or stress, and repair muscle tissue. With advancing age, there is a decrease in the efficiency of the regenerative response of Sc. Diagnosis occurs with the Sp established by direct assessments of muscle. However, the detection of biomarkers in real-time biofluids by liquid biopsy could represent a step-change in the understanding of the molecular biology and heterogeneity of Sp. A total of 13 potential proteogenomic biomarkers of Sp by their physiological and biological interaction with Sc have been previously described in the literature. Increases in the expression of GDF11, PGC-1α, Sirt1, Pax7, Pax3, Myf5, MyoD, CD34, MyoG, and activation of Notch signaling stimulate Sc activity and proliferation, which could modulate and delay Sp progression. On the contrary, intensified expression of GDF8, p16INK4a, Mrf4, and activation of the Wnt pathway would contribute to early Sp development by directly inducing reduced and/or altered Sc function, which would attenuate the restorative capacity of skeletal muscle. Additionally, tissue biopsy remains an important diagnostic tool. Proteomic profiling of aged muscle tissues has shown shifts toward protein isoforms characteristic of a fast-to-slow transition process and an elevated number of oxidized proteins. In addition, a strong association between age and plasma values of growth differentiation factor 15 (GDF-15) has been described and serpin family A member 3 (serpin A3n) was more secreted by atrophied muscle cells. The identification of these new biomarkers holds the potential to change personalized medicine because it could predict in real time the course of Sp by monitoring its evolution and assessing responses to potential therapeutic strategies.
Collapse
|
12
|
Dowling P, Gargan S, Zweyer M, Sabir H, Swandulla D, Ohlendieck K. Proteomic profiling of carbonic anhydrase CA3 in skeletal muscle. Expert Rev Proteomics 2021; 18:1073-1086. [PMID: 34890519 DOI: 10.1080/14789450.2021.2017776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Carbonic anhydrase (CA) is a key enzyme that mediates the reversible hydration of carbon dioxide. Skeletal muscles contain high levels of the cytosolic isoform CA3. This enzyme has antioxidative function and plays a crucial role in the maintenance of intracellular pH homeostasis. AREAS COVERED Since elevated levels of serum CA3, often in combination with other muscle-specific proteins, are routinely used as a marker of general muscle damage, it was of interest to examine recent analyses of this enzyme carried out by modern proteomics. This review summarizes the mass spectrometry-based identification and evaluation of CA3 in normal, adapting, dystrophic, and aging skeletal muscle tissues. EXPERT OPINION The mass spectrometric characterization of CA3 confirmed this enzyme as a highly useful marker of both physiological and pathophysiological alterations in skeletal muscles. Cytosolic CA3 is clearly enriched in slow-twitching type I fibers, which makes it an ideal marker for studying fiber type shifting and muscle adaptations. Importantly, neuromuscular diseases feature distinct alterations in CA3 in skeletal muscle tissues versus biofluids, such as serum. Characteristic changes of CA3 in age-related muscle wasting and dystrophinopathy established this enzyme as a suitable biomarker candidate for differential diagnosis and monitoring of disease progression and therapeutic impact.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Margit Zweyer
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Hemmen Sabir
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| |
Collapse
|
13
|
Lofaro FD, Cisterna B, Lacavalla MA, Boschi F, Malatesta M, Quaglino D, Zancanaro C, Boraldi F. Age-Related Changes in the Matrisome of the Mouse Skeletal Muscle. Int J Mol Sci 2021; 22:10564. [PMID: 34638903 PMCID: PMC8508832 DOI: 10.3390/ijms221910564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022] Open
Abstract
Aging is characterized by a progressive decline of skeletal muscle (SM) mass and strength which may lead to sarcopenia in older persons. To date, a limited number of studies have been performed in the old SM looking at the whole, complex network of the extracellular matrix (i.e., matrisome) and its aging-associated changes. In this study, skeletal muscle proteins were isolated from whole gastrocnemius muscles of adult (12 mo.) and old (24 mo.) mice using three sequential extractions, each one analyzed by liquid chromatography with tandem mass spectrometry. Muscle sections were investigated using fluorescence- and transmission electron microscopy. This study provided the first characterization of the matrisome in the old SM demonstrating several statistically significantly increased matrisome proteins in the old vs. adult SM. Several proteomic findings were confirmed and expanded by morphological data. The current findings shed new light on the mutually cooperative interplay between cells and the extracellular environment in the aging SM. These data open the door for a better understanding of the mechanisms modulating myocellular behavior in aging (e.g., by altering mechano-sensing stimuli as well as signaling pathways) and their contribution to age-dependent muscle dysfunction.
Collapse
Affiliation(s)
- Francesco Demetrio Lofaro
- Department of Life Sciences, University of Modena and Reggio Emilia, I-44100 Modena, Italy; (F.D.L.); (D.Q.)
| | - Barbara Cisterna
- Department of Neurological and Movement Sciences, University of Verona, I-37100 Verona, Italy; (B.C.); (M.A.L.); (M.M.)
| | - Maria Assunta Lacavalla
- Department of Neurological and Movement Sciences, University of Verona, I-37100 Verona, Italy; (B.C.); (M.A.L.); (M.M.)
| | - Federico Boschi
- Department of Computer Science, University of Verona, I-37100 Verona, Italy;
| | - Manuela Malatesta
- Department of Neurological and Movement Sciences, University of Verona, I-37100 Verona, Italy; (B.C.); (M.A.L.); (M.M.)
| | - Daniela Quaglino
- Department of Life Sciences, University of Modena and Reggio Emilia, I-44100 Modena, Italy; (F.D.L.); (D.Q.)
| | - Carlo Zancanaro
- Department of Neurological and Movement Sciences, University of Verona, I-37100 Verona, Italy; (B.C.); (M.A.L.); (M.M.)
| | - Federica Boraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, I-44100 Modena, Italy; (F.D.L.); (D.Q.)
| |
Collapse
|
14
|
Kalita B, Bano S, Vavachan VM, Taunk K, Seshadri V, Rapole S. Application of mass spectrometry based proteomics to understand diabetes: A special focus on interactomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140469. [DOI: 10.1016/j.bbapap.2020.140469] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/07/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
|
15
|
Jacobson KR, Lipp S, Acuna A, Leng Y, Bu Y, Calve S. Comparative Analysis of the Extracellular Matrix Proteome across the Myotendinous Junction. J Proteome Res 2020; 19:3955-3967. [PMID: 32830507 DOI: 10.1021/acs.jproteome.0c00248] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The myotendinous junction is a highly interdigitated interface designed to transfer muscle-generated force to tendon. Understanding how this interface is formed and organized, as well as identifying tendon- and muscle-specific extracellular matrix (ECM), is critical for designing effective regenerative therapies to restore functionality to damaged muscle-tendon units. However, a comparative analysis of the ECM proteome across this interface has not been conducted. The goal of this study was to resolve the distribution of ECM proteins that are uniformly expressed as well as those specific to each of the muscle, tendon, and junction tissues. The soleus muscles from 5-month-old wild-type C57BL/6 mice were harvested and dissected into the central muscle (M) away from tendon, the junction between muscle and tendon (J) and the tendon (T). Tissues were processed by either homogenizing in guanidine hydrochloride or fractionating to isolate the ECM from more soluble intracellular components and then analyzed using liquid chromatography-tandem mass spectrometry. Overall, we found that both tissue processing methods generated similar ECM profiles. Many ECM were found across the muscle-tendon unit, including type I collagen and associated fibril-regulating proteins. The ECM identified exclusively in M were primarily related to the basal lamina, whereas those specific to T and J tissue included thrombospondins and other matricellular ECM. Type XXII collagen (COL22A1) was restricted to J, and we identified COL5A3 as a potential marker of the muscle-tendon interface. Immunohistochemical analysis of key proteins confirmed the restriction of some basal lamina proteins to M, tenascin-C to T, and COL22A1 to J. COL5A3, PRELP, and POSTN were visualized in the tissue surrounding the junction, suggesting that these proteins play a role in stabilizing the interface. This comparative map provides a guide for tissue-specific ECM that can facilitate the spatial visualization of M, J, and T tissues and inform musculoskeletal regenerative therapies.
Collapse
Affiliation(s)
- Kathryn R Jacobson
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, Indiana 47907, United States
| | - Sarah Lipp
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Andrea Acuna
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Yue Leng
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Ye Bu
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Sarah Calve
- Purdue University Interdisciplinary Life Science Program, 155 S. Grant Street, West Lafayette, Indiana 47907, United States.,Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States.,Paul M. Rady Department of Mechanical Engineering, University of Colorado-Boulder, 1111 Engineering Center, 427 UCB, Boulder, Colorado 80309, United States
| |
Collapse
|
16
|
Kruse R, Sahebekhtiari N, Højlund K. The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance. Int J Mol Sci 2020; 21:ijms21155374. [PMID: 32731645 PMCID: PMC7432338 DOI: 10.3390/ijms21155374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction: Mitochondria are essential in energy metabolism and cellular survival, and there is growing evidence that insulin resistance in chronic metabolic disorders, such as obesity, type 2 diabetes (T2D), and aging, is linked to mitochondrial dysfunction in skeletal muscle. Protein profiling by proteomics is a powerful tool to investigate mechanisms underlying complex disorders. However, despite significant advances in proteomics within the past two decades, the technologies have not yet been fully exploited in the field of skeletal muscle proteome. Area covered: Here, we review the currently available studies characterizing the mitochondrial proteome in human skeletal muscle in insulin-resistant conditions, such as obesity, T2D, and aging, as well as exercise-mediated changes in the mitochondrial proteome. Furthermore, we outline technical challenges and limitations and methodological aspects that should be considered when planning future large-scale proteomics studies of mitochondria from human skeletal muscle. Authors’ view: At present, most proteomic studies of skeletal muscle or isolated muscle mitochondria have demonstrated a reduced abundance of proteins in several mitochondrial biological processes in obesity, T2D, and aging, whereas the beneficial effects of exercise involve an increased content of muscle proteins involved in mitochondrial metabolism. Powerful mass-spectrometry-based proteomics now provides unprecedented opportunities to perform in-depth proteomics of muscle mitochondria, which in the near future is expected to increase our understanding of the complex molecular mechanisms underlying the link between mitochondrial dysfunction and insulin resistance in chronic metabolic disorders.
Collapse
Affiliation(s)
- Rikke Kruse
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Navid Sahebekhtiari
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
- Correspondence: ; Tel.: +45-2532-06-48
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Kaplan N, Dong Y, Wang S, Yang W, Park JK, Wang J, Fiolek E, Perez White B, Chandel NS, Peng H, Lavker RM. FIH-1 engages novel binding partners to positively influence epithelial proliferation via p63. FASEB J 2019; 34:525-539. [PMID: 31914679 DOI: 10.1096/fj.201901512r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022]
Abstract
Whereas much is known about the genes regulated by ΔNp63α in keratinocytes, how ΔNp63α is regulated is less clear. During studies with the hydroxylase, factor inhibiting hypoxia-inducible factor 1 (FIH-1), we observed increases in epidermal ΔNp63α expression along with proliferative capacity in a conditional FIH-1 transgenic mouse. Conversely, loss of FIH-1 in vivo and in vitro attenuated ΔNp63α expression. To elucidate the FIH-1/p63 relationship, BioID proteomics assays identified FIH-1 binding partners that had the potential to regulate p63 expression. FIH-1 interacts with two previously unknown partners, Plectin1 and signal transducer and activator of transcription 1 (STAT1) leading to the regulation of ΔNp63α expression. Two known interactors of FIH-1, apoptosis-stimulating of P53 protein 2 (ASPP2) and histone deacetylase 1 (HDAC1), were also identified. Knockdown of ASPP2 upregulated ΔNp63α and reversed the decrease in ΔNp63α by FIH-1 depletion. Additionally, FIH-1 regulates growth arrest and DNA damage-45 alpha (GADD45α), a negative regulator of ΔNp63α by interacting with HDAC1. GADD45α knockdown rescued reduction in ΔNp63α by FIH-1 depletion. Collectively, our data reveal that FIH-1 positively regulates ΔNp63α in keratinocytes via variety of signaling partners: (a) Plectin1/STAT1, (b) ASPP2, and (c) HDAC1/GADD45α signaling pathways.
Collapse
Affiliation(s)
- Nihal Kaplan
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Ying Dong
- Department of Dermatology, Northwestern University, Chicago, IL, USA.,Department of Ophthalmology, The First Affiliated Hospital, Chinese PLA General Hospital, Beijing, China
| | - Sijia Wang
- Department of Dermatology, Northwestern University, Chicago, IL, USA.,Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wending Yang
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Jong Kook Park
- Department of Dermatology, Northwestern University, Chicago, IL, USA.,Department of Biomedical Science, College of Natural Sciences #8403, Hallym University, Chuncheon, Republic of Korea
| | - Junyi Wang
- Department of Dermatology, Northwestern University, Chicago, IL, USA.,Department of Ophthalmology, The First Affiliated Hospital, Chinese PLA General Hospital, Beijing, China
| | - Elaina Fiolek
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | | | | | - Han Peng
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| | - Robert M Lavker
- Department of Dermatology, Northwestern University, Chicago, IL, USA
| |
Collapse
|
19
|
Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| |
Collapse
|
20
|
Ubaida-Mohien C, Gonzalez-Freire M, Lyashkov A, Moaddel R, Chia CW, Simonsick EM, Sen R, Ferrucci L. Physical Activity Associated Proteomics of Skeletal Muscle: Being Physically Active in Daily Life May Protect Skeletal Muscle From Aging. Front Physiol 2019; 10:312. [PMID: 30971946 PMCID: PMC6443906 DOI: 10.3389/fphys.2019.00312] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/07/2019] [Indexed: 01/18/2023] Open
Abstract
Muscle strength declines with aging and increasing physical activity is the only intervention known to attenuate this decline. In order to adequately investigate both preventive and therapeutic interventions against sarcopenia, a better understanding of the biological changes that are induced by physical activity in skeletal muscle is required. To determine the effect of physical activity on the skeletal muscle proteome, we utilized liquid-chromatography mass spectrometry to obtain quantitative proteomics data on human skeletal muscle biopsies from 60 well-characterized healthy individuals (20-87 years) who reported heterogeneous levels of physical activity (not active, active, moderately active, and highly active). Over 4,000 proteins were quantified, and higher self-reported physical activity was associated with substantial overrepresentation of proteins associated with mitochondria, TCA cycle, structural and contractile muscle, and genome maintenance. Conversely, proteins related to the spliceosome, transcription regulation, immune function, and apoptosis, DNA damage, and senescence were underrepresented with higher self-reported activity. These differences in observed protein expression were related to different levels of physical activity in daily life and not intense competitive exercise. In most instances, differences in protein levels were directly opposite to those reported in the literature observed with aging. These data suggest that being physically active in daily life has strong and biologically detectable beneficial effects on muscle.
Collapse
Affiliation(s)
- Ceereena Ubaida-Mohien
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Marta Gonzalez-Freire
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Alexey Lyashkov
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Ruin Moaddel
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Chee W Chia
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Eleanor M Simonsick
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Ranjan Sen
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| | - Luigi Ferrucci
- Intramural Research Program, National Institute on Aging - National Institutes of Health, Baltimore, MD, United States
| |
Collapse
|
21
|
Murphy S, Zweyer M, Raucamp M, Henry M, Meleady P, Swandulla D, Ohlendieck K. Proteomic profiling of the mouse diaphragm and refined mass spectrometric analysis of the dystrophic phenotype. J Muscle Res Cell Motil 2019; 40:9-28. [PMID: 30888583 DOI: 10.1007/s10974-019-09507-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022]
Abstract
The diaphragm is a crucial muscle involved in active inspiration and whole body homeostasis. Previous biochemical, immunochemical and cell biological investigations have established the distribution and fibre type-specific expression of key diaphragm proteins. Building on these findings, it was of interest to establish the entire experimentally assessable diaphragm proteome and verify the presence of specific protein isoforms within this specialized subtype of skeletal muscle. A highly sensitive Orbitrap Fusion Tribrid mass spectrometer was used for the systematic identification of the mouse diaphragm-associated protein population. Proteomics established 2925 proteins by high confidence peptide identification. Bioinformatics was used to determine the distribution of the main protein classes, biological processes and subcellular localization within the diaphragm proteome. Following the establishment of the respiratory muscle proteome with special emphasis on protein isoform expression in the contractile apparatus, the extra-sarcomeric cytoskeleton, the extracellular matrix and the excitation-contraction coupling apparatus, the mass spectrometric analysis of the diaphragm was extended to the refined identification of proteome-wide changes in X-linked muscular dystrophy. The comparative mass spectrometric profiling of the dystrophin-deficient diaphragm from the mdx-4cv mouse model of Duchenne muscular dystrophy identified 289 decreased and 468 increased protein species. Bioinformatics was employed to analyse the clustering of changes in protein classes and potential alterations in interaction patterns of proteins involved in metabolism, the contractile apparatus, proteostasis and the extracellular matrix. The detailed pathoproteomic profiling of the mdx-4cv diaphragm suggests highly complex alterations in a variety of crucial cellular processes due to deficiency in the membrane cytoskeletal protein dystrophin.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.,Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, 53115, Bonn, Germany
| | - Maren Raucamp
- Institute of Physiology II, University of Bonn, 53115, Bonn, Germany
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, 53115, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
22
|
Murphy S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Proteomic profiling of giant skeletal muscle proteins. Expert Rev Proteomics 2019; 16:241-256. [DOI: 10.1080/14789450.2019.1575205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| |
Collapse
|
23
|
Profiling of nanoparticle–protein interactions by electrophoresis techniques. Anal Bioanal Chem 2018; 411:79-96. [DOI: 10.1007/s00216-018-1401-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/18/2018] [Accepted: 09/24/2018] [Indexed: 01/02/2023]
|
24
|
Kruse R, Højlund K. Proteomic study of skeletal muscle in obesity and type 2 diabetes: progress and potential. Expert Rev Proteomics 2018; 15:817-828. [PMID: 30251560 DOI: 10.1080/14789450.2018.1528147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Skeletal muscle is the major site of insulin-stimulated glucose uptake and imparts the beneficial effects of exercise, and hence is an important site of insulin resistance in obesity and type 2 diabetes (T2D). Despite extensive molecular biology-oriented research the molecular mechanisms underlying insulin resistance in skeletal muscle remain to be established. Areas covered: The proteomic capabilities have greatly improved over the last decades. This review summarizes the technical challenges in skeletal muscle proteomics studies as well as the results of quantitative proteomic studies of skeletal muscle in relation to obesity, T2D, and exercise. Expert commentary: Current available proteomic studies contribute to the view that insulin resistance in obesity and T2D is associated with increased glycolysis and reduced mitochondrial oxidative metabolism in skeletal muscle, and that the latter can be improved by exercise. Future proteomics studies should be designed to markedly intensify the identification of abnormalities in metabolic and signaling pathways in skeletal muscle of insulin-resistant individuals to increase the understanding of the pathogenesis of T2D, but more importantly to identify multiple novel targets of treatment of which at least some can be safely targeted by novel drugs to treat and prevent T2D and reduce risk of cardiovascular disease.
Collapse
Affiliation(s)
- Rikke Kruse
- a The Section of Molecular Diabetes and Metabolism, Department of Clinical Research and Department of Molecular Medicine , University of Southern Denmark , Odense , Denmark.,b Steno Diabetes Center Odense , Odense University Hospital , Odense , Denmark
| | - Kurt Højlund
- a The Section of Molecular Diabetes and Metabolism, Department of Clinical Research and Department of Molecular Medicine , University of Southern Denmark , Odense , Denmark.,b Steno Diabetes Center Odense , Odense University Hospital , Odense , Denmark
| |
Collapse
|
25
|
Mey JT, Haus JM. Dicarbonyl Stress and Glyoxalase-1 in Skeletal Muscle: Implications for Insulin Resistance and Type 2 Diabetes. Front Cardiovasc Med 2018; 5:117. [PMID: 30250846 PMCID: PMC6139330 DOI: 10.3389/fcvm.2018.00117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/09/2018] [Indexed: 01/01/2023] Open
Abstract
Glyoxalase-1 (GLO1) is a ubiquitously expressed cytosolic protein which plays a role in the natural maintenance of cellular health and is abundantly expressed in human skeletal muscle. A consequence of reduced GLO1 protein expression is cellular dicarbonyl stress, which is elevated in obesity, insulin resistance and type 2 diabetes (T2DM). Both in vitro and pre-clinical models suggest dicarbonyl stress per se induces insulin resistance and is prevented by GLO1 overexpression, implicating a potential role for GLO1 therapy in insulin resistance and type 2 diabetes (T2DM). Recent work has identified the therapeutic potential of novel natural agents as a GLO1 inducer, which resulted in improved whole-body metabolism in obese adults. Given skeletal muscle is a major contributor to whole-body glucose, lipid, and protein metabolism, such GLO1 inducers may act, in part, through mechanisms in skeletal muscle. Currently, investigations examining the specificity of dicarbonyl stress and GLO1 biology in human skeletal muscle are lacking. Recent work from our lab indicates that dysregulation of GLO1 in skeletal muscle may underlie human insulin resistance and that exercise training may impart therapeutic benefits. This minireview will summarize the existing human literature examining skeletal muscle GLO1 and highlight the emerging therapeutic concepts for GLO1 gain-of-function in conditions such as insulin resistance and cardiometabolic disease.
Collapse
Affiliation(s)
- Jacob T Mey
- Department of Pathobiology, Cleveland Clinic, Cleveland, OH, United States
| | - Jacob M Haus
- School of Kinesiology, University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
26
|
Danese E, Montagnana M, Lippi G. Proteomics and frailty: a clinical overview. Expert Rev Proteomics 2018; 15:657-664. [DOI: 10.1080/14789450.2018.1505511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Elisa Danese
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | | | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| |
Collapse
|
27
|
Ma D, Tu C, Sheng Q, Yang Y, Kan Z, Guo Y, Shyr Y, Scott IC, Lou X. Dynamics of Zebrafish Heart Regeneration Using an HPLC-ESI-MS/MS Approach. J Proteome Res 2018; 17:1300-1308. [PMID: 29369637 DOI: 10.1021/acs.jproteome.7b00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Failure to properly repair damaged due to myocardial infarction is a major cause of heart failure. In contrast with adult mammals, zebrafish hearts show remarkable regenerative capabilities after substantial damage. To characterize protein dynamics during heart regeneration, we employed an HPLC-ESI-MS/MS (mass spectrometry) approach. Myocardium tissues were taken from sham-operated fish and ventricle-resected sample at three different time points (2, 7, and 14 days); dynamics of protein expression were analyzed by an ion-current-based quantitative platform. More than 2000 protein groups were quantified in all 16 experiments. Two hundred and nine heart-regeneration-related protein groups were quantified and clustered into six time-course patterns. Functional analysis indicated that multiple molecular function and metabolic pathways were involved in heart regeneration. Interestingly, Ingenuity Pathway Analysis revealed that P53 signaling was inhibited during the heart regeneration, which was further verified by real-time quantitative polymerase chain reaction (Q-PCR). In summary, we applied systematic proteomics analysis on regenerating zebrafish heart, uncovered the dynamics of regenerative genes expression and regulatory pathways, and provided invaluable insight into design regenerative-based strategies in human hearts.
Collapse
Affiliation(s)
- Danjun Ma
- College of Mechanical Engineering, Dongguan University of Technology , 1 Daxue Road, Dongguan, Guangdong 523808, China
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo , 285 Kapoor Hall, Buffalo, New York 14260, United States
| | - Quanhu Sheng
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University School of Medicine , 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
| | - Yuxi Yang
- Model Animal Research Center, Nanjing University , Nanjing 210093, China
| | - Zhisheng Kan
- Department of Neurosurgery, Beijing Anzhen Hospital, Capital Medical University , Beijing 100029, China
| | - Yan Guo
- Department of Internal Medicine, University of New Mexico, Comprehensive Cancer Center , Albuquerque, New Mexico 87131, United States
| | - Yu Shyr
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University School of Medicine , 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children , Toronto, Ontario M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Xin Lou
- Model Animal Research Center, Nanjing University , Nanjing 210093, China
| |
Collapse
|
28
|
Ebhardt HA, Degen S, Tadini V, Schilb A, Johns N, Greig CA, Fearon KCH, Aebersold R, Jacobi C. Comprehensive proteome analysis of human skeletal muscle in cachexia and sarcopenia: a pilot study. J Cachexia Sarcopenia Muscle 2017; 8:567-582. [PMID: 28296247 PMCID: PMC5566647 DOI: 10.1002/jcsm.12188] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cancer cachexia (cancer-induced muscle wasting) is found in a subgroup of cancer patients leaving the patients with a poor prognosis for survival due to a lower tolerance of the chemotherapeutic drug. The cause of the muscle wasting in these patients is not fully understood, and no predictive biomarker exists to identify these patients early on. Skeletal muscle loss is an inevitable consequence of advancing age. As cancer frequently occurs in old age, identifying and differentiating the molecular mechanisms mediating muscle wasting in cancer cachexia vs. age-related sarcopenia are a challenge. However, the ability to distinguish between them is critical for early intervention, and simple measures of body weight may not be sufficiently sensitive to detect cachexia early. METHODS We used a range of omics approaches: (i) undepleted proteome was quantified using advanced high mass accuracy mass spectrometers in SWATH-MS acquisition mode; (ii) phospho epitopes were quantified using protein arrays; and (iii) morphology was assessed using fluorescent microscopy. RESULTS We quantified the soluble proteome of muscle biopsies from cancer cachexia patients and compared them with cohorts of cancer patients and healthy individuals with and without age-related muscle loss (aka age-related sarcopenia). Comparing the proteomes of these cohorts, we quantified changes in muscle contractile myosins and energy metabolism allowing for a clear identification of cachexia patients. In an in vitro time lapse experiment, we mimicked cancer cachexia and identified signal transduction pathways governing cell fusion to play a pivotal role in preventing muscle regeneration. CONCLUSIONS The work presented here lays the foundation for further understanding of muscle wasting diseases and holds the promise of overcoming ambiguous weight loss as a measure for defining cachexia to be replaced by a precise protein signature.
Collapse
Affiliation(s)
- H Alexander Ebhardt
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Simone Degen
- Novartis Institutes for BioMedical Research Basel, Novartis Pharma AG, Basel, Switzerland
| | - Valentina Tadini
- Novartis Institutes for BioMedical Research Basel, Novartis Pharma AG, Basel, Switzerland
| | - Alain Schilb
- Novartis Institutes for BioMedical Research Basel, Novartis Pharma AG, Basel, Switzerland
| | - Neil Johns
- Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, Scotland, UK
| | - Carolyn A Greig
- School of Sport, Exercise, and Rehabilitation Sciences and MRC-Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Kenneth C H Fearon
- Clinical Sciences (Surgery), University of Edinburgh, Edinburgh, Scotland, UK
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Carsten Jacobi
- Novartis Institutes for BioMedical Research Basel, Novartis Pharma AG, Basel, Switzerland
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Yu TY, Morton JD, Clerens S, Dyer JM. Cooking-Induced Protein Modifications in Meat. Compr Rev Food Sci Food Saf 2016; 16:141-159. [DOI: 10.1111/1541-4337.12243] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Tzer-Yang Yu
- Food & Bio-Based Products; AgResearch Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
- Wine, Food & Molecular Biosciences, Faculty of Agriculture and Life Sciences; Lincoln Univ; PO Box 84 Canterbury 7647 New Zealand
| | - James D. Morton
- Wine, Food & Molecular Biosciences; Faculty of Agriculture and Life Sciences, Lincoln Univ; PO Box 84 Canterbury 7647 New Zealand
- Biomolecular Interaction Centre; Univ. of Canterbury; Private Bag 4800 Christchurch 8140 New Zealand
| | - Stefan Clerens
- Food & Bio-Based Products; AgResearch Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
- Biomolecular Interaction Centre; Univ. of Canterbury; Private Bag 4800 Christchurch 8140 New Zealand
| | - Jolon M. Dyer
- Food & Bio-Based Products; AgResearch Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
- Riddet Inst; Massey Univ; Palmerston North 4442 New Zealand
- Wine, Food & Molecular Biosciences, Faculty of Agriculture and Life Sciences; Lincoln Univ; PO Box 84 Canterbury 7647 New Zealand
- Biomolecular Interaction Centre; Univ. of Canterbury; Private Bag 4800 Christchurch 8140 New Zealand
| |
Collapse
|
31
|
A Proof of Concept to Bridge the Gap between Mass Spectrometry Imaging, Protein Identification and Relative Quantitation: MSI~LC-MS/MS-LF. Proteomes 2016; 4:proteomes4040032. [PMID: 28248242 PMCID: PMC5260965 DOI: 10.3390/proteomes4040032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section. Then, we did a back-correlation of the m/z of the proteins detected by MALDI-MSI to those identified by label-free quantitation. This allowed us to compare the label-free quantitation of proteins obtained in LC-MS/MS with the peak intensities observed in MALDI-MSI. We managed to link identification to nine peaks observed by MALDI-MSI. The results showed that the MSI~LC-MS/MS-LF workflow (i) allowed us to study a representative muscle proteome compared to a classical bottom-up workflow; and (ii) was sparsely impacted by matrix deposition and laser ablation. This workflow, performed as a proof-of-concept, suggests that a single tissue section can be used to perform MALDI-MSI and protein extraction, identification, and relative quantitation.
Collapse
|
32
|
Murphy S, Dowling P, Ohlendieck K. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis. Proteomes 2016; 4:proteomes4030027. [PMID: 28248237 PMCID: PMC5217355 DOI: 10.3390/proteomes4030027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/16/2022] Open
Abstract
The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
33
|
Kruse R, Højlund K. Mitochondrial phosphoproteomics of mammalian tissues. Mitochondrion 2016; 33:45-57. [PMID: 27521611 DOI: 10.1016/j.mito.2016.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 12/31/2022]
Abstract
Mitochondria are essential for several biological processes including energy metabolism and cell survival. Accordingly, impaired mitochondrial function is involved in a wide range of human pathologies including diabetes, cancer, cardiovascular, and neurodegenerative diseases. Within the past decade a growing body of evidence indicates that reversible phosphorylation plays an important role in the regulation of a variety of mitochondrial processes as well as tissue-specific mitochondrial functions in mammals. The rapidly increasing number of mitochondrial phosphorylation sites and phosphoproteins identified is largely ascribed to recent advances in phosphoproteomic technologies such as fractionation, phosphopeptide enrichment, and high-sensitivity mass spectrometry. However, the functional importance and the specific kinases and phosphatases involved have yet to be determined for the majority of these mitochondrial phosphorylation sites. This review summarizes the progress in establishing the mammalian mitochondrial phosphoproteome and the technical challenges encountered while characterizing it, with a particular focus on large-scale phosphoproteomic studies of mitochondria from human skeletal muscle.
Collapse
Affiliation(s)
- Rikke Kruse
- Department of Endocrinology, Odense University Hospital, DK-5000, Odense, Denmark; The Section of Molecular Diabetes & Metabolism, Department of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, DK-5000, Odense, Denmark; The Section of Molecular Diabetes & Metabolism, Department of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark.
| |
Collapse
|
34
|
Turk R, Hsiao JJ, Smits MM, Ng BH, Pospisil TC, Jones KS, Campbell KP, Wright ME. Molecular Signatures of Membrane Protein Complexes Underlying Muscular Dystrophy. Mol Cell Proteomics 2016; 15:2169-85. [PMID: 27099343 PMCID: PMC5083101 DOI: 10.1074/mcp.m116.059188] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 01/16/2023] Open
Abstract
Mutations in genes encoding components of the sarcolemmal dystrophin-glycoprotein complex (DGC) are responsible for a large number of muscular dystrophies. As such, molecular dissection of the DGC is expected to both reveal pathological mechanisms, and provides a biological framework for validating new DGC components. Establishment of the molecular composition of plasma-membrane protein complexes has been hampered by a lack of suitable biochemical approaches. Here we present an analytical workflow based upon the principles of protein correlation profiling that has enabled us to model the molecular composition of the DGC in mouse skeletal muscle. We also report our analysis of protein complexes in mice harboring mutations in DGC components. Bioinformatic analyses suggested that cell-adhesion pathways were under the transcriptional control of NFκB in DGC mutant mice, which is a finding that is supported by previous studies that showed NFκB-regulated pathways underlie the pathophysiology of DGC-related muscular dystrophies. Moreover, the bioinformatic analyses suggested that inflammatory and compensatory mechanisms were activated in skeletal muscle of DGC mutant mice. Additionally, this proteomic study provides a molecular framework to refine our understanding of the DGC, identification of protein biomarkers of neuromuscular disease, and pharmacological interrogation of the DGC in adult skeletal muscle https://www.mda.org/disease/congenital-muscular-dystrophy/research.
Collapse
Affiliation(s)
- Rolf Turk
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | | | | | - Brandon H Ng
- ¶Department of Molecular Physiology and Biophysics
| | - Tyler C Pospisil
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Kayla S Jones
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Kevin P Campbell
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | | |
Collapse
|
35
|
Age- and Activity-Related Differences in the Abundance of Myosin Essential and Regulatory Light Chains in Human Muscle. Proteomes 2016; 4:proteomes4020015. [PMID: 28248225 PMCID: PMC5217348 DOI: 10.3390/proteomes4020015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/21/2022] Open
Abstract
Traditional methods for phenotyping skeletal muscle (e.g., immunohistochemistry) are labor-intensive and ill-suited to multixplex analysis, i.e., assays must be performed in a series. Addressing these concerns represents a largely unmet research need but more comprehensive parallel analysis of myofibrillar proteins could advance knowledge regarding age- and activity-dependent changes in human muscle. We report a label-free, semi-automated and time efficient LC-MS proteomic workflow for phenotyping the myofibrillar proteome. Application of this workflow in old and young as well as trained and untrained human skeletal muscle yielded several novel observations that were subsequently verified by multiple reaction monitoring (MRM). We report novel data demonstrating that human ageing is associated with lesser myosin light chain 1 content and greater myosin light chain 3 content, consistent with an age-related reduction in type II muscle fibers. We also disambiguate conflicting data regarding myosin regulatory light chain, revealing that age-related changes in this protein more closely reflect physical activity status than ageing per se. This finding reinforces the need to control for physical activity levels when investigating the natural process of ageing. Taken together, our data confirm and extend knowledge regarding age- and activity-related phenotypes. In addition, the MRM transitions described here provide a methodological platform that can be fine-tuned to suite multiple research needs and thus advance myofibrillar phenotyping.
Collapse
|
36
|
Gross SM, Lehman SL. Functional phosphorylation sites in cardiac myofilament proteins are evolutionarily conserved in skeletal myofilament proteins. Physiol Genomics 2016; 48:377-87. [PMID: 26993364 DOI: 10.1152/physiolgenomics.00112.2015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/11/2016] [Indexed: 01/14/2023] Open
Abstract
Protein phosphorylation plays an important role in regulating cardiac contractile function, but phosphorylation is not thought to play a regulatory role in skeletal muscle. To examine how myofilament phosphorylation arose in the human heart, we analyzed the amino acid sequences of 25 cardiac phosphorylation sites in animals ranging from fruit flies to humans. These analyses indicated that of the 25 human phosphorylation sites examined, 11 have been conserved across vertebrates and four have been sporadically present in vertebrates. Furthermore, all 11 of the cardiac sites found across vertebrates were present in skeletal muscle isoforms, along with three sites that were sporadically present. Based on the conservation of amino acid sequences between cardiac and skeletal contractile proteins, we tested for phosphorylation in mammalian skeletal muscle using several biochemical techniques and found evidence that multiple myofilament proteins were phosphorylated. Several of these phosphorylation sites were validated using mass spectrometry, including one site that is present in slow- and fast-twitch troponin I (TnI), but was lost in cardiac TnI. Thus, several myofilament phosphorylation sites present in the human heart likely arose in invertebrate muscle, have been evolutionarily conserved in skeletal muscle, and potentially have functional effects in both skeletal and cardiac muscle.
Collapse
Affiliation(s)
- Sean M Gross
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California; and Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon
| | - Steven L Lehman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California; and
| |
Collapse
|
37
|
Gizak A, Rakus D. Will Quantitative Proteomics Redefine Some of the Key Concepts in Skeletal Muscle Physiology? Proteomes 2016; 4:proteomes4010002. [PMID: 28248211 PMCID: PMC5217361 DOI: 10.3390/proteomes4010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 01/28/2023] Open
Abstract
Molecular and cellular biology methodology is traditionally based on the reasoning called “the mechanistic explanation”. In practice, this means identifying and selecting correlations between biological processes which result from our manipulation of a biological system. In theory, a successful application of this approach requires precise knowledge about all parameters of a studied system. However, in practice, due to the systems’ complexity, this requirement is rarely, if ever, accomplished. Typically, it is limited to a quantitative or semi-quantitative measurements of selected parameters (e.g., concentrations of some metabolites), and a qualitative or semi-quantitative description of expression/post-translational modifications changes within selected proteins. A quantitative proteomics approach gives a possibility of quantitative characterization of the entire proteome of a biological system, in the context of the titer of proteins as well as their post-translational modifications. This enables not only more accurate testing of novel hypotheses but also provides tools that can be used to verify some of the most fundamental dogmas of modern biology. In this short review, we discuss some of the consequences of using quantitative proteomics to verify several key concepts in skeletal muscle physiology.
Collapse
Affiliation(s)
- Agnieszka Gizak
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego 30, 50-205 Wroclaw, Poland.
| | - Dariusz Rakus
- Department of Animal Molecular Physiology, Wroclaw University, Cybulskiego 30, 50-205 Wroclaw, Poland.
| |
Collapse
|
38
|
Murphy S, Ohlendieck K. The biochemical and mass spectrometric profiling of the dystrophin complexome from skeletal muscle. Comput Struct Biotechnol J 2015; 14:20-7. [PMID: 26793286 PMCID: PMC4688399 DOI: 10.1016/j.csbj.2015.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 12/12/2022] Open
Abstract
The development of advanced mass spectrometric methodology has decisively enhanced the analytical capabilities for studies into the composition and dynamics of multi-subunit protein complexes and their associated components. Large-scale complexome profiling is an approach that combines the systematic isolation and enrichment of protein assemblies with sophisticated mass spectrometry-based identification methods. In skeletal muscles, the membrane cytoskeletal protein dystrophin of 427 kDa forms tight interactions with a variety of sarcolemmal, cytosolic and extracellular proteins, which in turn associate with key components of the extracellular matrix and the intracellular cytoskeleton. A major function of this enormous assembly of proteins, including dystroglycans, sarcoglycans, syntrophins, dystrobrevins, sarcospan, laminin and cortical actin, is postulated to stabilize muscle fibres during the physical tensions of continuous excitation-contraction-relaxation cycles. This article reviews the evidence from recent proteomic studies that have focused on the characterization of the dystrophin-glycoprotein complex and its central role in the establishment of the cytoskeleton-sarcolemma-matrisome axis. Proteomic findings suggest a close linkage of the core dystrophin complex with a variety of protein species, including tubulin, vimentin, desmin, annexin, proteoglycans and collagens. Since the almost complete absence of dystrophin is the underlying cause for X-linked muscular dystrophy, a more detailed understanding of the composition, structure and plasticity of the dystrophin complexome may have considerable biomedical implications.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| |
Collapse
|
39
|
Le Bihan MC, Barrio-Hernandez I, Mortensen TP, Henningsen J, Jensen SS, Bigot A, Blagoev B, Butler-Browne G, Kratchmarova I. Cellular Proteome Dynamics during Differentiation of Human Primary Myoblasts. J Proteome Res 2015; 14:3348-61. [DOI: 10.1021/acs.jproteome.5b00397] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marie-Catherine Le Bihan
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Inigo Barrio-Hernandez
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Tenna Pavia Mortensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Jeanette Henningsen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Søren Skov Jensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Anne Bigot
- Center
for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 75013 Paris, France
| | - Blagoy Blagoev
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Gillian Butler-Browne
- Center
for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 75013 Paris, France
| | - Irina Kratchmarova
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| |
Collapse
|
40
|
Murphy S, Henry M, Meleady P, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Simultaneous Pathoproteomic Evaluation of the Dystrophin-Glycoprotein Complex and Secondary Changes in the mdx-4cv Mouse Model of Duchenne Muscular Dystrophy. BIOLOGY 2015; 4:397-423. [PMID: 26067837 PMCID: PMC4498307 DOI: 10.3390/biology4020397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022]
Abstract
In skeletal muscle, the dystrophin-glycoprotein complex forms a membrane-associated assembly of relatively low abundance, making its detailed proteomic characterization in normal versus dystrophic tissues technically challenging. To overcome this analytical problem, we have enriched the muscle membrane fraction by a minimal differential centrifugation step followed by the comprehensive label-free mass spectrometric analysis of microsomal membrane preparations. This organelle proteomic approach successfully identified dystrophin and its binding partners in normal versus dystrophic hind limb muscles. The introduction of a simple pre-fractionation step enabled the simultaneous proteomic comparison of the reduction in the dystrophin-glycoprotein complex and secondary changes in the mdx-4cv mouse model of dystrophinopathy in a single analytical run. The proteomic screening of the microsomal fraction from dystrophic hind limb muscle identified the full-length dystrophin isoform Dp427 as the most drastically reduced protein in dystrophinopathy, demonstrating the remarkable analytical power of comparative muscle proteomics. Secondary pathoproteomic expression patterns were established for 281 proteins, including dystrophin-associated proteins and components involved in metabolism, signalling, contraction, ion-regulation, protein folding, the extracellular matrix and the cytoskeleton. Key findings were verified by immunoblotting. Increased levels of the sarcolemmal Na+/K+-ATPase in dystrophic leg muscles were also confirmed by immunofluorescence microscopy. Thus, the reduction of sample complexity in organelle-focused proteomics can be advantageous for the profiling of supramolecular protein complexes in highly intricate systems, such as skeletal muscle tissue.
Collapse
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland.
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Rustam R Mundegar
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Dieter Swandulla
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
41
|
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.
Collapse
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.
| |
Collapse
|
42
|
In-depth characterisation of the lamb meat proteome from longissimus lumborum. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
43
|
Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M. Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors. Mol Cell Proteomics 2015; 14:841-53. [PMID: 25616865 PMCID: PMC4390264 DOI: 10.1074/mcp.m114.044222] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Indexed: 11/07/2022] Open
Abstract
Skeletal muscle constitutes 40% of individual body mass and plays vital roles in locomotion and whole-body metabolism. Proteomics of skeletal muscle is challenging because of highly abundant contractile proteins that interfere with detection of regulatory proteins. Using a state-of-the art MS workflow and a strategy to map identifications from the C2C12 cell line model to tissues, we identified a total of 10,218 proteins, including skeletal muscle specific transcription factors like myod1 and myogenin and circadian clock proteins. We obtain absolute abundances for proteins expressed in a muscle cell line and skeletal muscle, which should serve as a valuable resource. Quantitation of protein isoforms of glucose uptake signaling pathways and in glucose and lipid metabolic pathways provides a detailed metabolic map of the cell line compared with tissue. This revealed unexpectedly complex regulation of AMP-activated protein kinase and insulin signaling in muscle tissue at the level of enzyme isoforms.
Collapse
Affiliation(s)
- Atul S Deshmukh
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Marta Murgia
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany; §Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padua, Italy
| | - Nagarjuna Nagaraj
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jonas T Treebak
- ¶The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Integrative Physiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jürgen Cox
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany; ‖The Novo Nordisk Foundation Center for Protein Research, Department for proteomics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
44
|
Brinkmeier H, Ohlendieck K. Chaperoning heat shock proteins: Proteomic analysis and relevance for normal and dystrophin-deficient muscle. Proteomics Clin Appl 2014; 8:875-95. [DOI: 10.1002/prca.201400015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/24/2014] [Accepted: 05/28/2014] [Indexed: 12/15/2022]
Affiliation(s)
| | - Kay Ohlendieck
- Department of Biology; National University of Ireland; Maynooth Co. Kildare Ireland
| |
Collapse
|
45
|
Burniston JG, Connolly J, Kainulainen H, Britton SL, Koch LG. Label-free profiling of skeletal muscle using high-definition mass spectrometry. Proteomics 2014; 14:2339-44. [PMID: 25065561 DOI: 10.1002/pmic.201400118] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/10/2014] [Accepted: 07/22/2014] [Indexed: 11/10/2022]
Abstract
We report automated and time-efficient (2 h per sample) profiling of muscle using ultra-performance LC coupled directly with high-definition MS (HDMS(E)). Soluble proteins extracted from rat gastrocnemius (n = 10) were digested with trypsin and analyzed in duplicate using a 90 min RPLC gradient. Protein identification and label-free quantitation were performed from HDMS(E) spectra analyzed using Progenesis QI for Proteomics software. In total 1514 proteins were identified. Of these, 811 had at least three unique peptides and were subsequently used to assess the dynamic range and precision of LC-HDMS(E) label-free profiling. Proteins analyzed by LC-HDMS(E) encompass the entire complement of glycolytic, β-oxidation, and tricarboxylic acid enzymes. In addition, numerous components of the electron transport chain and protein kinases involved in skeletal muscle regulation were detected. The dynamic range of protein abundances spanned four orders of magnitude. The correlation between technical replicates of the ten biological samples was R(2) = 0.9961 ± 0.0036 (95% CI = 0.9940 - 0.9992) and the technical CV averaged 7.3 ± 6.7% (95% CI = 6.87 - 7.79%). This represents the most sophisticated label-free profiling of skeletal muscle to date.
Collapse
Affiliation(s)
- Jatin G Burniston
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | | | | | | | | |
Collapse
|
46
|
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PLoS One 2014; 9:e102319. [PMID: 25029527 PMCID: PMC4100879 DOI: 10.1371/journal.pone.0102319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 06/18/2014] [Indexed: 12/25/2022] Open
Abstract
Computational models using metabolic reconstructions for in silico simulation of metabolic disorders such as type 2 diabetes mellitus (T2DM) can provide a better understanding of disease pathophysiology and avoid high experimentation costs. There is a limited amount of computational work, using metabolic reconstructions, performed in this field for the better understanding of T2DM. In this study, a new algorithm for generating tissue-specific metabolic models is presented, along with the resulting multi-confidence level (MCL) multi-tissue model. The effect of T2DM on liver, muscle, and fat in MKR mice was first studied by microarray analysis and subsequently the changes in gene expression of frank T2DM MKR mice versus healthy mice were applied to the multi-tissue model to test the effect. Using the first multi-tissue genome-scale model of all metabolic pathways in T2DM, we found out that branched-chain amino acids' degradation and fatty acids oxidation pathway is downregulated in T2DM MKR mice. Microarray data showed low expression of genes in MKR mice versus healthy mice in the degradation of branched-chain amino acids and fatty-acid oxidation pathways. In addition, the flux balance analysis using the MCL multi-tissue model showed that the degradation pathways of branched-chain amino acid and fatty acid oxidation were significantly downregulated in MKR mice versus healthy mice. Validation of the model was performed using data derived from the literature regarding T2DM. Microarray data was used in conjunction with the model to predict fluxes of various other metabolic pathways in the T2DM mouse model and alterations in a number of pathways were detected. The Type 2 Diabetes MCL multi-tissue model may explain the high level of branched-chain amino acids and free fatty acids in plasma of Type 2 Diabetic subjects from a metabolic fluxes perspective.
Collapse
|
47
|
Burniston JG, Kenyani J, Gray D, Guadagnin E, Jarman IH, Cobley JN, Cuthbertson DJ, Chen YW, Wastling JM, Lisboa PJ, Koch LG, Britton SL. Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity. J Proteomics 2014; 106:230-45. [PMID: 24769234 PMCID: PMC4150023 DOI: 10.1016/j.jprot.2014.04.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/03/2014] [Accepted: 04/09/2014] [Indexed: 12/11/2022]
Abstract
Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features.
Collapse
Affiliation(s)
- Jatin G Burniston
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK.
| | - Jenna Kenyani
- Department of Cellular and Molecular Physiology, University of Liverpool, Nuffield Building, Liverpool L69 3BX, UK
| | - Donna Gray
- Department of Obesity and Endocrinology, Clinical Sciences Center, University Hospital Anitree, Liverpool L9 7AL, UK
| | - Eleonora Guadagnin
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Ian H Jarman
- Department of Mathematics and Statistics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - James N Cobley
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Daniel J Cuthbertson
- Department of Obesity and Endocrinology, Clinical Sciences Center, University Hospital Anitree, Liverpool L9 7AL, UK
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University, Washington DC, USA
| | - Jonathan M Wastling
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park IC2, L3 5RF, UK
| | - Paulo J Lisboa
- Department of Mathematics and Statistics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Lauren G Koch
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-2200, USA; Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Steven L Britton
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-2200, USA; Department of Anesthesiology, University of Michigan, Ann Arbor, MI 48109-2200, USA
| |
Collapse
|
48
|
Zhao X, Bak S, Pedersen AJT, Jensen ON, Højlund K. Insulin Increases Phosphorylation of Mitochondrial Proteins in Human Skeletal Muscle in Vivo. J Proteome Res 2014; 13:2359-69. [DOI: 10.1021/pr401163t] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaolu Zhao
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
- College
of Life Science, Wuhan University, Wuhan, P. R. China 430072
| | - Steffen Bak
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
- Section of Molecular Diabetes & Metabolism, Institute of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | | | - Ole Nørregaard Jensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kurt Højlund
- Section of Molecular Diabetes & Metabolism, Institute of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
- Department
of Endocrinology, Odense University Hospital, DK-5000 Odense
M, Denmark
- Section
of Molecular Physiology, The August Krogh Centre, Department of Nutrition,
Exercise and Sports, University of Copenhagen, 2100 Copenhagen, Denmark
| |
Collapse
|
49
|
Al-Khalili L, de Castro Barbosa T, Östling J, Massart J, Katayama M, Nyström AC, Oscarsson J, Zierath JR. Profiling of human myotubes reveals an intrinsic proteomic signature associated with type 2 diabetes. TRANSLATIONAL PROTEOMICS 2014. [DOI: 10.1016/j.trprot.2013.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
|
50
|
Hussey SE, Sharoff CG, Garnham A, Yi Z, Bowen BP, Mandarino LJ, Hargreaves M. Effect of exercise on the skeletal muscle proteome in patients with type 2 diabetes. Med Sci Sports Exerc 2014; 45:1069-76. [PMID: 23274603 DOI: 10.1249/mss.0b013e3182814917] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PURPOSE Exercise training alters protein abundance in the muscle of healthy individuals, but the effect of exercise on these proteins in patients with type 2 diabetes (T2D) is unknown. The aim of this study was to determine how exercise training alters the skeletal muscle proteome in patients with T2D. METHODS Biopsies of the vastus lateralis were obtained before and after 4 wk of exercise training in six patients with T2D (54 ± 4 yr; body mass index (BMI), 29 ± 2) and six age- and BMI-matched control subjects (48 ± 2; BMI, 28 ± 3) studied at the baseline. The proteins were identified and quantified using normalized spectral abundance factors by multidimensional high-resolution mass spectrometry. RESULTS Of the 1329 proteins assigned at the baseline, 438 were present in at least half of all the muscle samples; of these, 15 proteins differed significantly between the patients with T2D and control subjects (P < 0.05). In the diabetic patients, the exercise training altered the abundance of 17 proteins (P < 0.05). Key training adaptations included an increase in proteins of the malate-aspartate shuttle and citric acid cycle, reduced the abundance of glycolytic proteins, and altered the abundance of cytoskeleton proteins. CONCLUSION The data from this study support the ability of exercise training to alter the abundance of proteins that regulate metabolism and cytoskeletal structure in patients with T2D. These findings open new avenues for future research.
Collapse
Affiliation(s)
- Sophie E Hussey
- Department of Physiology, The University of Melbourne, Australia
| | | | | | | | | | | | | |
Collapse
|