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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; 34:12565. [PMID: 38787292 PMCID: PMC11264233 DOI: 10.4081/ejtm.2024.12565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - 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.
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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; 34:12564. [PMID: 38787300 PMCID: PMC11264229 DOI: 10.4081/ejtm.2024.12564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - 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.
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Wang Q, Cui C, Zhang N, Lin W, Chai S, Chow SKH, Wong RMY, Hu Y, Law SW, Cheung WH. Effects of physical exercise on neuromuscular junction degeneration during ageing: A systematic review. J Orthop Translat 2024; 46:91-102. [PMID: 38817243 PMCID: PMC11137388 DOI: 10.1016/j.jot.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 06/01/2024] Open
Abstract
The neuromuscular junction (NMJ) is a specialized chemical synapse that converts neural impulses into muscle action. Age-associated NMJ degeneration, which involves nerve terminal and postsynaptic decline, denervation, and loss of motor units, significantly contributes to muscle weakness and dysfunction. Although physical training has been shown to make substantial modifications in NMJ of both young and aged animals, the results are often influenced by methodological variables in existing studies. Moreover, there is still lack of strong consensus on the specific effects of exercise on improving the morphology and function of the ageing NMJ. Consequently, the purpose of this study was to conduct a systematic review to elucidate the effects of exercise training on NMJ compartments in the elderly. We conducted a systematic review using PubMed, Embase, and Web of Science databases, employing relevant keywords. Two independent reviewers selected studies that detailed NMJ changes during exercise in ageing, written in English, and available in full text. In total, 20 papers were included. We examined the altered adaptation of the NMJ to exercise, focusing on presynaptic and postsynaptic structures and myofibers in older animals or humans. Our findings indicated that aged NMJs exhibited different adaptive responses to physical exercise compared to younger counterparts. Endurance training, compared with resistance and voluntary exercise regimens, was found to have a more pronounced effect on NMJ structural remodeling, particularly in fast twitch muscle fibers. Physical exercise was observed to promote the formation and maintenance of acetylcholine receptor (AChR) clusters by increasing the recombinant docking protein 7 (Dok7) expression and stabilizing Agrin and lipoprotein receptor-related protein 4 (LRP4). These insights suggest that research on exercise-related therapies could potentially attenuate the progression of neuromuscular degeneration. Translational potential of this article: This systematic review provides a detailed overview of the effects of different types of physical exercise on improving NMJ in the elderly, providing scientific support for the timely intervention of muscle degeneration in the elderly by physical exercise, and providing help for the development of new therapeutic interventions in the future.
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Affiliation(s)
- Qianjin Wang
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Can Cui
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Ning Zhang
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Wujian Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Senlin Chai
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Simon Kwoon-Ho Chow
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA, USA
| | - Ronald Man Yeung Wong
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Yong Hu
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Sheung Wai Law
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Wing-Hoi Cheung
- Musculoskeletal Research Laboratory, Department of Orthopaedics and Traumatology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
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Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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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.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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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: 24] [Impact Index Per Article: 24.0] [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.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - 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
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Abstract
The gradual loss of skeletal muscle mass during aging and associated decline in contractile strength can result in reduced fitness, frailty, and loss of independence. In order to better understand the molecular and cellular mechanisms that underlie sarcopenia of old age and the frailty syndrome, as well as identify novel therapeutic targets to treat age-related fiber wasting, it is crucial to develop a comprehensive biomarker signature of muscle aging. Fluorescence two-dimensional gel electrophoresis (2D-DIGE) in combination with sensitive mass spectrometry presents an ideal bioanalytical tool for biomarker discovery in biogerontology. This chapter outlines the application of the 2D-DIGE method for the comparative analysis of human biopsy specimens from middle-aged versus senescent individuals using a two-CyDye-based method.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Abstract
The global analysis of the proteome is an important tool in cell biology. Comparative proteomic evaluations can identify and compare the composition, dynamics, and modifications between different samples. Comparing tissue proteomes under different conditions is crucial for advancing the biomedical field. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a sensitive and robust biochemical method that can compare multiple protein samples over a broad dynamic range on the same analytical gel and can be used to establish differentially expressed protein profiles between different sample groups. 2D-DIGE involves fluorescently labeling protein samples with CyDye flours, via a two-dye or a three-dye system, pre-separation by isoelectric point, and molecular weight. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization, thus enabling accurate high-resolution analysis of differences in protein abundance between samples. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of two-dye and three-dye DIGE minimal labeling.
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Abstract
The combination of large-scale protein separation techniques, sophisticated mass spectrometry, and systems bioinformatics has led to the establishment of proteomics as a distinct discipline within the wider field of protein biochemistry. Both discovery proteomics and targeted proteomics are widely used in biological and biomedical research, whereby the analytical approaches can be broadly divided into proteoform-centric top-down proteomics versus peptide-centric bottom-up proteomics. This chapter outlines the scientific value of top-down proteomics and describes how fluorescence two-dimensional difference gel electrophoresis can be combined with the systematic analysis of crucial post-translational modifications. The concept of on-membrane digestion following the electrophoretic transfer of proteins and the usefulness of comparative two-dimensional immunoblotting are discussed.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Abstract
The skeletal muscle proteome consists of a large number of diverse protein species with a broad and dynamic concentration range. Since mature skeletal muscles are characterized by a distinctive combination of contractile cells with differing physiological and biochemical properties, it is essential to determine specific differences in the protein composition of fast, slow, and hybrid fibers. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a powerful comparative tool to analyze fiber type-specific differences between predominantly fast contracting versus slower twitching muscles. In this chapter, the application of the 2D-DIGE method for the comparative analysis of different subtypes of skeletal muscles is outlined in detail. A standardized proteomic workflow is described, involving sample preparation, protein extraction, differential fluorescence labeling using a 3-CyDye system, first-dimension isoelectric focusing, second-dimension slab gel electrophoresis, 2D-DIGE image analysis, protein digestion, and mass spectrometry.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system, particularly in the separation of intact proteins. A modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual protein species including protein isoforms and post-translational modifications. This chapter discusses the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research, particularly on recombinant Chinese hamster ovary cells, which are also discussed in this chapter.
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Affiliation(s)
- Paula Meleady
- School of Biotechnology, National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland.
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Ali S, Ammar Khan M, Rajput N, Naeem M, Zhang W, Li CB, Zhou G. Desmin as molecular chaperone for myofibrillar degradation during freeze-thaw cycles. Food Chem 2022; 386:132691. [PMID: 35339085 DOI: 10.1016/j.foodchem.2022.132691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/04/2022]
Abstract
This study investigated the relationship of secondary protein structures with textural attributes of chicken breast subjected to 6 freeze (-20 °C) thaw (4 °C for 12 h) cycles. 2DE identified 78 distinct protein spots. Moreover, WB indicated a remarkable increase in the degree of desmin degradation during multiple freeze-thaw (MFT). In addition, the TEM micrographs revealed that MFT remarkably increased the spacing between the muscle fibers, especially from cycles 3 to 5, slightly decreased H-zone, but a remarkable shrinkage of Z-lines, as well as degradation of myofibril structures (Z-line, I-bands, and M-lines). DSC showed shifts in first and second endothermic transition peaks during the 3rd and 5th cycles. Viscoelastic graphs revealed a cycle-dependent decrease in gel-forming ability (G') during MFT. Finally, the MFT chicken breast samples exhibited significantly decreased shear force in a cycle-dependent manner. This study highlighted the critical role of desmin in regulating myofibrillar degradation through various routes and mechanisms.
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Affiliation(s)
- Sher Ali
- Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, China; Department of Meat Science &Technology, Faculty of Animal Production and Technology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
| | - Muhammad Ammar Khan
- Department of Food Science & Technology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Nasir Rajput
- Faculty of Animal Husbandry & Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh, Pakistan
| | - Muhammad Naeem
- Faculty of Animal Husbandry & Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh, Pakistan
| | - Wangang Zhang
- Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, China
| | - Chun-Bao Li
- Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing and Quality Control, Synergetic Innovation Centre of Food Safety and Nutrition, College of Food Science and Technology, Nanjing Agricultural University, China
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MARQUES ITO, FERNANDES CCL, VASCONCELOS FR, ALVES JPM, MONTENEGRO AR, SILVA CPD, OLIVEIRA FBBD, FIGUEIREDO FC, MOURA AA, RONDINA D. Meat quality of culled adult goats finished with increased feeding plans. FOOD SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1590/fst.37721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tang Y, Xie T, Wu S, Yang Q, Liu T, Li C, Liu S, Shao Z, Zhang X. Quantitative proteomics revealed the molecular characteristics of distinct types of granulated somatotroph adenomas. Endocrine 2021; 74:375-386. [PMID: 34043183 DOI: 10.1007/s12020-021-02767-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/15/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE Somatotroph adenomas are obviously heterogeneous in clinical characteristics, imaging performance, pathological diagnosis and therapeutic effect. The heterogeneity of the tumors, especially for SG and DG type adenomas, have attracted great interest in identifying the specific pathological markers and therapeutic targets of them. However, previous analyses of the molecular characteristics of the subtypes of somatotroph adenomas were performed at genomic and transcriptome level. The proteomic differences between the two subtypes of somatotroph adenomas are still unknown. METHODS Tumor samples were surgically removed from 10 sporadic pituitary somatotroph adenoma patients and grouped according to the pathological type. Tandem mass tag (TMT)-based quantitative proteomic analysis was employed to analyze the proteomic differences between SG and DG tumors. RESULTS In total, 228 differentially expressed proteins were identified between SG adenomas and DG adenomas. They were enriched mainly in extracellular matrix (ECM)-receptor interaction, leukocyte transendothelial migration, arrhythmogenic right ventricular cardiomyopathy and DNA replication pathways. Protein-protein interaction (PPI) network analysis indicated that Cadherin-1 and Catenin beta-1 were the most important key proteins in the differences between SG and DG adenomas. Immunohistochemistry (IHC) confirmed the expression levels of the key proteins. CONCLUSIONS This study provides large-scale proteome molecular characteristics of distinct granulation subtypes of somatotroph adenomas. Compared with DG adenomas, The differential protein of SG adenomas mostly enrich in invasive and proliferative functions and pathways at the proteomic level. Cadherin-1 and Catenin beta-1 play key roles in the different biological characteristics of the two tumor subtypes.
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Affiliation(s)
- Yifan Tang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Xie
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Silin Wu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiaoqiao Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Tengfei Liu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Li
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuang Liu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiyong Shao
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xiaobiao Zhang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Digital Medical Research Center, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Medical Image Computing and Computer-Assisted Intervention, Shanghai, China.
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15
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Saburina IN, Kosheleva NV, Kopylov AT, Lipina TV, Krasina ME, Zurina IM, Gorkun AA, Girina SS, Pulin AA, Kaysheva AL, Morozov SG. Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three-dimensional culture. Proteomics 2021; 22:e2000304. [PMID: 34674377 DOI: 10.1002/pmic.202000304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/24/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022]
Abstract
Myocyte differentiation is featured by adaptation processes, including mitochondria repopulation and cytoskeleton re-organization. The difference between monolayer and spheroid cultured cells at the proteomic level is uncertain. We cultivated alveolar mucosa multipotent mesenchymal stromal cells in spheroids in a myogenic way for the proper conditioning of ECM architecture and cell morphology, which induced spontaneous myogenic differentiation of cells within spheroids. Electron microscopy analysis was used for the morphometry of mitochondria biogenesis, and proteomic was used complementary to unveil events underlying differences between two-dimensional/three-dimensional myoblasts differentiation. The prevalence of elongated mitochondria with an average area of 0.097 μm2 was attributed to monolayer cells 7 days after the passage. The population of small mitochondria with a round shape and area of 0.049 μm2 (p < 0.05) was observed in spheroid cells cultured under three-dimensional conditions. Cells in spheroids were quantitatively enriched in proteins of mitochondria biogenesis (DNM1L, IDH2, SSBP1), respiratory chain (ACO2, ATP5I, COX5A), extracellular proteins (COL12A1, COL6A1, COL6A2), and cytoskeleton (MYL6, MYL12B, MYH10). Most of the Rab-related transducers were inhibited in spheroid culture. The proteomic assay demonstrated delicate mechanisms of mitochondria autophagy and repopulation, cytoskeleton assembling, and biogenesis. Differences in the ultrastructure of mitochondria indicate active biogenesis under three-dimensional conditions.
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Affiliation(s)
- Irina N Saburina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
| | - Nastasia V Kosheleva
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia
| | - Arthur T Kopylov
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov University, Moscow, Russia.,Department of Proteomic Research, Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Tatiana V Lipina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Marina E Krasina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina M Zurina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Anastasiya A Gorkun
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Svetlana S Girina
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
| | - Andrey A Pulin
- Pirogov National Medical Surgical Center, Moscow, Russian Federation
| | - Anna L Kaysheva
- Department of Proteomic Research, Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Sergey G Morozov
- FSBSI Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
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16
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Ceballos-González CF, Bolívar-Monsalve EJ, Quevedo-Moreno DA, Lam-Aguilar LL, Borrayo-Montaño KI, Yee-de León JF, Zhang YS, Alvarez MM, Trujillo-de Santiago G. High-Throughput and Continuous Chaotic Bioprinting of Spatially Controlled Bacterial Microcosms. ACS Biomater Sci Eng 2021; 7:2408-2419. [PMID: 33979127 DOI: 10.1016/j.bprint.2020.e00125] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Microorganisms do not work alone but instead function as collaborative microsocieties. The spatial distribution of different bacterial strains (micro-biogeography) in a shared volumetric space and their degree of intimacy greatly influences their societal behavior. Current microbiological techniques are commonly focused on the culture of well-mixed bacterial communities and fail to reproduce the micro-biogeography of polybacterial societies. Here, we bioprinted fine-scale bacterial microcosms using chaotic flows induced by a printhead containing a static mixer. This straightforward approach (i.e., continuous chaotic bacterial bioprinting) enables the fabrication of hydrogel constructs with intercalated layers of bacterial strains. These multilayered constructs are used to analyze how the spatial distributions of bacteria affect their social behavior. For example, we show that bacteria within these biological microsystems engage in either cooperation or competition, depending on the degree of shared interface. The extent of inhibition in predator-prey scenarios (i.e., probiotic-pathogen bacteria) increases when bacteria are in greater intimacy. Furthermore, two Escherichia coli strains exhibit competitive behavior in well-mixed microenvironments, whereas stable coexistence prevails for longer times in spatially structured communities. We anticipate that chaotic bioprinting will contribute to the development of a greater complexity of polybacterial microsystems, tissue-microbiota models, and biomanufactured materials.
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Affiliation(s)
| | | | - Diego Alonso Quevedo-Moreno
- Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Li Lu Lam-Aguilar
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | | | | | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, Massachusetts United States
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
- Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
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17
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Almuslehi MSM, Sen MK, Shortland PJ, Mahns DA, Coorssen JR. CD8 T-cell Recruitment Into the Central Nervous System of Cuprizone-Fed Mice: Relevance to Modeling the Etiology of Multiple Sclerosis. Front Cell Neurosci 2020; 14:43. [PMID: 32210765 PMCID: PMC7076139 DOI: 10.3389/fncel.2020.00043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/14/2020] [Indexed: 11/24/2022] Open
Abstract
Cuprizone (CPZ)-feeding in mice induces atrophy of peripheral immune organs (thymus and spleen) and suppresses T-cell levels, thereby limiting its use as a model for studying the effects of the immune system in demyelinating diseases such as Multiple Sclerosis (MS). To investigate whether castration (Cx) can protect the peripheral immune organs from CPZ-induced atrophy and enable T-cell recruitment into the central nervous system (CNS) following a breach of the blood-brain barrier (BBB), three related studies were carried out. In Study 1, Cx prevented the dose-dependent reductions (0.1% < 0.2% CPZ) in thymic and splenic weight, size of the thymic medulla and splenic white pulp, and CD4 and CD8 (CD4/8) levels remained comparable to gonadally intact (Gi) control males. Importantly, 0.1% and 0.2% CPZ were equipotent at inducing central demyelination and glial activation. In Study 2, combining Cx with 0.1% CPZ-feeding and BBB disruption with pertussis toxin (PT) enhanced CD8+ T-cell recruitment into the CNS. The increased CD8+ T-cell level observed in the parenchyma of the cerebrum, cerebellum, brainstem and spinal cord were confirmed by flow cytometry and western blot analyses of CNS tissue. In Study 3, PT+0.1% CPZ-feeding to Gi female mice resulted in similar effects on the peripheral immune organs, CNS demyelination, and gliosis comparable to Gi males, indicating that testosterone levels alone were not responsible for the immune response seen in Study 2. The combination of Cx+0.1% CPZ-feeding+PT indicates that CPZ-induced demyelination can trigger an “inside-out” immune response when the peripheral immune system is spared and may provide a better model to study the initiating events in demyelinating conditions such as MS.
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Affiliation(s)
- Mohammed S M Almuslehi
- School of Medicine, Western Sydney University, Penrith, NSW, Australia.,Department of Physiology, College of Veterinary Medicine, Diyala University, Diyala, Iraq
| | - Monokesh K Sen
- School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Peter J Shortland
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - David A Mahns
- School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Jens R Coorssen
- Department of Health Sciences, Faculty of Applied Health Sciences, St. Catharines, ON, Canada.,Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON, Canada
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18
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Ma D, Li Y, Xiao W, Peng L, Wang L, Liao Z, Hu L. Achyranthes bidentata extract protects chondrocytes functions through suppressing glycolysis and apoptosis via MAPK/AKT signaling axis. Am J Transl Res 2020; 12:142-152. [PMID: 32051743 PMCID: PMC7013231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Osteoarthritis (OA) is considered to be a joint-associated disorder and one of leading reasons for disability, however, potential mechanism has never been clarified. The purpose of this research was to evaluate protective-effects of Achyranthes Bidentata extracts (ABE) on chondrocytes function in osteoarthritis. We performed a systematic investigation of transcriptional and proteomic landscapes to identify the underlying mechanisms behind effects of ABE on chondrocytic functions. OA animal models were generated in the present research. Chondrocytes were isolated and cultured, and then prepared for GeneChip analysis. Two-dimensional gel electrophoresis and LC-MS/MS analysis were conducted to analyze samples. Quantitative real-time PCR (qRT-PCR) and western blotting were used to evaluate expression of protein kinase B (AKT), β-tubulin and β-action. Apoptosis and glycolysis pathway were significantly compromised in chondrocytes with ABE stimulation as revealed by both transcriptional and proteomic data. Consistently, ABE suppressed chondrocytes apoptosis and glycolytic activity in vitro through modulating multiple genes, such as Plk2, Casp1/12 and Cers1 as well as Pkm2, Eno1/3 and Pgk2. Mechanically, ABE activated MAPK signaling pathway and suppressed AKT signaling pathway, therefore, reducing the glycolysis to provide survival benefits. We extended our analysis by verifying insulin-like growth factor 1 (IGF-1) and MAP kinase 1 (MEK1) in chondrocytes function. Depletion of either IGF-1 or MEK1 impaired AKT expression and phosphorylation, leading to the enhanced chondrocyte apoptosis and reduced cell proliferation. In conclusion, our study provided systematic view and molecular basis for ABE to serve as potential intervention of OA via suppressing AKT signaling.
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Affiliation(s)
- Dujun Ma
- Shenzhen Traditional Chinese Medicine HospitalShenzhen 518033, China
| | - Yuan Li
- The Second People’s Hospital of Futian District ShenzhenShenzhen 518000, China
| | - Wei Xiao
- Shenzhen Traditional Chinese Medicine HospitalShenzhen 518033, China
| | - Liping Peng
- Shenzhen Traditional Chinese Medicine HospitalShenzhen 518033, China
| | - Lixin Wang
- Shenzhen Traditional Chinese Medicine HospitalShenzhen 518033, China
| | - Zhouwei Liao
- Shenzhen Traditional Chinese Medicine HospitalShenzhen 518033, China
| | - Liekui Hu
- The Fourth Clinical Medical College of Guangzhou University of Chinese MedicineShenzhen 518033, China
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19
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Huang H, Zhao Y, Shang X, Ren H, Zhao Y, Liu X. CAIII expression in skeletal muscle is regulated by Ca2+–CaMKII–MEF2C signaling. Exp Cell Res 2019; 385:111672. [DOI: 10.1016/j.yexcr.2019.111672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022]
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20
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Schiaffino S, Reggiani C, Murgia M. Fiber type diversity in skeletal muscle explored by mass spectrometry-based single fiber proteomics. Histol Histopathol 2019; 35:239-246. [PMID: 31612964 DOI: 10.14670/hh-18-170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian skeletal muscles are composed of a variety of muscle fibers with specialized functional properties. Slow fibers are suited for long lasting and low intensity contractile activity, while various subtypes of fast fibers are optimized to produce high force and power even with a significant fatigue. The functional specialization of muscle fibers is based on selective gene expression regulation, which provides each fiber with a specific protein complement. The recent refinement of small-scale sample preparation, combined with the development of mass spectrometers characterized by high sensitivity, sequencing speed and mass accuracy, has allowed the characterization of the proteome of single muscle fibers with an unprecedented resolution. In the last few years, the first studies on the global proteomics of individual fibers of different types have been published. In this short review we discuss the methodological advancements which have opened the way to single fiber proteomics and the discovery power of this approach. We provide examples of how specific features of single fibers can be overlooked when whole muscle or multi-fiber samples are analyzed and can only be detected when a single fiber proteome is analyzed. Thus, novel subtype-specific metabolic features, most prominently mitochondrial specialization of fiber types have been revealed by single fiber proteomics. In the same way, specific adaptive responses of single fibers to aging or loss of neural input have been detected when single fibers were individually analyzed. We conclude that the fiber type-resolved proteomes represent a powerful tool which can be applied to a variety of physiological and pathological conditions.
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Affiliation(s)
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Institute for Kinesiology Research, Science and Research Center of Koper, Koper, Slovenia
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Max-Planck-Institute of Biochemistry, Martinsried, Germany
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21
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Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
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22
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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.
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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.
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23
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Murphy S, Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Proteomic profiling of giant skeletal muscle proteins. Expert Rev Proteomics 2019; 16:241-256. [DOI: 10.1080/14789450.2019.1575205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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24
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Yuan H, Jiang B, Zhao B, Zhang L, Zhang Y. Recent Advances in Multidimensional Separation for Proteome Analysis. Anal Chem 2018; 91:264-276. [DOI: 10.1021/acs.analchem.8b04894] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Bo Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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25
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Klein O, Strohschein K, Nebrich G, Fuchs M, Thiele H, Giavalisco P, Duda GN, Winkler T, Kobarg JH, Trede D, Geissler S. Unraveling local tissue changes within severely injured skeletal muscles in response to MSC-based intervention using MALDI Imaging mass spectrometry. Sci Rep 2018; 8:12677. [PMID: 30140012 PMCID: PMC6107672 DOI: 10.1038/s41598-018-30990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Pre-clinical and clinical studies are now beginning to demonstrate the high potential of cell therapies in enhancing muscle regeneration. We previously demonstrated functional benefit after the transplantation of autologous bone marrow mesenchymal stromal cells (MSC-TX) into a severe muscle crush trauma model. Despite our increasing understanding of the molecular and cellular mechanisms underlying MSC's regenerative function, little is known about the local molecular alterations and their spatial distribution within the tissue after MSC-TX. Here, we used MALDI imaging mass spectrometry (MALDI-IMS) in combination with multivariate statistical strategies to uncover previously unknown peptide alterations within severely injured skeletal muscles. Our analysis revealed that very early molecular alterations in response to MSC-TX occur largely in the region adjacent to the trauma and only to a small extent in the actual trauma region. Using "bottom up" mass spectrometry, we subsequently identified the proteins corresponding to the differentially expressed peptide intensity distributions in the specific muscle regions and used immunohistochemistry to validate our results. These findings extend our current understanding about the early molecular processes of muscle healing and highlights the critical role of trauma adjacent tissue during the early therapeutic response upon treatment with MSC.
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Affiliation(s)
- Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Kristin Strohschein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Grit Nebrich
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Michael Fuchs
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Herbert Thiele
- Fraunhofer - Inst. Medical Image Computing MEVIS, Maria-Goeppert-Straße 3, 23562, Lübeck, Germany
| | - Patrick Giavalisco
- Experimental Systems Biology Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, 14476, Golm, Germany
| | - Georg N Duda
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Tobias Winkler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan Hendrik Kobarg
- SCiLS, Zweigniederlassung Bremen der Bruker Daltonik, Fahrenheitstr. 1, 28359, Bremen, Germany
| | - Dennis Trede
- SCiLS, Zweigniederlassung Bremen der Bruker Daltonik, Fahrenheitstr. 1, 28359, Bremen, Germany
| | - Sven Geissler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
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26
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Murphy S, Henry M, Meleady P, Ohlendieck K. Utilization of dried and long-term stored polyacrylamide gels for the advanced proteomic profiling of mitochondrial contact sites from rat liver. Biol Methods Protoc 2018; 3:bpy008. [PMID: 32161802 PMCID: PMC6994098 DOI: 10.1093/biomethods/bpy008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 11/25/2022] Open
Abstract
Following subcellular fractionation, the complexity of proteins derived from a particular cellular compartment is often evaluated by gel electrophoretic analysis. For the proteomic cataloguing of these distinct protein populations and their biochemical characterization, gel electrophoretic protein separation can be conveniently combined with liquid chromatography mass spectrometry. Here we describe a gel-enhanced liquid chromatography mass spectrometry (GeLC-MS)/MS approach with a new bioanalytical focus on the proteomic profiling of mitochondrial contact sites from rat liver using the highly sensitive Orbitrap Fusion Tribrid mass spectrometer for optimum protein identification following extraction from dried and long-term stored gels. Mass spectrometric analysis identified 964 protein species in the mitochondrial contact site fraction, whereby 459 proteins were identified by ≥3 unique peptides. This included mitochondrial components of the supramolecular complexes that form the ATP synthase, the respiratory chain, ribosomal subunits and the cytochrome P450 system, as well as crucial components of the translocase complexes translocase of the inner membrane (TIM) and translocase of the outer membrane (TOM) of the two mitochondrial membranes. Proteomics also identified contact site markers, such as glutathione transferase, monoamine oxidase and the pore protein voltage dependent anion channel (VDAC)-1. Hence, this report demonstrates that the GeLC-MS/MS method can be used to study complex mixtures of proteins that have been embedded and stored in dried polyacrylamide gels for a long period of time. Careful re-swelling and standard in-gel digestion is suitable to produce peptide profiles from old gels that can be used to extract sophisticated proteomic maps and enable the subsequent bioinformatics analysis of the distribution of protein function and the determination of potential protein clustering within the contact site system.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, 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
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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27
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Goez MM, Torres-Madroñero MC, Röthlisberger S, Delgado-Trejos E. Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:63-72. [PMID: 29474888 PMCID: PMC6000252 DOI: 10.1016/j.gpb.2017.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 09/20/2017] [Accepted: 10/19/2017] [Indexed: 12/19/2022]
Abstract
Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image.
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Affiliation(s)
- Manuel Mauricio Goez
- Automatics, Electronics and Computer Science Research Group, Faculty of Engineering, Instituto Tecnologico Metropolitano, Medellin 050012, Colombia
| | - Maria Constanza Torres-Madroñero
- Automatics, Electronics and Computer Science Research Group, Faculty of Engineering, Instituto Tecnologico Metropolitano, Medellin 050012, Colombia.
| | - Sarah Röthlisberger
- Biomedical Innovation and Research Group, Faculty of Applied and Exact Sciences, Instituto Tecnologico Metropolitano, Medellin 050012, Colombia
| | - Edilson Delgado-Trejos
- Quality, Metrology and Production Research Group, Faculty of Economic and Management Sciences, Instituto Tecnologico Metropolitano, Medellin 050012, Colombia
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28
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Zhan X, Yang H, Peng F, Li J, Mu Y, Long Y, Cheng T, Huang Y, Li Z, Lu M, Li N, Li M, Liu J, Jungblut PR. How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome? Electrophoresis 2018; 39:965-980. [PMID: 29205401 DOI: 10.1002/elps.201700330] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 11/03/2017] [Accepted: 11/17/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- The State Key Laboratory of Medical Genetics; Central South University; Changsha Hunan P. R. China
| | - Haiyan Yang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Fang Peng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, Hunan University; Changsha Hunan P. R. China
| | - Yun Mu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Ying Long
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Tingting Cheng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Yuda Huang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Zhao Li
- Department of Neurosurgery; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Miaolong Lu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Maoyu Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs; Xiangya Hospital, Central South University; Changsha Hunan P. R. China
| | - Jianping Liu
- Bio-Analytical Chemistry Research Laboratory, Modern Analytical Testing Center; Central South University; Changsha Hunan P. R. China
| | - Peter R. Jungblut
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis; Berlin Germany
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29
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Murphy S, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Proteomic serum biomarkers for neuromuscular diseases. Expert Rev Proteomics 2018; 15:277-291. [DOI: 10.1080/14789450.2018.1429923] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn, Germany
| | | | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland
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30
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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system. In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual proteins species including protein isoforms and post-translational modifications. This review will discuss the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research (particularly on recombinant Chinese hamster ovary cells), which will also be discussed in the review chapter.
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Affiliation(s)
- Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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31
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Abstract
Gel-based proteomics has been widely used for the systematic cataloging of the protein constituents of defined biofluids, purified organelles, individual cell types, heterogeneous tissues and isolated organs, as well as being applied to comparative biochemical and biomedical analyses of complex biological specimens. Of the many electrophoretic techniques used in modern biochemical approaches, large-scale protein separation by difference gel electrophoresis (DIGE) has established itself as the most powerful analytical tool in comparative proteomics. Both 2-dye and 3-dye fluorescence systems with minimal or saturation labeling are routinely used. This chapter briefly describes the technical advantages of the pre-electrophoretic fluorescent labeling technique and discusses the bioanalytical usefulness of this highly successful electrophoretic method.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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32
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Comparative Testis Tissue Proteomics Using 2-Dye Versus 3-Dye DIGE Analysis. Methods Mol Biol 2017. [PMID: 29019134 DOI: 10.1007/978-1-4939-7268-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Comparative tissue proteomics aims to analyze alterations of the proteome in response to a stimulus. Two-dimensional difference gel electrophoresis (2D-DIGE) is a modified and advanced form of 2D gel electrophoresis. DIGE is a powerful biochemical method that compares two or three protein samples on the same analytical gel, and can be used to establish differentially expressed protein levels between healthy normal and diseased pathological tissue sample groups. Minimal DIGE labeling can be used via a 2-dye system with Cy3 and Cy5 or a 3-dye system with Cy2, Cy3, and Cy5 to fluorescently label samples with CyDye flours pre-electrophoresis. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization. This form of quantitative high-resolution proteomics facilitates the comparative analysis and evaluation of tissue protein compositions. Comparing tissue groups under different conditions is crucially important for advancing the biomedical field by characterization of cellular processes, understanding pathophysiological development and tissue biomarker discovery. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of 2-dye and 3-dye DIGE minimal labeling.
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Abstract
The skeletal muscle proteome consists of a large number of diverse protein species with a broad and dynamic concentration range. Since mature skeletal muscles are characterized by a specific combination of contractile cells with differing physiological and biochemical properties, it is essential to determine specific differences in the protein composition of fast, slow, and hybrid fibers. Fluorescence two-dimensional gel electrophoresis (DIGE) is a powerful comparative tool to analyze fiber type-specific differences between fast and slow muscles. In this chapter, the application of the DIGE method for the comparative analysis of different subtypes of skeletal muscles is outlined in detail. A standardized proteomic workflow is described, involving sample preparation, protein extraction, differential fluorescence labeling using a 3-dye system, first-dimension isoelectric focusing, second-dimension slab gel electrophoresis, DIGE image analysis, protein digestion, and mass spectrometry.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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34
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Capitanio D, Moriggi M, Gelfi C. Mapping the human skeletal muscle proteome: progress and potential. Expert Rev Proteomics 2017; 14:825-839. [PMID: 28780899 DOI: 10.1080/14789450.2017.1364996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies. Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies. Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.
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Affiliation(s)
- Daniele Capitanio
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Manuela Moriggi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Cecilia Gelfi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
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35
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Murphy S, Ohlendieck K. Mass spectrometric identification of dystrophin, the protein product of the Duchenne muscular dystrophy gene, in distinct muscle surface membranes. Int J Mol Med 2017; 40:1078-1088. [PMID: 28765879 PMCID: PMC5593493 DOI: 10.3892/ijmm.2017.3082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/22/2017] [Indexed: 12/21/2022] Open
Abstract
Supramolecular membrane complexes of low abundance are difficult to study by routine bioanalytical techniques. The plasmalemmal complex consisting of sarcoglycans, dystroglycans, dystrobrevins and syntrophins, which is closely associated with the membrane cytoskeletal protein dystrophin, represents such a high‑molecular‑mass protein assembly in skeletal muscles. The almost complete loss of the dystrophin isoform Dp427‑M and concomitant reduction in the dystrophin‑associated glycoprotein complex is the underlying cause of the highly progressive neuromuscular disorder named Duchenne muscular dystrophy. This gives the detailed characterization of the dystrophin complex considerable pathophysiological importance. In order to carry out a comprehensive mass spectrometric identification of the dystrophin‑glycoprotein complex, in this study, we used extensive subcellular fractionation and enrichment procedures prior to subproteomic analysis. Mass spectrometry identified high levels of full‑length dystrophin isoform Dp427‑M, α/β‑dystroglycans, α/β/γ/δ‑sarcoglycans, α1/β1/β2‑syntrophins and α/β‑dystrobrevins in highly purified sarcolemma vesicles. By contrast, lower levels were detected in transverse tubules and no components of the dystrophin complex were identified in triads. For comparative purposes, the presence of organellar marker proteins was studied in crude surface membrane preparations vs. enriched fractions from the sarcolemma, transverse tubules and triad junctions using gradient gel electrophoresis and on‑membrane digestion. This involved the subproteomic assessment of various ion‑regulatory proteins and excitation‑contraction coupling components. The comparative profiling of skeletal muscle fractions established a relatively restricted subcellular localization of the dystrophin‑glycoprotein complex in the muscle fibre periphery by proteomic means and clearly demonstrated the absence of dystrophin from triad junctions by sensitive mass spectrometric analysis.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co Kildare, Ireland
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36
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Coorssen J, Yergey A. Editorial for Special Issue: Approaches to Top-Down Proteomics: In Honour of Prof. Patrick H. O'Farrell. Proteomes 2017; 5:proteomes5030018. [PMID: 28737716 PMCID: PMC5620535 DOI: 10.3390/proteomes5030018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jens Coorssen
- Faculty of Graduate Studies, and the Departments of Health Sciences and Biological Sciences, Brock University, St. Catharines, L2S 3A1 ON, Canada.
| | - Alfred Yergey
- NIH, Building 10, Room 9D 52, Bethesda, MD 20892, USA.
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