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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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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; 24:2415. [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
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Deane CS, Phillips BE, Willis CRG, Wilkinson DJ, Smith K, Higashitani N, Williams JP, Szewczyk NJ, Atherton PJ, Higashitani A, Etheridge T. Proteomic features of skeletal muscle adaptation to resistance exercise training as a function of age. GeroScience 2022:10.1007/s11357-022-00658-5. [PMID: 36161583 PMCID: PMC10400508 DOI: 10.1007/s11357-022-00658-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/03/2022] [Indexed: 12/29/2022] Open
Abstract
Resistance exercise training (RET) can counteract negative features of muscle ageing but older age associates with reduced adaptive capacity to RET. Altered muscle protein networks likely contribute to ageing RET adaptation; therefore, associated proteome-wide responses warrant exploration. We employed quantitative sarcoplasmic proteomics to compare age-related proteome and phosphoproteome responses to RET. Thigh muscle biopsies were collected from eight young (25 ± 1.1 years) and eight older (67.5 ± 2.6 years) adults before and after 20 weeks supervised RET. Muscle sarcoplasmic fractions were pooled for each condition and analysed using Isobaric Tags for Relative and Absolute Quantification (iTRAQ) labelling, tandem mass spectrometry and network-based hub protein identification. Older adults displayed impaired RET-induced adaptations in whole-body lean mass, body fat percentage and thigh lean mass (P > 0.05). iTRAQ identified 73 differentially expressed proteins with age and/or RET. Despite possible proteomic stochasticity, RET improved ageing profiles for mitochondrial function and glucose metabolism (top hub; PYK (pyruvate kinase)) but failed to correct altered ageing expression of cytoskeletal proteins (top hub; YWHAZ (14-3-3 protein zeta/delta)). These ageing RET proteomic profiles were generally unchanged or oppositely regulated post-RET in younger muscle. Similarly, RET corrected expression of 10 phosphoproteins altered in ageing, but these responses were again different vs. younger adults. Older muscle is characterised by RET-induced metabolic protein profiles that, whilst not present in younger muscle, improve untrained age-related proteomic deficits. Combined with impaired cytoskeletal adhesion responses, these results provide a proteomic framework for understanding and optimising ageing muscle RET adaptation.
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Affiliation(s)
- Colleen S Deane
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, St. Luke's Campus, Exeter, EX1 2LU, UK
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Bethan E Phillips
- School of Medicine, MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Derby, UK
| | - Craig R G Willis
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
- Ohio Musculoskeletal and Neurological Institute, Ohio University, Athens, OH, USA
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, UK
| | - Daniel J Wilkinson
- School of Medicine, MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Derby, UK
| | - Ken Smith
- School of Medicine, MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Derby, UK
| | - Nahoko Higashitani
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - John P Williams
- School of Medicine, MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Derby, UK
- University Hospitals Derby & Burton NHS Foundation Trust, Royal Derby Hospital, Derby, UK
| | - Nathaniel J Szewczyk
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
- Ohio Musculoskeletal and Neurological Institute, Ohio University, Athens, OH, USA
| | - Philip J Atherton
- School of Medicine, MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research and National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Derby, UK
| | - Atsushi Higashitani
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, St. Luke's Campus, Exeter, EX1 2LU, UK.
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Stalmach A, Boehm I, Fernandes M, Rutter A, Skipworth RJE, Husi H. Gene Ontology (GO)-Driven Inference of Candidate Proteomic Markers Associated with Muscle Atrophy Conditions. Molecules 2022; 27:5514. [PMID: 36080280 PMCID: PMC9457532 DOI: 10.3390/molecules27175514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Skeletal muscle homeostasis is essential for the maintenance of a healthy and active lifestyle. Imbalance in muscle homeostasis has significant consequences such as atrophy, loss of muscle mass, and progressive loss of functions. Aging-related muscle wasting, sarcopenia, and atrophy as a consequence of disease, such as cachexia, reduce the quality of life, increase morbidity and result in an overall poor prognosis. Investigating the muscle proteome related to muscle atrophy diseases has a great potential for diagnostic medicine to identify (i) potential protein biomarkers, and (ii) biological processes and functions common or unique to muscle wasting, cachexia, sarcopenia, and aging alone. We conducted a meta-analysis using gene ontology (GO) analysis of 24 human proteomic studies using tissue samples (skeletal muscle and adipose biopsies) and/or biofluids (serum, plasma, urine). Whilst there were few similarities in protein directionality across studies, biological processes common to conditions were identified. Here we demonstrate that the GO analysis of published human proteomics data can identify processes not revealed by single studies. We recommend the integration of proteomics data from tissue samples and biofluids to yield a comprehensive overview of the human skeletal muscle proteome. This will facilitate the identification of biomarkers and potential pathways of muscle-wasting conditions for use in clinics.
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Affiliation(s)
- Angelique Stalmach
- Centre for Health Science, Division of Biomedical Sciences, Institute of Health Research and Innovation, School of Health, Social Care and Life Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | - Ines Boehm
- Edinburgh Cancer Research UK Tissue Group, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XR, UK
- Clinical Surgery, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Marco Fernandes
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Alison Rutter
- Centre for Health Science, Division of Biomedical Sciences, Institute of Health Research and Innovation, School of Health, Social Care and Life Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | - Richard J. E. Skipworth
- Clinical Surgery, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Holger Husi
- Centre for Health Science, Division of Biomedical Sciences, Institute of Health Research and Innovation, School of Health, Social Care and Life Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
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Chambon C, Sayd T, Bourillon S, Theron L, Niderkorn V. Digestomic data of proteolysis during whether post rumen digestion after tannin supplementation. Data Brief 2022; 43:108492. [PMID: 35928346 PMCID: PMC9343927 DOI: 10.1016/j.dib.2022.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
The protein degradation of alfalfa hay after tannin supplementation was monitored during wethers digestion. Three rumen-cannulated wethers were infused a tannin solution, and water for control, through the cannula. The digestion time-points samples were collected in vivo in the rumen and in vitro in the abomasum, and the small intestine compartments. The digestomic dataset was acquired by identifying and quantifying the peptides resulting from the protein degradation, using high-resolution LC-MS/MS mass spectrometry and label-free quantitation. The digestomic dataset is the compilation of proteomic data acquired in the rumen and peptidomic data acquired in the abomasum and in the small intestine. The proteomic analysis identified 20 Medicago proteins in the rumen fluid, based on 169 peptides of which 140 are unique. The peptidomic analysis identified 28 Medicago proteins in the abomasum, based on 575 peptides of which 363 are unique, and 11 Medicago proteins in the small intestine, based on 94 peptides of which 63 are unique. This digestomic dataset of proteolysis during sheep post rumen digestion after tannin supplementation reveals the protein regions protected by tannin supplementation, and could be reused in studies related to the protein use efficiency by ruminants.
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Affiliation(s)
- Christophe Chambon
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Plateforme d'Exploration du Métabolisme Composante Protéomique (PFEMcp), F-63122 Saint-Genès Champanelle, France
| | - Thierry Sayd
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UR 370, Qualité des produits animaux (QuaPA), F-63122 Saint-Genès Champanelle, France
| | - Sylvie Bourillon
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UR 370, Qualité des produits animaux (QuaPA), F-63122 Saint-Genès Champanelle, France
| | - Laetitia Theron
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UR 370, Qualité des produits animaux (QuaPA), F-63122 Saint-Genès Champanelle, France
| | - Vincent Niderkorn
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes Champanelle, France
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Barbé C, Salles J, Chambon C, Giraudet C, Sanchez P, Patrac V, Denis P, Boirie Y, Walrand S, Gueugneau M. Characterization of the Skeletal Muscle Proteome in Undernourished Old Rats. Int J Mol Sci 2022; 23:ijms23094762. [PMID: 35563153 PMCID: PMC9101871 DOI: 10.3390/ijms23094762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022] Open
Abstract
Aging is associated with a progressive loss of skeletal muscle mass and function termed sarcopenia. Various metabolic alterations that occur with aging also increase the risk of undernutrition, which can worsen age-related sarcopenia. However, the impact of undernutrition on aged skeletal muscle remains largely under-researched. To build a deeper understanding of the cellular and molecular mechanisms underlying age-related sarcopenia, we characterized the undernutrition-induced changes in the skeletal muscle proteome in old rats. For this study, 20-month-old male rats were fed 50% or 100% of their spontaneous intake for 12 weeks, and proteomic analysis was performed on both slow- and fast-twitch muscles. Proteomic profiling of undernourished aged skeletal muscle revealed that undernutrition has profound effects on muscle proteome independently of its effect on muscle mass. Undernutrition-induced changes in muscle proteome appear to be muscle-type-specific: slow-twitch muscle showed a broad pattern of differential expression in proteins important for energy metabolism, whereas fast-twitch muscle mainly showed changes in protein turnover between undernourished and control rats. This first proteomic analysis of undernourished aged skeletal muscle provides new molecular-level insight to explain phenotypic changes in undernourished aged muscle. We anticipate this work as a starting point to define new biomarkers associated with undernutrition-induced muscle loss in the elderly.
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Affiliation(s)
- Caroline Barbé
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Jérôme Salles
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Christophe Chambon
- Animal Products Quality Unit (QuaPA), INRAE, 63122 Clermont-Ferrand, France;
- Metabolomic and Proteomic Exploration Facility, Clermont Auvergne University, INRAE, 63122 Clermont-Ferrand, France
| | - Christophe Giraudet
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Phelipe Sanchez
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Véronique Patrac
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Philippe Denis
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Yves Boirie
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
- Department of Clinical Nutrition, Clermont-Ferrand University Hospital Center, 63000 Clermont-Ferrand, France
| | - Stéphane Walrand
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
- Department of Clinical Nutrition, Clermont-Ferrand University Hospital Center, 63000 Clermont-Ferrand, France
| | - Marine Gueugneau
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
- Correspondence: ; Tel.: +33-4-73-60-82-65
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A Single Bout of Ultra-Endurance Exercise Reveals Early Signs of Muscle Aging in Master Athletes. Int J Mol Sci 2022; 23:ijms23073713. [PMID: 35409073 PMCID: PMC8998696 DOI: 10.3390/ijms23073713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Accepted: 03/26/2022] [Indexed: 01/27/2023] Open
Abstract
Middle-aged and master endurance athletes exhibit similar physical performance and long-term muscle adaptation to aerobic exercise. Nevertheless, we hypothesized that the short-term plasticity of the skeletal muscle might be distinctly altered for master athletes when they are challenged by a single bout of prolonged moderate-intensity exercise. Six middle-aged (37Y) and five older (50Y) master highly-trained athletes performed a 24-h treadmill run (24TR). Vastus lateralis muscle biopsies were collected before and after the run and assessed for proteomics, fiber morphometry, intramyocellular lipid droplets (LD), mitochondrial oxidative activity, extracellular matrix (ECM), and micro-vascularisation. Before 24TR, muscle fiber type morphometry, intramyocellular LD, oxidative activity, ECM and micro-vascularisation were similar between master and middle-aged runners. For 37Y runners, 24TR was associated with ECM thickening, increased capillary-to-fiber interface, and an 89% depletion of LD in type-I fibers. In contrast, for 50Y runners, 24TR did not alter ECM and capillarization and poorly depleted LDs. Moreover, an impaired succinate dehydrogenase activity and functional class scoring of proteomes suggested reduced oxidative phosphorylation post-24TR exclusively in 50Y muscle. Collectively, our data support that middle-aged and master endurance athletes exhibit distinct transient plasticity in response to a single bout of ultra-endurance exercise, which may constitute early signs of muscle aging for master athletes.
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Sayd T, Chambon C, Popova M, Morgavi DP, Torrent A, Blinet S, Theron L, Niderkorn V. Impact of Tannin Supplementation on Proteolysis during Post-Ruminal Digestion in Wethers Using a Dynamic In Vitro System: A Plant ( Medicago sativa) Digestomic Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2221-2230. [PMID: 35157803 DOI: 10.1021/acs.jafc.1c07378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The aim of this study was to characterize the effects of tannins on plant protein during sheep digestion using a digestomic approach combining in vivo (rumen) conditions and an in vitro digestive system (abomasum and small intestine). Ruminal fluid from wethers infused with a tannin solution or water (control) was introduced into the digester, and protein degradation was followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Tannin infusion in the rumen led to a clear decrease in protein degradation-related fermentation end-products, whereas ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) protein was more abundant than in control wethers. In the simulated abomasum, peptidomic analysis showed more degradation products of RuBisCo in the presence of tannins. The effect of RuBisCo protection by tannins continued to impact Rubisco digestion into early-stage intestinal digestion but was no longer detectable in late-stage intestinal digestion. The peptidomics approach proved a potent tool for identifying and quantifying the type of protein hydrolyzed throughout the gastrointestinal tract.
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Affiliation(s)
- Thierry Sayd
- INRAE, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Christophe Chambon
- INRAE, UR 370, Plateforme Exploration du Métabolisme (PFEM) composante protéomique, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Angélique Torrent
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
| | - Sylvie Blinet
- INRAE, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Laetitia Theron
- INRAE, UR 370, Qualité des Produits Animaux (QuaPA), Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Vincent Niderkorn
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genes-Champanelle, France
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11
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Dowling P, Gargan S, Zweyer M, Sabir H, Swandulla D, Ohlendieck K. Proteomic profiling of carbonic anhydrase CA3 in skeletal muscle. Expert Rev Proteomics 2021; 18:1073-1086. [PMID: 34890519 DOI: 10.1080/14789450.2021.2017776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Carbonic anhydrase (CA) is a key enzyme that mediates the reversible hydration of carbon dioxide. Skeletal muscles contain high levels of the cytosolic isoform CA3. This enzyme has antioxidative function and plays a crucial role in the maintenance of intracellular pH homeostasis. AREAS COVERED Since elevated levels of serum CA3, often in combination with other muscle-specific proteins, are routinely used as a marker of general muscle damage, it was of interest to examine recent analyses of this enzyme carried out by modern proteomics. This review summarizes the mass spectrometry-based identification and evaluation of CA3 in normal, adapting, dystrophic, and aging skeletal muscle tissues. EXPERT OPINION The mass spectrometric characterization of CA3 confirmed this enzyme as a highly useful marker of both physiological and pathophysiological alterations in skeletal muscles. Cytosolic CA3 is clearly enriched in slow-twitching type I fibers, which makes it an ideal marker for studying fiber type shifting and muscle adaptations. Importantly, neuromuscular diseases feature distinct alterations in CA3 in skeletal muscle tissues versus biofluids, such as serum. Characteristic changes of CA3 in age-related muscle wasting and dystrophinopathy established this enzyme as a suitable biomarker candidate for differential diagnosis and monitoring of disease progression and therapeutic impact.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Margit Zweyer
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Hemmen Sabir
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
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12
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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: 18] [Impact Index Per Article: 6.0] [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.
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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.)
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13
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Gueugneau M, Coudy-Gandilhon C, Chambon C, Verney J, Taillandier D, Combaret L, Polge C, Walrand S, Roche F, Barthélémy JC, Féasson L, Béchet D. Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men. Int J Mol Sci 2021; 22:4205. [PMID: 33921590 PMCID: PMC8074053 DOI: 10.3390/ijms22084205] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Aging is associated with a progressive decline in muscle mass and function. Aging is also a primary risk factor for metabolic syndrome, which further alters muscle metabolism. However, the molecular mechanisms involved remain to be clarified. Herein we performed omic profiling to decipher in muscle which dominating processes are associated with healthy aging and metabolic syndrome in old men. (2) Methods: This study included 15 healthy young, 15 healthy old, and 9 old men with metabolic syndrome. Old men were selected from a well-characterized cohort, and each vastus lateralis biopsy was used to combine global transcriptomic and proteomic analyses. (3) Results: Over-representation analysis of differentially expressed genes (ORA) and functional class scoring of pathways (FCS) indicated that healthy aging was mainly associated with upregulations of apoptosis and immune function and downregulations of glycolysis and protein catabolism. ORA and FCS indicated that with metabolic syndrome the dominating biological processes were upregulation of proteolysis and downregulation of oxidative phosphorylation. Proteomic profiling matched 586 muscle proteins between individuals. The proteome of healthy aging revealed modifications consistent with a fast-to-slow transition and downregulation of glycolysis. These transitions were reduced with metabolic syndrome, which was more associated with alterations in NADH/NAD+ shuttle and β-oxidation. Proteomic profiling further showed that all old muscles overexpressed protein chaperones to preserve proteostasis and myofiber integrity. There was also evidence of aging-related increases in reactive oxygen species but better detoxifications of cytotoxic aldehydes and membrane protection in healthy than in metabolic syndrome muscles. (4) Conclusions: Most candidate proteins and mRNAs identified herein constitute putative muscle biomarkers of healthy aging and metabolic syndrome in old men.
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Affiliation(s)
- Marine Gueugneau
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Cécile Coudy-Gandilhon
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Christophe Chambon
- Metabolomic and Proteomic Exploration Facility, Université Clermont Auvergne, INRAE, 63000 Clermont-Ferrand, France;
| | - Julien Verney
- Laboratoire AME2P, Université Clermont Auvergne, 3533 Clermont-Ferrand, France;
| | - Daniel Taillandier
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Lydie Combaret
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Cécile Polge
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Stéphane Walrand
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Frédéric Roche
- Service de Physiologie Clinique et de l’Exercice, CHU Saint Etienne, 42055 Saint Etienne, France; (F.R.); (J.-C.B.)
- INSERM, SAINBIOSE, U1059, Dysfonction Vasculaire et Hémostase, Université Jean-Monnet, 42055 Saint-Etienne, France
| | - Jean-Claude Barthélémy
- Service de Physiologie Clinique et de l’Exercice, CHU Saint Etienne, 42055 Saint Etienne, France; (F.R.); (J.-C.B.)
- INSERM, SAINBIOSE, U1059, Dysfonction Vasculaire et Hémostase, Université Jean-Monnet, 42055 Saint-Etienne, France
| | - Léonard Féasson
- Unité de Myologie, Service de Physiologie Clinique et de l’Exercice, Centre Référent Maladies Neuromusculaires Euro-NmD, 42000 CHU de Saint-Etienne, France;
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université de Lyon, Université Jean Monnet Saint-Etienne, 69000 Lyon, France
| | - Daniel Béchet
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
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14
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Capitanio D, Barbacini P, Arosio B, Guerini FR, Torretta E, Trecate F, Cesari M, Mari D, Clerici M, Gelfi C. Can Serum Nitrosoproteome Predict Longevity of Aged Women? Int J Mol Sci 2020; 21:ijms21239009. [PMID: 33260845 PMCID: PMC7731247 DOI: 10.3390/ijms21239009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Aging is characterized by increase in reactive oxygen (ROS) and nitrogen (RNS) species, key factors of cardiac failure and disuse-induced muscle atrophy. This study focused on serum nitroproteome as a trait of longevity by adopting two complementary gel-based techniques: two-dimensional differential in gel electrophoresis (2-D DIGE) and Nitro-DIGE coupled with mass spectrometry of albumin-depleted serum of aged (A, n = 15) and centenarian (C, n = 15) versus young females (Y, n = 15). Results indicate spots differently expressed in A and C compared to Y and spots changed in A vs. C. Nitro-DIGE revealed nitrosated protein spots in A and C compared to Y and spots changed in A vs. C only (p-value < 0.01). Nitro-proteoforms of alpha-1-antitripsin (SERPINA1), alpha-1-antichimotripsin (SERPINA3), ceruloplasmin (CP), 13 proteoforms of haptoglobin (HP), and inactive glycosyltransferase 25 family member 3 (CERCAM) increased in A vs. Y and C. Conversely, nitrosation levels decreased in C vs. Y and A, for immunoglobulin light chain 1 (IGLC1), serotransferrin (TF), transthyretin (TTR), and vitamin D-binding protein (VDBP). Immunoblottings of alcohol dehydrogenase 5/S-nitrosoglutathione reductase (ADH5/GSNOR) and thioredoxin reductase 1 (TRXR1) indicated lower levels of ADH5 in A vs. Y and C, whereas TRXR1 decreased in A and C in comparison to Y. In conclusion, the study identified putative markers in C of healthy aging and high levels of ADH5/GSNOR that can sustain the denitrosylase activity, promoting longevity.
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Affiliation(s)
- Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, 20090 Segrate (MI), Italy; (D.C.); (P.B.)
| | - Pietro Barbacini
- Department of Biomedical Sciences for Health, University of Milan, 20090 Segrate (MI), Italy; (D.C.); (P.B.)
| | - Beatrice Arosio
- Geriatric Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy;
| | - Franca Rosa Guerini
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, 20148 Milan, Italy; (F.R.G.); (F.T.); (M.C.)
| | | | - Fabio Trecate
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, 20148 Milan, Italy; (F.R.G.); (F.T.); (M.C.)
| | - Matteo Cesari
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy;
- Geriatric Unit, IRCCS Istituti Clinici Scientifici Maugeri, 20138 Milan, Italy
| | - Daniela Mari
- Laboratorio Sperimentale di Ricerche di Neuroendocrinologia Geriatrica ed Oncologica, IRCCS Istituto Auxologico Italiano, 20145 Milan, Italy;
| | - Mario Clerici
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, 20148 Milan, Italy; (F.R.G.); (F.T.); (M.C.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, 20090 Segrate (MI), Italy; (D.C.); (P.B.)
- IRCCS Istituto Ortopedico Galeazzi, 20161 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5033-0475
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15
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Dalle C, Ostermann AI, Konrad T, Coudy-Gandilhon C, Decourt A, Barthélémy JC, Roche F, Féasson L, Mazur A, Béchet D, Schebb NH, Gladine C. Muscle Loss Associated Changes of Oxylipin Signatures During Biological Aging: An Exploratory Study From the PROOF Cohort. J Gerontol A Biol Sci Med Sci 2020; 74:608-615. [PMID: 30137216 DOI: 10.1093/gerona/gly187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Indexed: 12/26/2022] Open
Abstract
Characterizations of the multiple mechanisms determining biological aging are required to better understand the etiology and identify early biomarkers of sarcopenia. Oxylipins refer to a large family of signaling lipids involved in the regulation of various biological processes that become dysregulated during aging. To investigate whether comprehensive oxylipin profiling could provide an integrated and fine characterization of the early phases of sarcopenia, we performed a quantitative targeted metabolomics of oxylipins in plasma of 81-year-old subjects from the PROOF cohort with decreased (n = 12), stable (n = 16), or increased appendicular muscle mass (n = 14). Multivariate and univariate analyses identified significant and concordant changes of oxylipin profiles according to the muscle status. Of note, 90% of the most discriminant oxylipins were derived from EPA and DHA and were increased in the sarcopenic subjects. The oxylipins signatures of sarcopenic subjects revealed subtle activation of inflammatory resolution pathways, coagulation processes, and oxidative stress as well as the inhibition of angiogenesis. Heat maps highlighted relationships between oxylipins and the cardiometabolic health parameters which were mainly lost in sarcopenic subjects. This exploratory study supports that targeted metabolomics of oxylipins could provide relevant and subtle characterization of early disturbances associated with muscle loss during aging.
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Affiliation(s)
- Céline Dalle
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Annika Irmgard Ostermann
- Institute for Food Toxicology, University of Veterinary Medicine Hannover, Hannover, Germany.,Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
| | - Thade Konrad
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
| | - Cécile Coudy-Gandilhon
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Alice Decourt
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France.,Laboratoire Interuniversitaire de Biologie de la Motricité-EA 7424, Univ Lyon, UJM-Saint-Etienne, France
| | - Jean-Claude Barthélémy
- Service de Physiologie Clinique et de l'Exercice, CHU de St Etienne, Saint-Etienne, France.,Laboratoire SNA-EPIS-EA 4607, Univ Lyon, UJM-Saint-Etienne, France
| | - Frédéric Roche
- Service de Physiologie Clinique et de l'Exercice, CHU de St Etienne, Saint-Etienne, France.,Laboratoire SNA-EPIS-EA 4607, Univ Lyon, UJM-Saint-Etienne, France
| | - Léonard Féasson
- Laboratoire Interuniversitaire de Biologie de la Motricité-EA 7424, Univ Lyon, UJM-Saint-Etienne, France.,Service de Physiologie Clinique et de l'Exercice, CHU de St Etienne, Saint-Etienne, France.,Centre Référent Maladies Neuromusculaires Rares - Euro-NmD, CHU Saint-Etienne, Saint-Etienne, France
| | - André Mazur
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Daniel Béchet
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Nils Helge Schebb
- Institute for Food Toxicology, University of Veterinary Medicine Hannover, Hannover, Germany.,Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
| | - Cécile Gladine
- Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
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16
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Laakkonen EK, Soliymani R, Lalowski M. Estrogen regulates muscle bioenergetic signaling. Aging (Albany NY) 2020; 10:160-161. [PMID: 29410389 PMCID: PMC5842845 DOI: 10.18632/aging.101380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 02/02/2018] [Indexed: 11/25/2022]
Affiliation(s)
- Eija K Laakkonen
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, FIN-40014, Finland
| | - Rabah Soliymani
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, FI-00014, Finland
| | - Maciej Lalowski
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Helsinki, FI-00014, Finland
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17
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Zhang F, Xu N, Yu Y, Wu S, Li S, Wang W. Expression Profile of the Digestive Enzymes of Manis javanica Reveals Its Adaptation to Diet Specialization. ACS OMEGA 2019; 4:19925-19933. [PMID: 31788625 PMCID: PMC6882119 DOI: 10.1021/acsomega.9b02845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
The expression of animal digestive enzymes reflects important dietary adaptations. The pangolin, also known as scaly anteater, is a specialized myrmecophage that consumes mainly ants and termites, but its digestive enzymes have not been fully investigated. Therefore, in this study, we used shotgun proteomic analysis to examine the protein components of the saliva and intestinal juice of a Sunda pangolin (Manis javanica) that died shortly after being rescued. The intestinal juice contained greater variety of digestive enzymes, including α-amylase, maltase-glucoamylase, α,α-trehalase, sucrase-isomaltase, pepsin A, trypsin, pancreatic endopeptidase E, carboxypeptidase A1, carboxypeptidase B, dipeptidyl-peptidase 4, and pancreatic triacylglycerol lipase. The digestive enzymes identified in the saliva were maltase-glucoamylase and trypsin, and chitinase which was also found in the intestinal juice. Compared with other animals, the Sunda pangolin has less intestinal protease diversity and lacks key digestive enzymes, such as chymotrypsin and pancreatic elastase. The expression profile of the digestive enzymes of the Sunda pangolin reveals animal's adaptation to a diet consisting mainly of ants and termites. Our results will facilitate the preparation of artificial food for rescued pangolins and for those in captivity for conservation breeding efforts.
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Affiliation(s)
| | | | | | - Shibao Wu
- E-mail: . Phone: +86-20-85211372. Fax: +86-20-85215535 (S.W.)
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18
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Melouane A, Ghanemi A, Yoshioka M, St-Amand J. Functional genomics applications and therapeutic implications in sarcopenia. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:175-185. [PMID: 31416575 DOI: 10.1016/j.mrrev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/14/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022]
Abstract
The human genome contains around 20,000-25,000 genes coding for 30,000 proteins. Some proteins and genes represent therapeutic targets for human diseases. RNA and protein expression profiling tools allow the study of the molecular basis of aging and drug discovery validation. Throughout the life, there is an age-related and disease-related muscle decline. Sarcopenia is defined as a loss of muscle mass and a decrease in functional properties such as muscle strength and physical performance. Yet, there is still no consensus on the evaluation methods of sarcopenia prognosis. The main challenge of this complex biological phenomena is its multifactorial etiology. Thus, functional genomics methods attempt to shape the related scientific approaches via an innovative in-depth view on sarcopenia. Gene and drug high throughput screening combined with functional genomics allow the generation and the interpretation of a large amount of data related to sarcopenia and therapeutic progress. This review focuses on the application of selected functional genomics techniques such as RNA interference, RNA silencing, proteomics, transgenic mice, metabolomics, genomics, and epigenomics to better understand sarcopenia mechanisms.
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Affiliation(s)
- Aicha Melouane
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada
| | - Abdelaziz Ghanemi
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada
| | - Mayumi Yoshioka
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada
| | - Jonny St-Amand
- CREMI, CHU de Québec Research Center, Quebec, Quebec, G1V 4G2, Canada; Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, Quebec, G1V 4G2, Canada.
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19
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Gueugneau M, d'Hose D, Barbé C, de Barsy M, Lause P, Maiter D, Bindels LB, Delzenne NM, Schaeffer L, Gangloff YG, Chambon C, Coudy-Gandilhon C, Béchet D, Thissen JP. Increased Serpina3n release into circulation during glucocorticoid-mediated muscle atrophy. J Cachexia Sarcopenia Muscle 2018; 9:929-946. [PMID: 29989354 PMCID: PMC6204594 DOI: 10.1002/jcsm.12315] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/13/2018] [Accepted: 04/22/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Glucocorticoids (GC) play a major role in muscle atrophy. As skeletal muscle is a secretory organ, characterization of the muscle secretome elicited by muscle atrophy should allow to better understand the cellular mechanisms and to identify circulating biomarkers of this condition. Our project aimed to identify the changes in the muscle secretome associated with GC-induced muscle atrophy and susceptible to translate into circulation. METHODS We have identified the GC-induced changes in the secretome of C2 C12 muscle cells by proteomic analysis, and then, we have determined how these changes translate into the circulation of mice or human subjects exposed to high concentrations of GC. RESULTS This approach led us to identify Serpina3n as one of the most markedly secreted protein in response to GC. Our original in vitro results were confirmed in vivo by an increased expression of Serpina3n in skeletal muscle (3.9-fold; P < 0.01) and in the serum (two-fold; P < 0.01) of mice treated with GC. We also observed increased levels of the human orthologue Serpina3 in the serum of Cushing's syndrome patients compared with healthy controls matched for age and sex (n = 9/group, 2.5-fold; P < 0.01). An increase of Serpina3n was also demonstrated in muscle atrophy models mediated by GC such as cancer cachexia (four-fold; P < 0.01), sepsis (12.5-fold; P < 0.001), or diabetes (two-fold; P < 0.01). In contrast, levels of Serpina3n both in skeletal muscle and in the circulation were reduced in several models of muscle hypertrophy induced by myostatin inhibition (P < 0.01). Furthermore, a cluster of data suggests that the regulation of muscle Serpina3n involves mTOR, an essential determinant of the muscle cell size. CONCLUSIONS Taken together, these data suggest that Serpina3n may represent a circulating biomarker of muscle atrophy associated to GC and, broadly, a reflection of dynamic changes in muscle mass.
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Affiliation(s)
- Marine Gueugneau
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium.,INRA, UMR1019, Université Clermont Auvergne, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Donatienne d'Hose
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Caroline Barbé
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Marie de Barsy
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Pascale Lause
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Dominique Maiter
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), Université catholique de Louvain, Brussels, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), Université catholique de Louvain, Brussels, Belgium
| | - Laurent Schaeffer
- INMG, CNRS, UMR 5310, INSERM U1217, LBMC, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Yann-Gaël Gangloff
- INMG, CNRS, UMR 5310, INSERM U1217, LBMC, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Christophe Chambon
- INRA, Plateforme d'Exploration du Métabolisme Composante Protéomique, Saint Genès Champanelle, France
| | - Cécile Coudy-Gandilhon
- INRA, UMR1019, Université Clermont Auvergne, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Daniel Béchet
- INRA, UMR1019, Université Clermont Auvergne, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Clermont-Ferrand, France
| | - Jean-Paul Thissen
- Pole of Endocrinology, Diabetes and Nutrition, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
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20
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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
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21
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Iqbal J, Zhang K, Jin N, Zhao Y, Liu Q, Ni J, Shen L. Selenium positively affects the proteome of 3 × Tg-AD mice cortex by altering the expression of various key proteins: unveiling the mechanistic role of selenium in AD prevention. J Neurosci Res 2018; 96:1798-1815. [DOI: 10.1002/jnr.24309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/21/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Javed Iqbal
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
| | - Kaoyuan Zhang
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
| | - Na Jin
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
| | - Yuxi Zhao
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
| | - Qiong Liu
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
| | - Jiazuan Ni
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
| | - Liming Shen
- College of Life Sciences and Oceanography; Shenzhen University; Shenzhen P. R. China
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22
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Clonal variation in productivity and proteolytic clipping of an Fc-fusion protein in CHO cells: Proteomic analysis suggests a role for defective protein folding and the UPR. J Biotechnol 2018; 281:21-30. [PMID: 29860056 DOI: 10.1016/j.jbiotec.2018.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/27/2018] [Accepted: 05/30/2018] [Indexed: 11/21/2022]
Abstract
Product degradation, such as clipping, is a common quality issue in the production of Fc-fusion proteins from Chinese hamster ovary (CHO) cells. Degradation of proteins is mainly due to the action of either intracellular or extracellular host cell proteases. This study was carried out to understand more fundamentally the intracellular events that may play a role in determining why cell lines from the same cell line development project can vary with regards to the extent of Fc-fusion protein clipping. The cell lines that displayed the highest levels of clipping also produced less product than the cell lines with a lower level of clipping. In this study we applied differential quantitative label-free LC-MS/MS proteomic analysis to group clonally-derived cell lines (CDCLs) based on the level of clipping of the Fc-fusion protein. The analysis was carried out over two times points in culture and clones were designated as either having 'high' or 'low' clipping phenotypes. We have identified 200 differentially expressed proteins using quantitative label-free LC-MS/MS analysis between the two experimental groups. Functional assessment of the resultant proteomic data using Gene Ontology analysis showed a significant enrichment of biological processes and molecular functions related to protein folding, response to unfolded protein and protein translation. The levels of several proteases were also increased. This study identified protein targets that could be modified using cell line engineering approaches to improve the quality of recombinant Fc-fusion protein production in the biopharmaceutical industry.
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23
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Ping L, Duong DM, Yin L, Gearing M, Lah JJ, Levey AI, Seyfried NT. Global quantitative analysis of the human brain proteome in Alzheimer's and Parkinson's Disease. Sci Data 2018; 5:180036. [PMID: 29533394 PMCID: PMC5848788 DOI: 10.1038/sdata.2018.36] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/09/2018] [Indexed: 02/07/2023] Open
Abstract
Patients with Alzheimer's disease (AD) and Parkinson's disease (PD) often have overlap in clinical presentation and brain neuropathology suggesting that these two diseases share common underlying mechanisms. Currently, the molecular pathways linking AD and PD are incompletely understood. Utilizing Tandem Mass Tag (TMT) isobaric labeling and synchronous precursor selection-based MS3 (SPS-MS3) mass spectrometry, we performed an unbiased quantitative proteomic analysis of post-mortem human brain tissues (n=80) from four different groups defined as controls, AD, PD, and co-morbid AD/PD cases across two brain regions (frontal cortex and anterior cingulate gyrus). In total, we identified 11 840 protein groups representing 10 230 gene symbols, which map to ~65% of the protein coding genes in brain. The utility of including two reference standards in each TMT 10-plex assay to assess intra- and inter-batch variance is also described. Ultimately, this comprehensive human brain proteomic dataset serves as a valuable resource for various research endeavors including, but not limited to, the identification of disease-specific protein signatures and molecular pathways that are common in AD and PD.
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Affiliation(s)
- Lingyan Ping
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Marla Gearing
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James J. Lah
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan I. Levey
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
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24
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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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25
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Melouane A, Ghanemi A, Aubé S, Yoshioka M, St-Amand J. Differential gene expression analysis in ageing muscle and drug discovery perspectives. Ageing Res Rev 2018; 41:53-63. [PMID: 29102726 DOI: 10.1016/j.arr.2017.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022]
Abstract
Identifying therapeutic target genes represents the key step in functional genomics-based therapies. Within this context, the disease heterogeneity, the exogenous factors and the complexity of genomic structure and function represent important challenges. The functional genomics aims to overcome such obstacles via identifying the gene functions and therefore highlight disease-causing genes as therapeutic targets. Genomic technologies promise to reshape the research on ageing muscle, exercise response and drug discovery. Herein, we describe the functional genomics strategies, mainly differential gene expression methods microarray, serial analysis of gene expression (SAGE), massively parallel signature sequence (MPSS), RNA sequencing (RNA seq), representational difference analysis (RDA), and suppression subtractive hybridization (SSH). Furthermore, we review these illustrative approaches that have been used to discover new therapeutic targets for some complex diseases along with the application of these tools to study the modulation of the skeletal muscle transcriptome.
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26
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Laakkonen EK, Soliymani R, Karvinen S, Kaprio J, Kujala UM, Baumann M, Sipilä S, Kovanen V, Lalowski M. Estrogenic regulation of skeletal muscle proteome: a study of premenopausal women and postmenopausal MZ cotwins discordant for hormonal therapy. Aging Cell 2017; 16:1276-1287. [PMID: 28884514 PMCID: PMC5676059 DOI: 10.1111/acel.12661] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2017] [Indexed: 12/31/2022] Open
Abstract
Female middle age is characterized by a decline in skeletal muscle mass and performance, predisposing women to sarcopenia, functional limitations, and metabolic dysfunction as they age. Menopausal loss of ovarian function leading to low circulating level of 17β‐estradiol has been suggested as a contributing factor to aging‐related muscle deterioration. However, the underlying molecular mechanisms remain largely unknown and thus far androgens have been considered as a major anabolic hormone for skeletal muscle. We utilized muscle samples from 24 pre‐ and postmenopausal women to establish proteome‐wide profiles, associated with the difference in age (30–34 years old vs. 54–62 years old), menopausal status (premenopausal vs. postmenopausal), and use of hormone replacement therapy (HRT; user vs. nonuser). None of the premenopausal women used hormonal medication while the postmenopausal women were monozygotic (MZ) cotwin pairs of whom the other sister was current HRT user or the other had never used HRT. Label‐free proteomic analyses resulted in the quantification of 797 muscle proteins of which 145 proteins were for the first time associated with female aging using proteomics. Furthermore, we identified 17β‐estradiol as a potential upstream regulator of the observed differences in muscle energy pathways. These findings pinpoint the underlying molecular mechanisms of the metabolic dysfunction accruing upon menopause, thus having implications for understanding the complex functional interactions between female reproductive hormones and health.
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Affiliation(s)
- Eija K. Laakkonen
- Faculty of Sport and Health Sciences Gerontology Research Center University of Jyväskylä Jyväskylä Finland
| | - Rabah Soliymani
- Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core Facility University of Helsinki Helsinki Finland
| | - Sira Karvinen
- Faculty of Sport and Health Sciences Gerontology Research Center University of Jyväskylä Jyväskylä Finland
- Divisions of Rehabilitation Science and Physical Therapy Department of Rehabilitation Medicine Medical School University of Minnesota Minneapolis MN USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM University of Helsinki Helsinki Finland
| | - Urho M. Kujala
- Faculty of Sport and Health Sciences University of Jyväskylä Jyväskylä Finland
| | - Marc Baumann
- Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core Facility University of Helsinki Helsinki Finland
| | - Sarianna Sipilä
- Faculty of Sport and Health Sciences Gerontology Research Center University of Jyväskylä Jyväskylä Finland
| | - Vuokko Kovanen
- Faculty of Sport and Health Sciences University of Jyväskylä Jyväskylä Finland
| | - Maciej Lalowski
- Medicum, Biochemistry/Developmental Biology Meilahti Clinical Proteomics Core Facility University of Helsinki Helsinki Finland
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27
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Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P. Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 2017; 16:2339-2358. [DOI: 10.1021/acs.jproteome.6b00868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Henry
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Power
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Prashant Kaushik
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Coleman
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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28
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Correia S, Hébraud M, Chafsey I, Chambon C, Viala D, Sáenz Y, Capelo JL, Poeta P, Igrejas G. Comparative subproteomic analysis of clinically acquired fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B. Proteomics Clin Appl 2017; 11. [PMID: 28314077 DOI: 10.1002/prca.201600107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 02/21/2017] [Accepted: 03/07/2017] [Indexed: 02/06/2023]
Abstract
PURPOSE Antimicrobial resistance is a worldwide public health threat and Salmonella enterica subsp. enterica serotype Typhimurium phage type DT104B multiresistant strains with additional quinolone resistance have been responsible for global outbreaks and high mortality. Quinolone resistance is known to be multifactorial but is still far from a complete understanding. To give new insights about the resistance mechanisms involved, this work aimed to evaluate subproteome changes between an S. Typhimurium DT104B clinical strain that acquired fluoroquinolone resistance after treatment (Se20) and its pretreatment parental strain (Se6), and also subproteome variations in Se20 under ciprofloxacin (CIP) stress (Se20+CIP). EXPERIMENTAL DESIGN The proteomes were compared at the intracellular and membrane levels by a 2-DE∼LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 14 differentially abundant proteins were identified when comparing Se6 with Se20 and 91 were identified between Se20 and Se20+CIP. Several proteins with known and possible roles in quinolone resistance (AAC(6')-Ib-cr4, OmpD, OmpX, GlmS, GlmU, H-NS, etc.) were identified and discussed. CONCLUSIONS AND CLINICAL RELEVANCE The great number of proteins identified in this study provides important information about mechanism-related differential protein expression which supports the current knowledge and might lead to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
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Affiliation(s)
- Susana Correia
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Michel Hébraud
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne (UCA), UMR Microbiologie Environnement Digestif et Santé (MEDiS), site de Theix, France.,Institut National de la Recherche Agronomique (INRA), UR370 QuaPA, Plate-Forme d'Exploration du Métabolisme composante protéomique, site de Theix, France
| | - Ingrid Chafsey
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne (UCA), UMR Microbiologie Environnement Digestif et Santé (MEDiS), site de Theix, France
| | - Christophe Chambon
- Institut National de la Recherche Agronomique (INRA), UR370 QuaPA, Plate-Forme d'Exploration du Métabolisme composante protéomique, site de Theix, France
| | - Didier Viala
- Institut National de la Recherche Agronomique (INRA), UR370 QuaPA, Plate-Forme d'Exploration du Métabolisme composante protéomique, site de Theix, France
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logrono, Spain
| | - José Luis Capelo
- UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal.,ProteoMass Scientific Society, Faculty of Sciences and Technology, Caparica Campus, Caparica, Portugal
| | - Patrícia Poeta
- Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,UCIBIO-REQUIMTE, Faculty of Science and Technology, Nova University of Lisbon, Lisbon, Portugal
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29
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Bi B, Li F, Guo J, Li C, Jing R, Lv X, Chen X, Wang F, Azadzoi KM, Wang L, Liu Y, Yang JH. Label-free quantitative proteomics unravels the importance of RNA processing in glioma malignancy. Neuroscience 2017; 351:84-95. [PMID: 28341197 DOI: 10.1016/j.neuroscience.2017.03.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 11/30/2022]
Abstract
Glioma, one of the most common cancers in human, is classified to different grades according to the degrees of malignancy. Glioblastoma (GBM) is known to be the most malignant (Grade IV) whereas low-grade astrocytoma (LGA, Grade II) is relatively benign. The mechanism underlying the pathogenesis and progression of glioma malignancy remains unclear. Here we report a quantitative proteomic study to elucidate the differences between GBM and LGA using liquid chromatography and tandem mass spectrometry followed by label-free quantification. A total of 136 proteins were differentially expressed in GBM for at least five folds in comparison with LGA. Ontological analysis revealed a close correlation between GBM-associated proteins and RNA processing. Interaction network analysis indicated that the GBM-associated proteins in the RNA processing were linked to crucial signaling transduction modulators including epidermal growth factor receptor (EGFR), signal transducer and activator of transcription 1 (STAT1), and mitogen-activated protein kinase 1 (MAPK1), which were further connected to the proteins important for neuronal structural integrity, development and functions. Upregulation of 40S ribosomal protein S5 (RPS5), Ferritin Heavy chain (FTH1) and STAT1, and downregulation of tenascin R (TNR) were validated as representatives by immune assays. In summary, we revealed a panel of GBM-associated proteins and the important modulators centered at the RNA-processing network in glioma malignancy that may become novel biomarkers and help elucidate the underlying mechanism.
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Affiliation(s)
- Baibin Bi
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China; Departments of Neurosurgery and Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, China; Brain Science Research Institute of Shandong University, Jinan 250012, China.
| | - Feng Li
- Departments of Neurosurgery and Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, China; Brain Science Research Institute of Shandong University, Jinan 250012, China.
| | - Jisheng Guo
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China.
| | - Cuiling Li
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China.
| | - Ruirui Jing
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China.
| | - Xin Lv
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China.
| | - Xinjun Chen
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China.
| | - Fengqin Wang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China.
| | - Kazem M Azadzoi
- Departments of Surgery and Urology, VA Boston Healthcare System, Boston University School of Medicine, Boston, MA 02130, USA.
| | - Lin Wang
- Departments of Neurosurgery and Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Yuguang Liu
- Departments of Neurosurgery and Radiation Oncology, Qilu Hospital of Shandong University, Jinan 250012, China; Brain Science Research Institute of Shandong University, Jinan 250012, China.
| | - Jing-Hua Yang
- Cancer Research Center, Shandong University School of Medicine, Jinan 250012, China; Departments of Surgery and Urology, VA Boston Healthcare System, Boston University School of Medicine, Boston, MA 02130, USA.
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30
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Gonzalez-Freire M, Semba RD, Ubaida-Mohien C, Fabbri E, Scalzo P, Højlund K, Dufresne C, Lyashkov A, Ferrucci L. The Human Skeletal Muscle Proteome Project: a reappraisal of the current literature. J Cachexia Sarcopenia Muscle 2017; 8:5-18. [PMID: 27897395 PMCID: PMC5326819 DOI: 10.1002/jcsm.12121] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle is a large organ that accounts for up to half the total mass of the human body. A progressive decline in muscle mass and strength occurs with ageing and in some individuals configures the syndrome of 'sarcopenia', a condition that impairs mobility, challenges autonomy, and is a risk factor for mortality. The mechanisms leading to sarcopenia as well as myopathies are still little understood. The Human Skeletal Muscle Proteome Project was initiated with the aim to characterize muscle proteins and how they change with ageing and disease. We conducted an extensive review of the literature and analysed publically available protein databases. A systematic search of peer-reviewed studies was performed using PubMed. Search terms included 'human', 'skeletal muscle', 'proteome', 'proteomic(s)', and 'mass spectrometry', 'liquid chromatography-mass spectrometry (LC-MS/MS)'. A catalogue of 5431 non-redundant muscle proteins identified by mass spectrometry-based proteomics from 38 peer-reviewed scientific publications from 2002 to November 2015 was created. We also developed a nosology system for the classification of muscle proteins based on localization and function. Such inventory of proteins should serve as a useful background reference for future research on changes in muscle proteome assessed by quantitative mass spectrometry-based proteomic approaches that occur with ageing and diseases. This classification and compilation of the human skeletal muscle proteome can be used for the identification and quantification of proteins in skeletal muscle to discover new mechanisms for sarcopenia and specific muscle diseases that can be targeted for the prevention and treatment.
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Affiliation(s)
| | - Richard D Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Elisa Fabbri
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Paul Scalzo
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Alexey Lyashkov
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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Souza GHMF, Guest PC, Martins-de-Souza D. LC-MS E, Multiplex MS/MS, Ion Mobility, and Label-Free Quantitation in Clinical Proteomics. Methods Mol Biol 2017; 1546:57-73. [PMID: 27896757 DOI: 10.1007/978-1-4939-6730-8_4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteomic tools can only be implemented in clinical settings if high-throughput, automated, sensitive, and accurate methods are developed. This has driven researchers to the edge of mass spectrometry (MS)-based proteomics capacity. Here we provide an overview of recent achievements in mass spectrometric technologies and instruments. This includes development of high and ultra definition-MSE (HDMSE and UDMSE) through implementation of ion mobility (IM) MS towards sensitive and accurate label-free proteomics using ultra performance liquid chromatography (UPLC). Label free UPLC-HDMSE is less expensive than labeled-based quantitative proteomics and has no limits regarding the number of samples that can be analyzed and compared, which is an important requirement for supporting clinical applications.
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Affiliation(s)
- Gustavo Henrique Martins Ferreira Souza
- Mass Spectrometry Applications & Development Laboratory, Waters Corporation, 125, Alphaville Industrial, Barueri, 06455-020, Campinas, São Paulo, SP, Brazil.
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
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Ayyadevara S, Balasubramaniam M, Suri P, Mackintosh SG, Tackett AJ, Sullivan DH, Shmookler Reis RJ, Dennis RA. Proteins that accumulate with age in human skeletal-muscle aggregates contribute to declines in muscle mass and function in Caenorhabditis elegans. Aging (Albany NY) 2016; 8:3486-3497. [PMID: 27992858 PMCID: PMC5270681 DOI: 10.18632/aging.101141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/03/2016] [Indexed: 06/06/2023]
Abstract
Protein aggregation increases with age in normal tissues, and with pathology and age in Alzheimer's hippocampus and mouse cardiac muscle. We now ask whether human skeletal muscle accumulates aggregates with age. Detergent-insoluble protein aggregates were isolated from vastus lateralis biopsies from 5 young (23–27 years of age) and 5 older (64-80 years) adults. Aggregates, quantified after gel electrophoresis, contain 2.1-fold more protein (P<0.0001) when isolated from older subjects relative to young. Of 515 proteins identified by liquid chromatography coupled to tandem mass spectrometry, 56 (11%) were significantly more abundant in older muscle, while 21 (4%) were depleted with age (each P<0.05). Orthologs to seven of these proteins were then targeted in C. elegans by RNA interference. Six of the seven knockdown treatments decreased protein aggregation (range 6-45%, P<0.01 to <0.0001) and increased muscle mass (range 1.5- to 1.85-fold, P<0.01 to <0.0001) in aged nematodes, and rescued mobility (range 1.4 to 1.65-fold, P≤0.0005 each) in a nematode amyloidopathy model. We conclude that specific aggregate proteins, discovered as differentially abundant in aging human muscle, have orthologs that contribute functionally to aggregation and age-associated muscle loss in nematodes, and thus can be considered potential drug targets for sarcopenia in humans.
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Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Meenakshisundaram Balasubramaniam
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Pooja Suri
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J. Tackett
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Dennis H. Sullivan
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Geriatric Research, Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Robert J. Shmookler Reis
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- BioInformatics Program, University of Arkansas at Little Rock and University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Geriatric Research, Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Richard A. Dennis
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
- Reynolds Institute on Aging, Dept. of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Geriatric Research, Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
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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.
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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.
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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.
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Magalhães P, Pinto L, Gonçalves A, Araújo JE, Santos HM, Capelo JL, Saénz Y, de Toro M, Torres C, Chambon C, Hébraud M, Poeta P, Igrejas G. Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli? J Proteomics 2016; 145:103-111. [PMID: 27072110 DOI: 10.1016/j.jprot.2016.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 11/19/2022]
Abstract
UNLABELLED Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance. BIOLOGICAL SIGNIFICANCE This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein.
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Affiliation(s)
- Pedro Magalhães
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Luís Pinto
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Alexandre Gonçalves
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - José Eduardo Araújo
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal
| | - Hugo M Santos
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal; ProteoMass Scientific Society, Faculty of Sciences and Technology, Caparica, Portugal
| | - José Luis Capelo
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal; ProteoMass Scientific Society, Faculty of Sciences and Technology, Caparica, Portugal
| | - Yolanda Saénz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - María de Toro
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain; Instituto de Biomedicina y Biotecnologia de Cantabria IBBTEC, Universidad de Cantabria/CSIC, Santander, Spain
| | - Carmen Torres
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain; Department of Food and Agriculture, Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Christophe Chambon
- Institut National de la Recherche Agronomique, Centre Auvergne-Rhône-Alpes, Plate-Forme d'Exploration du Métabolisme composante protéomique (PFEMcp), France
| | - Michel Hébraud
- Institut National de la Recherche Agronomique, Centre Auvergne-Rhône-Alpes, Plate-Forme d'Exploration du Métabolisme composante protéomique (PFEMcp), France; Institut National de la Recherche Agronomique, Centre Auvergne-Rhône-Alpes, UR454 Microbiologie, France
| | - Patrícia Poeta
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal; Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal.
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Dowling P, Murphy S, Ohlendieck K. Proteomic profiling of muscle fibre type shifting in neuromuscular diseases. Expert Rev Proteomics 2016; 13:783-99. [DOI: 10.1080/14789450.2016.1209416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Guo J, Wang X, Lü X, Jing R, Li J, Li C, Wang D, Bi B, Chen X, Wang F, Sun S, Gong J, Azadzoi KM, Yang JH. Unraveling molecular effects of ADAR1 overexpression in HEK293T cells by label-free quantitative proteomics. Cell Cycle 2016; 15:1591-601. [PMID: 27104882 DOI: 10.1080/15384101.2016.1176657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
ADAR1 is a double-stranded RNA (dsRNA) editing enzyme that specifically converts adenosine to inosine. ADAR1 is ubiquitously expressed in eukaryotes and participate in various cellular processes such as differentiation, proliferation and immune responses. We report here a new proteomics study of HEK293T cells with and without ADAR1 overexpression. The up- and down-regulated proteins by ADAR1 overexpression are identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by label-free protein quantification. Totally 1,495 proteins (FDR < 0.01) are identified, among which 211 are up- and 159 are down-regulated for at least 1.5-fold (n = 3, p < 0.05). Gene ontology analysis reveals that these ADAR1-regulated proteins are involved in protein translation and cell cycle regulation. Bioinformatics analysis identifies a closely related network consistent for the protein translation machinery and a tightly connected network through proliferating cell nuclear antigen (PCNA)-interactions. Up-regulation of the proteins in the PCNA-mediated cell proliferation network is confirmed by Western blotting. In addition, ADAR1 overexpression is confirmed to increase cell proliferation in HEK293T cells and A549 cells. We conclude that ADAR1 overexpression modulates the protein translation and cell cycle networks through PCNA-mediated protein-protein interaction to promote cell proliferation in HEK293 cells.
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Affiliation(s)
- Jisheng Guo
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Xiaoyue Wang
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Xin Lü
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Ruirui Jing
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Junqiang Li
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - CuiLing Li
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Daoguang Wang
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Baibin Bi
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Xinjun Chen
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Fengqin Wang
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Shengnan Sun
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Jing Gong
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China
| | - Kazem M Azadzoi
- b Departments of Surgery and Urology , VA Boston Healthcare System, Boston University School of Medicine , Boston , MA , USA
| | - Jing-Hua Yang
- a Cancer Research Center, Shandong University School of Medicine , Jinan , China.,b Departments of Surgery and Urology , VA Boston Healthcare System, Boston University School of Medicine , Boston , MA , USA
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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.
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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
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Carter HN, Chen CCW, Hood DA. Mitochondria, muscle health, and exercise with advancing age. Physiology (Bethesda) 2016; 30:208-23. [PMID: 25933821 DOI: 10.1152/physiol.00039.2014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Skeletal muscle health is dependent on the optimal function of its mitochondria. With advancing age, decrements in numerous mitochondrial variables are evident in muscle. Part of this decline is due to reduced physical activity, whereas the remainder appears to be attributed to age-related alterations in mitochondrial synthesis and degradation. Exercise is an important strategy to stimulate mitochondrial adaptations in older individuals to foster improvements in muscle function and quality of life.
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Affiliation(s)
- Heather N Carter
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Chris C W Chen
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - David A Hood
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
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Ikwuobe J, Bellary S, Griffiths HR. Innovative biomarkers for predicting type 2 diabetes mellitus: relevance to dietary management of frailty in older adults. Biogerontology 2016; 17:511-27. [PMID: 26897532 DOI: 10.1007/s10522-016-9634-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 01/18/2016] [Indexed: 01/01/2023]
Abstract
Type 2 diabetes mellitus (T2DM) increases in prevalence in the elderly. There is evidence for significant muscle loss and accelerated cognitive impairment in older adults with T2DM; these comorbidities are critical features of frailty. In the early stages of T2DM, insulin sensitivity can be improved by a "healthy" diet. Management of insulin resistance by diet in people over 65 years of age should be carefully re-evaluated because of the risk for falling due to hypoglycaemia. To date, an optimal dietary programme for older adults with insulin resistance and T2DM has not been described. The use of biomarkers to identify those at risk for T2DM will enable clinicians to offer early dietary advice that will delay onset of disease and of frailty. Here we have used an in silico literature search for putative novel biomarkers of T2DM risk and frailty. We suggest that plasma bilirubin, plasma, urinary DPP4-positive microparticles and plasma pigment epithelium-derived factor merit further investigation as predictive biomarkers for T2DM and frailty risk in older adults. Bilirubin is screened routinely in clinical practice. Measurement of specific microparticle frequency in urine is less invasive than a blood sample so is a good choice for biomonitoring. Future studies should investigate whether early dietary changes, such as increased intake of whey protein and micronutrients that improve muscle function and insulin sensitivity, affect biomarkers and can reduce the longer term complication of frailty in people at risk for T2DM.
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Affiliation(s)
- John Ikwuobe
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Birmingham, B4 7ET, UK
| | - Srikanth Bellary
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Birmingham, B4 7ET, UK
| | - Helen R Griffiths
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Birmingham, B4 7ET, UK.
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Unraveling Molecular Differences of Gastric Cancer by Label-Free Quantitative Proteomics Analysis. Int J Mol Sci 2016; 17:ijms17010069. [PMID: 26805816 PMCID: PMC4730314 DOI: 10.3390/ijms17010069] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/16/2015] [Accepted: 12/25/2015] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer (GC) has significant morbidity and mortality worldwide and especially in China. Its molecular pathogenesis has not been thoroughly elaborated. The acknowledged biomarkers for diagnosis, prognosis, recurrence monitoring and treatment are lacking. Proteins from matched pairs of human GC and adjacent tissues were analyzed by a coupled label-free Mass Spectrometry (MS) approach, followed by functional annotation with software analysis. Nano-LC-MS/MS, quantitative real-time polymerase chain reaction (qRT-PCR), western blot and immunohistochemistry were used to validate dysregulated proteins. One hundred forty-six dysregulated proteins with more than twofold expressions were quantified, 22 of which were first reported to be relevant with GC. Most of them were involved in cancers and gastrointestinal disease. The expression of a panel of four upregulated nucleic acid binding proteins, heterogeneous nuclear ribonucleoprotein hnRNPA2B1, hnRNPD, hnRNPL and Y-box binding protein 1 (YBX-1) were validated by Nano-LC-MS/MS, qRT-PCR, western blot and immunohistochemistry assays in ten GC patients’ tissues. They were located in the keynotes of a predicted interaction network and might play important roles in abnormal cell growth. The label-free quantitative proteomic approach provides a deeper understanding and novel insight into GC-related molecular changes and possible mechanisms. It also provides some potential biomarkers for clinical diagnosis.
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Goeminne LJE, Argentini A, Martens L, Clement L. Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines. J Proteome Res 2015; 14:2457-65. [PMID: 25827922 DOI: 10.1021/pr501223t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative label-free mass spectrometry is increasingly used to analyze the proteomes of complex biological samples. However, the choice of appropriate data analysis methods remains a major challenge. We therefore provide a rigorous comparison between peptide-based models and peptide-summarization-based pipelines. We show that peptide-based models outperform summarization-based pipelines in terms of sensitivity, specificity, accuracy, and precision. We also demonstrate that the predefined FDR cutoffs for the detection of differentially regulated proteins can become problematic when differentially expressed (DE) proteins are highly abundant in one or more samples. Care should therefore be taken when data are interpreted from samples with spiked-in internal controls and from samples that contain a few very highly abundant proteins. We do, however, show that specific diagnostic plots can be used for assessing differentially expressed proteins and the overall quality of the obtained fold change estimates. Finally, our study also illustrates that imputation under the "missing by low abundance" assumption is beneficial for the detection of differential expression in proteins with low abundance, but it negatively affects moderately to highly abundant proteins. Hence, imputation strategies that are commonly implemented in standard proteomics software should be used with care.
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Affiliation(s)
- Ludger J E Goeminne
- ∥Department of Plant Systems Biology, VIB, Ghent University, 9052 Ghent, Belgium
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Tu C, Beharry KD, Shen X, Li J, Wang L, Aranda JV, Qu J. Proteomic profiling of the retinas in a neonatal rat model of oxygen-induced retinopathy with a reproducible ion-current-based MS1 approach. J Proteome Res 2015; 14:2109-2120. [PMID: 25780855 DOI: 10.1021/pr501238m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Investigation of the retina proteome during hypoxia-induced retinal neovascularization is valuable for understanding pathogenesis of retinopathy of prematurity (ROP). Here we employed a reproducible ion-current-based MS1 quantification approach (ICB) to explore the retinal proteomic changes in early stage of ROP in a rat model of oxygen-induced retinopathy (OIR). Retina proteins, which are rich in membrane proteins, were efficiently extracted by a detergent-cocktail and subjected to precipitation/on-pellet-digestion, followed by nano-LC-MS analysis on a 75-cm column with a 7-h gradient. The high reproducibility of sample preparation and chromatography separation enabled excellent peak alignment and contributed to the superior performance of ICB over parallel label-free approaches. In this study, sum-of-intensity with rejection was incorporated to determine the protein ratios. In total, 1325 unique protein groups were quantified from rat retinas (n = 4/group) with at least two distinct peptides at a protein FDR of 1%. Thirty-two significantly altered proteins were observed with confidence, and the elevated glial fibrillary acidic protein and decreased crystalline proteins in OIR retinas agree well with previous studies. Selected key alterations were further validated by Western blot analysis. Interestingly, Rab21/RhoA/ROCK2/moesin signaling pathway was found to be involved in retinal neovascularization of OIR. Moreover, highly elevated annexin A3, a potential angiogenic mediator, was observed in OIR retinas and may serve as a potential therapeutic target. In conclusion, reproducible ICB profiling enabled reliable discovery of many altered mediators and pathways in OIR retinas, thereby providing new insights into molecular mechanisms involved in pathogenesis of ROP.
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Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Kay D Beharry
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,Department of Ophthalmology, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,SUNY Eye Institute, Syracuse, New York 13202, United States
| | - Xiaomeng Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Lianshui Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Jacob V Aranda
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,Department of Ophthalmology, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,SUNY Eye Institute, Syracuse, New York 13202, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
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Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, Polge C, Taillandier D, Attaix D, Friguet B, Maier AB, Butler-Browne G, Béchet D. Proteomics of muscle chronological ageing in post-menopausal women. BMC Genomics 2014; 15:1165. [PMID: 25532418 PMCID: PMC4523020 DOI: 10.1186/1471-2164-15-1165] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/16/2014] [Indexed: 12/18/2022] Open
Abstract
Background Muscle ageing contributes to both loss of functional autonomy and increased morbidity. Muscle atrophy accelerates after 50 years of age, but the mechanisms involved are complex and likely result from the alteration of a variety of interrelated functions. In order to better understand the molecular mechanisms underlying muscle chronological ageing in human, we have undertaken a top-down differential proteomic approach to identify novel biomarkers after the fifth decade of age. Results Muscle samples were compared between adult (56 years) and old (78 years) post-menopausal women. In addition to total muscle extracts, low-ionic strength extracts were investigated to remove high abundance myofibrillar proteins and improve the detection of low abundance proteins. Two-dimensional gel electrophoreses with overlapping IPGs were used to improve the separation of muscle proteins. Overall, 1919 protein spots were matched between all individuals, 95 were differentially expressed and identified by mass spectrometry, and they corresponded to 67 different proteins. Our results suggested important modifications in cytosolic, mitochondrial and lipid energy metabolism, which may relate to dysfunctions in old muscle force generation. A fraction of the differentially expressed proteins were linked to the sarcomere and cytoskeleton (myosin light-chains, troponin T, ankyrin repeat domain-containing protein-2, vinculin, four and a half LIM domain protein-3), which may account for alterations in contractile properties. In line with muscle contraction, we also identified proteins related to calcium signal transduction (calsequestrin-1, sarcalumenin, myozenin-1, annexins). Muscle ageing was further characterized by the differential regulation of several proteins implicated in cytoprotection (catalase, peroxiredoxins), ion homeostasis (carbonic anhydrases, selenium-binding protein 1) and detoxification (aldo-keto reductases, aldehyde dehydrogenases). Notably, many of the differentially expressed proteins were central for proteostasis, including heat shock proteins and proteins involved in proteolysis (valosin-containing protein, proteasome subunit beta type-4, mitochondrial elongation factor-Tu). Conclusions This study describes the most extensive proteomic analysis of muscle ageing in humans, and identified 34 new potential biomarkers. None of them were previously recognized as differentially expressed in old muscles, and each may represent a novel starting point to elucidate the mechanisms of muscle chronological ageing in humans.
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Affiliation(s)
- Marine Gueugneau
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France. .,Pôle Endocrinologie, Diabétologie et Nutrition, Institut de Recherches Expérimentales et Cliniques, Université Catholique de Louvain, B-1200, Brussels, Belgium.
| | - Cécile Coudy-Gandilhon
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Ophélie Gourbeyre
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Christophe Chambon
- INRA, Plateforme d'Exploration du Métabolisme, Composante Protéique, F-63122, Saint Genès Champanelle, France.
| | - Lydie Combaret
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Cécile Polge
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Daniel Taillandier
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Didier Attaix
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
| | - Bertrand Friguet
- UPMC Université Paris 06, UMR 8256, Biological Adaptation and Ageing - IBPS, CNRS-UMR 8256, INSERM U1164, Sorbonne Universités, F-75005, Paris, France.
| | - Andrea B Maier
- Department of Internal Medicine, Section of Gerontology and Geriatrics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Gillian Butler-Browne
- Institut de Myologie, Centre de Recherches en Myologie UMR 974 76, INSERM U974, CNRS FRE 3617, Sorbonne Universités, UPMC Université Paris 06, F-75013, Paris, France.
| | - Daniel Béchet
- INRA, UMR 1019, Centre de Recherche en Nutrition Humaine, Université d'Auvergne, F-63122, Saint Genès Champanelle, France. .,Clermont Université, Université d'Auvergne, F-63000, Clermont-Ferrand, France.
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Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma. Tumour Biol 2014; 36:939-51. [PMID: 25315187 DOI: 10.1007/s13277-014-2694-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/30/2014] [Indexed: 01/22/2023] Open
Abstract
Renal cell carcinoma (RCC) is one of the most common malignancies in adults, and there is still no acknowledged biomarker for its diagnosis, prognosis, recurrence monitoring, and treatment stratification. Besides, little is known about the post-translational modification (PTM) of proteins in RCC. Here, we performed quantitative proteomic analysis on 12 matched pairs of clear cell RCC (ccRCC) and adjacent kidney tissues using liquid chromatography-tandem mass spectrometry (nanoLCMS/MS) and Progenesis LC-MS software (label-free) to identify and quantify the dysregulated proteins. A total of 1872 and 1927 proteins were identified in ccRCC and adjacent kidney tissues, respectively. Among these proteins, 1037 proteins were quantified by Progenesis LC-MS, and 213 proteins were identified as dysregulated proteins between ccRCC and adjacent tissues. Pathway analysis using IPA, STRING, and David tools was performed, which demonstrated the enrichment of cancer-related signaling pathways and biological processes such as mitochondrial dysfunction, metabolic pathway, cell death, and acetylation. Dysregulation of two mitochondrial proteins, acetyl-CoA acetyltransferase 1 (ACAT1) and manganese superoxide dismutase (MnSOD) were selected and confirmed by Western blotting and immunohistochemistry assays using another 6 pairs of ccRCC and adjacent tissues. Further mass spectrometry analysis indicated that both ACAT1 and MnSOD had characterized acetylation at lysine residues, which is the first time to identify acetylation of ACAT1 and MnSOD in ccRCC. Collectively, these data revealed a number of dysregulated proteins and signaling pathways by label-free quantitative proteomic approach in RCC, which shed light on potential diagnostic or prognostic biomarkers and therapeutic molecular targets for clinical intervention of RCC.
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Holland A, Dowling P, Ohlendieck K. New pathobiochemical insights into dystrophinopathy from the proteomics of senescent mdx mouse muscle. Front Aging Neurosci 2014; 6:109. [PMID: 24917816 PMCID: PMC4042888 DOI: 10.3389/fnagi.2014.00109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/18/2014] [Indexed: 01/08/2023] Open
Abstract
Primary abnormalities in the dystrophin gene cause X-linked muscular dystrophy, a highly progressive muscle wasting disorder of childhood. A spontaneous animal model of Duchenne muscular dystrophy is the mdx mouse, which presents a highly interesting phenotype that exhibits considerable variations in the degree of fiber degeneration in different subtypes of muscles. The idea that aging exacerbates the dystrophic mdx phenotype, as previously indicated by a large number of biochemical and cell biological studies, was clearly confirmed by comparative muscle proteomics. Here we outline recent findings of age-dependent changes in the dystrophin-deficient muscle proteome and contrast these results with the previously established proteomic profile of sarcopenic muscle. Besides comparable perturbations of various biochemical functions, especially striking are similarities in the cellular stress response associated with a drastic up-regulation of small αB-crystallin-like heat shock proteins. Hence, the comparison of large-scale proteomic data sets of natural muscle aging with dystrophic sarcopenia promises to shed light on the differential effect of sarcopenia of old age vs. senescent abnormalities on a mutant dystrophic background.
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Affiliation(s)
- Ashling Holland
- Department of Biology, National University of Ireland Maynooth, Ireland
| | - Paul Dowling
- Department of Biology, National University of Ireland Maynooth, Ireland
| | - Kay Ohlendieck
- Department of Biology, National University of Ireland Maynooth, Ireland
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