1
|
Beller NC, Hummon AB. Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis. Mol Omics 2022; 18:579-590. [PMID: 35723214 PMCID: PMC9378559 DOI: 10.1039/d2mo00077f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The field of proteomics is continually improving, requiring the development of new quantitative methods. Stable isotope labeling in cell culture (SILAC) is a metabolic labeling technique originating in the early 2000s. By incorporating isotopically labeled amino acids into the media used for cell culture, unlabeled versus labeled cells can be differentiated by the mass spectrometer. Traditional SILAC labeling has been expanded to pulsed applications allowing for a new quantitative dimension of proteomics - temporal analysis. The complete introduction of Heavy SILAC labeling chased with surplus unlabeled medium mimics traditional pulse-chase experiments and allows for the loss of heavy signal to track proteomic changes over time. In a similar fashion, pulsed SILAC (pSILAC) monitors the initial incorporation of a heavy label across a period of time, which allows for the rate of protein label integration to be assessed. These innovative techniques have aided in inspiring numerous SILAC-based temporal and spatial labeling applications, including super SILAC, spike-in SILAC, spatial SILAC, and a revival in label multiplexing. This review reflects upon the evolution of SILAC and the pulsed SILAC application, introduces advances in SILAC labeling, and proposes future perspectives for this novel and exciting field.
Collapse
Affiliation(s)
- Nicole C Beller
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA, 43210.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA, 43210.
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA, 43210
| |
Collapse
|
2
|
Bøtker HE, Hausenloy D, Andreadou I, Antonucci S, Boengler K, Davidson SM, Deshwal S, Devaux Y, Di Lisa F, Di Sante M, Efentakis P, Femminò S, García-Dorado D, Giricz Z, Ibanez B, Iliodromitis E, Kaludercic N, Kleinbongard P, Neuhäuser M, Ovize M, Pagliaro P, Rahbek-Schmidt M, Ruiz-Meana M, Schlüter KD, Schulz R, Skyschally A, Wilder C, Yellon DM, Ferdinandy P, Heusch G. Practical guidelines for rigor and reproducibility in preclinical and clinical studies on cardioprotection. Basic Res Cardiol 2018; 113:39. [PMID: 30120595 PMCID: PMC6105267 DOI: 10.1007/s00395-018-0696-8] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/18/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Hans Erik Bøtker
- Department of Cardiology, Aarhus University Hospital, Palle-Juul Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Derek Hausenloy
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
- The National Institute of Health Research, University College London Hospitals Biomedial Research Centre, Research and Development, London, UK
- National Heart Research Institute Singapore, National Heart Centre, Singapore, Singapore
- Yon Loo Lin School of Medicine, National University Singapore, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Salvatore Antonucci
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Kerstin Boengler
- Institute for Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Sean M Davidson
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
| | - Soni Deshwal
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Fabio Di Lisa
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Moises Di Sante
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Panagiotis Efentakis
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Saveria Femminò
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - David García-Dorado
- Experimental Cardiology, Vall d'Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Zoltán Giricz
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Borja Ibanez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), IIS-Fundación Jiménez Díaz, CIBERCV, Madrid, Spain
| | - Efstathios Iliodromitis
- Second Department of Cardiology, Faculty of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Nina Kaludercic
- Department of Biomedical Sciences, CNR Institute of Neuroscience, University of Padova, Via Ugo Bassi 58/B, 35121, Padua, Italy
| | - Petra Kleinbongard
- Institute for Pathophysiology, West German Heart and Vascular Center, University of Essen Medical School, Essen, Germany
| | - Markus Neuhäuser
- Department of Mathematics and Technology, Koblenz University of Applied Science, Remagen, Germany
- Institute for Medical Informatics, Biometry, and Epidemiology, University Hospital Essen, Essen, Germany
| | - Michel Ovize
- Explorations Fonctionnelles Cardiovasculaires, Hôpital Louis Pradel, Lyon, France
- UMR, 1060 (CarMeN), Université Claude Bernard, Lyon1, Villeurbanne, France
| | - Pasquale Pagliaro
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - Michael Rahbek-Schmidt
- Department of Cardiology, Aarhus University Hospital, Palle-Juul Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Marisol Ruiz-Meana
- Experimental Cardiology, Vall d'Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d'Hebron, Pg. Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | | | - Rainer Schulz
- Institute for Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Andreas Skyschally
- Institute for Pathophysiology, West German Heart and Vascular Center, University of Essen Medical School, Essen, Germany
| | - Catherine Wilder
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
| | - Derek M Yellon
- The Hatter Cardiovascular Institute, University College London, 67 Chenies Mews, London, WC1E 6HX, UK
| | - Peter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Gerd Heusch
- Institute for Pathophysiology, West German Heart and Vascular Center, University of Essen Medical School, Essen, Germany.
| |
Collapse
|
3
|
Kleinbongard P, Gedik N, Kirca M, Stoian L, Frey U, Zandi A, Thielmann M, Jakob H, Peters J, Kamler M, Heusch G. Mitochondrial and Contractile Function of Human Right Atrial Tissue in Response to Remote Ischemic Conditioning. J Am Heart Assoc 2018; 7:e009540. [PMID: 30371229 PMCID: PMC6201459 DOI: 10.1161/jaha.118.009540] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/27/2018] [Indexed: 01/02/2023]
Abstract
Background Remote ischemic preconditioning ( RIPC ) by repeated brief cycles of limb ischemia/reperfusion attenuates myocardial ischemia/reperfusion injury. We aimed to identify a functional parameter reflecting the RIPC -induced protection in human. Therefore, we measured mitochondrial function in right atrial tissue and contractile function of isolated right atrial trabeculae before and during hypoxia/reoxygenation from patients undergoing coronary artery bypass grafting with RIPC or placebo, respectively. Methods and Results One hundred thirty-seven patients under isoflurane anesthesia underwent RIPC (3×5 minutes blood pressure cuff inflation on the left upper arm/5 minutes deflation, n=67) or placebo (cuff uninflated, n=70), and right atrial appendages were harvested before ischemic cardioplegic arrest. Myocardial protection by RIPC was assessed from serum troponin I/T concentrations over 72 hours after surgery. Atrial tissue was obtained for isolation of mitochondria ( RIPC /placebo: n=10/10). Trabeculae were dissected for contractile function measurements at baseline and after hypoxia/reoxygenation (60 min/30 min) and for western blot analysis after hypoxia/reoxygenation ( RIPC /placebo, n=57/60). Associated with cardioprotection by RIPC (26% decrease in the area under the curve of troponin I/T), mitochondrial adenosine diphosphate-stimulated complex I respiration (+10%), adenosine triphosphate production (+46%), and calcium retention capacity (+37%) were greater, whereas reactive oxygen species production (-24%) was less with RIPC than placebo. Contractile function was improved by RIPC (baseline, +7%; reoxygenation, +24%). Expression and phosphorylation of proteins, which have previously been associated with cardioprotection, were not different between RIPC and placebo. Conclusions Cardioprotection by RIPC goes along with improved mitochondrial and contractile function of human right atrial tissue. Clinical Trial Registration URL: https://www.clinicaltrials.gov . Unique identifier: NCT 01406678.
Collapse
Affiliation(s)
- Petra Kleinbongard
- Institut für PathophysiologieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Nilguen Gedik
- Institut für PathophysiologieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Mücella Kirca
- Institut für PathophysiologieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Leanda Stoian
- Institut für PathophysiologieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Ulrich Frey
- Klinik für Anästhesiologie und IntensivmedizinUniversitätsklinikum EssenGermany
| | - Afsaneh Zandi
- Herzchirurgie Essen‐HuttropWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Matthias Thielmann
- Klinik für Thorax‐ und Kardiovaskuläre ChirurgieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Heinz Jakob
- Klinik für Thorax‐ und Kardiovaskuläre ChirurgieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Jürgen Peters
- Klinik für Anästhesiologie und IntensivmedizinUniversitätsklinikum EssenGermany
| | - Markus Kamler
- Herzchirurgie Essen‐HuttropWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| | - Gerd Heusch
- Institut für PathophysiologieWestdeutsches Herz‐ und GefäßzentrumUniversitätsklinikum EssenGermany
| |
Collapse
|
4
|
Claydon AJ, Beynon R. Proteome dynamics: revisiting turnover with a global perspective. Mol Cell Proteomics 2012; 11:1551-65. [PMID: 23125033 DOI: 10.1074/mcp.o112.022186] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Although bulk protein turnover has been measured with the use of stable isotope labeled tracers for over half a century, it is only recently that the same approach has become applicable to the level of the proteome, permitting analysis of the turnover of many proteins instead of single proteins or an aggregated protein pool. The optimal experimental design for turnover studies is dependent on the nature of the biological system under study, which dictates the choice of precursor label, protein pool sampling strategy, and treatment of data. In this review we discuss different approaches and, in particular, explore how complexity in experimental design and data processing increases as we shift from unicellular to multicellular systems, in particular animals.
Collapse
Affiliation(s)
- Amy J Claydon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | | |
Collapse
|
5
|
Li L, Nelson CJ, Solheim C, Whelan J, Millar AH. Determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15N labeling of two-dimensional gel-separated protein spots. Mol Cell Proteomics 2012; 11:M111.010025. [PMID: 22215636 DOI: 10.1074/mcp.m111.010025] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. The control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. However, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and even when proteins accumulate it is unclear whether enhanced synthesis or decreased degradation is responsible. We have used a (15)N labeling strategy with inorganic nitrogen sources coupled to a two-dimensional fluorescence difference gel electrophoresis and mass spectrometry analysis of two-dimensional IEF/SDS-PAGE gel spots to define the rate of protein synthesis (K(S)) and degradation (K(D)) of Arabidopsis cell culture proteins. Through analysis of MALDI-TOF/TOF mass spectra from 120 protein spots, we were able to quantify K(S) and K(D) for 84 proteins across six functional groups and observe over 65-fold variation in protein degradation rates. K(S) and K(D) correlate with functional roles of the proteins in the cell and the time in the cell culture cycle. This approach is based on progressive (15)N labeling that is innocuous for the plant cells and, because it can be used to target analysis of proteins through the use of specific gel spots, it has broad applicability.
Collapse
Affiliation(s)
- Lei Li
- Australian Research Council Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks, M316, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | | | | | | |
Collapse
|
6
|
Aryal UK, Stöckel J, Welsh EA, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM. Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light. J Proteome Res 2011; 11:609-19. [PMID: 22060561 DOI: 10.1021/pr200959x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Understanding the dynamic nature of protein abundances provides insights into protein turnover not readily apparent from conventional, static mass spectrometry measurements. This level of data is particularly informative when surveying protein abundances in biological systems subjected to large perturbations or alterations in environment such as cyanobacteria. Our current analysis expands upon conventional proteomic approaches in cyanobacteria by measuring dynamic changes of the proteome using a (13)C(15)N-l-leucine metabolic labeling in Cyanothece ATCC51142. Metabolically labeled Cyanothece ATCC51142 cells grown under nitrogen-sufficient conditions in continuous light were monitored longitudinally for isotope incorporation over a 48 h period, revealing 414 proteins with dynamic changes in abundances. In particular, proteins involved in carbon fixation, pentose phosphate pathway, cellular protection, redox regulation, protein folding, assembly, and degradation showed higher levels of isotope incorporation, suggesting that these biochemical pathways are important for growth under continuous light. Calculation of relative isotope abundances (RIA) values allowed the measurement of actual active protein synthesis over time for different biochemical pathways under high light exposure. Overall results demonstrated the utility of "non-steady state" pulsed metabolic labeling for systems-wide dynamic quantification of the proteome in Cyanothece ATCC51142 that can also be applied to other cyanobacteria.
Collapse
Affiliation(s)
- Uma K Aryal
- Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Penque D. Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery. Proteomics Clin Appl 2008; 3:155-72. [DOI: 10.1002/prca.200800025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
8
|
Grussenmeyer T, Meili-Butz S, Dieterle T, Traunecker E, Carrel TP, Lefkovits I. Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing. J Proteome Res 2008; 7:5211-20. [PMID: 19367704 DOI: 10.1021/pr8005292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. It has been found that the silver-stained readout offers a convenient approach for quantitation if a linear range for gel loading is defined. In addition, a broad range of a 10-fold input (loading 20-200 microg per gel) fulfills the linearity criteria, although at the lowest input (20 microg) a portion of protein species will remain undetected. The method is reliable and reproducible within a range of 65-200 microg input. The normalization procedure using the sum of all spot intensities from a silver-stained 2D pattern has been shown to be less reliable than other approaches, namely, normalization through median or through involvement of interquartile range. A special refinement of the normalization through virtual segmentation of pattern, and calculation of normalization factor for each stratum provides highly satisfactory results. The presented results not only provide evidence for the usefulness of silver-stained gels for quantitative evaluation, but they are directly applicable to the research endeavor of monitoring alterations in cardiovascular pathophysiology.
Collapse
|
9
|
Doherty MK, Hammond DE, Clague MJ, Gaskell SJ, Beynon RJ. Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC. J Proteome Res 2008; 8:104-12. [DOI: 10.1021/pr800641v] [Citation(s) in RCA: 250] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Mary K. Doherty
- Proteomics and Functional Genomics Research Group, Department of Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdon, The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Crown Street, Liverpool L69 3BX, United Kingdom, and Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Dean E. Hammond
- Proteomics and Functional Genomics Research Group, Department of Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdon, The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Crown Street, Liverpool L69 3BX, United Kingdom, and Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael J. Clague
- Proteomics and Functional Genomics Research Group, Department of Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdon, The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Crown Street, Liverpool L69 3BX, United Kingdom, and Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Simon J. Gaskell
- Proteomics and Functional Genomics Research Group, Department of Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdon, The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Crown Street, Liverpool L69 3BX, United Kingdom, and Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Robert J. Beynon
- Proteomics and Functional Genomics Research Group, Department of Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdon, The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, Crown Street, Liverpool L69 3BX, United Kingdom, and Michael Barber Centre for Mass Spectrometry, Manchester Interdisciplinary Biocentre, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
10
|
Proteomik. ZEITSCHRIFT FUR HERZ THORAX UND GEFASSCHIRURGIE 2008. [DOI: 10.1007/s00398-008-0610-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|