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El‐Harasis MA, Quintana JA, Martinez‐Parachini JR, Jackson GG, Varghese BT, Yoneda ZT, Murphy BS, Crawford DM, Tomasek K, Su YR, Wells QS, Roden DM, Michaud GF, Saavedra P, Estrada JC, Richardson TD, Kanagasundram AN, Shen ST, Montgomery JA, Ellis CR, Crossley GH, Eberl M, Gillet L, Ziegler A, Shoemaker MB. Recurrence After Atrial Fibrillation Ablation and Investigational Biomarkers of Cardiac Remodeling. J Am Heart Assoc 2024; 13:e031029. [PMID: 38471835 PMCID: PMC11010019 DOI: 10.1161/jaha.123.031029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/23/2023] [Indexed: 03/14/2024]
Abstract
BACKGROUND Recurrence after atrial fibrillation (AF) ablation remains common. We evaluated the association between recurrence and levels of biomarkers of cardiac remodeling, and their ability to improve recurrence prediction when added to a clinical prediction model. METHODS AND RESULTS Blood samples collected before de novo catheter ablation were analyzed. Levels of bone morphogenetic protein-10, angiopoietin-2, fibroblast growth factor-23, insulin-like growth factor-binding protein-7, myosin-binding protein C3, growth differentiation factor-15, interleukin-6, N-terminal pro-brain natriuretic peptide, and high-sensitivity troponin T were measured. Recurrence was defined as ≥30 seconds of an atrial arrhythmia 3 to 12 months postablation. Multivariable logistic regression was performed using biomarker levels along with clinical covariates: APPLE score (Age >65 years, Persistent AF, imPaired eGFR [<60 ml/min/1.73m2], LA diameter ≥43 mm, EF <50%; which includes age, left atrial diameter, left ventricular ejection fraction, persistent atrial fibrillation, and estimated glomerular filtration rate), preablation rhythm, sex, height, body mass index, presence of an implanted continuous monitor, year of ablation, and additional linear ablation. A total of 1873 participants were included. A multivariable logistic regression showed an association between recurrence and levels of angiopoietin-2 (odds ratio, 1.08 [95% CI, 1.02-1.15], P=0.007) and interleukin-6 (odds ratio, 1.02 [95% CI, 1.003-1.03]; P=0.02). The area under the receiver operating characteristic curve of a model that only contained clinical predictors was 0.711. The addition of any of the 9 studied biomarkers to the predictive model did not result in a statistically significant improvement in the area under the receiver operating characteristic curve. CONCLUSIONS Higher angiopoietin-2 and interleukin-6 levels were associated with recurrence after atrial fibrillation ablation in multivariable modeling. However, the addition of biomarkers to a clinical prediction model did not significantly improve recurrence prediction.
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Affiliation(s)
- Majd A. El‐Harasis
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Joseph A. Quintana
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | | | - Gregory G. Jackson
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Bibin T. Varghese
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Zachary T. Yoneda
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Brittany S. Murphy
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Diane M. Crawford
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Kelsey Tomasek
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Yan Ru Su
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Quinn S. Wells
- Departments of Medicine, Pharmacology, and Biomedical InformaticsVanderbilt University Medical CenterNashvilleTN
| | - Dan M. Roden
- Departments of Medicine, Pharmacology, and Biomedical InformaticsVanderbilt University Medical CenterNashvilleTN
| | - Gregory F. Michaud
- Division of Cardiovascular Medicine, Massachusetts General HospitalBostonMA
| | - Pablo Saavedra
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Juan Carlos Estrada
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Travis D. Richardson
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | | | - Sharon T. Shen
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Jay A. Montgomery
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - Christopher R. Ellis
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
| | - George H. Crossley
- Division of Cardiovascular MedicineVanderbilt University Medical CenterNashvilleTN
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Diep AN, Schyns J, Gourzones C, Goffin E, Papadopoulos I, Moges S, Minner F, Ek O, Bonhomme G, Paridans M, Gillain N, Husson E, Garigliany M, Darcis G, Saegerman C, Desmecht D, Guillaume M, A F D, Bureau F, Gillet L. How do successive vaccinations and SARS-CoV-2 infections impact humoral immunity dynamics: An 18-month longitudinal study. J Infect 2024; 88:183-186. [PMID: 37981216 DOI: 10.1016/j.jinf.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Affiliation(s)
- A N Diep
- Biostatistics and Research Method Center - Public Health Department, Liège University, 4000 Liège, Belgium
| | - J Schyns
- Laboratory of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium; COVID-19 Platform, Liège University, 4000 Liège, Belgium
| | - C Gourzones
- COVID-19 Platform, Liège University, 4000 Liège, Belgium; Laboratory of Immunology-Vaccinology, FARAH, Liège University, 4000 Liège, Belgium
| | - E Goffin
- COVID-19 Platform, Liège University, 4000 Liège, Belgium; Laboratory of Immunology-Vaccinology, FARAH, Liège University, 4000 Liège, Belgium
| | - I Papadopoulos
- Biostatistics and Research Method Center - Public Health Department, Liège University, 4000 Liège, Belgium
| | - S Moges
- Biostatistics and Research Method Center - Public Health Department, Liège University, 4000 Liège, Belgium
| | - F Minner
- COVID-19 Platform, Liège University, 4000 Liège, Belgium
| | - O Ek
- COVID-19 Platform, Liège University, 4000 Liège, Belgium
| | - G Bonhomme
- Department of Pathology, FARAH, Liège University, 4000 Liège, Belgium
| | - M Paridans
- From Biostatistics to Health Promotion Research Unit, Public Health Department, Liège University, 4000 Liège, Belgium
| | - N Gillain
- Biostatistics and Research Method Center - Public Health Department, Liège University, 4000 Liège, Belgium; From Biostatistics to Health Promotion Research Unit, Public Health Department, Liège University, 4000 Liège, Belgium
| | - E Husson
- Biostatistics and Research Method Center - Public Health Department, Liège University, 4000 Liège, Belgium; From Biostatistics to Health Promotion Research Unit, Public Health Department, Liège University, 4000 Liège, Belgium
| | - M Garigliany
- Department of Pathology, FARAH, Liège University, 4000 Liège, Belgium
| | - G Darcis
- Infectious Diseases Department, University Hospital of Liège, 4000 Liège, Belgium
| | - C Saegerman
- Research Unit in Epidemiology and Risk Analysis applied to Veterinary Sciences, FARAH, Liège University, 4000 Liège, Belgium
| | - D Desmecht
- Department of Pathology, FARAH, Liège University, 4000 Liège, Belgium
| | - M Guillaume
- From Biostatistics to Health Promotion Research Unit, Public Health Department, Liège University, 4000 Liège, Belgium
| | - Donneau A F
- Biostatistics and Research Method Center - Public Health Department, Liège University, 4000 Liège, Belgium
| | - F Bureau
- Laboratory of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium; COVID-19 Platform, Liège University, 4000 Liège, Belgium
| | - L Gillet
- COVID-19 Platform, Liège University, 4000 Liège, Belgium; Laboratory of Immunology-Vaccinology, FARAH, Liège University, 4000 Liège, Belgium.
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3
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Zila N, Eichhoff OM, Steiner I, Mohr T, Bileck A, Cheng PF, Leitner A, Gillet L, Sajic T, Goetze S, Friedrich B, Bortel P, Strobl J, Reitermaier R, Hogan SA, Martínez Gómez JM, Staeger R, Tuchmann F, Peters S, Stary G, Kuttke M, Elbe-Bürger A, Hoeller C, Kunstfeld R, Weninger W, Wollscheid B, Dummer R, French LE, Gerner C, Aebersold R, Levesque MP, Paulitschke V. Proteomic Profiling of Advanced Melanoma Patients to Predict Therapeutic Response to Anti-PD-1 Therapy. Clin Cancer Res 2024; 30:159-175. [PMID: 37861398 DOI: 10.1158/1078-0432.ccr-23-0562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/17/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
PURPOSE Despite high clinical need, there are no biomarkers that accurately predict the response of patients with metastatic melanoma to anti-PD-1 therapy. EXPERIMENTAL DESIGN In this multicenter study, we applied protein depletion and enrichment methods prior to various proteomic techniques to analyze a serum discovery cohort (n = 56) and three independent serum validation cohorts (n = 80, n = 12, n = 17). Further validation analyses by literature and survival analysis followed. RESULTS We identified several significantly regulated proteins as well as biological processes such as neutrophil degranulation, cell-substrate adhesion, and extracellular matrix organization. Analysis of the three independent serum validation cohorts confirmed the significant differences between responders (R) and nonresponders (NR) observed in the initial discovery cohort. In addition, literature-based validation highlighted 30 markers overlapping with previously published signatures. Survival analysis using the TCGA database showed that overexpression of 17 of the markers we identified correlated with lower overall survival in patients with melanoma. CONCLUSIONS Ultimately, this multilayered serum analysis led to a potential marker signature with 10 key markers significantly altered in at least two independent serum cohorts: CRP, LYVE1, SAA2, C1RL, CFHR3, LBP, LDHB, S100A8, S100A9, and SAA1, which will serve as the basis for further investigation. In addition to patient serum, we analyzed primary melanoma tumor cells from NR and found a potential marker signature with four key markers: LAMC1, PXDN, SERPINE1, and VCAN.
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Affiliation(s)
- Nina Zila
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Division of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Ossia M Eichhoff
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Irene Steiner
- Center for Medical Data Science, Institute of Medical Statistics, Medical University of Vienna, Vienna, Austria
| | - Thomas Mohr
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Phil F Cheng
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tatjana Sajic
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- ETH PHRT Swiss Multi-Omics Center (SMOC), Zurich, Switzerland
| | - Betty Friedrich
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Patricia Bortel
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Johanna Strobl
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - René Reitermaier
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Sabrina A Hogan
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ramon Staeger
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Felix Tuchmann
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Sophie Peters
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Georg Stary
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Mario Kuttke
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | | | - Christoph Hoeller
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Rainer Kunstfeld
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lars E French
- Department of Dermatology and Allergy University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | - Christopher Gerner
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
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4
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Weith M, Großbach J, Clement‐Ziza M, Gillet L, Rodríguez‐López M, Marguerat S, Workman CT, Picotti P, Bähler J, Aebersold R, Beyer A. Genetic effects on molecular network states explain complex traits. Mol Syst Biol 2023; 19:e11493. [PMID: 37485750 PMCID: PMC10407735 DOI: 10.15252/msb.202211493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023] Open
Abstract
The complexity of many cellular and organismal traits results from the integration of genetic and environmental factors via molecular networks. Network structure and effect propagation are best understood at the level of functional modules, but so far, no concept has been established to include the global network state. Here, we show when and how genetic perturbations lead to molecular changes that are confined to small parts of a network versus when they lead to modulation of network states. Integrating multi-omics profiling of genetically heterogeneous budding and fission yeast strains with an array of cellular traits identified a central state transition of the yeast molecular network that is related to PKA and TOR (PT) signaling. Genetic variants affecting this PT state globally shifted the molecular network along a single-dimensional axis, thereby modulating processes including energy and amino acid metabolism, transcription, translation, cell cycle control, and cellular stress response. We propose that genetic effects can propagate through large parts of molecular networks because of the functional requirement to centrally coordinate the activity of fundamental cellular processes.
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Affiliation(s)
- Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | - Jan Großbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | | | - Ludovic Gillet
- Department of BiologyInstitute of Molecular Systems Biology, ETH ZürichZürichSwitzerland
| | - María Rodríguez‐López
- Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Samuel Marguerat
- Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Christopher T Workman
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Paola Picotti
- Department of BiologyInstitute of Molecular Systems Biology, ETH ZürichZürichSwitzerland
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems Biology, ETH ZürichZürichSwitzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
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5
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Vanhersecke L, Gillet L, Le Douget JE, Schmauch B, Maussion C, Italiano A, Soubeyran I, Le Loarer F. 10P Deep learning-based prediction of patient’s TLS status from HE images in pan-cancer cohort. Immuno-Oncology and Technology 2022. [DOI: 10.1016/j.iotech.2022.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Schnabel RB, Marinelli EA, Arbelo E, Boriani G, Boveda S, Buckley CM, Camm AJ, Casadei B, Chua W, Dagres N, de Melis M, Desteghe L, Diederichsen SZ, Duncker D, Eckardt L, Eisert C, Engler D, Fabritz L, Freedman B, Gillet L, Goette A, Guasch E, Svendsen JH, Hatem SN, Haeusler KG, Healey JS, Heidbuchel H, Hindricks G, Hobbs FDR, Hübner T, Kotecha D, Krekler M, Leclercq C, Lewalter T, Lin H, Linz D, Lip GYH, Løchen ML, Lucassen W, Malaczynska-Rajpold K, Massberg S, Merino JL, Meyer R, Mont L, Myers MC, Neubeck L, Niiranen T, Oeff M, Oldgren J, Potpara TS, Psaroudakis G, Pürerfellner H, Ravens U, Rienstra M, Rivard L, Scherr D, Schotten U, Shah D, Sinner MF, Smolnik R, Steinbeck G, Steven D, Svennberg E, Thomas D, True Hills M, van Gelder IC, Vardar B, Palà E, Wakili R, Wegscheider K, Wieloch M, Willems S, Witt H, Ziegler A, Daniel Zink M, Kirchhof P. Early diagnosis and better rhythm management to improve outcomes in patients with atrial fibrillation: the 8th AFNET/EHRA consensus conference. Europace 2022; 25:6-27. [PMID: 35894842 PMCID: PMC9907557 DOI: 10.1093/europace/euac062] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Despite marked progress in the management of atrial fibrillation (AF), detecting AF remains difficult and AF-related complications cause unacceptable morbidity and mortality even on optimal current therapy. This document summarizes the key outcomes of the 8th AFNET/EHRA Consensus Conference of the Atrial Fibrillation NETwork (AFNET) and the European Heart Rhythm Association (EHRA). Eighty-three international experts met in Hamburg for 2 days in October 2021. Results of the interdisciplinary, hybrid discussions in breakout groups and the plenary based on recently published and unpublished observations are summarized in this consensus paper to support improved care for patients with AF by guiding prevention, individualized management, and research strategies. The main outcomes are (i) new evidence supports a simple, scalable, and pragmatic population-based AF screening pathway; (ii) rhythm management is evolving from therapy aimed at improving symptoms to an integrated domain in the prevention of AF-related outcomes, especially in patients with recently diagnosed AF; (iii) improved characterization of atrial cardiomyopathy may help to identify patients in need for therapy; (iv) standardized assessment of cognitive function in patients with AF could lead to improvement in patient outcomes; and (v) artificial intelligence (AI) can support all of the above aims, but requires advanced interdisciplinary knowledge and collaboration as well as a better medico-legal framework. Implementation of new evidence-based approaches to AF screening and rhythm management can improve outcomes in patients with AF. Additional benefits are possible with further efforts to identify and target atrial cardiomyopathy and cognitive impairment, which can be facilitated by AI.
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Affiliation(s)
- Renate B Schnabel
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Department of Cardiology, University Heart & Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,German Centre for Cardiovascular Research (DZHK) partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | | | - Elena Arbelo
- Arrhythmia Section, Cardiology Department, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain,IDIBAPS, Institut d'Investigació August Pi i Sunyer, Barcelona, Spain,CIBERCV, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Giuseppe Boriani
- Cardiology Division, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Polyclinic of Modena, Modena, Italy
| | - Serge Boveda
- Cardiology—Heart Rhythm Management Department, Clinique Pasteur, 45 Avenue de Lombez, 31076 Toulouse, France,Universiteit Ziekenhuis, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - A John Camm
- Cardiology Clinical Academic Group, Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Barbara Casadei
- RDM, Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Winnie Chua
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
| | - Nikolaos Dagres
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany
| | - Mirko de Melis
- Medtronic Bakken Research Center, Maastricht, The Netherlands
| | - Lien Desteghe
- Research Group Cardiovascular Diseases, University of Antwerp, Antwerp, Belgium,Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium,Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium,Heart Centre Hasselt, Jessa Hospital, Hasselt, Belgium
| | - Søren Zöga Diederichsen
- Department of Cardiology, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - David Duncker
- Hannover Heart Rhythm Center, Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Lars Eckardt
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Division of Electrophysiology, Department of Cardiology and Angiology, Münster, Germany
| | | | - Daniel Engler
- Department of Cardiology, University Heart & Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,German Centre for Cardiovascular Research (DZHK) partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Larissa Fabritz
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Department of Cardiology, University Heart & Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,German Centre for Cardiovascular Research (DZHK) partner site Hamburg/Kiel/Lübeck, Hamburg, Germany,Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK,University Center of Cardiovascular Science Hamburg, Hamburg, Germany
| | - Ben Freedman
- Heart Research Institute, The University of Sydney, Sydney, Australia
| | | | - Andreas Goette
- Atrial Fibrillation Network (AFNET), Muenster, Germany,St Vincenz Hospital, Paderborn, Germany
| | - Eduard Guasch
- Arrhythmia Section, Cardiology Department, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain,IDIBAPS, Institut d'Investigació August Pi i Sunyer, Barcelona, Spain,CIBERCV, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jesper Hastrup Svendsen
- Department of Cardiology, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Karl Georg Haeusler
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Department of Neurology, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Jeff S Healey
- Population Health Research Institute, McMaster University Hamilton, ON, Canada
| | - Hein Heidbuchel
- Research Group Cardiovascular Diseases, University of Antwerp, Antwerp, Belgium,Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium
| | - Gerhard Hindricks
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, Leipzig, Germany
| | | | | | - Dipak Kotecha
- University of Birmingham & University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | | | - Thorsten Lewalter
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Hospital Munich South, Department of Cardiology, Munich, Germany,Department of Cardiology, University of Bonn, Bonn, Germany
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dominik Linz
- Department of Cardiology, Maastricht University Medical Center and Cardiovascular Research Institute Maastricht, Maastricht, The Netherlands,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gregory Y H Lip
- Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, UK,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Maja Lisa Løchen
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Wim Lucassen
- Amsterdam UMC (location AMC), Department General Practice, Amsterdam, The Netherlands
| | | | - Steffen Massberg
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany,German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Jose L Merino
- Arrhythmia & Robotic EP Unit, La Paz University Hospital, IDIPAZ, Madrid, Spain
| | | | - Lluıs Mont
- Arrhythmia Section, Cardiology Department, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain,IDIBAPS, Institut d'Investigació August Pi i Sunyer, Barcelona, Spain,CIBERCV, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | | | - Lis Neubeck
- Arrhythmia & Robotic EP Unit, La Paz University Hospital, IDIPAZ, Madrid, Spain
| | - Teemu Niiranen
- Medtronic, Dublin, Ireland,Centre for Cardiovascular Health Edinburgh Napier University, Edinburgh, UK
| | - Michael Oeff
- Atrial Fibrillation Network (AFNET), Muenster, Germany
| | - Jonas Oldgren
- University of Turku and Turku University Hospital, Turku, Finland
| | | | - George Psaroudakis
- Uppsala Clinical Research Center and Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Helmut Pürerfellner
- School of Medicine, Belgrade University, Cardiology Clinic, University Clinical Centre of Serbia, Belgrade, Serbia
| | - Ursula Ravens
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Bayer AG, Leverkusen, Germany
| | - Michiel Rienstra
- Ordensklinikum Linz, Elisabethinen, Cardiological Department, Linz, Austria
| | - Lena Rivard
- Institute of Experimental Cardiovascular Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Daniel Scherr
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ulrich Schotten
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Montreal Heart Institute, University of Montreal, Montreal, Canada
| | - Dipen Shah
- Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Moritz F Sinner
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Amsterdam UMC (location AMC), Department General Practice, Amsterdam, The Netherlands,Royal Brompton Hospital, London, UK
| | | | - Gerhard Steinbeck
- Atrial Fibrillation Network (AFNET), Muenster, Germany,MUMC+, Maastricht, The Netherlands
| | - Daniel Steven
- Atrial Fibrillation Network (AFNET), Muenster, Germany,University Hospital of Geneva, Cardiac Electrophysiology Unit, Geneva, Switzerland
| | - Emma Svennberg
- Center for Cardiology at Clinic Starnberg, Starnberg, Germany
| | - Dierk Thomas
- Atrial Fibrillation Network (AFNET), Muenster, Germany,University Hospital Cologne, Heart Center, Department of Electrophysiology, Cologne, Germany,Karolinska Institutet, Department of Medicine Huddinge, Karolinska University Hospital, Stockholm, Sweden,Department of Cardiology, Medical University Hospital, Heidelberg, Germany
| | - Mellanie True Hills
- HCR (Heidelberg Center for Heart Rhythm Disorders), Medical University Hospital Heidelberg, Heidelberg, Germany
| | - Isabelle C van Gelder
- DZHK (German Center for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Burcu Vardar
- Uppsala Clinical Research Center and Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Elena Palà
- StopAfib.org, American Foundation for Women’s Health, Decatur, TX, USA
| | - Reza Wakili
- Atrial Fibrillation Network (AFNET), Muenster, Germany,Department of Cardiology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Karl Wegscheider
- Atrial Fibrillation Network (AFNET), Muenster, Germany,German Centre for Cardiovascular Research (DZHK) partner site Hamburg/Kiel/Lübeck, Hamburg, Germany,Neurovascular Research Laboratory, Vall d’Hebron Institute of Research (VHIR), Autonomous University of Barcelona, Barcelona, Spain
| | - Mattias Wieloch
- Department of Cardiology and Vascular Medicine, Westgerman Heart and Vascular Center, University of Duisburg-Essen, Essen, Germany,Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Germany
| | - Stephan Willems
- Atrial Fibrillation Network (AFNET), Muenster, Germany,German Centre for Cardiovascular Research (DZHK) partner site Hamburg/Kiel/Lübeck, Hamburg, Germany,Department of Coagulation Disorders, Skane University Hospital, Lund University, Malmö, Sweden
| | | | | | - Matthias Daniel Zink
- Asklepios Hospital St Georg, Department of Cardiology and Internal Intensive Care Medicine, Faculty of Medicine, Semmelweis University Campus Hamburg, Hamburg, Germany
| | - Paulus Kirchhof
- Corresponding author. Tel: +49 40 7410 52438; Fax: +49 40 7410 55862. E-mail address:
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7
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Grossbach J, Gillet L, Clément‐Ziza M, Schmalohr CL, Schubert OT, Schütter M, Mawer JSP, Barnes CA, Bludau I, Weith M, Tessarz P, Graef M, Aebersold R, Beyer A. The impact of genomic variation on protein phosphorylation states and regulatory networks. Mol Syst Biol 2022; 18:e10712. [PMID: 35574625 PMCID: PMC9109056 DOI: 10.15252/msb.202110712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high‐quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well‐defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation.
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Affiliation(s)
- Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Ludovic Gillet
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
| | - Mathieu Clément‐Ziza
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Lesaffre International Marcq‐en‐Barœul France
| | - Corinna L Schmalohr
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Olga T Schubert
- Department of Human Genetics University of California, Los Angeles Los Angeles CA USA
| | | | | | | | - Isabell Bludau
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany
| | - Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Peter Tessarz
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Martin Graef
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Ruedi Aebersold
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Faculty of Science University of Zurich Zurich Switzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Institute for Genetics Faculty of Mathematics and Natural Sciences University of Cologne Cologne Germany
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8
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Fossati A, Frommelt F, Uliana F, Martelli C, Vizovisek M, Gillet L, Collins B, Gstaiger M, Aebersold R. System-Wide Profiling of Protein Complexes Via Size Exclusion Chromatography-Mass Spectrometry (SEC-MS). Methods Mol Biol 2021; 2259:269-294. [PMID: 33687722 DOI: 10.1007/978-1-0716-1178-4_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In living cells, most proteins are organized in stable or transient functional assemblies, protein complexes, which control a multitude of vital cellular processes such as cell cycle progression, metabolism, and signal transduction. Over several decades, specific protein complexes have been analyzed by structural biology methods, initially X-ray crystallography and more recently single particle cryoEM. In parallel, mass spectrometry (MS)-based methods including in vitro affinity-purification coupled to MS or in vivo protein proximity-dependent labeling methods have proven particularly effective to detect complexes, thus nominating new assemblies for structural analysis. Those approaches, however, are either of limited in throughput or require specifically engineered protein systems.In this chapter, we present protocols for a workflow that supports the parallel analysis of multiple complexes from the same biological sample with respect to abundance, subunit composition, and stoichiometry. It consists of the separation of native complexes by size-exclusion chromatography (SEC) and the subsequent mass spectrometric analysis of the proteins in consecutive SEC fractions. In particular, we describe (1) optimized conditions to achieve native protein complex separation by SEC, (2) the preparation of the SEC fractions for MS analysis, (3) the acquisition of the MS data at high throughput via SWATH/DIA (data-independent analysis) mass spectrometry and short chromatographic gradients, and (4) a set of bioinformatic tools for the targeted analysis of protein complexes. Altogether, the parallel measurement of a high number of complexes from a single biological sample results in unprecedented system-level insights into the remodeling of cellular protein complexes in response to perturbations of a broad range of cellular systems.
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Affiliation(s)
- Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Matej Vizovisek
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Ben Collins
- School of Biological Sciences, Queen's University of Belfast, Belfast, UK
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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9
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Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 2020; 38:374. [DOI: 10.1038/s41587-020-0457-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. iScience 2019; 21:664-680. [PMID: 31733513 PMCID: PMC6889472 DOI: 10.1016/j.isci.2019.10.059] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022] Open
Abstract
Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses. High-quality NCI-60 proteotypes created using pressure cycling technology and SWATH-MS Proteotypes improve drug response prediction in multi-omics regression analysis ∼3000 measured proteins allow investigation into protein complex stoichiometry CellMinerCDB (discover.nci.nih.gov/cellminercdb) portal allows dataset exploration
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Affiliation(s)
- Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Augustin Luna
- cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ching Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Zhicheng Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Wei Liu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Yaoting Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Huanhuan Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Michael P Menden
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany; Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Chao Xu
- Faculty of Software, Fujian Normal University, Fuzhou, China
| | - Laurence Calzone
- Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France
| | - Loredana Martignetti
- Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech 75005, Paris, France
| | - Chiara Auwerx
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Marija Buljan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Murat Iskar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ran Bi
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Jiangnan Zhang
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Huanhuan Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Chenhuan Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Qing Zhong
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; Cancer Data Science Group, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia
| | | | - Uwe Schmitt
- Scientific IT Services, ETH Zurich, Zurich, Switzerland
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Dr., Atlanta, GA 30332, USA
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P. R. China; Guomics Laboratory of Proteomic Big Data, Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Mathew J Garnett
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chris Sander
- cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
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11
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Zhu Y, Weiss T, Zhang Q, Sun R, Wang B, Yi X, Wu Z, Gao H, Cai X, Ruan G, Zhu T, Xu C, Lou S, Yu X, Gillet L, Blattmann P, Saba K, Fankhauser CD, Schmid MB, Rutishauser D, Ljubicic J, Christiansen A, Fritz C, Rupp NJ, Poyet C, Rushing E, Weller M, Roth P, Haralambieva E, Hofer S, Chen C, Jochum W, Gao X, Teng X, Chen L, Zhong Q, Wild PJ, Aebersold R, Guo T. High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification. Mol Oncol 2019; 13:2305-2328. [PMID: 31495056 PMCID: PMC6822243 DOI: 10.1002/1878-0261.12570] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/09/2019] [Accepted: 09/03/2019] [Indexed: 11/06/2022] Open
Abstract
Formalin‐fixed, paraffin‐embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT)‐SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B‐cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh‐frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.
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Affiliation(s)
- Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Rui Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Bo Wang
- Department of Pathology, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Yi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zhicheng Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Huanhuan Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Guan Ruan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tiansheng Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chao Xu
- College of Mathematics and Informatics, Digital Fujian Institute of Big Data Security Technology, Fujian Normal University, Fuzhou, China
| | - Sai Lou
- Phase I Clinical Research Center, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xiaoyan Yu
- Department of Pathology, The Second Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Karim Saba
- Department of Urology, University Hospital Zurich, University of Zurich, Switzerland
| | | | - Michael B Schmid
- Department of Urology, University Hospital Zurich, University of Zurich, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Jelena Ljubicic
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Ailsa Christiansen
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Christine Fritz
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Cedric Poyet
- Department of Urology, University Hospital Zurich, University of Zurich, Switzerland
| | - Elisabeth Rushing
- Department of Neuropathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Patrick Roth
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, University of Zurich, Switzerland
| | - Eugenia Haralambieva
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland
| | - Silvia Hofer
- Division of Medical Oncology, Lucerne Cantonal Hospital and Cancer Center, Switzerland
| | | | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, Switzerland
| | - Xiaofei Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Lirong Chen
- Department of Pathology, The Second Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, China
| | - Qing Zhong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland.,Children's Medical Research Institute, University of Sydney, Australia
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Switzerland.,Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,Faculty of Science, University of Zurich, Switzerland
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
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12
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Rougier JS, Essers MC, Gillet L, Guichard S, Sonntag S, Shmerling D, Abriel H. A Distinct Pool of Na v1.5 Channels at the Lateral Membrane of Murine Ventricular Cardiomyocytes. Front Physiol 2019; 10:834. [PMID: 31333492 PMCID: PMC6619393 DOI: 10.3389/fphys.2019.00834] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/17/2019] [Indexed: 01/22/2023] Open
Abstract
Background: In cardiac ventricular muscle cells, the presence of voltage-gated sodium channels Nav1.5 at the lateral membrane depends in part on the interaction between the dystrophin–syntrophin complex and the Nav1.5 C-terminal PDZ-domain-binding sequence Ser-Ile-Val (SIV motif). α1-Syntrophin, a PDZ-domain adaptor protein, mediates the interaction between Nav1.5 and dystrophin at the lateral membrane of cardiac cells. Using the cell-attached patch-clamp approach on cardiomyocytes expressing Nav1.5 in which the SIV motif is deleted (ΔSIV), sodium current (INa) recordings from the lateral membrane revealed a SIV-motif-independent INa. Since immunostaining has suggested that Nav1.5 is expressed in transverse (T-) tubules, this remaining INa might be carried by channels in the T-tubules. Of note, a recent study using heterologous expression systems showed that α1-syntrophin also interacts with the Nav1.5 N-terminus, which may explain the SIV-motif independent INa at the lateral membrane of cardiomyocytes. Aim: To address the role of α1-syntrophin in regulating the INa at the lateral membrane of cardiac cells. Methods and Results: Patch-clamp experiments in cell-attached configuration were performed on the lateral membranes of wild-type, α1-syntrophin knockdown, and ΔSIV ventricular mouse cardiomyocytes. Compared to wild-type, a reduction of the lateral INa was observed in myocytes from α1-syntrophin knockdown hearts. Similar to ΔSIV myocytes, a remaining INa was still recorded. In addition, cell-attached INa recordings from lateral membrane did not differ significantly between non-detubulated and detubulated ΔSIV cardiomyocytes. Lastly, we obtained evidence suggesting that cell-attached patch-clamp experiments on the lateral membrane cannot record currents carried by channels in T-tubules such as calcium channels. Conclusion: Altogether, these results suggest the presence of a sub-pool of sodium channels at the lateral membrane of cardiomyocytes that is independent of α1-syntrophin and the PDZ-binding motif of Nav1.5, located in membrane domains outside of T-tubules. The question of a T-tubular pool of Nav1.5 channels, however, remains open.
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Affiliation(s)
| | - Maria C Essers
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Ludovic Gillet
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.,Pain Center, Department of Anesthesiology, Lausanne University Hospital, Lausanne, Switzerland.,Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Sabrina Guichard
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | | | | | - Hugues Abriel
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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Chevalier M, Vermij SH, Wyler K, Gillet L, Keller I, Abriel H. Corrigendum: Transcriptomic analyses of murine ventricular cardiomyocytes. Sci Data 2018; 5:180216. [PMID: 30299437 PMCID: PMC6176784 DOI: 10.1038/sdata.2018.216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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14
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Chevalier M, Vermij SH, Wyler K, Gillet L, Keller I, Abriel H. Transcriptomic analyses of murine ventricular cardiomyocytes. Sci Data 2018; 5:180170. [PMID: 30129933 PMCID: PMC6103258 DOI: 10.1038/sdata.2018.170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
Mice are used universally as model organisms for studying heart physiology, and a plethora of genetically modified mouse models exist to study cardiac disease. Transcriptomic data for whole-heart tissue are available, but not yet for isolated ventricular cardiomyocytes. Our lab therefore collected comprehensive RNA-seq data from wildtype murine ventricular cardiomyocytes as well as from knockout models of the ion channel regulators CASK, dystrophin, and SAP97. We also elucidate ion channel expression from wild-type cells to help forward the debate about which ion channels are expressed in cardiomyocytes. Researchers studying the heart, and especially cardiac arrhythmias, may benefit from these cardiomyocyte-specific transcriptomic data to assess expression of genes of interest.
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Affiliation(s)
- Morgan Chevalier
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Sarah H Vermij
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Kurt Wyler
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, 3012 Bern, Switzerland
| | - Ludovic Gillet
- Pain Center, Department of Anesthesiology, University Hospital Center (CHUV) and Faculty of Biology and Medicine (FBM), University of Lausanne, 1011 Lausanne, Switzerland.,Department of Fundamental Neurosciences, Faculty of Biology and Medicine (FBM), University of Lausanne, 1005 Lausanne, Switzerland
| | - Irene Keller
- Department for BioMedical Research and Swiss Institute of Bioinformatics, University of Bern, 3007 Bern, Switzerland
| | - Hugues Abriel
- Ion Channels and Channelopathies Laboratory, Institute for Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
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Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol 2018; 14:e8126. [PMID: 30104418 PMCID: PMC6088389 DOI: 10.15252/msb.20178126] [Citation(s) in RCA: 563] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/16/2023] Open
Abstract
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH-MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH-MS data, a strategy based on peptide-centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH-MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH-MS data using peptide-centric scoring. Furthermore, concepts on how to improve SWATH-MS data acquisition, potential trade-offs of parameter settings and alternative data analysis strategies are discussed.
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Affiliation(s)
- Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sabine Amon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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16
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Delguste M, Koehler M, Gillet L, Alsteens D. Topography imaging of herpesvirus in native condition using atomic force microscopy. Clin Microbiol Infect 2018; 24:610-611. [DOI: 10.1016/j.cmi.2018.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/15/2018] [Accepted: 03/12/2018] [Indexed: 10/17/2022]
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17
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Tschager T, Rösch S, Gillet L, Widmayer P. A better scoring model for de novo peptide sequencing: the symmetric difference between explained and measured masses. Algorithms Mol Biol 2017; 12:12. [PMID: 28603547 PMCID: PMC5464308 DOI: 10.1186/s13015-017-0104-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/19/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Given a peptide as a string of amino acids, the masses of all its prefixes and suffixes can be found by a trivial linear scan through the amino acid masses. The inverse problem is the idealde novopeptide sequencing problem: Given all prefix and suffix masses, determine the string of amino acids. In biological reality, the given masses are measured in a lab experiment, and measurements by necessity are noisy. The (real, noisy) de novo peptide sequencing problem therefore has a noisy input: a few of the prefix and suffix masses of the peptide are missing and a few other masses are given in addition. For this setting, we ask for an amino acid string that explains the given masses as accurately as possible. RESULTS Past approaches interpreted accuracy by searching for a string that explains as many masses as possible. We feel, however, that it is not only bad to not explain a mass that appears, but also to explain a mass that does not appear. We propose to minimize the symmetric difference between the set of given masses and the set of masses that the string explains. For this new optimization problem, we propose an efficient algorithm that computes both the best and the k best solutions. Proof-of-concept experiments on measurements of synthesized peptides show that our approach leads to better results compared to finding a string that explains as many given masses as possible. CONCLUSIONS We conclude that considering the symmetric difference as optimization goal can improve the identification rates for de novo peptide sequencing. A preliminary version of this work has been presented at WABI 2016.
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18
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Tonus C, Connan D, Waroux O, Vandenhove B, Wayet J, Gillet L, Desmecht D, Antoine N, Ectors F, Grobet L. Cryopreservation of chicken primordial germ cells by vitrification and slow freezing: A comparative study. Theriogenology 2017; 88:197-206. [DOI: 10.1016/j.theriogenology.2016.09.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 11/25/2022]
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19
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Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nat Methods 2016; 13:777-83. [PMID: 27479329 PMCID: PMC5008461 DOI: 10.1038/nmeth.3954] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 06/14/2016] [Indexed: 12/16/2022]
Abstract
Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets.
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Affiliation(s)
- Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Giuseppe D'Agostino
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Matteo Zanella
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Pedro Navarro
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Lars Malmström
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,S3IT, University of Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
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20
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Roels E, Dourcy M, Holopainen S, Rajamäki MM, Gillet L, Ehlers B, Clercx C. No Evidence of Herpesvirus Infection in West Highland White Terriers With Canine Idiopathic Pulmonary Fibrosis. Vet Pathol 2016; 53:1210-1212. [PMID: 27106742 DOI: 10.1177/0300985816641991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In humans, horses, and rodents, an association between pulmonary fibrotic disorders and gammaherpesvirus infection has been suggested. In dogs, canine idiopathic pulmonary fibrosis (CIPF), a progressive fibrotic lung disease of unknown origin and poorly understood pathophysiology, has been reported to occur in West Highland white terriers (WHWTs). The present study investigated the potential association between CIPF and herpesvirus infection. A PCR assay, using a mixture of degenerate and deoxyinosine-substituted primers targeting highly conserved regions of the DNA polymerase gene (DPOL) of herpesviruses, was applied on both lung and blood samples from WHWTs affected with CIPF and controls. Herpesvirus DPOL sequence could not be amplified from any of 46 lung samples (28 affected WHWTs and 18 control dogs of various breeds) and 38 blood samples (19 CIPF WHWTs and 19 control age-matched WHWTs) included. An association between CIPF and herpesvirus infection is therefore unlikely. Investigation of other causes of the disease is warranted.
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Affiliation(s)
- E Roels
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - M Dourcy
- Department of Infectious and Parasitic Diseases, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - S Holopainen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - M M Rajamäki
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - L Gillet
- Department of Infectious and Parasitic Diseases, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - B Ehlers
- Robert Koch-Institute, Berlin, Germany
| | - C Clercx
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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21
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Roger S, Gillet L, Le Guennec JY, Besson P. Voltage-gated sodium channels and cancer: is excitability their primary role? Front Pharmacol 2015; 6:152. [PMID: 26283962 PMCID: PMC4518325 DOI: 10.3389/fphar.2015.00152] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/09/2015] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium channels (NaV) are molecular characteristics of excitable cells. Their activation, triggered by membrane depolarization, generates transient sodium currents that initiate action potentials in neurons and muscle cells. Sodium currents were discovered by Hodgkin and Huxley using the voltage clamp technique and reported in their landmark series of papers in 1952. It was only in the 1980's that sodium channel proteins from excitable membranes were molecularly characterized by Catterall and his collaborators. Non-excitable cells can also express NaV channels in physiological conditions as well as in pathological conditions. These NaV channels can sustain biological roles that are not related to the generation of action potentials. Interestingly, it is likely that the abnormal expression of NaV in pathological tissues can reflect the re-expression of a fetal phenotype. This is especially true in epithelial cancer cells for which these channels have been identified and sodium currents recorded, while it was not the case for cells from the cognate normal tissues. In cancers, the functional activity of NaV appeared to be involved in regulating the proliferative, migrative, and invasive properties of cells. This review is aimed at addressing the non-excitable roles of NaV channels with a specific emphasis in the regulation of cancer cell biology.
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Affiliation(s)
- Sébastien Roger
- Inserm UMR1069, Nutrition, Croissance et Cancer, Université François-Rabelais de Tours Tours, France ; Département de Physiologie Animale, UFR Sciences and Techniques, Université François-Rabelais de Tours Tours, France
| | - Ludovic Gillet
- Department of Clinical Research, University of Bern Bern, Switzerland
| | | | - Pierre Besson
- Inserm UMR1069, Nutrition, Croissance et Cancer, Université François-Rabelais de Tours Tours, France
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22
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Driffort V, Gillet L, Bon E, Marionneau-Lambot S, Oullier T, Joulin V, Collin C, Pagès JC, Jourdan ML, Chevalier S, Bougnoux P, Le Guennec JY, Besson P, Roger S. Ranolazine inhibits NaV1.5-mediated breast cancer cell invasiveness and lung colonization. Mol Cancer 2014; 13:264. [PMID: 25496128 PMCID: PMC4295566 DOI: 10.1186/1476-4598-13-264] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/03/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Na(V)1.5 voltage-gated sodium channels are abnormally expressed in breast tumours and their expression level is associated with metastatic occurrence and patients' death. In breast cancer cells, Na(V)1.5 activity promotes the proteolytic degradation of the extracellular matrix and enhances cell invasiveness. FINDINGS In this study, we showed that the extinction of Na(V)1.5 expression in human breast cancer cells almost completely abrogated lung colonisation in immunodepressed mice (NMRI nude). Furthermore, we demonstrated that ranolazine (50 μM) inhibited Na(V)1.5 currents in breast cancer cells and reduced Na(V)1.5-related cancer cell invasiveness in vitro. In vivo, the injection of ranolazine (50 mg/kg/day) significantly reduced lung colonisation by Na(V)1.5-expressing human breast cancer cells. CONCLUSIONS Taken together, our results demonstrate the importance of Na(V)1.5 in the metastatic colonisation of organs by breast cancer cells and indicate that small molecules interfering with Na(V) activity, such as ranolazine, may represent powerful pharmacological tools to inhibit metastatic development and improve cancer treatments.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Pierre Besson
- Inserm UMR1069, Nutrition, Croissance et Cancer, Université François-Rabelais de Tours, 10 Boulevard Tonnellé, Tours 37032, France.
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23
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Gillet L, Rougier JS, Shy D, Sonntag S, Mougenot N, Essers M, Shmerling D, Balse E, Hatem SN, Abriel H. Cardiac-specific ablation of synapse-associated protein SAP97 in mice decreases potassium currents but not sodium current. Heart Rhythm 2014; 12:181-92. [PMID: 25447080 DOI: 10.1016/j.hrthm.2014.09.057] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Membrane-associated guanylate kinase (MAGUK) proteins are important determinants of ion channel organization in the plasma membrane. In the heart, the MAGUK protein SAP97, encoded by the DLG1 gene, interacts with several ion channels via their PDZ domain-binding motif and regulates their function and localization. OBJECTIVE The purpose of this study was to assess in vivo the role of SAP97 in the heart by generating a genetically modified mouse model in which SAP97 is suppressed exclusively in cardiomyocytes. METHODS SAP97(fl/fl) mice were generated by inserting loxP sequences flanking exons 1-3 of the SAP97 gene. SAP97(fl/fl) mice were crossed with αMHC-Cre mice to generate αMHC-Cre/SAP97(fl/fl) mice, thus resulting in a cardiomyocyte-specific deletion of SAP97. Quantitative reverse transcriptase-polymerase chain reaction, western blots, and immunostaining were performed to measure mRNA and protein expression levels, and ion channel localization. The patch-clamp technique was used to record ion currents and action potentials. Echocardiography and surface ECGs were performed on anesthetized mice. RESULTS Action potential duration was greatly prolonged in αMHC-Cre/SAP97(fl/fl) cardiomyocytes compared to SAP97(fl/fl) controls, but maximal upstroke velocity was unchanged. This was consistent with the decreases observed in IK1, Ito, and IKur potassium currents and the absence of effect on the sodium current INa. Surface ECG revealed an increased corrected QT interval in αMHC-Cre/SAP97(fl/fl) mice. CONCLUSION These data suggest that ablation of SAP97 in the mouse heart mainly alters potassium channel function. Based on the important role of SAP97 in regulating the QT interval, DLG1 may be a susceptibility gene to be investigated in patients with congenital long QT syndrome.
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Affiliation(s)
- Ludovic Gillet
- Department of Clinical Research, University of Bern, Bern, Switzerland.
| | | | - Diana Shy
- Department of Clinical Research, University of Bern, Bern, Switzerland
| | | | - Nathalie Mougenot
- Plateau d'Expérimentation Coeur, Muscle, Vaisseaux, Université Pierre et Marie Curie, Paris, France
| | - Maria Essers
- Department of Clinical Research, University of Bern, Bern, Switzerland
| | | | - Elise Balse
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR S1166, Institut de Recherche Sur Les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France; Institute of Cardiometabolism & Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Stéphane N Hatem
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR S1166, Institut de Recherche Sur Les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, UMR S1166, Paris, France; Institute of Cardiometabolism & Nutrition, ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Hugues Abriel
- Department of Clinical Research, University of Bern, Bern, Switzerland.
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Affiliation(s)
- Diana Shy
- From the Department of Clinical Research, Ion Channel Research Group, University of Bern, Bern, Switzerland
| | - Ludovic Gillet
- From the Department of Clinical Research, Ion Channel Research Group, University of Bern, Bern, Switzerland
| | - Hugues Abriel
- From the Department of Clinical Research, Ion Channel Research Group, University of Bern, Bern, Switzerland
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25
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Gillet L, Shy D, Abriel H. Elucidating sodium channel NaV1.5 clustering in cardiac myocytes using super-resolution techniques. Cardiovasc Res 2014; 104:231-3. [DOI: 10.1093/cvr/cvu221] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Shy D, Gillet L, Ogrodnik J, Albesa M, Verkerk AO, Wolswinkel R, Rougier JS, Barc J, Essers MC, Syam N, Marsman RF, van Mil AM, Rotman S, Redon R, Bezzina CR, Remme CA, Abriel H. PDZ domain-binding motif regulates cardiomyocyte compartment-specific NaV1.5 channel expression and function. Circulation 2014; 130:147-60. [PMID: 24895455 DOI: 10.1161/circulationaha.113.007852] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Sodium channel NaV1.5 underlies cardiac excitability and conduction. The last 3 residues of NaV1.5 (Ser-Ile-Val) constitute a PDZ domain-binding motif that interacts with PDZ proteins such as syntrophins and SAP97 at different locations within the cardiomyocyte, thus defining distinct pools of NaV1.5 multiprotein complexes. Here, we explored the in vivo and clinical impact of this motif through characterization of mutant mice and genetic screening of patients. METHODS AND RESULTS To investigate in vivo the regulatory role of this motif, we generated knock-in mice lacking the SIV domain (ΔSIV). ΔSIV mice displayed reduced NaV1.5 expression and sodium current (INa), specifically at the lateral myocyte membrane, whereas NaV1.5 expression and INa at the intercalated disks were unaffected. Optical mapping of ΔSIV hearts revealed that ventricular conduction velocity was preferentially decreased in the transversal direction to myocardial fiber orientation, leading to increased anisotropy of ventricular conduction. Internalization of wild-type and ΔSIV channels was unchanged in HEK293 cells. However, the proteasome inhibitor MG132 rescued ΔSIV INa, suggesting that the SIV motif is important for regulation of NaV1.5 degradation. A missense mutation within the SIV motif (p.V2016M) was identified in a patient with Brugada syndrome. The mutation decreased NaV1.5 cell surface expression and INa when expressed in HEK293 cells. CONCLUSIONS Our results demonstrate the in vivo significance of the PDZ domain-binding motif in the correct expression of NaV1.5 at the lateral cardiomyocyte membrane and underline the functional role of lateral NaV1.5 in ventricular conduction. Furthermore, we reveal a clinical relevance of the SIV motif in cardiac disease.
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Affiliation(s)
- Diana Shy
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Ludovic Gillet
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Jakob Ogrodnik
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Maxime Albesa
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Arie O Verkerk
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Rianne Wolswinkel
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Jean-Sébastien Rougier
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Julien Barc
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Maria C Essers
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Ninda Syam
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Roos F Marsman
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Anneke M van Mil
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Samuel Rotman
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Richard Redon
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Connie R Bezzina
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Carol Ann Remme
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.)
| | - Hugues Abriel
- From the Department of Clinical Research, University of Bern, Bern, Switzerland (D.S., L.G., J.O., M.A., J.-S.R., M.C.E., N.S., H.A.); Department of Anatomy, Embryology and Physiology (A.O.V.) and Department of Clinical and Experimental Cardiology (R.W., J.B., R.F.M., C.R.B., C.A.R.), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; ICIN-Netherlands Heart Institute, Utrecht, The Netherlands (J.B.); Center for Human and Clinical Genetics, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands (A.M.v.M.); Institute of Pathology, University of Lausanne, Lausanne, Switzerland (S.R.); Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche 1087, L'Institut du Thorax, Nantes, France (R.R.); Centre National de la Recherche Scientifique Unité Mixte de Recherche 6291, Nantes, France (R.R.); Université de Nantes, Nantes, France (R.R.); and Centre Hospitalier Universitaire Nantes, L'Institut du Thorax, Service de Cardiologie, Nantes, France (R.R.).
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Gillet L, Shy D, Sonntag S, Rougier JS, Verkerk A, Essers M, Marsman R, Shmerling D, Bezzina C, Remme CA, Abriel H. 0150: PDZ domain proteins interacting with Nav1.5 differentially regulate Nav1.5 channel pools in mouse cardiomyocytes. Archives of Cardiovascular Diseases Supplements 2014. [DOI: 10.1016/s1878-6480(14)71373-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
Evaluation of: Noorman M, Hakim S, Kessler E et al. Remodeling of the cardiac sodium channel, connexin43, and plakoglobin at the intercalated disk in patients with arrhythmogenic cardiomyopathy. Heart Rhythm 10(3), 412-419 (2013). Arrhythmogenic cardiomyopathy (AC) is a heart muscle disease characterized by a progressive replacement of the ventricular myocardium with adipose and fibrous tissue. This disease is often associated with mutations in genes encoding desmosomal proteins in the majority of patients. Based on results obtained from recent experimental models, a disturbed distribution of gap junction proteins and cardiac sodium channels may also be observed in AC phenotypes, secondary to desmosomal dysfunction. The study from Noorman et al. examined heart sections from patients diagnosed with AC and performed immunohistochemical analyses of N-cadherin, PKP2, PKG, Cx43 and the cardiac sodium channel NaV1.5. Altered expression/distribution of Cx43, PKG and NaV1.5 was found in most cases of patients with AC. The altered expression and/or distribution of NaV1.5 channels in AC hearts may play a mechanistic role in the arrhythmias leading to sudden cardiac death in AC patients. Thus, NaV1.5 should be considered as a supplemental element in the evaluation of risk stratification and management strategies. However, additional experiments are required to clearly understand the mechanisms leading to AC phenotypes.
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Affiliation(s)
- Ludovic Gillet
- Department of Clinical Research, Ion Channel Research Group, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
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Shy D, Gillet L, Abriel H. Cardiac sodium channel NaV1.5 distribution in myocytes via interacting proteins: the multiple pool model. Biochim Biophys Acta 2012; 1833:886-94. [PMID: 23123192 DOI: 10.1016/j.bbamcr.2012.10.026] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/18/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022]
Abstract
The cardiac sodium current (INa) is responsible for the rapid depolarization of cardiac cells, thus allowing for their contraction. It is also involved in regulating the duration of the cardiac action potential (AP) and propagation of the impulse throughout the myocardium. Cardiac INa is generated by the voltage-gated Na(+) channel, NaV1.5, a 2016-residue protein which forms the pore of the channel. Over the past years, hundreds of mutations in SCN5A, the human gene coding for NaV1.5, have been linked to many cardiac electrical disorders, including the congenital and acquired long QT syndrome, Brugada syndrome, conduction slowing, sick sinus syndrome, atrial fibrillation, and dilated cardiomyopathy. Similar to many membrane proteins, NaV1.5 has been found to be regulated by several interacting proteins. In some cases, these different proteins, which reside in distinct membrane compartments (i.e. lateral membrane vs. intercalated disks), have been shown to interact with the same regulatory domain of NaV1.5, thus suggesting that several pools of NaV1.5 channels may co-exist in cardiac cells. The aim of this review article is to summarize the recent works that demonstrate its interaction with regulatory proteins and illustrate the model that the sodium channel NaV1.5 resides in distinct and different pools in cardiac cells. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.
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Affiliation(s)
- Diana Shy
- Department of Clinical Research, University of Bern, Bern, Switzerland
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Veillard F, Saidi A, Burden RE, Scott CJ, Gillet L, Lecaille F, Lalmanach G. Cysteine cathepsins S and L modulate anti-angiogenic activities of human endostatin. J Biol Chem 2011; 286:37158-67. [PMID: 21896479 DOI: 10.1074/jbc.m111.284869] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Human endostatin, a potent anti-angiogenic protein, is generated by release of the C terminus of collagen XVIII. Here, we propose that cysteine cathepsins are involved in both the liberation and activation of bioactive endostatin fragments, thus regulating their anti-angiogenic properties. Cathepsins B, S, and L efficiently cleaved in vitro FRET peptides that encompass the hinge region corresponding to the N terminus of endostatin. However, in human umbilical vein endothelial cell-based assays, silencing of cathepsins S and L, but not cathepsin B, impaired the generation of the ∼22-kDa endostatin species. Moreover, cathepsins L and S released two peptides from endostatin with increased angiostatic properties and both encompassing the NGR sequence, a vasculature homing motif. The G10T peptide (residues 1455-1464: collagen XVIII numbering) displayed compelling anti-proliferative (EC(50) = 0.23 nm) and proapoptotic properties. G10T inhibited aminopeptidase N (APN/CD13) and reduced tube formation of endothelial cells in a manner similar to bestatin. Combination of G10T with bestatin resulted in no further increase in anti-angiogenic activity. Taken together, these data suggest that endostatin-derived peptides may represent novel molecular links between cathepsins and APN/CD13 in the regulation of angiogenesis.
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Affiliation(s)
- Florian Veillard
- INSERM U618, Protéases et Vectorisation Pulmonaires, Université François Rabelais, 37000 Tours, France
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Brisson L, Gillet L, Calaghan S, Besson P, Le Guennec JY, Roger S, Gore J. NaV1.5 enhances breast cancer cell invasiveness by increasing NHE1-dependent H+ efflux in caveolae. Oncogene 2010; 30:2070-6. [DOI: 10.1038/onc.2010.574] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Thirion M, Machiels B, Farnir F, Donofrio G, Gillet L, Dewals B, Vanderplasschen A. Bovine herpesvirus 4 ORF73 is dispensable for virus growth in vitro, but is essential for virus persistence in vivo. J Gen Virol 2010; 91:2574-84. [DOI: 10.1099/vir.0.023192-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Depla M, Uzbekov R, Hourioux C, Blanchard E, Le Gouge A, Gillet L, Roingeard P. Ultrastructural and quantitative analysis of the lipid droplet clustering induced by hepatitis C virus core protein. Cell Mol Life Sci 2010; 67:3151-61. [PMID: 20422251 DOI: 10.1007/s00018-010-0373-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 04/01/2010] [Accepted: 04/08/2010] [Indexed: 12/16/2022]
Abstract
Hepatitis C virus (HCV) release is linked to the formation of lipid droplet (LD) clusters in the perinuclear area of infected cells, induced by the core protein. We used electron microscopy (EM) to monitor and compare the number and size of LD in cells producing the mature and immature forms of the HCV core protein, and 3D EM to reconstruct whole cells producing the mature core protein. Only the mature protein coated the LD and induced their clustering and emergence from endoplasmic reticulum membranes enriched in this protein. We found no particular association between LD clusters and the centrosome in reconstructed cells. The LD clustering induced by the mature core protein was associated with an increase in LD synthesis potentially due, at least in part, to the ability of this protein to coat the LD. These observations provide useful information for further studies of the mechanisms involved in HCV-induced steatosis.
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Affiliation(s)
- Marion Depla
- INSERM U966, Faculté de Médecine, Université François Rabelais, CHRU de Tours, 10 boulevard Tonnellé, 37032, Tours Cedex, France
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Roger S, Gillet L, Baroja-Mazo A, Surprenant A, Pelegrin P. C-terminal calmodulin-binding motif differentially controls human and rat P2X7 receptor current facilitation. J Biol Chem 2010; 285:17514-24. [PMID: 20378545 DOI: 10.1074/jbc.m109.053082] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P2X(7) receptors (P2X(7)R) are ATP-gated calcium-permeable cationic channels structurally unique among the P2X family by their much longer intracellular C-terminal tail. P2X(7)Rs show several unusual biophysical properties, in particular marked facilitation of currents and leftward shift in agonist affinity in response to repeated or prolonged agonist applications. We previously found the facilitation at rat P2X(7)R resulted from a Ca(2+)-calmodulin-dependent process and a distinct calcium-independent process. However, P2X(7)Rs show striking species differences; thus, this study compared the properties of ATP-evoked facilitation of currents in HEK293 cells transiently expressing the human or rat P2X(7)R as well as rat/human, human/rat chimeric, and mutated P2X(7)Rs. Facilitation at the human P2X(7)R was 5-fold slower than at the rat P2X(7)R. Facilitation did not resulting from an increase of receptor addressing the plasma membrane. We found the human P2X(7)R shows only calcium-independent facilitation with no evidence for calmodulin-dependent processes, nor does it contain the novel 1-5-16 calmodulin binding domain present in the C terminus of rat P2X(7)R. Replacement of three critical residues of this binding domain from the rat into the human P2X(7)R (T541I, C552S, and G559V) reconstituted the Ca(2+)-calmodulin-dependent facilitation, leaving the calcium-independent facilitation unaltered. The leftward shift in the ATP concentration-response curve with repeated agonist applications appears to be a property of the calcium-independent facilitation process because it was not altered in any of the chimeric or mutated P2X(7)Rs. The absence of Ca(2+)-dependent facilitation at the human P2X(7)R may represent a protective adaptation of the innate immune response in which P2X(7)R plays significant roles.
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Affiliation(s)
- Sébastien Roger
- Inserm U921, Université François Rabelais de Tours, 10 Boulevard Tonnellé, 37032 Tours, France.
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Gillet L, Roger S, Bougnoux P, Le Guennec JY, Besson P. Beneficial effects of omega-3 long-chain fatty acids in breast cancer and cardiovascular diseases: voltage-gated sodium channels as a common feature? Biochimie 2010; 93:4-6. [PMID: 20167245 DOI: 10.1016/j.biochi.2010.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
Abstract
Cancers are among the leading causes of death worldwide. Voltage-gated sodium channels, among other ion channels, appear as new molecular players in epithelial cancers. Highly metastatic breast cancer cells express Na(V)1.5, the main isoform expressed in cardiac cells, where the current generated by the flux of sodium ions is responsible for the excitability. Breast cancer cells are not excitable and the protein activity regulates cell invasiveness, through the modulation of activity of acidic cathepsins, a characteristic involved in the metastatic phenotype. Interestingly, it is known that ω-3 LC-PUFA can exert beneficial effects by preventing post-myocardial infarction arrhythmias and by reducing the incidence of metastatic breast cancer. In this review, we compare the effects of some ω-3 LC-PUFA on Na(V)1.5 expressed in both cardiac and MDA-MB-231 breast cancer cells. We propose that some of the effects of ω-3 LC-PUFA act through common mechanisms involved in both diseases.
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Affiliation(s)
- Ludovic Gillet
- Inserm U921, Nutrition Croissance Cancer, Université François-Rabelais, Faculté de médecine, 10 Bd Tonnellé, 37032 Tours Cedex, France
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Gillet L, Roger S, Besson P, Lecaille F, Gore J, Bougnoux P, Lalmanach G, Le Guennec JY. Voltage-gated Sodium Channel Activity Promotes Cysteine Cathepsin-dependent Invasiveness and Colony Growth of Human Cancer Cells. J Biol Chem 2009; 284:8680-91. [PMID: 19176528 DOI: 10.1074/jbc.m806891200] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Voltage-gated sodium channels (Na(V)) are functionally expressed in highly metastatic cancer cells derived from nonexcitable epithelial tissues (breast, prostate, lung, and cervix). MDA-MB-231 breast cancer cells express functional sodium channel complexes, consisting of Na(V)1.5 and associated auxiliary beta-subunits, that are responsible for a sustained inward sodium current at the membrane potential. Although these channels do not regulate cellular multiplication or migration, their inhibition by the specific blocker tetrodotoxin impairs both the extracellular gelatinolytic activity (monitored with DQ-gelatin) and cell invasiveness leading to the attenuation of colony growth and cell spreading in three-dimensional Matrigel-composed matrices. MDA-MB-231 cells express functional cysteine cathepsins, which we found play a predominant role ( approximately 65%) in cancer invasiveness. Matrigel invasion is significantly decreased in the presence of specific inhibitors of cathepsins B and S (CA-074 and Z-FL-COCHO, respectively), and co-application of tetrodotoxin does not further reduce cell invasion. This suggests that cathepsins B and S are involved in invasiveness and that their proteolytic activity partly depends on Na(V) function. Inhibiting Na(V) has no consequence for cathepsins at the transcription, translation, and secretion levels. However, Na(V) activity leads to an intracellular alkalinization and a perimembrane acidification favorable for the extracellular activity of these acidic proteases. We propose that Na(v) enhance the invasiveness of cancer cells by favoring the pH-dependent activity of cysteine cathepsins. This general mechanism could lead to the identification of new targets allowing the therapeutic prevention of metastases.
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Affiliation(s)
- Ludovic Gillet
- INSERM U921, Nutrition, Croissance et Cancer, and INSERM U618, Protéases et Vectorisation Pulmonaires, Université François Rabelais, FacultédeMédecine, 37032 Tours, France
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Tran TA, Gillet L, Roger S, Besson P, White E, Le Guennec JY. Non-anti-mitotic concentrations of taxol reduce breast cancer cell invasiveness. Biochem Biophys Res Commun 2008; 379:304-8. [PMID: 19111674 DOI: 10.1016/j.bbrc.2008.12.073] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 12/10/2008] [Indexed: 11/26/2022]
Abstract
Taxol is widely used in breast cancer chemotherapy. Its effects are primarily attributed to its anti-mitotic activity. Microtubule perturbators also exert antimetastatic activities which cannot be explained solely by the inhibition of proliferation. Voltage-dependent sodium channels (Na(V)) are abnormally expressed in the highly metastatic breast cancer cell line MDA-MB-231 and not in MDA-MB-468 cell line. Inhibiting Na(V) activity with tetrodotoxin is responsible for an approximately 0.4-fold reduction of MDA-MB-231 cell invasiveness. In this study, we focused on the effect of a single, 2-h application of 10 nM taxol on the two cell lines MDA-MB-231 and MDA-MB-468. At this concentration, taxol had no effect on proliferation after 7 days and on migration in any cell line. However it led to a 40% reduction of transwell invasion of MDA-MB-231 cells. There was no additive effect when taxol and tetrodotoxin were simultaneously applied. Na(V) activity, as assessed by patch-clamp, indicates that it was changed by taxol pre-treatment. We conclude that taxol can exert anti-tumoral activities, in cells expressing Na(V), at low doses that have no effect on cell proliferation. This effect might be due to a modulation of signalling pathways involving sodium channels.
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Thireau J, Poisson D, Zhang BL, Gillet L, Le Pécheur M, Andres C, London J, Babuty D. Increased heart rate variability in mice overexpressing the Cu/Zn superoxide dismutase. Free Radic Biol Med 2008; 45:396-403. [PMID: 18513493 DOI: 10.1016/j.freeradbiomed.2008.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 03/25/2008] [Accepted: 04/08/2008] [Indexed: 11/23/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) is implicated in various pathological conditions including Down's syndrome, neurodegenerative diseases, and afflictions of the autonomic nervous system (ANS). To assess the SOD1 contribution to ANS dysfunction, especially its influence on cardiac regulation, we studied the heart rate variability (HRV) and cardiac arrhythmias in conscious 12-month-old male and female transgenic mice for the human SOD1 gene (TghSOD1). TghSOD1 mice presented heart rate reduction as compared with control FVB/N individuals. All HRV parameters reflecting parasympathetic activity were increased in TghSOD1. Pharmacological studies confirmed that the parasympathetic tone was exacerbated and the sympathetic pathway was functional in TghSOD1 mice. A high frequency of atrioventricular block and premature ventricular contractions was observed in TghSOD1. By biochemical assays we found that SOD1 activities were multiplied by 9 and 4 respectively in the heart and brainstem of transgenic mice. A twofold decrease in cholinesterase activity was observed in the heart but not in the brainstem. We demonstrate that SOD1 overexpression induces an ANS dysfunction by an exacerbated vagal tone that may be related to impaired cardiac activity of the cholinesterases and may explain the high occurrence of arrhythmias.
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Affiliation(s)
- Jérôme Thireau
- Centre National de Recherche Scientifique, Unité Mixte de Recherche 6542 Laboratoire de Physiologie des Cellules Cardiaques et Vasculaires, Université François-Rabelais, Tours, France
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Gillet L, Roger S, Besson P, Gore J, Bougnoux P, Lecaille F, Lalmanach G, Le Guennec J. Voltage-gated sodium channels activity promotes cysteine cathepsins-dependent invasiveness of human cancer cell lines. EJC Suppl 2008. [DOI: 10.1016/s1359-6349(08)71448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Daix V, Schroeder H, Praet N, Georgin JP, Chiappino I, Gillet L, de Fays K, Decrem Y, Leboulle G, Godfroid E, Bollen A, Pastoret PP, Gern L, Sharp PM, Vanderplasschen A. Ixodes ticks belonging to the Ixodes ricinus complex encode a family of anticomplement proteins. Insect Mol Biol 2007; 16:155-66. [PMID: 17298559 DOI: 10.1111/j.1365-2583.2006.00710.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The alternative pathway of complement is an important innate defence against pathogens including ticks. This component of the immune system has selected for pathogens that have evolved countermeasures. Recently, a salivary protein able to inhibit the alternative pathway was cloned from the American tick Ixodes scapularis (Valenzuela et al., 2000; J. Biol. Chem. 275, 18717-18723). Here, we isolated two different sequences, similar to Isac, from the transcriptome of I. ricinus salivary glands. Expression of these sequences revealed that they both encode secreted proteins able to inhibit the complement alternative pathway. These proteins, called I. ricinus anticomplement (IRAC) protein I and II, are coexpressed constitutively in I. ricinus salivary glands and are upregulated during blood feeding. Also, we demonstrated that they are the products of different genes and not of alleles of the same locus. Finally, phylogenetic analyses demonstrate that ticks belonging to the Ixodes ricinus complex encode a family of relatively small anticomplement molecules undergoing diversification by positive Darwinian selection.
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Affiliation(s)
- V Daix
- Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Looze Y, Gillet L, Deconinck M, Leonis J, Gelbcke M. Carbon-13 Nuclear Magnetic Resonance Study of 5′-Substituted-5′-Oeoxyadenosine Derivatives. ANAL LETT 2006. [DOI: 10.1080/00032718008078008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Dewals B, Boudry C, Gillet L, Markine-Goriaynoff N, de Leval L, Haig DM, Vanderplasschen A. Cloning of the genome of Alcelaphine herpesvirus 1 as an infectious and pathogenic bacterial artificial chromosome. J Gen Virol 2006; 87:509-517. [PMID: 16476972 DOI: 10.1099/vir.0.81465-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alcelaphine herpesvirus 1 (AlHV-1), carried asymptomatically by wildebeest, causes malignant catarrhal fever (MCF) following cross-species transmission to a variety of susceptible species of the order Artiodactyla. The study of MCF pathogenesis has been impeded by an inability to produce recombinant virus, mainly due to the fact that AlHV-1 becomes attenuated during passage in culture. In this study, these difficulties were overcome by cloning the entire AlHV-1 genome as a stable, infectious and pathogenic bacterial artificial chromosome (BAC). A modified loxP-flanked BAC cassette was inserted in one of the two large non-coding regions of the AlHV-1 genome. This insertion allowed the production of an AlHV-1 BAC clone stably maintained in bacteria and able to regenerate virions when transfected into permissive cells. The loxP-flanked BAC cassette was excised from the genome of reconstituted virions by growing them in permissive cells stably expressing Cre recombinase. Importantly, BAC-derived AlHV-1 virions replicated comparably to the virulent (low-passage) AlHV-1 parental strain and induced MCF in rabbits that was indistinguishable from that of the virulent parental strain. The availability of the AlHV-1 BAC is an important advance for the study of MCF that will allow the identification of viral genes involved in MCF pathogenesis, as well as the production of attenuated recombinant candidate vaccines.
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Affiliation(s)
- B Dewals
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - C Boudry
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - L Gillet
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - N Markine-Goriaynoff
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - L de Leval
- Department of Pathology, Faculty of Medicine, University of Liège, B-4000 Liège, Belgium
| | - D M Haig
- The Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK
| | - A Vanderplasschen
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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Cejka P, Mojas N, Gillet L, Schär P, Jiricny J. Homologous recombination rescues mismatch-repair-dependent cytotoxicity of S(N)1-type methylating agents in S. cerevisiae. Curr Biol 2006; 15:1395-400. [PMID: 16085492 DOI: 10.1016/j.cub.2005.07.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 06/13/2005] [Accepted: 06/15/2005] [Indexed: 11/30/2022]
Abstract
Resistance of mammalian cells to S(N)1-type methylating agents such as N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) generally arises through increased expression of methylguanine methyltransferase (MGMT), which reverts the cytotoxic O(6)-methylguanine ((Me)G) to guanine, or through inactivation of the mismatch repair (MMR) system, which triggers cell death through aberrant processing of (Me)G/T mispairs generated during DNA replication when MGMT capacity is exceeded. Given that MMR and (Me)G-detoxifying proteins are functionally conserved through evolution, and that MMR-deficient Escherichia coli dam(-) strains are also resistant to MNNG, the finding that MMR status did not affect the sensitivity of Saccharomyces cerevisiae to MNNG was unexpected. Because (Me)G residues in DNA trigger homologous recombination (HR), we wondered whether the efficient HR in S. cerevisiae might alleviate the cytotoxic effects of (Me)G processing. We now show that HR inactivation sensitizes S. cerevisiae to MNNG and that, as in human cells, defects in the MMR genes MLH1 and MSH2 rescue this sensitivity. Inactivation of the EXO1 gene, which encodes the only exonuclease implicated in MMR to date, failed to rescue the hypersensitivity, which implies that scExo1 is not involved in the processing of (Me)G residues by the S. cerevisiae MMR system.
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Affiliation(s)
- Petr Cejka
- Institute of Molecular Cancer Research, University of Zürich, August Forel-Strasse 7, CH-8008 Zürich, Switzerland
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Bona C, Dewals B, Wiggers L, Coudijzer K, Vanderplasschen A, Gillet L. Short Communication: Pasteurization of Milk Abolishes Bovine Herpesvirus 4 Infectivity. J Dairy Sci 2005; 88:3079-83. [PMID: 16107396 DOI: 10.3168/jds.s0022-0302(05)72989-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bovine herpesvirus 4 (BoHV-4) is a gammaherpesvirus highly prevalent in the cattle population that has been isolated from the milk and the serum of healthy infected cows. Several studies reported the sensitivity and the permissiveness of some human cells to BoHV-4 infection. Moreover, our recent study demonstrated that some human cells sensitive but not permissive to BoHV-4 support a persistent infection protecting them from tumor necrosis factor-alpha-induced apoptosis. Together, these observations suggested that BoHV-4 could represent a danger for public health. To evaluate the risk of human infection by BoHV-4 through milk or serum derivatives, we investigated the resistance of BoHV-4 to the mildest thermal treatments usually applied to these products. The results demonstrated that milk pasteurization and thermal decomplementation of serum abolish BoHV-4 infectivity by inactivation of its property to enter permissive cells. Consequently, our results demonstrate that these treatments drastically reduce the risk of human infection by BoHV-4 through treated milk or serum derivatives.
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Affiliation(s)
- C Bona
- Immunology-Vaccinology (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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Gillet L, Daix V, Donofrio G, Wagner M, Koszinowski UH, China B, Ackermann M, Markine-Goriaynoff N, Vanderplasschen A. Development of bovine herpesvirus 4 as an expression vector using bacterial artificial chromosome cloning. J Gen Virol 2005; 86:907-917. [PMID: 15784885 DOI: 10.1099/vir.0.80718-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several features make bovine herpesvirus 4 (BoHV-4) attractive as a backbone for use as a viral expression vector and/or as a model to study gammaherpesvirus biology. However, these developments have been impeded by the difficulty in manipulating its large genome using classical homologous recombination in eukaryotic cells. In the present study, the feasibility of exploiting bacterial artificial chromosome (BAC) cloning and prokaryotic recombination technology for production of BoHV-4 recombinants was explored. Firstly, the BoHV-4 genome was BAC cloned using two potential insertion sites. Both sites of insertion gave rise to BoHV-4 BAC clones stably maintained in bacteria and able to regenerate virions when transfected into permissive cells. Reconstituted virus replicated comparably to wild-type parental virus and the loxP-flanked BAC cassette was excised by growing them on permissive cells stably expressing Cre recombinase. Secondly, BoHV-4 recombinants expressing Ixodes ricinus anti-complement protein I or II (IRAC I/II) were produced using a two-step mutagenesis procedure in Escherichia coli. Both recombinants induced expression of high levels of functional IRAC molecules in the supernatant of infected cells. This study demonstrates that BAC cloning and prokaryotic recombination technology are powerful tools for the development of BoHV-4 as an expression vector and for further fundamental studies of this gammaherpesvirus.
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Affiliation(s)
- L Gillet
- Department of Infectious and Parasitic Diseases (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - V Daix
- Department of Infectious and Parasitic Diseases (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - G Donofrio
- Dipartimento di Salute Animale, Facoltà di Medicina Veterinaria, Sezione di Malattie Infettive degli Animali, Università degli Studi di Parma, I-43100 Parma, Italy
| | - M Wagner
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - U H Koszinowski
- Department of Virology, Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
| | - B China
- Food Sciences Department (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - M Ackermann
- Institute for Virology, University of Zurich, CH-8057 Zurich, Switzerland
| | - N Markine-Goriaynoff
- Department of Infectious and Parasitic Diseases (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - A Vanderplasschen
- Department of Infectious and Parasitic Diseases (B43b), Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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Abstract
Bovine subclinical mastitis can be defined as a moderated inflammatory disease characterized by a persistent accumulation of neutrophils in milk. As GMCSF-mediated delay of neutrophil apoptosis contributes to the accumulation of inflammatory cells at the site of inflammation in many human diseases, we sought to determine whether subclinical mastitis in cows is also associated with a GMCSF-dependent increase in milk-neutrophil survival. We first addressed the hypothesis that GMCSF delays bovine neutrophil apoptosis by activation of the signal transducer and activator of transcription (STAT) family members STAT3 and STAT5, which are critical regulators of the expression of various Bcl-2 family proteins. Granulocyte-macrophage colony-stimulating factor significantly delayed apoptosis of blood neutrophils obtained from healthy cows. In these cells, GMCSF activated STAT5, but not STAT3, and induced an increase in the mRNA of the antiapoptotic Bcl-2 member, Bcl-xL. Granulocyte-macrophage colony-stimulating factor-dependent STAT5 activation and up-regulation of Bcl-xL mRNA were blocked by the Jak inhibitor, AG-490. This inhibition was associated with abrogation of the prosurvival effect of GMCSF, demonstrating a key role for STAT5 in delayed neutrophil apoptosis. We further found that GMCSF expression was increased in milk cells from cows affected with subclinical mastitis. Neutrophils from these cows demonstrated a significant delay of apoptosis as compared with neutrophils obtained from healthy cows and were unresponsive to GMCSF. Active STAT5 complexes were detected in these neutrophils. Finally, in the presence of AG-490, apoptosis was induced and a time-dependent down-regulation of Bcl-xL mRNA was observed in milk neutrophils from mastitis-affected cows. These results indicate that neutrophil survival is enhanced in milk of subclinical mastitis-affected cows and suggest a role for a GMCSF-activated STAT5 signaling pathway in this phenomenon. This pathway could thus represent a target for the control of persistent accumulation of neutrophils in the bovine mammary gland.
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Affiliation(s)
- P Boutet
- Department of Physiology, University of Liége, Belgium.
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Gillet L, Minner F, Detry B, Farnir F, Willems L, Lambot M, Thiry E, Pastoret PP, Schynts F, Vanderplasschen A. Investigation of the susceptibility of human cell lines to bovine herpesvirus 4 infection: demonstration that human cells can support a nonpermissive persistent infection which protects them against tumor necrosis factor alpha-induced apoptosis. J Virol 2004; 78:2336-47. [PMID: 14963130 PMCID: PMC369250 DOI: 10.1128/jvi.78.5.2336-2347.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine herpesvirus 4 (BoHV-4) is a gammaherpesvirus that has a worldwide distribution in the population of cattle. Many factors make human contamination by BoHV-4 likely to occur. In this study, we performed in vitro experiments to assess the risk and the consequences of human infection by BoHV-4. First, by using a recombinant BoHV-4 strain expressing enhanced green fluorescent protein under the control of the human cytomegalovirus immediate-early gene promoter, we tested 21 human cell lines for their sensitivity and their permissiveness to BoHV-4 infection. These experiments revealed that human cell lines from lymphoid and myeloid origins were resistant to infection, whereas epithelial cells, carcinoma cells, or adenocarcinoma cells isolated from various organs were sensitive but poorly permissive to BoHV-4 infection. Second, by using the HeLa cell line as a model of human cells sensitive but not permissive to BoHV-4 infection, we investigated the resistance of infected cells to apoptosis and the persistence of the infection through cellular divisions. The results obtained can be summarized as follows. (i) BoHV-4 nonpermissive infection of HeLa cells protects them against tumor necrosis factor alpha-induced apoptosis. (ii) BoHV-4 infection of HeLa cells persists in cell culture; however, the percentage of infected cells decreases with time due to erratic transmission of the viral genome through cell division. (iii) BoHV-4 infection has no effect on the rate of HeLa cell division. Altogether, these data suggest that BoHV-4 could infect humans. This study also stresses the importance of considering the insidious effects of nonpermissive infection when the biosafety of animal gammaherpesviruses for humans is being considered.
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Affiliation(s)
- L Gillet
- Immunology-Vaccinology, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
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Ferry G, Gillet L, Bruneau V, Banales JM, Beauverger P, Cogé F, Galizzi JP, Scalbert E, Okamoto T, Urata H, Boutin JA. Development of new assays and improved procedures for the purification of recombinant human chymase. Eur J Biochem 2001; 268:5885-93. [PMID: 11722576 DOI: 10.1046/j.0014-2956.2001.02544.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chymase mediates a major alternative way of angiotensin II production from angiotensin I beside angiotensin converting enzyme in the final step of the renin-angiotensin system. This enzyme is also involved in other physio-pathological processes such as angiogenesis, atherosclerosis and inflammation. Several purification attempts of natural or recombinant chymase were reported in the literature. Most of these reports were not successful in obtaining the recombinant enzyme in a highly active form and in large quantity. In the present study, we describe a facile route for the purification of the human recombinant chymase. Chymase being produced as inactive prochymase, to be cathepsin C-activated, newly raised anti-chymase Ig were used to follow the purification. In order to complete the available tools for the search of chymase inhibitors, we developed and assessed a new 96-well plate based assay for the measurement of enzyme activity, as well as a low throughput, HPLC-based one. The assays used an original derivative of angiotensin I, or the native hormone. Chymase was produced in CHO cells and appropriately matured. The amount of enzyme obtained at the end of the process is compatible with the medium-throughput screening (up to 10,000 points per day), about 800 microg x L(-1) of culture medium with a specific activity of 6.16 mmol of angiotensin I cleaved per minute per mg of protein. All the biological and technical tools are now available for the discovery of new classes of chymase inhibitors.
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Affiliation(s)
- G Ferry
- Division de Pharmacologie Moléculaire et Cellulaire, Institut de Recherches Servier, Croissy sur Seine, France; Fukuoka University, Department of Cardiology, Fukuoka, Japan; Institut de Recherches Internationales Servier, Courbevoie, France
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Robberecht P, Gillet L, Chatelain P, De Neef P, Camus JC, Vincent M, Sassard J, Christophe J. Specific decrease of secretin/VIP-stimulated adenylate cyclase in the heart from the Lyon strain of hypertensive rats. Peptides 1984; 5:355-8. [PMID: 6473161 DOI: 10.1016/0196-9781(84)90233-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cardiac adenylate cyclase activity of genetically hypertensive rats from the Lyon strain (LH) was compared to that of Lyon normotensive rats (LN) and that of low blood pressure Lyon rats (LL). The major finding was a 30-35% decrease of secretin- and VIP-stimulated adenylate cyclase activity in cardiac membranes of LH rats that was already obvious in 5 week-old prehypertensive animals: this alteration was apparently specific for the cardiac secretin/VIP-stimulated adenylate cyclase activity, the same activity in membranes from brain, anterior pituitary, and liver being similar in LH, LN and LL rats. It is tempting to conclude that a selective alteration of functional cardiac secretin/VIP receptors in LH rats reflects a local hyperactivity of the sympathetic adrenergic system.
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Gillet L, Robberecht P, Waelbroeck M, Camus JC, De Neef P, König W, Christophe J. Interaction of Gila monster venom with secretin receptors in rat pancreatic membranes. Peptides 1984; 5:407-9. [PMID: 6089139 DOI: 10.1016/0196-9781(84)90244-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The stimulatory effect of Gila monster venom on adenylate cyclase activity in rat pancreatic membranes was compared to that of porcine secretin and porcine VIP. The maximal effect exerted by the venom was identical to that of VIP but significantly lower than that of secretin. The effect of Gila monster venom could, however, be attributed to its interaction with secretin receptors rather than with VIP receptors, at variance with its previously described action on guinea pig pancreatic acini. Adenylate cyclase activation by both Gila monster venom and secretin in rat pancreatic membranes was, indeed: (1) dose-dependently inhibited by two secretin fragments secretin-(4-27) and secretin-(7-27), and (2) more severely depressed than VIP stimulation, after pretreating pancreatic membranes with dithiothreitol (DTT).
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