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Sabbag A, Essayagh B, Barrera JDR, Basso C, Berni A, Cosyns B, Deharo JC, Deneke T, Di Biase L, Enriquez-Sarano M, Donal E, Imai K, Lim HS, Marsan NA, Turagam MK, Peichl P, Po SS, Haugaa KH, Shah D, de Riva Silva M, Bertrand P, Saba M, Dweck M, Townsend SN, Ngarmukos T, Fenelon G, Santangeli P, Sade LE, Corrado D, Lambiase P, Sanders P, Delacrétaz E, Jahangir A, Kaufman ES, Saggu DK, Pierard L, Delgado V, Lancellotti P. EHRA expert consensus statement on arrhythmic mitral valve prolapse and mitral annular disjunction complex in collaboration with the ESC Council on valvular heart disease and the European Association of Cardiovascular Imaging endorsed cby the Heart Rhythm Society, by the Asia Pacific Heart Rhythm Society, and by the Latin American Heart Rhythm Society. Europace 2022; 24:1981-2003. [PMID: 35951656 DOI: 10.1093/europace/euac125] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Avi Sabbag
- The Davidai Center for Rhythm Disturbances and Pacing, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Benjamin Essayagh
- Department of Cardiovascular Medicine, Simone Veil Hospital, Cannes 06400, France.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester 55905, Minnesota
| | | | - Cristina Basso
- Dipartimento di Scienze Cardio-Toraco-Vascolari e Sanità Pubblica, Università degli Studi di Padova, Padova 35128, Italy
| | - Ana Berni
- Cardiology and Cardiac Electrophysiology, EP Lab. Hospital Angeles Pedregal. Mexico City 10700, Board member, Mexican Society of Cardiology
| | - Bernard Cosyns
- Cardiology Department, Centrum voor hart en vaatziekten, Universitair Ziekenhuis Brussel, Free University of Brussels, Brussels 1090, Belgium
| | - Jean-Claude Deharo
- Department of Cardiology, L'hôpital de la Timone, Marseille, 13005, France
| | - Thomas Deneke
- Clinic for Interventional Electrophysiology, Heart Center RHÖN-KLINIKUM Campus Bad Neustadt, 97616, Germany
| | - Luigi Di Biase
- Albert Einstein College of Medicine at Montefiore Hospital, New York, NY 10467, USA
| | | | - Erwan Donal
- Service de Cardiologie, CCP-CHU Pontchaillou, Rennes 35033, France
| | - Katsuhiko Imai
- Department of Cardiovascular Surgery, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Hiroshima 737-0023, Japan
| | - Han S Lim
- Department of Cardiology, Austin and Northern Health, University of Melbourne, Melbourne 3010, Australia
| | | | - Mohit K Turagam
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Petr Peichl
- Department of Cardiology, Institute for Clinical and Experimental Medicine (IKEM), Prague 73117, Czech Republic
| | - Sunny S Po
- Heart Rhythm Institute and Section of Cardiovascular Diseases, University of Oklahoma Health Sciences Center, Oklahoma City, OK 0372, USA
| | - Kristina Hermann Haugaa
- ProCardio Center for Innovation, Department of Cardiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Dipen Shah
- Cantonal Hospital, Cardiology Department, CH-1211 Geneva, Switzerland
| | - Marta de Riva Silva
- Department of Cardiology, Leiden University Medical Center, Leiden 2333, The Netherlands
| | - Philippe Bertrand
- Ziekenhuis Oost-Limburg, Hasselt University, Genk, Hasselt 3600, Belgium
| | - Magdi Saba
- Consultant and Reader in Cardiac Electrophysiology, Director, Advanced Ventricular Arrhythmia Training and Research Program, St. George's Hospital NHS Foundation Trust, St. George's, University of London, SW17 0QT, UK
| | - Marc Dweck
- Centre for cardiovascular science, University of Edinburgh, EH16 4TJ, UK
| | - Santiago Nava Townsend
- Instituto Nacional De Cardiologia Ich, Electrophysiology Department, Mexico Df 14080, Mexico
| | - Tachapong Ngarmukos
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 73170, Thailand
| | - Guilherme Fenelon
- Coordenador - Centro de Arritmia, Hospital Israelita Albert Einstein, São Paulo - SP, 05652-900, Brazil
| | | | - Leyla Elif Sade
- University of Pittsburgh, UPMC, Heart and Vascular Institute, ittsburgh, PA 15219, USA.,C.H.U. du Sart-Tilman, Universite de Liege, Liege 4000, Belgium
| | - Domenico Corrado
- Full Professor of Cardiovascular Medicine, Director, Inherited Arrhythmogenic Cardiomyopathies and Sports Cardiology Unit, Dept. of Cardiac, Thoracic and Vascular Sciences, University of Padua Medical School, Padova 35122, Italy
| | - Pier Lambiase
- UCL & Barts Heart Centre, Co-Director of Cardiovascular Research Barts NHS Trust, Inherited Arrhythmia Clinical Lead, UCL MRC DTP Theme Lead, BHRS Committee Research Lead, Institute of Cardiovascular Science, UCL, Department of Cardiology, Barts Heart Centre E1 1BB, UK
| | - Prashanthan Sanders
- Centre for Heart Rhythm Disorders, University of Adelaide, South Australia 5000, Australia
| | - Etienne Delacrétaz
- Clinique Cecil Hirslanden Lausanne & University Hospital Fribourg, Cardiology 1003, Switzerland
| | - Arshad Jahangir
- University of Wisconsin School of Medicine and Public Health, Milwaukee, MI 53705, USA
| | - Elizabeth S Kaufman
- Clinical Electrophysiologist, MetroHealth Medical Center, Professor, Case Western Reserve University 44106, USA
| | - Daljeet Kaur Saggu
- Consultant Cardiologist and Electrophysiologist, AIG HOSPITAL, Hyderabad 500032, India
| | - Luc Pierard
- C.H.U. du Sart-Tilman, Universite de Liege, Liege 4000, Belgium
| | - Victoria Delgado
- Heart Institute, Hospital University Germans Trias i Pujol, Badalona 08916, Spain
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Kawecki F, Gluais M, Claverol S, Dusserre N, McAllister T, L'Heureux N. Inter-donor variability of extracellular matrix production in long-term cultures of human fibroblasts. Biomater Sci 2022; 10:3935-3950. [PMID: 35700514 PMCID: PMC9275472 DOI: 10.1039/d1bm01933c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several tissue engineering approaches are based on the ability of mesenchymal cells to endogenously synthesize an extracellular matrix (ECM) in vitro, which can be seen as a form of biomaterial. Accordingly, the inter-donor variability of cell-assembled extracellular matrix (CAM) production is a key parameter to understand in order to progress towards clinical applications, especially for autologous strategies. In this study, CAMs were produced, under good manufacturing process conditions, from skin fibroblasts of 21 patients as part of a clinical trial to evaluate a tissue-engineered vascular graft. The inter-donor variability of CAM strength, thickness, hydroxyproline, and glycosaminoglycan was substantial (coefficient of variability of 33%, 19%, 24%, and 19%, respectively), but a significant correlation was observed between all four properties (Pearson r: 0.43 to 0.70; p-value ≤ 0.05). A CAM matrisome analysis, performed by mass spectrometry, revealed the presence of 70 ECM-related proteins. Our study shows that the relative abundance of 16 proteins (15 non-collagenous) correlated with CAM thickness. These proteins also correlated with CAM hydroxyproline content, as well as 21 other proteins that included fibrillar collagens and non-collagenous proteins. However, data demonstrated that only the relative abundance of type I collagen subunit alpha-1 was correlated to CAM strength. This study is the most extensive evaluation of CAM inter-donor variability to date and will help tissue engineers working with this type of biomaterial to design strategies that take into account this variability, especially for autologous tissue manufacturing. Several tissue engineering approaches are based on the ability of mesenchymal cells to endogenously synthesize an extracellular matrix (ECM) in vitro, which can be seen as a form of biomaterial.![]()
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Affiliation(s)
- Fabien Kawecki
- Univ. Bordeaux, Inserm, BioTis, UMR1026, F-33000 Bordeaux, France.
| | - Maude Gluais
- Univ. Bordeaux, Inserm, BioTis, UMR1026, F-33000 Bordeaux, France.
| | - Stéphane Claverol
- Centre de Génomique Fonctionnelle, Plateforme Protéome, University of Bordeaux, F-33000, Bordeaux, France
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3
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Ayagama T, Bose SJ, Capel RA, Priestman DA, Berridge G, Fischer R, Galione A, Platt FM, Kramer H, Burton RA. A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue. iScience 2021; 24:102949. [PMID: 34466782 PMCID: PMC8384914 DOI: 10.1016/j.isci.2021.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/04/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022] Open
Abstract
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
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Affiliation(s)
- Thamali Ayagama
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Samuel J. Bose
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Rebecca A. Capel
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | | | - Georgina Berridge
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Antony Galione
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Frances M. Platt
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN UK
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4
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Fajarda O, Duarte-Pereira S, Silva RM, Oliveira JL. Merging microarray studies to identify a common gene expression signature to several structural heart diseases. BioData Min 2020; 13:8. [PMID: 32670412 PMCID: PMC7346458 DOI: 10.1186/s13040-020-00217-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature deaths. A large amount of microarray data is available in public repositories and can be used to identify differentially expressed genes. However, most of the microarray datasets are composed of a reduced number of samples and to obtain more reliable results, several datasets have to be merged, which is a challenging task. The identification of differentially expressed genes is commonly done using statistical methods. Nonetheless, these methods are based on the definition of an arbitrary threshold to select the differentially expressed genes and there is no consensus on the values that should be used. RESULTS Nine publicly available microarray datasets from studies of different heart diseases were merged to form a dataset composed of 689 samples and 8354 features. Subsequently, the adjusted p-value and fold change were determined and by combining a set of adjusted p-values cutoffs with a list of different fold change thresholds, 12 sets of differentially expressed genes were obtained. To select the set of differentially expressed genes that has the best accuracy in classifying samples from patients with heart diseases and samples from patients with no heart condition, the random forest algorithm was used. A set of 62 differentially expressed genes having a classification accuracy of approximately 95% was identified. CONCLUSIONS We identified a gene expression signature common to different cardiac diseases and supported our findings by showing their involvement in the pathophysiology of the heart. The approach used in this study is suitable for the identification of gene expression signatures, and can be extended to different diseases.
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Affiliation(s)
- Olga Fajarda
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Sara Duarte-Pereira
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
| | - Raquel M. Silva
- IEETA/DETI, University of Aveiro, Aveiro, 3810-193 Portugal
- Department of Medical Sciences and iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, 3810-193 Portugal
- Current Address: Universidade Católica Portuguesa, Faculdade de Medicina Dentária, CIIS-Centro de Investigação Interdisciplinar em Saúde, Campus de Viseu, Viseu, 3504-505 Portugal
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5
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Huang Y, Zhang Q, Liu Y, Jiang B, Xie J, Gong T, Jia B, Liu X, Yao J, Cao W, Shen H, Yang P. Aperture-controllable nano-electrospray emitter and its application in cardiac proteome analysis. Talanta 2020; 207:120340. [PMID: 31594582 DOI: 10.1016/j.talanta.2019.120340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/31/2019] [Accepted: 09/07/2019] [Indexed: 12/01/2022]
Abstract
The emitter clogging is the most common hardware failure of nano-electrospray ionization, to improve the durability and electrospray stability of fused silica emitters, we demonstrate a means of fabricating nano-electrospray emitters with controllable aperture size and gradually-narrowed channel on the tip. We simulated the fluid morphologies in the emitter channels by computational fluid dynamics and found more stable flow on aperture-controllable nano-electrospray emitter. Besides, we found the unstable flow sections of commercial emitters match the actual clogging sections very well, indicating the main cause of emitter clogging is unstable flow. We further tested the emitters by nano-LC-MS based proteome analysis. Compared with the commercial emitter, aperture-controllable nano-electrospray emitters promoted the total ion chromatogram intensity by 25%, the number of identified proteins by 6.58%, and the number of identified peptides by 7.87%. In total, 989 proteins were identified from 1 μg of extracted mouse cardiac proteins. After the optimization by using mouse samples, we analyzed clinical auricular dextral tissues from patients undergoing cardiac surgery and found 16 proteins related to atrial fibrillation. Overall, aperture-controllable nano-electrospray emitter exhibits better sensitivity and reproducibility in the application of nano-LC-MS cardiac proteome analysis.
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Affiliation(s)
- Yuanyu Huang
- Department of Chemistry and Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Quanqing Zhang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Yingchao Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Biyun Jiang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Juanjuan Xie
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Tianqi Gong
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Bin Jia
- Department of Chemistry and Zhongshan Hospital, Fudan University, Shanghai, 200433, China
| | - Xiaohui Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jun Yao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Weiqian Cao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Fifth People's Hospital of Shanghai, NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 201100, China
| | - Huali Shen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
| | - Pengyuan Yang
- Department of Chemistry and Zhongshan Hospital, Fudan University, Shanghai, 200433, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
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Federspiel JD, Tandon P, Wilczewski CM, Wasson L, Herring LE, Venkatesh SS, Cristea IM, Conlon FL. Conservation and divergence of protein pathways in the vertebrate heart. PLoS Biol 2019; 17:e3000437. [PMID: 31490923 PMCID: PMC6750614 DOI: 10.1371/journal.pbio.3000437] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/18/2019] [Accepted: 08/14/2019] [Indexed: 12/18/2022] Open
Abstract
Heart disease is the leading cause of death in the western world. Attaining a mechanistic understanding of human heart development and homeostasis and the molecular basis of associated disease states relies on the use of animal models. Here, we present the cardiac proteomes of 4 model vertebrates with dual circulatory systems: the pig (Sus scrofa), the mouse (Mus musculus), and 2 frogs (Xenopus laevis and Xenopus tropicalis). Determination of which proteins and protein pathways are conserved and which have diverged within these species will aid in our ability to choose the appropriate models for determining protein function and to model human disease. We uncover mammalian- and amphibian-specific, as well as species-specific, enriched proteins and protein pathways. Among these, we find and validate an enrichment in cell-cycle-associated proteins within Xenopus laevis. To further investigate functional units within cardiac proteomes, we develop a computational approach to profile the abundance of protein complexes across species. Finally, we demonstrate the utility of these data sets for predicting appropriate model systems for studying given cardiac conditions by testing the role of Kielin/chordin-like protein (Kcp), a protein found as enriched in frog hearts compared to mammals. We establish that germ-line mutations in Kcp in Xenopus lead to valve defects and, ultimately, cardiac failure and death. Thus, integrating these findings with data on proteins responsible for cardiac disease should lead to the development of refined, species-specific models for protein function and disease states.
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Affiliation(s)
| | - Panna Tandon
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Caralynn M. Wilczewski
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lauren Wasson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laura E. Herring
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Ileana M. Cristea
- Princeton University, Princeton, New Jersey, United States of America
| | - Frank L. Conlon
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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7
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Narasimhan M, Kannan S, Chawade A, Bhattacharjee A, Govekar R. Clinical biomarker discovery by SWATH-MS based label-free quantitative proteomics: impact of criteria for identification of differentiators and data normalization method. J Transl Med 2019; 17:184. [PMID: 31151397 PMCID: PMC6545036 DOI: 10.1186/s12967-019-1937-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND SWATH-MS has emerged as the strategy of choice for biomarker discovery due to the proteome coverage achieved in acquisition and provision to re-interrogate the data. However, in quantitative analysis using SWATH, each sample from the comparison group is run individually in mass spectrometer and the resulting inter-run variation may influence relative quantification and identification of biomarkers. Normalization of data to diminish this variation thereby becomes an essential step in SWATH data processing. In most reported studies, data normalization methods used are those provided in instrument-based data analysis software or those used for microarray data. This study, for the first time provides an experimental evidence for selection of normalization method optimal for biomarker identification. METHODS The efficiency of 12 normalization methods to normalize SWATH-MS data was evaluated based on statistical criteria in 'Normalyzer'-a tool which provides comparative evaluation of normalization by different methods. Further, the suitability of normalized data for biomarker discovery was assessed by evaluating the clustering efficiency of differentiators, identified from the normalized data based on p-value, fold change and both, by hierarchical clustering in Genesis software v.1.8.1. RESULTS Conventional statistical criteria identified VSN-G as the optimal method for normalization of SWATH data. However, differentiators identified from VSN-G normalized data failed to segregate test and control groups. We thus assessed data normalized by eleven other methods for their ability to yield differentiators which segregate the study groups. Datasets in our study demonstrated that differentiators identified based on p-value from data normalized with Loess-R stratified the study groups optimally. CONCLUSION This is the first report of experimentally tested strategy for SWATH-MS data processing with an emphasis on identification of clinically relevant biomarkers. Normalization of SWATH-MS data by Loess-R method and identification of differentiators based on p-value were found to be optimal for biomarker discovery in this study. The study also demonstrates the need to base the choice of normalization method on the application of the data.
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Affiliation(s)
- Mythreyi Narasimhan
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210 India
- BARC Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094 India
| | - Sadhana Kannan
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210 India
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Atanu Bhattacharjee
- Section of Biostatistics, Centre for Cancer Epidemiology, Tata Memorial Centre, Kharghar, Navi Mumbai 410210 India
| | - Rukmini Govekar
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210 India
- BARC Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094 India
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8
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Heiland JJ, Geissler D, Piendl SK, Warias R, Belder D. Supercritical-Fluid Chromatography On-Chip with Two-Photon-Excited-Fluorescence Detection for High-Speed Chiral Separations. Anal Chem 2019; 91:6134-6140. [DOI: 10.1021/acs.analchem.9b00726] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Josef J. Heiland
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - David Geissler
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Sebastian K. Piendl
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Rico Warias
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany
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9
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Haghighi F, Talebpour Z, Nezhad AS. Towards fully integrated liquid chromatography on a chip: Evolution and evaluation. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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10
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Tan HT, Chung MCM. Label-Free Quantitative Phosphoproteomics Reveals Regulation of Vasodilator-Stimulated Phosphoprotein upon Stathmin-1 Silencing in a Pair of Isogenic Colorectal Cancer Cell Lines. Proteomics 2018; 18:e1700242. [PMID: 29460479 DOI: 10.1002/pmic.201700242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/10/2018] [Indexed: 02/06/2023]
Abstract
In this communication, we present the phosphoproteome changes in an isogenic pair of colorectal cancer cell lines, viz., the poorly metastatic HCT-116 and the highly metastatic derivative E1, upon stathmin-1 (STMN1) knockdown. The aim was to better understand how the alterations of the phosphoproteins in these cells are involved in cancer metastasis. After the phosphopeptides were enriched using the TiO2 HAMMOC approach, comparative proteomics analysis was carried out using sequential window acquisition of all theoretical mass spectra-MS. Following bioinformatics analysis using MarkerView and OneOmics platforms, we identified a list of regulated phosphoproteins that may play a potential role in signaling, maintenance of cytoskeletal structure, and focal adhesion. Among these phosphoproteins, was the actin cytoskeleton regulator protein, vasodilator-stimulated phosphoprotein (VASP), where its change in phosphorylation status was found to be concomitant with STMN1-associated roles in metastasis. We further showed that silencing of stathmin-1 altered the expression, subcellular localization and phosphorylation status of VASP, which suggested that it might be associated with remodeling of the cell cytoskeleton in colorectal cancer metastasis.
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Affiliation(s)
- Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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11
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Doll S, Dreßen M, Geyer PE, Itzhak DN, Braun C, Doppler SA, Meier F, Deutsch MA, Lahm H, Lange R, Krane M, Mann M. Region and cell-type resolved quantitative proteomic map of the human heart. Nat Commun 2017; 8:1469. [PMID: 29133944 PMCID: PMC5684139 DOI: 10.1038/s41467-017-01747-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/13/2017] [Indexed: 12/16/2022] Open
Abstract
The heart is a central human organ and its diseases are the leading cause of death worldwide, but an in-depth knowledge of the identity and quantity of its constituent proteins is still lacking. Here, we determine the healthy human heart proteome by measuring 16 anatomical regions and three major cardiac cell types by high-resolution mass spectrometry-based proteomics. From low microgram sample amounts, we quantify over 10,700 proteins in this high dynamic range tissue. We combine copy numbers per cell with protein organellar assignments to build a model of the heart proteome at the subcellular level. Analysis of cardiac fibroblasts identifies cellular receptors as potential cell surface markers. Application of our heart map to atrial fibrillation reveals individually distinct mitochondrial dysfunctions. The heart map is available at maxqb.biochem.mpg.de as a resource for future analyses of normal heart function and disease. The human heart is composed of distinct regions and cell types, but relatively little is known about their specific protein composition. Here, the authors present a region- and cell type-specific proteomic map of the healthy human heart, revealing functional differences and potential cell type markers.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Martina Dreßen
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Munich, 80636, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Christian Braun
- Forensic Institute, Ludwig-Maximilians-University, Munich, 80336, Germany
| | - Stefanie A Doppler
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Munich, 80636, Germany
| | - Florian Meier
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Marcus-Andre Deutsch
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Munich, 80636, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, 80802, Germany
| | - Harald Lahm
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Munich, 80636, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Munich, 80636, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, 80802, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Munich, 80636, Germany. .,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, 80802, Germany.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany. .,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.
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12
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Markby GR, Summers KM, MacRae VE, Corcoran BM. Comparative Transcriptomic Profiling and Gene Expression for Myxomatous Mitral Valve Disease in the Dog and Human. Vet Sci 2017; 4:vetsci4030034. [PMID: 29056693 PMCID: PMC5644653 DOI: 10.3390/vetsci4030034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 12/28/2022] Open
Abstract
Myxomatous mitral valve disease is the single most important mitral valve disease in both dogs and humans. In the case of the dog it is ubiquitous, such that all aged dogs will have some evidence of the disease, and for humans it is known as Barlow's disease and affects up to 3% of the population, with an expected increase in prevalence as the population ages. Disease in the two species show many similarities and while both have the classic myxomatous degeneration only in humans is there extensive fibrosis. This dual pathology of the human disease markedly affects the valve transcriptome and the difference between the dog and human is dominated by changes in genes associated with fibrosis. This review will briefly examine the comparative valve pathology and then, in more detail, the transcriptomic profiling and gene expression reported so far for both species.
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Affiliation(s)
- Greg R Markby
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
| | - Kim M Summers
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
| | - Vicky E MacRae
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
| | - Brendan M Corcoran
- Roslin Institute, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easterbush Veterinary Centre, Roslin, Scotland EH25 9RG, UK.
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13
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Banfi C, Guarino A, Brioschi M, Ghilardi S, Mastrullo V, Tremoli E, Polvani G. Optimized Protocol for the Extraction of Proteins from the Human Mitral Valve. J Vis Exp 2017. [PMID: 28654069 DOI: 10.3791/55762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Analysis of the cellular proteome can help to elucidate the molecular mechanisms underlying diseases due to the development of technologies that permit the large-scale identification and quantification of the proteins present in complex biological systems.The knowledge gained from a proteomic approach can potentially lead to a better understanding of the pathogenic mechanisms underlying diseases, allowing for the identification of novel diagnostic and prognostic disease markers, and, hopefully, of therapeutic targets. However, the cardiac mitral valve represents a very challenging sample for proteomic analysis because of the low cellularity in proteoglycan and collagen-enriched extracellular matrix. This makes it challenging to extract proteins for a global proteomic analysis. This work describes a protocol that is compatible with subsequent protein analysis, such as quantitative proteomics and immunoblotting. This can allow for the correlation of data concerning protein expression with data on quantitative mRNA expression and non-quantitative immunohistochemical analysis. Indeed, these approaches, when performed together, will lead to a more comprehensive understanding of the molecular mechanisms underlying diseases, from mRNA to post-translational protein modification. Thus, this method can be relevant to researchers interested in the study of cardiac valve physiopathology.
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Affiliation(s)
| | - Anna Guarino
- Cardiovascular Tissue Bank of Milan, Centro Cardiologico Monzino IRCCS
| | | | | | | | | | - Gianluca Polvani
- Cardiovascular Tissue Bank of Milan, Centro Cardiologico Monzino IRCCS; Department of Clinical Sciences and Community Health, Cardiovascular Section, University of Milan; Department of Cardiovascular Disease, Development and Innovation Cardiac Surgery Unit, Centro Cardiologico Monzino IRCCS
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14
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Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600278] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Faculty of Sciences and Technology; University of Coimbra; Coimbra Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Institute for Interdisciplinary Research (III); University of Coimbra; Coimbra Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
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15
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Brioschi M, Baetta R, Ghilardi S, Gianazza E, Guarino A, Parolari A, Polvani G, Tremoli E, Banfi C. Normal human mitral valve proteome: A preliminary investigation by gel-based and gel-free proteomic approaches. Electrophoresis 2016; 37:2633-2643. [PMID: 27450324 DOI: 10.1002/elps.201600081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 12/24/2022]
Abstract
The mitral valve is a highly complex structure which regulates blood flow from the left atrium to the left ventricle (LV) avoiding a significant forward gradient during diastole or regurgitation during systole. The integrity of the mitral valve is also essential for the maintenance of normal LV size, geometry, and function. Significant advances in the comprehension of the biological, functional, and mechanical behavior of the mitral valve have recently been made. However, current knowledge of protein components in the normal human mitral valve is still limited and complicated by the low cellularity of this tissue and the presence of high abundant proteins from the extracellular matrix. We employed here an integrated proteomic approach to analyse the protein composition of the normal human mitral valve and reported confident identification of 422 proteins, some of which have not been previously described in this tissue. In particular, we described the ability of pre-MS separation technique based on liquid-phase IEF and SDS-PAGE to identify the largest number of proteins. We also demonstrated that some of these proteins, e.g. αB-Crystallin, septin-11, four-and-a-half LIM domains protein 1, and dermatopontin, are synthesised by interstitial cells isolated from human mitral valves. These initial results provide a valuable basis for future studies aimed at analysing in depth the mitral valve protein composition and at investigating potential pathogenetic molecular mechanisms. Data are available via ProteomeXchange with identifier PXD004397.
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Affiliation(s)
| | | | | | | | - Anna Guarino
- Centro Cardiologico Monzino, IRCCS, Milan, Italy.,Banca Tessuti Cardiovascolari Regione Lombardia, Centro Cardiologico Monzino IRCCS Milan, Milan, Italy
| | - Alessandro Parolari
- Dipartimento di Chirurgia cardiaca, IRCCS Policlinico San Donato, Milan, Italy
| | - Gianluca Polvani
- Centro Cardiologico Monzino, IRCCS, Milan, Italy.,Università degli Studi di Milano, Dipartimento di Scienze Cliniche e di Comunità, Sezione Cardiovascolare, Milan, Italy
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