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Lai Z, Wang C, Liu X, Sun H, Guo Z, Shao J, Li K, Chen J, Wang J, Lei X, Shu K, Feng Y, Kong D, Sun W, Liu B. Characterization of the proteome of stable and unstable carotid atherosclerotic plaques using data-independent acquisition mass spectrometry. J Transl Med 2024; 22:247. [PMID: 38454421 PMCID: PMC10921703 DOI: 10.1186/s12967-023-04723-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Currently, noninvasive imaging techniques and circulating biomarkers are still insufficient to accurately assess carotid plaque stability, and an in-depth understanding of the molecular mechanisms that contribute to plaque instability is still lacking. METHODS We established a clinical study cohort containing 182 patients with carotid artery stenosis. After screening, 39 stable and 49 unstable plaques were included in the discovery group, and quantitative proteomics analysis based on data independent acquisition was performed for these plaque samples. Additionally, 35 plaques were included in the validation group to validate the proteomics results by immunohistochemistry analysis. RESULTS A total of 397 differentially expressed proteins were identified in stable and unstable plaques. These proteins are primarily involved in ferroptosis and lipid metabolism-related functions and pathways. Plaque validation results showed that ferroptosis- and lipid metabolism-related proteins had different expression trends in stable plaques versus unstable fibrous cap regions and lipid core regions. Ferroptosis- and lipid metabolism-related mechanisms in plaque stability were discussed. CONCLUSIONS Our results may provide a valuable strategy for revealing the mechanisms affecting plaque stability and will facilitate the discovery of specific biomarkers to broaden the therapeutic scope.
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Affiliation(s)
- Zhichao Lai
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Chaonan Wang
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
- Department of Hemangiomas & Vascular Malformations, Plastic Surgery Hospital, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Xiaoyan Liu
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Dongdansantiao 9St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Haidan Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Dongdansantiao 9St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Zhengguang Guo
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Dongdansantiao 9St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Jiang Shao
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Kang Li
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Junye Chen
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Pathophysiology, Peking Union Medical College, Beijing, China
| | - Jiaxian Wang
- Eight-Year Program of Clinical Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Peking Union Medical College, Beijing, China
| | - Xiangling Lei
- Eight-Year Program of Clinical Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Peking Union Medical College, Beijing, China
| | - Keqiang Shu
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Yuyao Feng
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Deqiang Kong
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China
| | - Wei Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking, Union Medical College, Dongdansantiao 9St, Dongcheng District, Beijing, 100730, People's Republic of China.
| | - Bao Liu
- Department of Vascular Surgery, Chinese Academy of Medical Science, Peking Union Medical College Hospital, Peking Union Medical College, Shuaifuyuan 1St, Dongcheng District, Beijing, 100730, People's Republic of China.
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2
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Kalailingam P, Mohd‐Kahliab K, Ngan SC, Iyappan R, Melekh E, Lu T, Zien GW, Sharma B, Guo T, MacNeil AJ, MacPherson REK, Tsiani EL, O'Leary DD, Lim KL, Su IH, Gao Y, Richards AM, Kalaria RN, Chen CP, McCarthy NE, Sze SK. Immunotherapy targeting isoDGR-protein damage extends lifespan in a mouse model of protein deamidation. EMBO Mol Med 2023; 15:e18526. [PMID: 37971164 PMCID: PMC10701600 DOI: 10.15252/emmm.202318526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Aging results from the accumulation of molecular damage that impairs normal biochemical processes. We previously reported that age-linked damage to amino acid sequence NGR (Asn-Gly-Arg) results in "gain-of-function" conformational switching to isoDGR (isoAsp-Gly-Arg). This integrin-binding motif activates leukocytes and promotes chronic inflammation, which are characteristic features of age-linked cardiovascular disorders. We now report that anti-isoDGR immunotherapy mitigates lifespan reduction of Pcmt1-/- mouse. We observed extensive accumulation of isoDGR and inflammatory cytokine expression in multiple tissues from Pcmt1-/- and naturally aged WT animals, which could also be induced via injection of isoDGR-modified plasma proteins or synthetic peptides into young WT animals. However, weekly injection of anti-isoDGR mAb (1 mg/kg) was sufficient to significantly reduce isoDGR-protein levels in body tissues, decreased pro-inflammatory cytokine concentrations in blood plasma, improved cognition/coordination metrics, and extended the average lifespan of Pcmt1-/- mice. Mechanistically, isoDGR-mAb mediated immune clearance of damaged isoDGR-proteins via antibody-dependent cellular phagocytosis (ADCP). These results indicate that immunotherapy targeting age-linked protein damage may represent an effective intervention strategy in a range of human degenerative disorders.
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Affiliation(s)
| | | | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Ranjith Iyappan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Evelin Melekh
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Tian Lu
- iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life SciencesWestlake UniversityHangzhouChina
| | - Gan Wei Zien
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Bhargy Sharma
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Tiannan Guo
- iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life SciencesWestlake UniversityHangzhouChina
| | - Adam J MacNeil
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Rebecca EK MacPherson
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Evangelia Litsa Tsiani
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Deborah D O'Leary
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Kah Leong Lim
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| | - I Hsin Su
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yong‐Gui Gao
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - A Mark Richards
- Department of CardiologyNational University Heart CentreSingaporeSingapore
- Department of CardiologyUniversity of OtagoChristchurchNew Zealand
| | - Raj N Kalaria
- Institute of Neuroscience, Campus for Ageing and VitalityNewcastle UniversityNewcastle upon TyneUK
| | - Christopher P Chen
- Memory, Aging and Cognition CentreNational University Health SystemSingaporeSingapore
| | - Neil E McCarthy
- Centre for Immunobiology, The Blizard Institute, Bart's and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Siu Kwan Sze
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
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3
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Nieddu G, Formato M, Lepedda AJ. Searching for Atherosclerosis Biomarkers by Proteomics: A Focus on Lesion Pathogenesis and Vulnerability. Int J Mol Sci 2023; 24:15175. [PMID: 37894856 PMCID: PMC10607641 DOI: 10.3390/ijms242015175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Plaque rupture and thrombosis are the most important clinical complications in the pathogenesis of stroke, coronary arteries, and peripheral vascular diseases. The identification of early biomarkers of plaque presence and susceptibility to ulceration could be of primary importance in preventing such life-threatening events. With the improvement of proteomic tools, large-scale technologies have been proven valuable in attempting to unravel pathways of atherosclerotic degeneration and identifying new circulating markers to be utilized either as early diagnostic traits or as targets for new drug therapies. To address these issues, different matrices of human origin, such as vascular cells, arterial tissues, plasma, and urine, have been investigated. Besides, proteomics was also applied to experimental atherosclerosis in order to unveil significant insights into the mechanisms influencing atherogenesis. This narrative review provides an overview of the last twenty years of omics applications to the study of atherogenesis and lesion vulnerability, with particular emphasis on lipoproteomics and vascular tissue proteomics. Major issues of tissue analyses, such as plaque complexity, sampling, availability, choice of proper controls, and lipoproteins purification, will be raised, and future directions will be addressed.
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Affiliation(s)
| | | | - Antonio Junior Lepedda
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (G.N.); (M.F.); Antonio Junior Lepedda (A.J.L.)
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4
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Chen YC, Smith M, Ying YL, Makridakis M, Noonan J, Kanellakis P, Rai A, Salim A, Murphy A, Bobik A, Vlahou A, Greening DW, Peter K. Quantitative proteomic landscape of unstable atherosclerosis identifies molecular signatures and therapeutic targets for plaque stabilization. Commun Biol 2023; 6:265. [PMID: 36914713 PMCID: PMC10011552 DOI: 10.1038/s42003-023-04641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Atherosclerotic plaque rupture leading to myocardial infarction is a major global health burden. Applying the tandem stenosis (TS) mouse model, which distinctively exhibits the characteristics of human plaque instability/rupture, we use quantitative proteomics to understand and directly compare unstable and stable atherosclerosis. Our data highlight the disparate natures and define unique protein signatures of unstable and stable atherosclerosis. Key proteins and pathway networks are identified such as the innate immune system, and neutrophil degranulation. The latter includes calprotectin S100A8/A9, which we validate in mouse and human unstable plaques, and we demonstrate the plaque-stabilizing effects of its inhibition. Overall, we provide critical insights into the unique proteomic landscape of unstable atherosclerosis (as distinct from stable atherosclerosis and vascular tissue). We further establish the TS model as a reliable preclinical tool for the discovery and testing of plaque-stabilizing drugs. Finally, we provide a knowledge resource defining unstable atherosclerosis that will facilitate the identification and validation of long-sought-after therapeutic targets and drugs for plaque stabilization.
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Affiliation(s)
- Yung-Chih Chen
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Meaghan Smith
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ya-Lan Ying
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Manousos Makridakis
- Proteomics Research Unit, Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jonathan Noonan
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Kanellakis
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Alin Rai
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia
| | - Agus Salim
- Department of Bioinformatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Andrew Murphy
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
- Haematopoiseis and Leukocyte Biology Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Alex Bobik
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Immunology, Monash University, Centre for Inflammatory Disease, School of Clinical Sciences, Monash Health, Melbourne, VIC, Australia
| | - Antonia Vlahou
- Proteomics Research Unit, Biotechnology Division, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - David W Greening
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
| | - Karlheinz Peter
- Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
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5
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Lautenbacher L, Samaras P, Muller J, Grafberger A, Shraideh M, Rank J, Fuchs ST, Schmidt TK, The M, Dallago C, Wittges H, Rost B, Krcmar H, Kuster B, Wilhelm M. ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Res 2022; 50:D1541-D1552. [PMID: 34791421 PMCID: PMC8728203 DOI: 10.1093/nar/gkab1026] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022] Open
Abstract
ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our efforts to continuously develop and expand ProteomicsDB. The major focus over the last two years was improving the findability, accessibility, interoperability and reusability (FAIR) of the data as well as its implementation. For this purpose, we release a new application programming interface (API) that provides systematic access to essentially all data in ProteomicsDB. Second, we release a new open-source user interface (UI) and show the advantages the scientific community gains from such software. With the new interface, two new visualizations of protein primary, secondary and tertiary structure as well an updated spectrum viewer were added. Furthermore, we integrated ProteomicsDB with our deep-neural-network Prosit that can predict the fragmentation characteristics and retention time of peptides. The result is an automatic processing pipeline that can be used to reevaluate database search engine results stored in ProteomicsDB. In addition, we extended the data content with experiments investigating different human biology as well as a newly supported organism.
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Affiliation(s)
- Ludwig Lautenbacher
- Technical University of Munich, Computational Mass Spectrometry, 85354 Freising, Bavaria, Germany
| | - Patroklos Samaras
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Julian Muller
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Andreas Grafberger
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Marwin Shraideh
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Johannes Rank
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Simon T Fuchs
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Tobias K Schmidt
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Matthew The
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
| | - Christian Dallago
- Technical University of Munich, Department for Bioinformatics and Computational Biology, 85748 Garching, Bavaria, Germany
- Technical University of Munich, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), 85748 Garching, Bavaria, Germany
| | - Holger Wittges
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Burkhard Rost
- Technical University of Munich, Department for Bioinformatics and Computational Biology, 85748 Garching, Bavaria, Germany
- Technical University of Munich, Institute for Advanced Study (TUM-IAS), 85748 Freising, Bavaria, Germany
| | - Helmut Krcmar
- Technical University of Munich, Chair for Information Systems, 85748 Garching, Bavaria, Germany
- Technical University of Munich, SAP University Competence Center, 85748 Garching, Bavaria, Germany
| | - Bernhard Kuster
- Technical University of Munich, Chair of Proteomics and Bioanalytics, 85354 Freising, Bavaria, Germany
- Technical University of Munich, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), 85354 Freising, Bavaria, Germany
| | - Mathias Wilhelm
- Technical University of Munich, Computational Mass Spectrometry, 85354 Freising, Bavaria, Germany
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6
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Wierer M, Werner J, Wobst J, Kastrati A, Cepele G, Aherrahrou R, Sager HB, Erdmann J, Dichgans M, Flockerzi V, Civelek M, Dietrich A, Mann M, Schunkert H, Kessler T. A proteomic atlas of the neointima identifies novel druggable targets for preventive therapy. Eur Heart J 2021; 42:1773-1785. [PMID: 33829256 PMCID: PMC8104955 DOI: 10.1093/eurheartj/ehab140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/30/2020] [Accepted: 02/19/2021] [Indexed: 11/21/2022] Open
Abstract
Aims In-stent restenosis is a complication after coronary stenting associated with morbidity and mortality. Here, we sought to investigate the molecular processes underlying neointima formation and to identify new treatment and prevention targets. Methods and results Neointima formation was induced by wire injury in mouse femoral arteries. High-accuracy proteomic measurement of single femoral arteries to a depth of about 5000 proteins revealed massive proteome remodelling, with more than half of all proteins exhibiting expression differences between injured and non-injured vessels. We observed major changes in the composition of the extracellular matrix and cell migration processes. Among the latter, we identified the classical transient receptor potential channel 6 (TRPC6) to drive neointima formation. While Trpc6
−/− mice presented reduced neointima formation compared to wild-type mice (1.44 ± 0.39 vs. 2.16 ± 0.48, P = 0.01), activating or repressing TRPC6 in human vascular smooth muscle cells resulted in increased [vehicle 156.9 ± 15.8 vs. 1-oleoyl-2-acetyl-sn-glycerol 179.1 ± 8.07 (103 pixels), P = 0.01] or decreased migratory capacity [vehicle 130.0 ± 26.1 vs. SAR7334 111.4 ± 38.0 (103 pixels), P = 0.04], respectively. In a cohort of individuals with angiographic follow-up (n = 3068, males: 69.9%, age: 59 ± 11 years, follow-up 217.1 ± 156.4 days), homozygous carriers of a common genetic variant associated with elevated TRPC6 expression were at increased risk of restenosis after coronary stenting (adjusted odds ratio 1.49, 95% confidence interval 1.08–2.05; P = 0.01). Conclusions Our study provides a proteomic atlas of the healthy and injured arterial wall that can be used to define novel factors for therapeutic targeting. We present TRPC6 as an actionable target to prevent neointima formation secondary to vascular injury and stent implantation.
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Affiliation(s)
- Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Planegg, Germany
| | - Julia Werner
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
| | - Jana Wobst
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e. V.), partner site Munich Heart Alliance, Munich, Germany
| | - Adnan Kastrati
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e. V.), partner site Munich Heart Alliance, Munich, Germany
| | - Ganildo Cepele
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
| | - Redouane Aherrahrou
- Department of Biomedical Engineering, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Hendrik B Sager
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e. V.), partner site Munich Heart Alliance, Munich, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,German Centre for Cardiovascular Research (DZHK e. V.), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Veit Flockerzi
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, Homburg, Germany
| | - Mete Civelek
- Department of Biomedical Engineering, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Alexander Dietrich
- Walther-Straub-Institute of Pharmacology and Toxicology, Member of the Center for Lung Research (DZL), Ludwig-Maximilians-University, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Planegg, Germany
| | - Heribert Schunkert
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e. V.), partner site Munich Heart Alliance, Munich, Germany
| | - Thorsten Kessler
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany.,German Centre for Cardiovascular Research (DZHK e. V.), partner site Munich Heart Alliance, Munich, Germany
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7
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Park JE, JebaMercy G, Pazhanchamy K, Guo X, Ngan SC, Liou KCK, Lynn SE, Ng SS, Meng W, Lim SC, Leow MKS, Richards AM, Pennington DJ, de Kleijn DPV, Sorokin V, Ho HH, McCarthy NE, Sze SK. Aging-induced isoDGR-modified fibronectin activates monocytic and endothelial cells to promote atherosclerosis. Atherosclerosis 2021; 324:58-68. [PMID: 33831670 DOI: 10.1016/j.atherosclerosis.2021.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND AIMS Aging is the primary risk factor for cardiovascular disease (CVD), but the mechanisms underlying age-linked atherosclerosis remain unclear. We previously observed that long-lived vascular matrix proteins can acquire 'gain-of-function' isoDGR motifs that might play a role in atherosclerotic pathology. METHODS IsoDGR-specific mAb were generated and used for ELISA-based measurement of motif levels in plasma samples from patients with coronary artery diseases (CAD) and non-CAD controls. Functional consequences of isoDGR accumulation in age-damaged fibronectin were determined by bioassay for capacity to activate monocytes, macrophages, and endothelial cells (signalling activity, pro-inflammatory cytokine expression, and recruitment/adhesion potential). Mice deficient in the isoDGR repair enzyme PCMT1 were used to assess motif distribution and macrophage localisation in vivo. RESULTS IsoDGR-modified fibronectin and fibrinogen levels in patient plasma were significantly enhanced in CAD and further associated with smoking status. Functional assays demonstrated that isoDGR-modified fibronectin activated both monocytes and macrophages via integrin receptor 'outside in' signalling, triggering an ERK:AP-1 cascade and expression of pro-inflammatory cytokines MCP-1 and TNFα to drive additional recruitment of circulating leukocytes. IsoDGR-modified fibronectin also induced endothelial cell expression of integrin β1 to further enhance cellular adhesion and matrix deposition. Analysis of murine aortic tissues confirmed accumulation of isoDGR-modified proteins co-localised with CD68+ macrophages in vivo. CONCLUSIONS Age-damaged fibronectin features isoDGR motifs that increase binding to integrins on the surface of monocytes, macrophages, and endothelial cells. Subsequent activation of 'outside-in' signalling elicits a range of potent cytokines and chemokines that drive additional leukocyte recruitment to the developing atherosclerotic matrix.
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Affiliation(s)
- Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Gnanasekaran JebaMercy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Kalailingam Pazhanchamy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Xue Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - SoFong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Ken Cheng Kang Liou
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Soe EinSi Lynn
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Ser Sue Ng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Wei Meng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551
| | - Su Chi Lim
- Diabetes Center, Khoo Teck Puat Hospital, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Melvin Khee-Shing Leow
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore; Lee Kong Chian School of Medicine, NTU, Singapore; Department of Endocrinology, Tan Tock Seng Hospital, Singapore
| | - A Mark Richards
- Cardiovascular Research Institute, National University of Singapore, Singapore, 119228; Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, 8140, New Zealand
| | - Daniel J Pennington
- Centre for Immunobiology, The Blizard Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, UMC Utrecht, Utrecht University, Utrecht, the Netherlands; Netherlands Heart Institute, Utrecht, the Netherlands
| | - Vitaly Sorokin
- Department of Cardiac, Thoracic and Vascular Surgery, National University Heart Centre, National University Health System, Singapore, 119228
| | - Hee Hwa Ho
- Department of Cardiology, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433
| | - Neil E McCarthy
- Centre for Immunobiology, The Blizard Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551.
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8
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Sze SK, JebaMercy G, Ngan SC. Profiling the 'deamidome' of complex biosamples using mixed-mode chromatography-coupled tandem mass spectrometry. Methods 2020; 200:31-41. [PMID: 32418626 DOI: 10.1016/j.ymeth.2020.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/26/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Deamidation is a spontaneous degenerative protein modification (DPM) that disrupts the structure and function of both endogenous proteins and various therapeutic agents. While deamidation has long been recognized as a critical event in human aging and multiple degenerative diseases, research progress in this field has been restricted by the technical challenges associated with studying this DPM in complex biological samples. Asparagine (Asn) deamidation generates L-aspartic acid (L-Asp), D-aspartic acid (D-Asp), L-isoaspartic acid (L-isoAsp) or D-isoaspartic acid (D-isoAsp) residues at the same position of Asn in the affected protein, but each of these amino acids displays similar hydrophobicity and cannot be effectively separated by reverse phase liquid chromatography. The Asp and isoAsp isoforms are also difficult to resolve using mass spectrometry since they have the same mass and fragmentation pattern in MS/MS. Moreover, the 13C peaks of the amidated peptide are often misassigned as monoisotopic peaks of the corresponding deamidated peptides in protein database searches. Furthermore, typical protein isolation and proteomic sample preparation methods induce artificial deamidation that cannot be distinguished from the physiological forms. To better understand the role of deamidation in biological aging and degenerative pathologies, new technologies are now being developed to address these analytical challenges, including mixed mode electrostatic-interaction modified hydrophilic interaction liquid chromatography (emHILIC). When coupled to high resolution, high accuracy tandem mass spectrometry this technology enables unprecedented, proteome-wide study of the 'deamidome' of complex samples. The current article therefore reviews recent advances in sample preparation methods, emHILIC-MS/MS technology, and MS instrumentation / data processing approaches to achieving accurate and reliable characterization of protein deamidation in complex biological and clinical samples.
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Affiliation(s)
- Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Gnanasekaran JebaMercy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - SoFong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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9
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Parker SJ, Chen L, Spivia W, Saylor G, Mao C, Venkatraman V, Holewinski RJ, Mastali M, Pandey R, Athas G, Yu G, Fu Q, Troxlair D, Vander Heide R, Herrington D, Van Eyk JE, Wang Y. Identification of Putative Early Atherosclerosis Biomarkers by Unsupervised Deconvolution of Heterogeneous Vascular Proteomes. J Proteome Res 2020; 19:2794-2806. [PMID: 32202800 DOI: 10.1021/acs.jproteome.0c00118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coronary artery disease remains a leading cause of death in industrialized nations, and early detection of disease is a critical intervention target to effectively treat patients and manage risk. Proteomic analysis of mixed tissue homogenates may obscure subtle protein changes that occur uniquely in underlying tissue subtypes. The unsupervised 'convex analysis of mixtures' (CAM) tool has previously been shown to effectively segregate cellular subtypes from mixed expression data. In this study, we hypothesized that CAM would identify proteomic information specifically informative to early atherosclerosis lesion involvement that could lead to potential markers of early disease detection. We quantified the proteome of 99 paired abdominal aorta (AA) and left anterior descending coronary artery (LAD) specimens (N = 198 specimens total) acquired during autopsy of young adults free of diagnosed cardiac disease. The CAM tool was then used to segregate protein subsets uniquely associated with different underlying tissue types, yielding markers of normal and fibrous plaque (FP) tissues in LAD and AA (N = 62 lesions markers). CAM-derived FP marker expression was validated against pathologist estimated luminal surface involvement of FP, as well as in an orthogonal cohort of "pure" fibrous plaque, fatty streak, and normal vascular specimens. A targeted mass spectrometry (MS) assay quantified 39 of 62 CAM-FP markers in plasma from women with angiographically verified coronary artery disease (CAD, N = 46) or free from apparent CAD (control, N = 40). Elastic net variable selection with logistic regression reduced this list to 10 proteins capable of classifying CAD status in this cohort with <6% misclassification error, and a mean area under the receiver operating characteristic curve of 0.992 (confidence interval 0.968-0.998) after cross validation. The proteomics-CAM workflow identified lesion-specific molecular biomarker candidates by distilling the most representative molecules from heterogeneous tissue types.
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Affiliation(s)
- Sarah J Parker
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Lulu Chen
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia 24061, United States
| | - Weston Spivia
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Georgia Saylor
- Department of Cardiovascular Medicine, Wake Forest University, Winston-Salem, North Carolina 27101, United States
| | - Chunhong Mao
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Vidya Venkatraman
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Ronald J Holewinski
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Mitra Mastali
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Rakhi Pandey
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Grace Athas
- Department of Pathology, Louisiana State University, New Orleans, Louisiana 70112, United States
| | - Guoqiang Yu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia 24061, United States
| | - Qin Fu
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Dana Troxlair
- Department of Pathology, Louisiana State University, New Orleans, Louisiana 70112, United States
| | - Richard Vander Heide
- Department of Pathology, Louisiana State University, New Orleans, Louisiana 70112, United States
| | - David Herrington
- Department of Cardiovascular Medicine, Wake Forest University, Winston-Salem, North Carolina 27101, United States
| | - Jennifer E Van Eyk
- Heart Institute & Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, Virginia 24061, United States
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10
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Functional pathways associated with human carotid atheroma: a proteomics analysis. Hypertens Res 2019; 42:362-373. [PMID: 30617313 DOI: 10.1038/s41440-018-0192-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/24/2018] [Accepted: 08/14/2018] [Indexed: 01/14/2023]
Abstract
Advances in large-scale analysis are becoming very useful in understanding health and disease. Here, we used high-throughput mass spectrometry to identify differentially expressed proteins between early and advanced lesions. Carotid endarterectomy samples were collected and dissected into early and advanced atherosclerotic lesion portions. Proteins were extracted and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Differentially expressed proteins were identified and verified using multiple reaction monitoring (MRM), on which advanced systems biology and enrichment analyses were performed. The identified proteins were further compared to the transcriptomic data of 32 paired samples obtained from early and advanced atherosclerotic lesions. A total of 95 proteins were upregulated, and 117 proteins were downregulated in advanced lesions compared to early atherosclerotic lesions (p < 0.05). The upregulated proteins were associated with proatherogenic processes, whereas downregulated proteins were involved in extracellular matrix organization and vascular smooth muscle cytoskeleton. Many of the identified proteins were linked to various "upstream regulators", among which TGFβ had the highest connections. Specifically, a total of 19 genes were commonly upregulated, and 30 genes were downregulated at the mRNA and protein levels. These genes were involved in vascular smooth muscle cell activity, for which enriched transcription factors were identified. This study deciphers altered pathways in atherosclerosis and identifies upstream regulators that could be candidate targets for treatment.
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11
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Hansmeier N, Buttigieg J, Kumar P, Pelle S, Choi KY, Kopriva D, Chao TC. Identification of Mature Atherosclerotic Plaque Proteome Signatures Using Data-Independent Acquisition Mass Spectrometry. J Proteome Res 2017; 17:164-176. [DOI: 10.1021/acs.jproteome.7b00487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Nicole Hansmeier
- Department
of Biology/Chemistry, Division of Microbiology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Josef Buttigieg
- Department
of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada
| | - Pankaj Kumar
- Department
of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada
| | - Shaneen Pelle
- Department
of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada
| | - Kyoo Yoon Choi
- Department
of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada
| | - David Kopriva
- Regina Qu’Appelle Health Region and University of Saskatchewan, 1440-14th Avenue, Regina, Saskatchewan S4P 0W5, Canada
| | - Tzu-Chiao Chao
- Department
of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S 0A2, Canada
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12
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Ucciferri N, Rocchiccioli S, Comelli L, Marconi M, Ferrari M, Pelosi G, Cecchettini A. Extracellular matrix characterization in plaques from carotid endarterectomy by a proteomics approach. Talanta 2017; 174:341-346. [DOI: 10.1016/j.talanta.2017.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 05/19/2017] [Accepted: 06/02/2017] [Indexed: 11/30/2022]
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13
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Monocyte adhesion to atherosclerotic matrix proteins is enhanced by Asn-Gly-Arg deamidation. Sci Rep 2017; 7:5765. [PMID: 28720870 PMCID: PMC5515959 DOI: 10.1038/s41598-017-06202-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/09/2017] [Indexed: 12/25/2022] Open
Abstract
Atherosclerosis arises from leukocyte infiltration and thickening of the artery walls and constitutes a major component of vascular disease pathology, but the molecular events underpinning this process are not fully understood. Proteins containing an Asn-Gly-Arg (NGR) motif readily undergo deamidation of asparagine to generate isoDGR structures that bind to integrin αvβ3 on circulating leukocytes. Here we report the identification of isoDGR motifs in human atherosclerotic plaque components including extracellular matrix (ECM) proteins fibronectin and tenascin C, which have been strongly implicated in human atherosclerosis. We further demonstrate that deamidation of NGR motifs in fibronectin and tenascin C leads to increased adhesion of the monocytic cell line U937 and enhanced binding of primary human monocytes, except in the presence of a αvβ3-blocking antibody or the αv-selective inhibitor cilengitide. In contrast, under the same deamidating conditions monocyte-macrophages displayed only weak binding to the alternative ECM component vitronectin which lacks NGR motifs. Together, these findings confirm a critical role for isoDGR motifs in mediating leukocyte adhesion to the ECM via integrin αvβ3 and suggest that protein deamidation may promote the pathological progression of human atherosclerosis by enhancing monocyte recruitment to developing plaques.
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14
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Mokou M, Lygirou V, Vlahou A, Mischak H. Proteomics in cardiovascular disease: recent progress and clinical implication and implementation. Expert Rev Proteomics 2017; 14:117-136. [DOI: 10.1080/14789450.2017.1274653] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marika Mokou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Harald Mischak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
- Mosaiques Diagnostics, Hannover, Germany
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15
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Zhang S, Weng T, Cheruba E, Guo T, Chan H, Sze SK, Koh CG. Phosphatase POPX2 Exhibits Dual Regulatory Functions in Cancer Metastasis. J Proteome Res 2016; 16:698-711. [PMID: 27976581 DOI: 10.1021/acs.jproteome.6b00748] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer metastasis is a complex mechanism involving multiple processes. Previously, our integrative proteome, transcriptome, and phosphoproteome study reported that the levels of serine/threonine phosphatase POPX2 were positively correlated with cancer cell motility through modulating MAPK signaling. Surprisingly, here we found that POPX2 knockdown cells induced more numerous and larger tumor nodules in lungs in longer term animal studies. Interestingly, our analysis of DNA microarray data from cancer patient samples that are available in public databases shows that low POPX2 expression is linked to distant metastasis and poor survival rate. These observations suggest that lower levels of POPX2 may favor tumor progression in later stages of metastasis. We hypothesize that POPX2 may do so by modulation of angiogenesis. Secretome analysis of POPX2-knockdown MDA-MB-231 cells using LC-MS/MS-based SILAC quantitative proteomics and cytokine array show that silencing of POPX2 leads to increased secretion of exosomes, which may, in turn, induce multiple pro-angiogenic cytokines. This study, combined with our previous findings, suggests that a single ubiquitously expressed phosphatase POPX2 influences cancer metastasis via modulating multiple biological processes including MAPK signaling and exosome cytokine secretion.
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Affiliation(s)
- Songjing Zhang
- School of Biological Sciences, Nanyang Technological University , Singapore 637551.,Mechanobiology Institute , Singapore 117411
| | - Ting Weng
- School of Biological Sciences, Nanyang Technological University , Singapore 637551.,Mechanobiology Institute , Singapore 117411
| | | | - Tiannan Guo
- School of Biological Sciences, Nanyang Technological University , Singapore 637551
| | - Hei Chan
- School of Biological Sciences, Nanyang Technological University , Singapore 637551
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University , Singapore 637551
| | - Cheng-Gee Koh
- School of Biological Sciences, Nanyang Technological University , Singapore 637551.,Mechanobiology Institute , Singapore 117411
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16
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Adav SS, Sze SK. Insight of brain degenerative protein modifications in the pathology of neurodegeneration and dementia by proteomic profiling. Mol Brain 2016; 9:92. [PMID: 27809929 PMCID: PMC5094070 DOI: 10.1186/s13041-016-0272-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/16/2016] [Indexed: 02/06/2023] Open
Abstract
Dementia is a syndrome associated with a wide range of clinical features including progressive cognitive decline and patient inability to self-care. Due to rapidly increasing prevalence in aging society, dementia now confers a major economic, social, and healthcare burden throughout the world, and has therefore been identified as a public health priority by the World Health Organization. Previous studies have established dementia as a 'proteinopathy' caused by detrimental changes in brain protein structure and function that promote misfolding, aggregation, and deposition as insoluble amyloid plaques. Despite clear evidence that pathological cognitive decline is associated with degenerative protein modifications (DPMs) arising from spontaneous chemical modifications to amino acid side chains, the molecular mechanisms that promote brain DPMs formation remain poorly understood. However, the technical challenges associated with DPM analysis have recently become tractable due to powerful new proteomic techniques that facilitate detailed analysis of brain tissue damage over time. Recent studies have identified that neurodegenerative diseases are associated with the dysregulation of critical repair enzymes, as well as the misfolding, aggregation and accumulation of modified brain proteins. Future studies will further elucidate the mechanisms underlying dementia pathogenesis via the quantitative profiling of the human brain proteome and associated DPMs in distinct phases and subtypes of disease. This review summarizes recent developments in quantitative proteomic technologies, describes how these techniques have been applied to the study of dementia-linked changes in brain protein structure and function, and briefly outlines how these findings might be translated into novel clinical applications for dementia patients. In this review, only spontaneous protein modifications such as deamidation, oxidation, nitration glycation and carbamylation are reviewed and discussed.
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Affiliation(s)
- Sunil S. Adav
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Siu Kwan Sze
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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17
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Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms. Nat Commun 2016; 7:10750. [PMID: 26892159 PMCID: PMC4762895 DOI: 10.1038/ncomms10750] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 01/18/2016] [Indexed: 11/26/2022] Open
Abstract
Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a ‘last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections. Pathogenic bacteria can aggregate to form biofilms and develop tolerance to antibiotics. Here, the authors use a proteomics approach to study the development of tolerance to the antibiotic colistin in Pseudomonas aeruginosa biofilms, and show that co-treatment with a second compound kills the tolerant cells.
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18
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Zhang Y, Bilbao A, Bruderer T, Luban J, Strambio-De-Castillia C, Lisacek F, Hopfgartner G, Varesio E. The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition. J Proteome Res 2015; 14:4359-71. [PMID: 26302369 DOI: 10.1021/acs.jproteome.5b00543] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As tryptic peptides and metabolites are not equally distributed along the mass range, the probability of cross fragment ion interference is higher in certain windows when fixed Q1 SWATH windows are applied. We evaluated the benefits of utilizing variable Q1 SWATH windows with regards to selectivity improvement. Variable windows based on equalizing the distribution of either the precursor ion population (PIP) or the total ion current (TIC) within each window were generated by an in-house software, swathTUNER. These two variable Q1 SWATH window strategies outperformed, with respect to quantification and identification, the basic approach using a fixed window width (FIX) for proteomic profiling of human monocyte-derived dendritic cells (MDDCs). Thus, 13.8 and 8.4% additional peptide precursors, which resulted in 13.1 and 10.0% more proteins, were confidently identified by SWATH using the strategy PIP and TIC, respectively, in the MDDC proteomic sample. On the basis of the spectral library purity score, some improvement warranted by variable Q1 windows was also observed, albeit to a lesser extent, in the metabolomic profiling of human urine. We show that the novel concept of "scheduled SWATH" proposed here, which incorporates (i) variable isolation windows and (ii) precursor retention time segmentation further improves both peptide and metabolite identifications.
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Affiliation(s)
- Ying Zhang
- University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland
| | - Aivett Bilbao
- University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland.,SIB Swiss Institute of Bioinformatics , Proteome Informatics Group, Geneva, Switzerland
| | - Tobias Bruderer
- University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland
| | - Jeremy Luban
- University of Massachusetts , Medical School, Program in Molecular Medicine, Worcester, Massachusetts 01605, United States
| | - Caterina Strambio-De-Castillia
- University of Massachusetts , Medical School, Program in Molecular Medicine, Worcester, Massachusetts 01605, United States
| | - Frédérique Lisacek
- SIB Swiss Institute of Bioinformatics , Proteome Informatics Group, Geneva, Switzerland.,University of Geneva , Faculty of Sciences, Geneva, Switzerland
| | - Gérard Hopfgartner
- University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland
| | - Emmanuel Varesio
- University of Geneva , Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, Geneva, Switzerland
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19
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Delporte C, Noyon C, Raynal P, Dufour D, Nève J, Abts F, Haex M, Zouaoui Boudjeltia K, Van Antwerpen P. Advancement in stationary phase for peptide separation helps in protein identification: Application to atheroma plaque proteomics using nano-chip liquid chromatography and mass spectrometry. J Chromatogr A 2015; 1385:116-23. [DOI: 10.1016/j.chroma.2015.01.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/01/2015] [Accepted: 01/14/2015] [Indexed: 12/14/2022]
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