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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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2
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HDL-Associated Proteins in Subjects with Polycystic Ovary Syndrome: A Proteomic Study. Cells 2023; 12:cells12060855. [PMID: 36980195 PMCID: PMC10047209 DOI: 10.3390/cells12060855] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Introduction. Serum lipoproteins, with the exception of high-density lipoprotein cholesterol (HDL-C), are increased in polycystic ovary syndrome (PCOS) and their levels may reflect the associated obesity and insulin resistance, but the nature of this association is not fully explained. Therefore, proteomic analysis of key proteins in lipoprotein metabolism was performed. Methods. In this cohort study, plasma was collected from 234 women (137 with PCOS and 97 controls without PCOS). Somalogic proteomic analysis was undertaken for the following 19 proteins involved in lipoprotein, and particularly HDL, metabolism: alpha-1-antichymotrypsin; alpha-1-antitrypsin; apolipoproteins A-1, B, D, E, E2, E3, E4, L1, and M; clusterin; complement C3; hemopexin; heparin cofactor II; kininogen-1; serum amyloid A-1; amyloid beta A-4; and paraoxonase-1. Results. The levels of apolipoprotein E were higher in PCOS (p = 0.012). However, the other isoforms of ApoE, ApoE2, E3, and E4, did not differ when compared with controls. ApoM was lower in PCOS (p = 0.000002). Complement C3 was higher in PCOS (p = 0.037), as was heparin cofactor II (HCFII) (p = 0.0004). The levels of the other proteins associated with lipoprotein metabolism did not differ between PCOS and controls. Conclusions. These data contribute to the concern of the deleterious dyslipidemia found in PCOS, with the novel combination reported here of higher levels of ApoE, C3 and HCFII together with lower ApoM. The dysregulation of these proteins could circumvent the protective effect of HDL-C and contribute to a more atherogenic profile that may increase cardiovascular risk.
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Vyletelová V, Nováková M, Pašková Ľ. Alterations of HDL's to piHDL's Proteome in Patients with Chronic Inflammatory Diseases, and HDL-Targeted Therapies. Pharmaceuticals (Basel) 2022; 15:1278. [PMID: 36297390 PMCID: PMC9611871 DOI: 10.3390/ph15101278] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/03/2022] [Accepted: 10/14/2022] [Indexed: 09/10/2023] Open
Abstract
Chronic inflammatory diseases, such as rheumatoid arthritis, steatohepatitis, periodontitis, chronic kidney disease, and others are associated with an increased risk of atherosclerotic cardiovascular disease, which persists even after accounting for traditional cardiac risk factors. The common factor linking these diseases to accelerated atherosclerosis is chronic systemic low-grade inflammation triggering changes in lipoprotein structure and metabolism. HDL, an independent marker of cardiovascular risk, is a lipoprotein particle with numerous important anti-atherogenic properties. Besides the essential role in reverse cholesterol transport, HDL possesses antioxidative, anti-inflammatory, antiapoptotic, and antithrombotic properties. Inflammation and inflammation-associated pathologies can cause modifications in HDL's proteome and lipidome, transforming HDL from atheroprotective into a pro-atherosclerotic lipoprotein. Therefore, a simple increase in HDL concentration in patients with inflammatory diseases has not led to the desired anti-atherogenic outcome. In this review, the functions of individual protein components of HDL, rendering them either anti-inflammatory or pro-inflammatory are described in detail. Alterations of HDL proteome (such as replacing atheroprotective proteins by pro-inflammatory proteins, or posttranslational modifications) in patients with chronic inflammatory diseases and their impact on cardiovascular health are discussed. Finally, molecular, and clinical aspects of HDL-targeted therapies, including those used in therapeutical practice, drugs in clinical trials, and experimental drugs are comprehensively summarised.
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Affiliation(s)
| | | | - Ľudmila Pašková
- Department of Cell and Molecular Biology of Drugs, Faculty of Pharmacy, Comenius University, 83232 Bratislava, Slovakia
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4
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Xu Y, Wu S, Wang P, Wei L, Li H. Label-free quantitative proteomic analysis of the mechanism of salt stress promoting selenium enrichment in Lactobacillus rhamnosus. J Proteomics 2022; 265:104663. [PMID: 35738527 DOI: 10.1016/j.jprot.2022.104663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Lactobacillus rhamnosus can metabolize selenite into organic selenium and Se0. In this paper, label-free quantitative proteomics was applied to explore the mechanism of salt stress promoting selenium enrichment of L.rhamnosus. 397 proteins were up-regulated and 147 proteins were down-regulated of selenium-enriched L.rhamnosus under salt stress. The differentially expressed proteins (DEPs) were mainly involved in metabolism, membrane transport and genetic information processing. The results of quantitative real-time PCR showed that gene opuA, metN, trxR and ldh of Se-enriched L.rhamnosus with salt stress were significantly up-regulated. However, the expression levels of gene luxS, groEL, dnaK and pgk were down-regulated. It was indicated that L.rhamnosus promoted part of amino acids combining with selenium into selenoamino acids with salt stress. Secondly, sodium chloride stimulated the expression of key enzymes involved in metabolism to provide energy for the process of Se-enrichment. In addition, NaCl induced the expression of enzymes and genes involved in the synthesis of selenoproteins. SIGNIFICANCE: It was indicated that L.rhamnosus promoted part of amino acids combining with selenium into selenoamino acids with salt stress. Secondly, sodium chloride stimulated the expression of key enzymes involved in metabolism to provide energy for the process of Se-enrichment. In addition, NaCl induced the expression of enzymes and genes involved in the synthesis of selenoproteins.
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Affiliation(s)
- Ying Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Shufang Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Panxue Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Lina Wei
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Hongliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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Yin X, Takov K, Straube R, Voit-Bak K, Graessler J, Julius U, Tselmin S, Rodionov RN, Barbir M, Walls M, Theofilatos K, Mayr M, Bornstein SR. Precision Medicine Approach for Cardiometabolic Risk Factors in Therapeutic Apheresis. Horm Metab Res 2022; 54:238-249. [PMID: 35413745 DOI: 10.1055/a-1776-7943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Lipoprotein apheresis (LA) is currently the most powerful intervention possible to reach a maximal reduction of lipids in patients with familial hypercholesterolemia and lipoprotein(a) hyperlipidemia. Although LA is an invasive method, it has few side effects and the best results in preventing further major cardiovascular events. It has been suggested that the highly significant reduction of cardiovascular complications in patients with severe lipid disorders achieved by LA is mediated not only by the potent reduction of lipid levels but also by the removal of other proinflammatory and proatherogenic factors. Here we performed a comprehensive proteomic analysis of patients on LA treatment using intra-individually a set of differently sized apheresis filters with the INUSpheresis system. This study revealed that proteomic analysis correlates well with routine clinical chemistry in these patients. The method is eminently suited to discover new biomarkers and risk factors for cardiovascular disease in these patients. Different filters achieve reduction and removal of proatherogenic proteins in different quantities. This includes not only apolipoproteins, C-reactive protein, fibrinogen, and plasminogen but also proteins like complement factor B (CFAB), protein AMBP, afamin, and the low affinity immunoglobulin gamma Fc region receptor III-A (FcγRIIIa) among others that have been described as atherosclerosis and metabolic vascular diseases promoting factors. We therefore conclude that future trials should be designed to develop an individualized therapy approach for patients on LA based on their metabolic and vascular risk profile. Furthermore, the power of such cascade filter treatment protocols may improve the prevention of cardiometabolic disease and its complications.
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Affiliation(s)
- X Yin
- Kings College London, London, UK
| | - K Takov
- Kings College London, London, UK
| | - R Straube
- Zentrum für Apherese- und Hämofiltration am INUS Tagesklinikum, Cham, Germany
| | - K Voit-Bak
- Zentrum für Apherese- und Hämofiltration am INUS Tagesklinikum, Cham, Germany
| | - J Graessler
- Department and Outpatient Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
| | - U Julius
- Department and Outpatient Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
| | - S Tselmin
- Department and Outpatient Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Roman N Rodionov
- Department and Outpatient Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
| | - M Barbir
- Royal Brompton Hospital, London, UK
| | | | | | - M Mayr
- Kings College London, London, UK
- Technische Universität Dresden, Dresden, Germany
| | - S R Bornstein
- Kings College London, London, UK
- Department and Outpatient Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany
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Wang W, Wu J, Liu P, Tang X, Pang H, Xie T, Xu F, Shao J, Chen Y, Liu B, Zheng Y. Urinary Proteomics Identifying Novel Biomarkers for the Diagnosis and Phenotyping of Carotid Artery Stenosis. Front Mol Biosci 2021; 8:714706. [PMID: 34447787 PMCID: PMC8383446 DOI: 10.3389/fmolb.2021.714706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/26/2021] [Indexed: 01/12/2023] Open
Abstract
Background: Carotid artery stenosis (CAS) is caused by the formation of atherosclerotic plaques inside the arterial wall and accounts for 20–30% of all strokes. The development of an early, noninvasive diagnostic method and the identification of high-risk patients for ischemic stroke is essential to the management of CAS in clinical practice. Methods: We used the data-independent acquisition (DIA) technique to conduct a urinary proteomic study in patients with CAS and healthy controls. We identified the potential diagnosis and risk stratification biomarkers of CAS. And Ingenuity pathway analysis was used for functional annotation of differentially expressed proteins (DEPs). Furthermore, receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic values of DEPs. Results: A total of 194 DEPs were identified between CAS patients and healthy controls by DIA quantification. The bioinformatics analysis showed that these DEPs were correlated with the pathogenesis of CAS. We further identified 32 DEPs in symptomatic CAS compared to asymptomatic CAS, and biological function analysis revealed that these proteins are mainly related to immune/inflammatory pathways. Finally, a biomarker panel of six proteins (ACP2, PLD3, HLA-C, GGH, CALML3, and IL2RB) exhibited potential diagnostic value in CAS and good discriminative power for differentiating symptomatic and asymptomatic CAS with high sensitivity and specificity. Conclusions: Our study identified novel potential urinary biomarkers for noninvasive early screening and risk stratification of CAS.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianqiang Wu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Liu
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyue Tang
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiyu Pang
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Xie
- State Key Laboratory of Complex Severe and Rare Diseases, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fang Xu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiang Shao
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuexin Chen
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bao Liu
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuehong Zheng
- State Key Laboratory of Complex Severe and Rare Disease, Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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7
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Shin JW, Lee JH, Kim H, Lee DH, Baek KH, Sunwoo JS, Byun JI, Kim TJ, Jun JS, Han D, Jung KY. Bioinformatic analysis of proteomic data for iron, inflammation, and hypoxic pathways in restless legs syndrome. Sleep Med 2020; 75:448-455. [PMID: 32992101 DOI: 10.1016/j.sleep.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/13/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE/BACKGROUND We performed bioinformatic analysis of proteomic data to identify the biomarkers of restless legs syndrome (RLS) and provide insights into the putative pathomechanisms, including iron deficiency, inflammation, and hypoxic pathways. PATIENTS/METHODS Patients with drug-naïve idiopathic RLS were recruited at a university hospital from June 2017 to February 2018. Serum samples from patients with RLS (n = 7) and healthy sex- and age-matched controls (n = 6) were evaluated by proteomic analysis. For differentially expressed proteins (DEPs) in patients with RLS, compared to those in controls, the expression profiles and protein-protein interaction (PPI) network were characterized between dysregulated proteins and extracted proteins involved in iron deficiency, hypoxia, and inflammation responses using the String database (http://string-DB.org). The PPI network was visualized by Cytoscape ver. 3. 7. 1. Statistical analyses of the validation Western blot assays were performed using a Student's t-test. RESULTS Interactome network analysis revealed a relationship among the eight proteins, their associated genes, and 150, 47, and 11 proteins related to iron deficiency, inflammation, and hypoxic pathways, respectively. All DEPs were well associated with inflammation, and complement 3, complement C4A, alpha-2 HS glycoprotein, and alpha-2 macroglobulin precursor were found to be in hub positions of networks involved in PPIs including iron deficiency, hypoxia pathway, and inflammation. C3 and C4A were verified using western blotting. CONCLUSIONS We identified key molecules that represent the selected cellular pathways as protein biomarkers by PPI network analysis. Changes in inflammation can mediate or affect the pathomechanism of RLS and can thus act as systemic biomarkers.
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Affiliation(s)
- Jung-Won Shin
- Department of Neurology, CHA University, Bundang CHA Medical Center, Republic of Korea
| | - Jung-Hun Lee
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Republic of Korea
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Republic of Korea
| | - Da-Hye Lee
- Department of Biomedical Science, CHA University, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, Republic of Korea
| | - Jun-Sang Sunwoo
- Department of Neurosurgery, Seoul National University Hospital, Republic of Korea
| | - Jung-Ick Byun
- Department of Neurology, Kyung Hee University Hospital at Gangdong, Republic of Korea
| | - Tae-Joon Kim
- Department of Neurology, Ajou University School of Medicine, Republic of Korea
| | - Jin-Sun Jun
- Department of Neurology, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Republic of Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Republic of Korea.
| | - Ki-Young Jung
- Seoul National University College of Medicine, Department of Neurology, Seoul National University Hospital, Republic of Korea.
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Comparative Proteomic Investigation of Plasma Reveals Novel Potential Biomarker Groups for Acute Aortic Dissection. DISEASE MARKERS 2020; 2020:4785068. [PMID: 32256857 PMCID: PMC7106916 DOI: 10.1155/2020/4785068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 12/03/2022]
Abstract
Acute aortic dissection (AAD) is a catastrophic cardiovascular disease with high disability and mortality due to multiple fatal complications. However, the molecular changes of the serum proteome after AAD are not very clear. Here, we performed isobaric tags for relative and absolute quantitation- (iTRAQ-) based comparative proteomic analysis to investigate the proteome profile changes after AAD by collecting plasma samples from 20 AAD patients and 20 controls. Out of the 345 identified proteins, 266 were considered as high-quality quantified proteins (95%confident peptides ≥ 2), of which 25 proteins were accumulated and 12 were reduced in AAD samples. Gene ontology enrichment analysis showed that the 25 AAD-accumulated proteins were enriched in high-density lipoprotein particles for the cellular component category and protein homodimerization acidity for the molecular function category. Protein-protein interaction network analysis showed that serum amyloid A proteins (SAAs), complement component proteins, and carboxypeptidase N catalytic chain proteins (CPNs) possessed the key nodes of the network. The expression levels of six selected AAD-accumulated proteins, B2-GP1, CPN1, F9, LBP, SAA1, and SAA2, were validated by ELISA. Moreover, ROC analysis showed that the AUCs of B2-GP1 and CPN1 were 0.808 and 0.702, respectively. Our data provide insights into molecular change profiles in proteome levels after AAD and indicate that B2-GP1 and CPN1 are potential biomarkers for AAD.
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Wang Z, Korantzopoulos P, Liu T. Carotid Atherosclerosis in Patients with Atrial Fibrillation. Curr Atheroscler Rep 2019; 21:55. [PMID: 31781980 DOI: 10.1007/s11883-019-0808-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW This review aims to explore the relationship between AF and carotid atherosclerosis, and the impact on the outcomes of cardiovascular and cerebrovascular events. Also, our aim is to critically review current knowledge and delineate future directions for effective treatment or prevention as well as strategies for improvement of the quality of life and survival. RECENT FINDINGS Atrial fibrillation (AF) is the most common arrhythmia, increasing the risk of stroke and cardiovascular morbidity and mortality representing a significant worldwide public health problem. On the other hand, carotid artery atherosclerosis can also significantly increase the risk of stroke, transient ischemic attack (TIA), and death. Firstly, we report epidemiological data on AF patients in different countries and regions having carotid artery abnormalities such as carotid artery plaque formation, atherosclerotic, and even stenosis. Despite geographical variations, these abnormalities were more frequent in AF patients and correlated with the duration of AF and the value of CHA2DS2-VASc score. Moreover, it is evident that AF patients with carotid artery abnormalities have significantly increased risk of adverse outcomes from the heart and brain. According to the CHA(2)DS2 (-VASc) score, AF patients are managed with anticoagulation therapy. Reviewing existing data on the treatment for stroke prevention in patients with AF, carotid artery disease, or both, we found that antiplatelet therapy could be combined with anticoagulant therapy appropriately in certain circumstances. In addition, some emerging technologies, such as the percutaneous permanent carotid filter, may be used safely and effectively to prevent the occurrence of stroke in patients both with AF and carotid artery atherosclerosis.
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Affiliation(s)
- Zhaojia Wang
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | | | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, China.
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10
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iTRAQ-based proteomic analysis of responses of Lactobacillus plantarum FS5-5 to salt tolerance. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1425-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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11
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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12
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Jiang TT, Shi LY, Chen J, Wei LL, Li M, Hu YT, Gan L, Liu CM, Tu HH, Li ZB, Yi WJ, Li JC. Screening and identification of potential protein biomarkers for evaluating the efficacy of intensive therapy in pulmonary tuberculosis. Biochem Biophys Res Commun 2018; 503:2263-2270. [PMID: 29959917 DOI: 10.1016/j.bbrc.2018.06.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 11/16/2022]
Abstract
This research aimed to discover potential biomarkers for evaluating the therapeutic efficacy of intensive therapy in pulmonary tuberculosis (TB). Protein profiles in 2-months intensively treated TB patients, untreated TB patients, and healthy controls were investigated with iTRAQ-2DLC-MS/MS technique. 71 differential proteins were identified in 2-months intensively treated TB patients. Significant differences in complement component C7 (CO7), apolipoprotein A-IV (APOA4), apolipoprotein C-II (APOC2), and angiotensinogen (ANGT) were found by ELISA validation. CO7 and ANGT were also found significantly different in sputum negative patients, compared with sputum positive patients after intensive treatment. Clinical analysis showed that after 2-months intensive treatment several indicators were significantly changed, and the one-year cure rate of sputum negative patients were significantly higher than sputum positive patients. Diagnostic models consisting of APOC2, CO7 and APOA4 were established to distinguish intensively treated TB patients from untreated TB patients and healthy controls with the AUC value of 0.910 and 0.935. Meanwhile, ANGT and CO7 were combined to identify sputum negative and sputum positive TB patients after intensive treatment with 89.36% sensitivity, 71.43% specificity, and the AUC value of 0.853. The results showed that APOC2, CO7, APOA4, and ANGT may be potential biomarkers for evaluating the efficacy of intensive anti-TB therapy.
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Affiliation(s)
- Ting-Ting Jiang
- South China University of Technology School of Medicine, Guangzhou, 510006, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310013, China
| | - Jing Chen
- Institute of Cell Biology, Zhejiang University, Hangzhou, 310058, China
| | - Li-Liang Wei
- Department of Pneumology, Shaoxing Municipal Hospital, Shaoxing, 312000, China
| | - Meng Li
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310013, China
| | - Yu-Ting Hu
- South China University of Technology School of Medicine, Guangzhou, 510006, China
| | - Lin Gan
- South China University of Technology School of Medicine, Guangzhou, 510006, China
| | - Chang-Ming Liu
- Institute of Cell Biology, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University, Hangzhou, 310058, China
| | - Zhi-Bin Li
- Institute of Cell Biology, Zhejiang University, Hangzhou, 310058, China
| | - Wen-Jing Yi
- Institute of Cell Biology, Zhejiang University, Hangzhou, 310058, China
| | - Ji-Cheng Li
- South China University of Technology School of Medicine, Guangzhou, 510006, China; Institute of Cell Biology, Zhejiang University, Hangzhou, 310058, China.
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13
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Lygirou V, Latosinska A, Makridakis M, Mullen W, Delles C, Schanstra JP, Zoidakis J, Pieske B, Mischak H, Vlahou A. Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease. J Transl Med 2018; 16:104. [PMID: 29665821 PMCID: PMC5905170 DOI: 10.1186/s12967-018-1476-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/06/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis. METHODS LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change. RESULTS Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related protein 2 [LRP2], protein SZT2) for which a mechanism of action is suggested. CONCLUSIONS This proteomic study provides a comprehensive dataset to be used for integrative and functional studies in the field. The observed protein changes reflect known CVD-related processes (e.g. lipid uptake, inflammation) but also novel hypotheses for further investigation including a potential pleiotropic role of LPR2 but also links of SZT2 to CVD.
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Affiliation(s)
- Vasiliki Lygirou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece
| | | | - Manousos Makridakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jerome Zoidakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece
| | - Burkert Pieske
- Deutsches Herzzentrum Berlin, Augustenburger Pl. 1, 13353, Berlin, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Antonia Vlahou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27, Athens, Greece.
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Hernández-Aguilera A, Nielsen SH, Bonache C, Fernández-Arroyo S, Martín-Paredero V, Fibla M, Karsdal MA, Genovese F, Menendez JA, Camps J, Joven J. Assessment of extracellular matrix-related biomarkers in patients with lower extremity artery disease. J Vasc Surg 2018; 68:1135-1142.e6. [PMID: 29615349 DOI: 10.1016/j.jvs.2017.12.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/21/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND The prevalence of lower extremity artery disease (LEAD) is high (20%-25%) in the population older than 65 years, but patients are seldom identified until the disease is advanced. Circulating markers of disease activity might provide patients with a key opportunity for timely treatment. We tested the hypothesis that measuring blood-specific fragments generated during degradation of the extracellular matrix (ECM) could provide further insight into the pathophysiologic mechanism of arterial remodeling. METHODS The protein profile of diseased arteries from patients undergoing infrainguinal limb revascularization was assessed by a liquid chromatography and tandem mass spectrometry, nontargeted proteomic approach. The information retrieved was the basis for measurement of neoepitope fragments of ECM proteins in the blood of 195 consecutive patients with LEAD by specific enzyme-linked immunosorbent assays. RESULTS Histologic and proteomic analyses confirmed the structural disorganization of affected arteries. Fourteen of 81 proteins were identified as differentially expressed in diseased arteries with respect to healthy tissues. Most of them were related to ECM components, and the difference in expression was used in multivariate analyses to establish that severe arterial lesions in LEAD patients have a specific proteome. Analysis of neoepitope fragments in blood revealed that fragments of versican and collagen type IV, alone or in combination, segregated patients with mild to moderate symptoms (intermittent claudication, Fontaine I-II) from those with severe LEAD (critical limb ischemia, Fontaine III-IV). CONCLUSIONS We propose noninvasive candidate biomarkers with the ability to be clinically useful across the LEAD spectrum.
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Affiliation(s)
- Anna Hernández-Aguilera
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Signe Holm Nielsen
- Fibrosis Biology and Biomarkers, Nordic Bioscience, Herlev, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cristina Bonache
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | | | - Montserrat Fibla
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain; Department of Pathology, Hospital Universitari Joan XXIII, Tarragona, Spain
| | - Morten A Karsdal
- Fibrosis Biology and Biomarkers, Nordic Bioscience, Herlev, Denmark
| | | | - Javier A Menendez
- Molecular Oncology Group, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain.
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Mourino-Alvarez L, Baldan-Martin M, Rincon R, Martin-Rojas T, Corbacho-Alonso N, Sastre-Oliva T, Barderas MG. Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis. Expert Rev Proteomics 2017; 14:701-713. [PMID: 28689450 DOI: 10.1080/14789450.2017.1353912] [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] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.
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Affiliation(s)
- Laura Mourino-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | | | - Raul Rincon
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tatiana Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Nerea Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tamara Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Maria G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
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