1
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Shelbaya K, Arthur V, Yang Y, Dorbala P, Buckley L, Claggett B, Skali H, Dufresne L, Yang TY, Engert JC, Thanassoulis G, Floyd J, Austin TR, Bortnick A, Kizer J, Freitas RCC, Singh SA, Aikawa E, Hoogeveen RC, Ballantyne C, Yu B, Coresh J, Blaha MJ, Matsushita K, Shah AM. Large-Scale Proteomics Identifies Novel Biomarkers and Circulating Risk Factors for Aortic Stenosis. J Am Coll Cardiol 2024; 83:577-591. [PMID: 38296402 DOI: 10.1016/j.jacc.2023.11.021] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Limited data exist regarding risk factors for aortic stenosis (AS). The plasma proteome is a promising phenotype for discovery of novel biomarkers and potentially causative mechanisms. OBJECTIVES The aim of this study was to discover novel biomarkers with potentially causal associations with AS. METHODS We measured 4,877 plasma proteins (SomaScan aptamer-affinity assay) among ARIC (Atherosclerosis Risk In Communities) study participants in mid-life (visit 3 [V3]; n = 11,430; age 60 ± 6 years) and in late-life (V5; n = 4,899; age 76 ± 5 years). We identified proteins cross-sectionally associated with aortic valve (AV) peak velocity (AVmax) and dimensionless index by echocardiography at V5 and with incident AV-related hospitalization after V3 with the use of multivariable linear and Cox proportional hazard regression. We assessed associations of candidate proteins with changes in AVmax over 6 years and with AV calcification with the use of cardiac computed tomography, replicated analysis in an independent sample, performed Mendelian randomization, and evaluated gene expression in explanted human AV tissue. RESULTS Fifty-two proteins cross-sectionally were associated with AVmax and dimensionless index at V5 and with risk of incident AV-related hospitalization after V3. Among 3,413 participants in the Cardiovascular Health Study, 6 of those proteins were significantly associated with adjudicated moderate or severe AS, including matrix metalloproteinase 12 (MMP12), complement C1q tumor necrosis factor-related protein 1 (C1QTNF1), and growth differentiation factor-15. MMP12 was also associated with greater increase in AVmax over 6 years, greater degree of AV calcification, and greater expression in calcific compared with normal or fibrotic AV tissue. C1QTNF1 had consistent potential causal effects on both AS and AVmax according to Mendelian randomization analysis. CONCLUSIONS These findings identify MMP12 as a potential novel circulating biomarker of AS risk and C1QTNF1 as a new putative target to prevent AS progression.
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Affiliation(s)
| | | | - Yimin Yang
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Pranav Dorbala
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Leo Buckley
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Brian Claggett
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Hicham Skali
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Line Dufresne
- McGill University Health Centre, Montreal, Quebec, Canada
| | - Ta-Yu Yang
- McGill University Health Centre, Montreal, Quebec, Canada
| | - James C Engert
- McGill University Health Centre, Montreal, Quebec, Canada
| | | | - James Floyd
- Cardiovascular Health Research Unit, Seattle, Washington, USA
| | - Thomas R Austin
- Cardiovascular Health Research Unit, Seattle, Washington, USA
| | - Anna Bortnick
- Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jorge Kizer
- Veterans Affairs Medical Center, San Francisco, California, USA
| | | | - Sasha A Singh
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Elena Aikawa
- Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | - Bing Yu
- University of Texas Health Science School of Public Health, Houston, Texas, USA
| | - Josef Coresh
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J Blaha
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Amil M Shah
- Brigham and Women's Hospital, Boston, Massachusetts, USA; University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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2
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Semenova D, Zabirnyk A, Lobov A, Boyarskaya N, Kachanova O, Uspensky V, Zainullina B, Denisov E, Gerashchenko T, Kvitting JPE, Kaljusto ML, Thiede B, Kostareva A, Stensløkken KO, Vaage J, Malashicheva A. Multi-omics of in vitro aortic valve calcification. Front Cardiovasc Med 2022; 9:1043165. [PMID: 36407442 PMCID: PMC9669078 DOI: 10.3389/fcvm.2022.1043165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 09/10/2023] Open
Abstract
Heart valve calcification is an active cellular and molecular process that partly remains unknown. Osteogenic differentiation of valve interstitial cells (VIC) is a central mechanism in calcific aortic valve disease (CAVD). Studying mechanisms in CAVD progression is clearly needed. In this study, we compared molecular mechanisms of osteogenic differentiation of human VIC isolated from healthy donors or patients with CAVD by RNA-seq transcriptomics in early timepoint (48 h) and by shotgun proteomics at later timepoint (10th day). Bioinformatic analysis revealed genes and pathways involved in the regulation of VIC osteogenic differentiation. We found a high amount of stage-specific differentially expressed genes and good accordance between transcriptomic and proteomic data. Functional annotation of differentially expressed proteins revealed that osteogenic differentiation of VIC involved many signaling cascades such as: PI3K-Akt, MAPK, Ras, TNF signaling pathways. Wnt, FoxO, and HIF-1 signaling pathways were modulated only at the early timepoint and thus probably involved in the commitment of VIC to osteogenic differentiation. We also observed a significant shift of some metabolic pathways in the early stage of VIC osteogenic differentiation. Lentiviral overexpression of one of the most upregulated genes (ZBTB16, PLZF) increased calcification of VIC after osteogenic stimulation. Analysis with qPCR and shotgun proteomics suggested a proosteogenic role of ZBTB16 in the early stages of osteogenic differentiation.
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Affiliation(s)
- Daria Semenova
- Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
- Almazov National Medical Research Center Russia, St. Petersburg, Russia
| | - Arsenii Zabirnyk
- Heart Physiology Research Group, Division of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Arseniy Lobov
- Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | | | - Olga Kachanova
- Almazov National Medical Research Center Russia, St. Petersburg, Russia
| | - Vladimir Uspensky
- Almazov National Medical Research Center Russia, St. Petersburg, Russia
| | - Bozhana Zainullina
- Centre for Molecular and Cell Technologies, St. Petersburg State University, St. Petersburg, Russia
| | - Evgeny Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Tatiana Gerashchenko
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - John-Peder Escobar Kvitting
- Heart Physiology Research Group, Division of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | | | - Bernd Thiede
- Heart Physiology Research Group, Division of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anna Kostareva
- Almazov National Medical Research Center Russia, St. Petersburg, Russia
| | - Kåre-Olav Stensløkken
- Heart Physiology Research Group, Division of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jarle Vaage
- Heart Physiology Research Group, Division of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Anna Malashicheva
- Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
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3
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Bogdanova M, Zabirnyk A, Malashicheva A, Semenova D, Kvitting JPE, Kaljusto ML, Perez MDM, Kostareva A, Stensløkken KO, Sullivan GJ, Rutkovskiy A, Vaage J. Models and Techniques to Study Aortic Valve Calcification in Vitro, ex Vivo and in Vivo. An Overview. Front Pharmacol 2022; 13:835825. [PMID: 35721220 PMCID: PMC9203042 DOI: 10.3389/fphar.2022.835825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022] Open
Abstract
Aortic valve stenosis secondary to aortic valve calcification is the most common valve disease in the Western world. Calcification is a result of pathological proliferation and osteogenic differentiation of resident valve interstitial cells. To develop non-surgical treatments, the molecular and cellular mechanisms of pathological calcification must be revealed. In the current overview, we present methods for evaluation of calcification in different ex vivo, in vitro and in vivo situations including imaging in patients. The latter include echocardiography, scanning with computed tomography and magnetic resonance imaging. Particular emphasis is on translational studies of calcific aortic valve stenosis with a special focus on cell culture using human primary cell cultures. Such models are widely used and suitable for screening of drugs against calcification. Animal models are presented, but there is no animal model that faithfully mimics human calcific aortic valve disease. A model of experimentally induced calcification in whole porcine aortic valve leaflets ex vivo is also included. Finally, miscellaneous methods and aspects of aortic valve calcification, such as, for instance, biomarkers are presented.
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Affiliation(s)
- Maria Bogdanova
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Arsenii Zabirnyk
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital, Oslo, Norway
| | - Anna Malashicheva
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Daria Semenova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Mari-Liis Kaljusto
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
| | | | - Anna Kostareva
- Almazov National Medical Research Centre, Saint Petersburg, Russia.,Department of Woman and Children Health, Karolinska Institute, Stockholm, Sweden
| | - Kåre-Olav Stensløkken
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gareth J Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Norwegian Center for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,Institute of Immunology, Oslo University Hospital, Oslo, Norway.,Hybrid Technology Hub - Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Arkady Rutkovskiy
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Pulmonary Diseases, Oslo University Hospital, Oslo, Norway
| | - Jarle Vaage
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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4
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Lim J, Aguilan JT, Sellers RS, Nagajyothi F, Weiss LM, Angeletti RH, Bortnick AE. Lipid mass spectrometry imaging and proteomic analysis of severe aortic stenosis. J Mol Histol 2020; 51:559-571. [PMID: 32794037 DOI: 10.1007/s10735-020-09905-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
Severe aortic stenosis (AS) is prevalent in adults ≥ 65 years, a significant cause of morbidity and mortality, with no medical therapy. Lipid and proteomic alterations of human AS tissue were determined using mass spectrometry imaging (MSI) and liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to understand histopathology, potential biomarkers of disease, and progression from non-calcified to calcified phenotype. A reproducible MSI method was developed using healthy murine aortic valves (n = 3) and subsequently applied to human AS (n = 2). Relative lipid levels were spatially mapped and associated with different microdomains. Proteomics for non-calcified and calcified microdomains were performed to ascertain differences in expression. Increased pro-osteogenic and inflammatory lysophosphatidylcholine (LPC) 16:0 and 18:0 were co-localized with calcified microdomains. Proteomics analysis identified differential patterns in calcified microdomains with high LPC and low cholesterol as compared to non-calcified microdomains with low LPC and high cholesterol. Calcified microdomains had higher levels of: apolipoproteins (Apo) B-100 (p < 0.001) and Apo A-IV (p < 0.001), complement C3 and C4-B (p < 0.001), C5 (p = 0.007), C8 beta chain (p = 0.013) and C9 (p = 0.010), antithrombotic proteins alpha-2-macroglobulin (p < 0.0001) and antithrombin III (p = 0.002), and higher anti-calcific fetuin-A (p = 0.02), while the osteoblast differentiating factor transgelin (p < 0.0001), extracellular matrix proteins versican, prolargin, and lumican ( p < 0.001) and regulator protein complement factor H (p < 0.001) were higher in non-calcified microdomains. A combined lipidomic and proteomic approach provided insight into factors potentially contributing to progression from non-calcified to calcific disease in severe AS. Additional studies of these candidates and protein networks could yield new targets for slowing progression of AS.
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Affiliation(s)
- Jihyeon Lim
- Janssen Research and Development, Malvern, PA, USA
| | - Jennifer T Aguilan
- Laboratory for Macromolecular Analysis & Proteomics, Bronx, NY, USA.,Department of Pathology, Montefiore Health System and Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Fnu Nagajyothi
- Department of Pathology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Louis M Weiss
- Laboratory for Macromolecular Analysis & Proteomics, Bronx, NY, USA
| | - Ruth Hogue Angeletti
- Laboratory for Macromolecular Analysis & Proteomics, Bronx, NY, USA.,Department of Biochemistry, Montefiore Health System and Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Montefiore Health System and Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anna E Bortnick
- Department of Medicine, Division of Cardiology, Montefiore Health System and Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Division of Geriatrics, Montefiore Health System and Albert Einstein College of Medicine, Bronx, NY, USA. .,Jack D. Weiler Hospital, 1825 Eastchester Road, Suite 2S-46, Bronx, NY, 10461, USA.
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5
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Huang D, Mao X, Peng J, Cheng M, Bai T, Du M, Huang K, Liu B, Yang L, Huang K, Zhang F. Role of adipokine zinc-α 2-glycoprotein in coronary heart disease. Am J Physiol Endocrinol Metab 2019; 317:E1055-E1062. [PMID: 31526290 DOI: 10.1152/ajpendo.00075.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Zinc-α2-glycoprotein (AZGP1) is a newly identified adipokine that is associated with lipid metabolism and vascular fibrosis. Although adipokines contribute to lipid dysfunction and its related diseases, including stroke and coronary heart disease (CHD), the role of AZGP1 remains unclear. In this study, the role of AZGP1 in atherosclerosis and CHD was investigated. Serum AZGP1 levels from control (n = 84) and CHD (n = 91) patients were examined by ELISA and its relationship with various clinical parameters was analyzed. Immunohistochemistry and immunofluorescence were used to detect the expression of AZGP1 and its receptor in coronary atherosclerotic arteries. THP-1 and human embryonic kidney 293 cells were used to verify its anti-inflammatory role in atherosclerosis. Serum AZGP1 levels in CHD patients were lower than controls (P < 0.01) and independently associated with CHD prevalence (P = 0.021). AZGP1 levels also inversely correlated with the Gensini score. Immunohistochemistry and immunofluorescence showed that AZGP1 and its receptor β3-adrenoceptor (β3-AR) colocalized in lipid-rich areas of atherosclerotic plaques, particularly around macrophages. In vitro, AZGP1 had no effect on foam cell formation but showed anti-inflammatory effects through its regulation of JNK/AP-1 signaling. In summary, AZGP1 is an anti-inflammatory agent that can be targeted for CHD treatment.
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Affiliation(s)
- Dandan Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxiang Mao
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiangtong Peng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Cheng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Du
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Liu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liu Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengxiao Zhang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Oda T, Yamaguchi A, Ishida R, Nikai T, Shimizu K, Matsumoto KI. Plasma proteomic changes during therapeutic hypothermia in resuscitated patients after cardiac arrest. Exp Ther Med 2019; 18:1069-1080. [PMID: 31316602 PMCID: PMC6601400 DOI: 10.3892/etm.2019.7649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/02/2019] [Indexed: 12/29/2022] Open
Abstract
Hypothermia is used for several h during cardiac and aortic surgery to protect ischemic organs. Therapeutic hypothermia (TH) is used for ≤24 h as a treatment for comatose patients after the return of spontaneous circulation (ROSC) following cardiac arrest. The proteomic approach may provide unbiased data on alterations in the abundance of proteins during TH. The objective of this study was to assess the effects of cooling/rewarming on the plasma proteome during TH after ROSC and to identify the mechanism underlying its therapeutic effects. A total of nine comatose adult patients, resuscitated shortly after cardiac arrest, were cooled to 34°C for 24 h and slowly rewarmed to 36°C. A quantitative gel-free proteomic analysis was performed using the isobaric tag for relative and absolute quantification labeling tandem mass spectrometry. Plasma samples were obtained prior to cooling and rewarming, and immediately after rewarming, from all patients during TH after ROSC. A total of 92 high-confidence proteins were identified. Statistically significant alterations were observed (>1.2-fold increase or <0.833-fold decrease) in the levels of 15 of those proteins (P=0.003–0.047), mainly proteins belonging to the acute-phase response or platelet degranulation. Unexpectedly, the levels of free hemoglobin (hemoglobin subunits α and β) were significantly downregulated during TH (P<0.05). The level of the terminal complement complex (SC5b-9) showed significant reduction after cooling (P=0.023). Although the acute-phase response proteins were upregulated, the abundance of complement proteins did not change, and the levels of SC5b-9 and free hemoglobin decreased during TH in patients after ROSC.
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Affiliation(s)
- Teiji Oda
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Shimane University Faculty of Medicine, Izumo, Shimane 693-8501, Japan
| | - Akane Yamaguchi
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Shimane University Faculty of Medicine, Izumo, Shimane 693-8501, Japan
| | - Ryosuke Ishida
- Department of Emergency and Critical Care Medicine, Shimane Prefectural Central Hospital, Izumo, Shimane 693-8555, Japan
| | - Tetsuro Nikai
- Department of Anesthesiology, Shimane University Faculty of Medicine, Izumo, Shimane 693-8501, Japan
| | - Koji Shimizu
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Shimane University Faculty of Medicine, Izumo, Shimane 693-8501, Japan
| | - Ken-Ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research, Shimane University, Izumo, Shimane 693-8501, Japan
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7
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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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8
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Trindade F, Ferreira R, Magalhães B, Leite-Moreira A, Falcão-Pires I, Vitorino R. How to use and integrate bioinformatics tools to compare proteomic data from distinct conditions? A tutorial using the pathological similarities between Aortic Valve Stenosis and Coronary Artery Disease as a case-study. J Proteomics 2017; 171:37-52. [PMID: 28336332 DOI: 10.1016/j.jprot.2017.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/28/2017] [Accepted: 03/19/2017] [Indexed: 11/25/2022]
Abstract
Nowadays we are surrounded by a plethora of bioinformatics tools, powerful enough to deal with the large amounts of data arising from proteomic studies, but whose application is sometimes hard to find. Therefore, we used a specific clinical problem - to discriminate pathophysiology and potential biomarkers between two similar cardiovascular diseases, aortic valve stenosis (AVS) and coronary artery disease (CAD) - to make a step-by-step guide through four bioinformatics tools: STRING, DisGeNET, Cytoscape and ClueGO. Proteome data was collected from articles available on PubMed centered on proteomic studies enrolling subjects with AVS or CAD. Through the analysis of gene ontology provided by STRING and ClueGO we could find specific biological phenomena associated with AVS, such as down-regulation of elastic fiber assembly, and with CAD, such as up-regulation of plasminogen activation. Moreover, through Cytoscape and DisGeNET we could pinpoint surrogate markers either for AVS (e.g. popeye domain containing protein 2 and 28S ribosomal protein S36, mitochondrial) or for CAD (e.g. ankyrin repeat and SOCS box protein 7) which deserve future validation. Data recycling and integration as well as research orientation are among the main advantages of resorting to bioinformatics analysis, hence these tutorials can be of great convenience for proteomics investigators. BIOLOGICAL SIGNIFICANCE As we saw for aortic valve stenosis and coronary artery disease, it can be of great relevance to perform preliminary bioinformatics analysis with already published proteomics data. It not only saves us time in the lab (avoiding work duplication) as it points out new hypothesis to explain the phenotypical presentation of the diseases as well as new surrogate markers with clinical relevance, deserving future scrutiny. These essential steps can be easily overcome if one follows the steps proposed in our tutorial for STRING, DisGeNET, Cytoscape and ClueGO utilization.
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Affiliation(s)
- Fábio Trindade
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Porto, Portugal.
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Beatriz Magalhães
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Adelino Leite-Moreira
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Inês Falcão-Pires
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Rui Vitorino
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
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