1
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Wang J, Wang J, Zhong J, Liu H, Li W, Chen M, Xu L, Zhang W, Zhang Z, Wei Z, Guo J, Wang X, Sui J, Liu X, Zhang S, Wang X. LRG1 promotes atherosclerosis by inducing macrophage M1-like polarization. Proc Natl Acad Sci U S A 2024; 121:e2405845121. [PMID: 39178231 PMCID: PMC11363312 DOI: 10.1073/pnas.2405845121] [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: 03/21/2024] [Accepted: 06/05/2024] [Indexed: 08/25/2024] Open
Abstract
Atherosclerosis is a chronic inflammatory disease of the arterial wall characterized by the accumulation of cholesterol-rich lipoproteins in macrophages. How macrophages commit to proinflammatory polarization under atherosclerosis conditions is not clear. Report here that the level of a circulating protein, leucine-rich alpha-2 glycoprotein 1 (LRG1), is elevated in the atherosclerotic tissue and serum samples from patients with coronary artery disease (CAD). LRG1 stimulated macrophages to proinflammatory M1-like polarization through the activation of extracellular signal-regulated kinase 1/2 (ERK1/2) and c-Jun N-terminal kinase (JNK) pathways. The LRG1 knockout mice showed significantly delayed atherogenesis progression and reduced levels of macrophage-related proinflammatory cytokines in a high-fat diet-induced Apoe-/- mouse atherosclerosis model. An anti-LRG1 neutralizing antibody also effectively blocked LRG1-induced macrophage M1-like polarization in vitro and conferred therapeutic benefits to animals with ApoE deficiency-induced atherosclerosis. LRG1 may therefore serve as an additional biomarker for CAD and targeting LRG1 could offer a potential therapeutic strategy for CAD patients by mitigating the proinflammatory response of macrophages.
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Affiliation(s)
- Juan Wang
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Jing Wang
- National Institute of Biological Sciences, Beijing102206, China
| | - Jiuchang Zhong
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Hongbin Liu
- Department of Cardiology, The Second Medical Center, Beijing 301 Hospital, Beijing100853, China
| | - Weiming Li
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Mulei Chen
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Li Xu
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Wenbin Zhang
- National Institute of Biological Sciences, Beijing102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing102206, China
| | - Ze Zhang
- National Institute of Biological Sciences, Beijing102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing102206, China
| | - Zhizhong Wei
- National Institute of Biological Sciences, Beijing102206, China
| | - Jia Guo
- National Institute of Biological Sciences, Beijing102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing102206, China
| | - Xinyu Wang
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing102206, China
| | - Xingpeng Liu
- Heart-Center of Beijing Chao-Yang hospital, Capital Medical University, Beijing Key Laboratory of Hypertension, Beijing100020, China
| | - Sitao Zhang
- National Institute of Biological Sciences, Beijing102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing102206, China
| | - Xiaodong Wang
- National Institute of Biological Sciences, Beijing102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing102206, China
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2
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Balasubramanian P, Vijayarangam V, Deviparasakthi MKG, Palaniyandi T, Ravi M, Natarajan S, Viswanathan S, Baskar G, Wahab MRA, Surendran H. Implications and progression of peroxiredoxin 2 (PRDX2) in various human diseases. Pathol Res Pract 2024; 254:155080. [PMID: 38219498 DOI: 10.1016/j.prp.2023.155080] [Citation(s) in RCA: 1] [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] [Received: 11/14/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
Peroxiredoxin 2 (PRDX2), a characteristic 2-Cys enzyme is one of the foremost effective scavenger proteins against reactive oxygen species (ROS) and hydrogen peroxide (H2O2) defending cells against oxidative stress. Dysregulation of this antioxidant raises the quantity of ROS and oxidative stress implicated in several diseases. PRDX2 lowers the generation of ROS that takes part in controlling several signalling pathways occurring in neurons, protecting them from stress caused by oxidation and an inflammatory harm. Depending on the aetiological variables, the kind of cancer, and the stage of tumour development, PRDX2 may behave either as an onco-suppressor or a promoter. However, overexpression of PRDX2 may be linked to the development of numerous cancers, including those of the colon, cervix, breast, and prostate. PRDX2 also plays a beneficial effect in inflammatory diseases. PRDX2 being a thiol-specific peroxidase, is known to control proinflammatory reactions. The spilling of PRDX2, on the other hand, accelerates cognitive impairment following a stroke by triggering an inflammatory reflex. PRDX2 expression patterns in vascular cells tend to be crucial to its involvement in cardiovascular diseases. In vascular smooth muscle cells, if the protein tyrosine phosphatase is restricted, PRDX2 could avoid the neointimal thickening which relies on platelet derived growth factor (PDGF), a vital component of vascular remodelling. A proper PRDX2 balance is therefore crucial. The imbalance causes a number of illnesses, including cancers, inflammatory diseases, cardiovascular ailments, and neurological and neurodegenerative problems which are discussed in this review.
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Affiliation(s)
| | - Varshini Vijayarangam
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | | | - Thirunavukkarasu Palaniyandi
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India; Department of Anatomy, Biomedical Research Unit and Laboratory Animal Centre, Saveetha Dental College and Hospital, SIMATS, Saveetha University, Chennai, India.
| | - Maddaly Ravi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Sudhakar Natarajan
- Department of Tuberculosis, ICMR - National Institute for Research in Tuberculosis (NIRT), Chennai, India
| | - Sandhiya Viswanathan
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | - Gomathy Baskar
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
| | | | - Hemapreethi Surendran
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai, India
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3
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Ge X, Yu Z, Guo X, Li L, Ye L, Ye M, Yuan J, Zhu C, Hu W, Hou Y. Complement and complement regulatory proteins are upregulated in lungs of COVID-19 patients. Pathol Res Pract 2023; 247:154519. [PMID: 37244049 PMCID: PMC10165854 DOI: 10.1016/j.prp.2023.154519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/18/2023] [Accepted: 05/06/2023] [Indexed: 05/29/2023]
Abstract
We explored the pathological changes and the activation of local complement system in COVID-19 pneumonia. Lung paraffin sections of COVID-19 infected patients were analyzed by HE (hematoxylin-eosin) staining. The deposition of complement C3, the deposition of C3b/iC3b/C3d and C5b-9, and the expression of complement regulatory proteins, CD59, CD46 and CD55 were detected by immunohistochemistry. In COVID-19 patients' lung tissues, fibrin exudation, mixed with erythrocyte, alveolar macrophage and shed pneumocyte are usually observed in the alveoli. The formation of an "alveolar emboli" structure may contribute to thrombosis and consolidation in lung tissue. In addition, we also found that compared to normal tissue, the lung tissues of COVID-19 patients displayed the hyper-activation of complement that is represented by extensive deposition of C3, C3b/iC3b/C3d and C5b-9, and the increased expression level of complement regulatory proteins CD55, and especially CD59 but not CD46. The thrombosis and consolidation in lung tissues may contribute to the pathogenesis of COVID-19. The increased expression of CD55 and CD59 may reflect a feedback of self-protection on the complement hyper-activation. Further, the increased C3 deposition and the strongly activated complement system in lung tissues may suggest the rationale of complement-targeted therapeutics in conquering COVID-19.
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Affiliation(s)
- Xiaowen Ge
- Department of Pathology, Zhongshan Hospital, Fudan University, Fenglin Road 180, Shanghai 200032, PR China
| | - Zhui Yu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, PR China
| | - Xinxin Guo
- Department of Pathology, Zhongshan Hospital, Fudan University, Fenglin Road 180, Shanghai 200032, PR China
| | - Ling Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Dongan Road 270, Shanghai 200032, PR China
| | - Ling Ye
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, PR China
| | - Maosong Ye
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, PR China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China
| | - Chouwen Zhu
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, PR China
| | - Weiguo Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Dongan Road 270, Shanghai 200032, PR China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Fenglin Road 180, Shanghai 200032, PR China.
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4
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Khairnar RC, Parihar N, Prabhavalkar KS, Bhatt LK. Emerging targets signaling for inflammation in Parkinson's disease drug discovery. Metab Brain Dis 2022; 37:2143-2161. [PMID: 35536461 DOI: 10.1007/s11011-022-00999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/29/2022] [Indexed: 10/18/2022]
Abstract
Parkinson's disease (PD) patients not only show motor features such as bradykinesia, tremor, and rigidity but also non-motor features such as anxiety, depression, psychosis, memory loss, attention deficits, fatigue, sexual dysfunction, gastrointestinal issues, and pain. Many pharmacological treatments are available for PD patients; however, these treatments are partially or transiently effective since they only decrease the symptoms. As these therapies are unable to restore dopaminergic neurons and stop the development of Parkinson's disease, therefore, the need for an effective therapeutic approach is required. The current review summarizes novel targets for PD, that can be utilized to identify disease-modifying treatments.
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Affiliation(s)
- Rhema Chandan Khairnar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Niraj Parihar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Kedar S Prabhavalkar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India.
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5
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Highly pathogenic coronavirus N protein aggravates inflammation by MASP-2-mediated lectin complement pathway overactivation. Signal Transduct Target Ther 2022; 7:318. [PMID: 36100602 PMCID: PMC9470675 DOI: 10.1038/s41392-022-01133-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 12/30/2022] Open
Abstract
Excessive inflammatory responses contribute to the pathogenesis and lethality of highly pathogenic human coronaviruses, but the underlying mechanism remains unclear. In this study, the N proteins of highly pathogenic human coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), middle east respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were found to bind MASP-2, a key serine protease in the lectin pathway of complement activation, resulting in excessive complement activation by potentiating MBL-dependent MASP-2 activation, and the deposition of MASP-2, C4b, activated C3 and C5b-9. Aggravated inflammatory lung injury was observed in mice infected with adenovirus expressing the N protein. Complement hyperactivation was also observed in SARS-CoV-2-infected patients. Either blocking the N protein:MASP-2 interaction, MASP-2 depletion or suppressing complement activation can significantly alleviate N protein-induced complement hyperactivation and lung injury in vitro and in vivo. Altogether, these data suggested that complement suppression may represent a novel therapeutic approach for pneumonia induced by these highly pathogenic coronaviruses.
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6
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Camilli C, Hoeh AE, De Rossi G, Moss SE, Greenwood J. LRG1: an emerging player in disease pathogenesis. J Biomed Sci 2022; 29:6. [PMID: 35062948 PMCID: PMC8781713 DOI: 10.1186/s12929-022-00790-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
The secreted glycoprotein leucine-rich α-2 glycoprotein 1 (LRG1) was first described as a key player in pathogenic ocular neovascularization almost a decade ago. Since then, an increasing number of publications have reported the involvement of LRG1 in multiple human conditions including cancer, diabetes, cardiovascular disease, neurological disease, and inflammatory disorders. The purpose of this review is to provide, for the first time, a comprehensive overview of the LRG1 literature considering its role in health and disease. Although LRG1 is constitutively expressed by hepatocytes and neutrophils, Lrg1-/- mice show no overt phenotypic abnormality suggesting that LRG1 is essentially redundant in development and homeostasis. However, emerging data are challenging this view by suggesting a novel role for LRG1 in innate immunity and preservation of tissue integrity. While our understanding of beneficial LRG1 functions in physiology remains limited, a consistent body of evidence shows that, in response to various inflammatory stimuli, LRG1 expression is induced and directly contributes to disease pathogenesis. Its potential role as a biomarker for the diagnosis, prognosis and monitoring of multiple conditions is widely discussed while dissecting the mechanisms underlying LRG1 pathogenic functions. Emphasis is given to the role that LRG1 plays as a vasculopathic factor where it disrupts the cellular interactions normally required for the formation and maintenance of mature vessels, thereby indirectly contributing to the establishment of a highly hypoxic and immunosuppressive microenvironment. In addition, LRG1 has also been reported to affect other cell types (including epithelial, immune, mesenchymal and cancer cells) mostly by modulating the TGFβ signalling pathway in a context-dependent manner. Crucially, animal studies have shown that LRG1 inhibition, through gene deletion or a function-blocking antibody, is sufficient to attenuate disease progression. In view of this, and taking into consideration its role as an upstream modifier of TGFβ signalling, LRG1 is suggested as a potentially important therapeutic target. While further investigations are needed to fill gaps in our current understanding of LRG1 function, the studies reviewed here confirm LRG1 as a pleiotropic and pathogenic signalling molecule providing a strong rationale for its use in the clinic as a biomarker and therapeutic target.
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Affiliation(s)
- Carlotta Camilli
- Institute of Ophthalmology, University College London, London, UK.
| | - Alexandra E Hoeh
- Institute of Ophthalmology, University College London, London, UK
| | - Giulia De Rossi
- Institute of Ophthalmology, University College London, London, UK
| | - Stephen E Moss
- Institute of Ophthalmology, University College London, London, UK
| | - John Greenwood
- Institute of Ophthalmology, University College London, London, UK
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7
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Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D’Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. mSystems 2021; 6:e0009521. [PMID: 34698547 PMCID: PMC8547481 DOI: 10.1128/msystems.00095-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).
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Affiliation(s)
- Halie M. Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Alexandra J. Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Ashwin N. Skelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth Sell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John J. Dziak
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Lucy D’Agostino McGowan
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Stephen Capone
- St. George’s University School of Medicine, St. George’s, Grenada
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - YoSon Park
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Mai
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuchen Sun
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
| | - Joel D. Boerckel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - James Brian Byrd
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Jinhui Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - John P. Barton
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, USA
| | - Rishi Raj Goel
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Tiago Lubiana
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - COVID-19 Review Consortium
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen, Germany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Mercer University, Macon, Georgia, USA
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
- Georgia State University, Atlanta, Georgia, USA
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
- St. George’s University School of Medicine, St. George’s, Grenada
- Department of Computer Science, University of Virginia, Charlottesville, Virginia, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Clinical Sciences, Lund University, Lund, Sweden
- University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
- Azimuth1, McLean, Virginia, USA
- Allen Institute for Immunology, Seattle, Washington, USA
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
- Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, USA
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Philadelphia, Pennsylvania, USA
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8
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Yaneske E, Zampieri G, Bertoldi L, Benvenuto G, Angione C. Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals an increased shift to glycolytic energy production. FEBS Lett 2021; 595:2350-2365. [PMID: 34409594 PMCID: PMC8427129 DOI: 10.1002/1873-3468.14180] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/02/2021] [Accepted: 08/15/2021] [Indexed: 01/08/2023]
Abstract
Cancer is considered a high‐risk condition for severe illness resulting from COVID‐19. The interaction between severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and human metabolism is key to elucidating the risk posed by COVID‐19 for cancer patients and identifying effective treatments, yet it is largely uncharacterised on a mechanistic level. We present a genome‐scale map of short‐term metabolic alterations triggered by SARS‐CoV‐2 infection of cancer cells. Through transcriptomic‐ and proteomic‐informed genome‐scale metabolic modelling, we characterise the role of RNA and fatty acid biosynthesis in conjunction with a rewiring in energy production pathways and enhanced cytokine secretion. These findings link together complementary aspects of viral invasion of cancer cells, while providing mechanistic insights that can inform the development of treatment strategies.
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Affiliation(s)
- Elisabeth Yaneske
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, UK
| | - Guido Zampieri
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, UK.,Department of Biology, University of Padua, Italy
| | | | | | - Claudio Angione
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, UK.,Healthcare Innovation Centre, Teesside University, Middlesbrough, UK.,Centre for Digital Innovation, Teesside University, Middlesbrough, UK
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9
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Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nat Commun 2021; 12:4314. [PMID: 34262047 PMCID: PMC8280215 DOI: 10.1038/s41467-021-24467-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/04/2021] [Indexed: 02/08/2023] Open
Abstract
Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyze the transcriptomes of 611,398 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observe a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD AT2 cells express higher levels of genes linked directly to the efficiency of viral replication and the innate immune response. Additionally, we identify basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.
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Affiliation(s)
- Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nichelle I Winters
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chitra Joseph
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | | | - Arun C Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lance M Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica B Blackburn
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley W Richmond
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Andrew G Nicholson
- National Heart and Lung Institute, Imperial College, London, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - William A Wallace
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Pathology, Edinburgh University Medical School, Edinburgh, UK
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - R Gisli Jenkins
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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10
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Elevated Expression Levels of Lung Complement Anaphylatoxin, Neutrophil Chemoattractant Chemokine IL-8, and RANTES in MERS-CoV-Infected Patients: Predictive Biomarkers for Disease Severity and Mortality. J Clin Immunol 2021; 41:1607-1620. [PMID: 34232441 PMCID: PMC8260346 DOI: 10.1007/s10875-021-01061-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
The complement system, a network of highly-regulated proteins, represents a vital part of the innate immune response. Over-activation of the complement system plays an important role in inflammation, tissue damage, and infectious disease severity. The prevalence of MERS-CoV in Saudi Arabia remains significant and cases are still being reported. The role of complement in Middle East Respiratory Syndrome coronavirus (MERS-CoV) pathogenesis and complement-modulating treatment strategies has received limited attention, and studies involving MERS-CoV-infected patients have not been reported. This study offers the first insight into the pulmonary expression profile including seven complement proteins, complement regulatory factors, IL-8, and RANTES in MERS-CoV infected patients without underlying chronic medical conditions. Our results significantly indicate high expression levels of complement anaphylatoxins (C3a and C5a), IL-8, and RANTES in the lungs of MERS-CoV-infected patients. The upregulation of lung complement anaphylatoxins, C5a, and C3a was positively correlated with IL-8, RANTES, and the fatality rate. Our results also showed upregulation of the positive regulatory complement factor P, suggesting positive regulation of the complement during MERS-CoV infection. High levels of lung C5a, C3a, factor P, IL-8, and RANTES may contribute to the immunopathology, disease severity, ARDS development, and a higher fatality rate in MERS-CoV-infected patients. These findings highlight the potential prognostic utility of C5a, C3a, IL-8, and RANTES as biomarkers for MERS-CoV disease severity and mortality. To further explore the prediction of functional partners (proteins) of highly expressed proteins (C5a, C3a, factor P, IL-8, and RANTES), the computational protein–protein interaction (PPI) network was constructed, and six proteins (hub nodes) were identified.
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11
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Kang S, Yang M, He S, Wang Y, Chen X, Chen YQ, Hong Z, Liu J, Jiang G, Chen Q, Zhou Z, Zhou Z, Huang Z, Huang X, He H, Zheng W, Liao HX, Xiao F, Shan H, Chen S. A SARS-CoV-2 antibody curbs viral nucleocapsid protein-induced complement hyperactivation. Nat Commun 2021; 12:2697. [PMID: 33976229 PMCID: PMC8113585 DOI: 10.1038/s41467-021-23036-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/30/2021] [Indexed: 12/14/2022] Open
Abstract
Although human antibodies elicited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-reactive antibodies. Herein, we isolate and profile a panel of 32 N protein-specific monoclonal antibodies (mAbs) from a quick recovery coronavirus disease-19 (COVID-19) convalescent patient who has dominant antibody responses to the SARS-CoV-2 N protein rather than to the SARS-CoV-2 spike (S) protein. The complex structure of the N protein RNA binding domain with the highest binding affinity mAb (nCoV396) reveals changes in the epitopes and antigen’s allosteric regulation. Functionally, a virus-free complement hyperactivation analysis demonstrates that nCoV396 specifically compromises the N protein-induced complement hyperactivation, which is a risk factor for the morbidity and mortality of COVID-19 patients, thus laying the foundation for the identification of functional anti-N protein mAbs. While SARS-CoV-2 S protein targeting monoclonal antibodies (mAbs) are well studied, little is known about N protein-targeting mAbs. Here, Kang et al. provide the crystal structure of the N protein RNA binding domain with a mAb derived from a convalescent patient and show that it compromises the N protein-induced complement hyperactivation.
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Affiliation(s)
- Sisi Kang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Mei Yang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Suhua He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Yueming Wang
- Institute of Biomedicine, Jinan University, Guangzhou, China.,Zhuhai Trinomab Biotechnology Co., Ltd, Zhuhai, China
| | - Xiaoxue Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Zhongsi Hong
- Department of Infectious Disease, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jing Liu
- Department of Respiratory Disease, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Guanmin Jiang
- Department of Clinical laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Qiuyue Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Ziliang Zhou
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhechong Zhou
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhaoxia Huang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Xi Huang
- Center for Infection and Immunity, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Huanhuan He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Weihong Zheng
- Institute of Biomedicine, Jinan University, Guangzhou, China.,Zhuhai Trinomab Biotechnology Co., Ltd, Zhuhai, China
| | - Hua-Xin Liao
- Institute of Biomedicine, Jinan University, Guangzhou, China. .,Zhuhai Trinomab Biotechnology Co., Ltd, Zhuhai, China.
| | - Fei Xiao
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China. .,Department of Infectious Disease, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hong Shan
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China. .,Department of Intervention Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
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12
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Malaquias MAS, Gadotti AC, Motta-Junior JDS, Martins APC, Azevedo MLV, Benevides APK, Cézar-Neto P, Panini do Carmo LA, Zeni RC, Raboni SM, Fonseca AS, Machado-Souza C, Moreno-Amaral AN, de Noronha L. The role of the lectin pathway of the complement system in SARS-CoV-2 lung injury. Transl Res 2021; 231:55-63. [PMID: 33221483 PMCID: PMC7677075 DOI: 10.1016/j.trsl.2020.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/23/2022]
Abstract
Although some evidence showed the activation of complement systems in COVID-19 patients, proinflammatory status and lectin pathway remain unclear. Thus, the present study aimed to demonstrate the role of MBL and ficolin-3 in the complement system activation and compared to pandemic Influenza A virus H1N1 subtype infection (H1N1pdm09) and control patients. A total of 27 lungs formalin-fixed paraffin-embedded samples (10 from H1N1 group, 6 from the COVID-19 group, and 11 from the control group) were analyzed by immunohistochemistry using anti-IL-6, TNF-alfa, CD163, MBL e FCN3 antibodies. Genotyping of target polymorphisms in the MBL2 gene was performed by real-time PCR. Proinflammatory cytokines such as IL-6 and TNF-alpha presented higher tissue expression in the COVID-19 group compared to H1N1 and control groups. The same results were observed for ICAM-1 tissue expression. Increased expression of the FCN3 was observed in the COVID-19 group and H1N1 group compared to the control group. The MBL tissue expression was higher in the COVID-19 group compared to H1N1 and control groups. The genotypes AA for rs180040 (G/A), GG for rs1800451 (G/A) and CC for rs5030737 (T/C) showed a higher prevalence in the COVID-19 group. The intense activation of the lectin pathway, with particular emphasis on the MBL pathway, together with endothelial dysfunction and a massive proinflammatory cytokines production, possibly lead to a worse outcome in patients infected with SARS-Cov-2. Moreover, 3 SNPs of our study presented genotypes that might be correlated with high MBL tissue expression in the COVID-19 pulmonary samples.
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Affiliation(s)
- Mineia Alessandra Scaranello Malaquias
- Postdoctoral Researcher Postgraduate Program in Health Sciences School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil.
| | - Ana Carolina Gadotti
- Postgraduate Program of Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | - Jarbas da Silva Motta-Junior
- Postgraduate Program of Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | - Ana Paula Camargo Martins
- Laboratory of Experimental Pathology, School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | - Marina Luise Viola Azevedo
- Laboratory of Experimental Pathology, School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | - Ana Paula Kubaski Benevides
- Laboratory of Experimental Pathology, School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | - Plínio Cézar-Neto
- School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | | | - Rafaela Chiuco Zeni
- School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
| | - Sonia Mara Raboni
- Laboratory of Virology, Hospital de Clínicas, Federal University of Paraná - UFPR, Curitiba, PR, Brazil
| | - Aline Simoneti Fonseca
- Faculdades Pequeno Príncipe (FPP). Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, PR, Brazil
| | - Cleber Machado-Souza
- Faculdades Pequeno Príncipe (FPP). Instituto de Pesquisa Pelé Pequeno Príncipe (IPPPP), Curitiba, PR, Brazil
| | - Andrea Novais Moreno-Amaral
- Anemia and Immunology Research Laboratory (LabAIRe), School of Medicine, Pontifical Catholic University of Parana - PUCPR, Curitiba, PR, Brazil
| | - Lucia de Noronha
- Laboratory of Experimental Pathology, School of Medicine, Pontifícia Universidade Católica do Paraná - PUCPR, Curitiba, PR, Brazil
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13
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Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Sun Y, Mai D, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. ARXIV 2021:arXiv:2102.01521v4. [PMID: 33594340 PMCID: PMC7885912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 12/03/2021] [Indexed: 12/02/2022]
Abstract
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.
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Affiliation(s)
- Halie M Rando
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America; Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, United States of America · Funded by the Gordon and Betty Moore Foundation (GBMF 4552); the National Human Genome Research Institute (R01 HG010067)
| | - Adam L MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Alexandra J Lee
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America · Funded by the Gordon and Betty Moore Foundation (GBMF 4552)
| | - Ronan Lordan
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5158, USA
| | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502285, Telangana, India
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen 72076, Germany
| | - Ashwin N Skelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States of America · Funded by NIH Medical Scientist Training Program T32 GM07170
| | - Elizabeth Sell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - John J Dziak
- Edna Bennett Pierce Prevention Research Center, The Pennsylvania State University, University Park, PA, United States of America
| | - Lamonica Shinholster
- Mercer University, Macon, GA, United States of America · Funded by the Center for Global Genomics and Health Equity at the University of Pennsylvania
| | - Lucy D'Agostino McGowan
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Nils Wellhausen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sergey Knyazev
- Georgia State University, Atlanta, GA, United States of America
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Stephen Capone
- St. George's University School of Medicine, St. George's, Grenada
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA, United States of America
| | - YoSon Park
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America · Funded by NHGRI R01 HG10067
| | - Yuchen Sun
- Department of Computer Science, University of Virginia, Charlottesville, VA, United States of America
| | - David Mai
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel D Boerckel
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States of America
| | | | - James Brian Byrd
- University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America · Funded by NIH K23HL128909; FastGrants
| | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Jinhui Wang
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Gregory L Szeto
- Allen Institute for Immunology, Seattle, WA, United States of America
| | - John P Barton
- Department of Physics and Astronomy, University of California-Riverside, Riverside, California, United States of America
| | - Rishi Raj Goel
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States of America
| | - Tiago Lubiana
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Morgridge Institute for Research, Madison, Wisconsin, United States of America · Funded by John W. and Jeanne M. Rowe Center for Research in Virology
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, Pennsylvania, United States of America; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America; Center for Health AI, University of Colorado School of Medicine, Aurora, Colorado, United States of America · Funded by the Gordon and Betty Moore Foundation (GBMF 4552); the National Human Genome Research Institute (R01 HG010067)
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14
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Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.20.347187. [PMID: 33106805 PMCID: PMC7587778 DOI: 10.1101/2020.10.20.347187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyzed the transcriptomes of 605,904 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observed a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD epithelial cells expressed higher levels of genes linked directly to the efficiency of viral replication and innate immune response. Additionally, we identified basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.
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Affiliation(s)
- Linh T. Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nichelle I. Winters
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chitra Joseph
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | | | - Arun C. Habermann
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lance M. Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J. Taylor
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica B. Blackburn
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bradley W. Richmond
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
| | - Andrew G. Nicholson
- National Heart and Lung Institute, Imperial College, London, SW3 6LY, UK
- Royal Brompton and Harefield NHS Foundation Trust, Department of Histopathology, Sydney Street, London, SW3 6NP, UK
| | - Doris Rassl
- Pathology Research, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - William A. Wallace
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
- Division of Pathology, Edinburgh University Medical School, Edinburgh, UK
| | - Ivan O. Rosas
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - R. Gisli Jenkins
- Respiratory Medicine NIHR Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
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15
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Oroojalian F, Haghbin A, Baradaran B, Hemmat N, Shahbazi MA, Baghi HB, Mokhtarzadeh A, Hamblin MR. Novel insights into the treatment of SARS-CoV-2 infection: An overview of current clinical trials. Int J Biol Macromol 2020; 165:18-43. [PMID: 32991900 PMCID: PMC7521454 DOI: 10.1016/j.ijbiomac.2020.09.204] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022]
Abstract
The emergence of the global pandemic caused by the novel SARS-CoV-2 virus has motivated scientists to find a definitive treatment or a vaccine against it in the shortest possible time. Current efforts towards this goal remain fruitless without a full understanding of the behavior of the virus and its adaptor proteins. This review provides an overview of the biological properties, functional mechanisms, and molecular components of SARS-CoV-2, along with investigational therapeutic and preventive approaches for this virus. Since the proteolytic cleavage of the S protein is critical for virus penetration into cells, a set of drugs, such as chloroquine, hydroxychloroquine, camostat mesylate have been tested in clinical trials to suppress this event. In addition to angiotensin-converting enzyme 2, the role of CD147 in the viral entrance has also been proposed. Mepolizumab has shown to be effective in blocking the virus's cellular entrance. Antiviral drugs, such as remdesivir, ritonavir, oseltamivir, darunavir, lopinavir, zanamivir, peramivir, and oseltamivir, have also been tested as treatments for COVID-19. Regarding preventive vaccines, the whole virus, vectors, nucleic acids, and structural subunits have been suggested for vaccine development. Mesenchymal stem cells and natural killer cells could also be used against SARS-CoV-2. All the above-mentioned strategies, as well as the role of nanomedicine for the diagnosis and treatment of SARS-CoV-2 infection, have been discussed in this review.
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Affiliation(s)
- Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran; Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Ali Haghbin
- Department of Pediatrics, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran; Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nima Hemmat
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad-Ali Shahbazi
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa.
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16
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Whetton AD, Preston GW, Abubeker S, Geifman N. Proteomics and Informatics for Understanding Phases and Identifying Biomarkers in COVID-19 Disease. J Proteome Res 2020; 19:4219-4232. [PMID: 32657586 PMCID: PMC7384384 DOI: 10.1021/acs.jproteome.0c00326] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 02/07/2023]
Abstract
The emergence of novel coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 coronavirus, has necessitated the urgent development of new diagnostic and therapeutic strategies. Rapid research and development, on an international scale, has already generated assays for detecting SARS-CoV-2 RNA and host immunoglobulins. However, the complexities of COVID-19 are such that fuller definitions of patient status, trajectory, sequelae, and responses to therapy are now required. There is accumulating evidence-from studies of both COVID-19 and the related disease SARS-that protein biomarkers could help to provide this definition. Proteins associated with blood coagulation (D-dimer), cell damage (lactate dehydrogenase), and the inflammatory response (e.g., C-reactive protein) have already been identified as possible predictors of COVID-19 severity or mortality. Proteomics technologies, with their ability to detect many proteins per analysis, have begun to extend these early findings. To be effective, proteomics strategies must include not only methods for comprehensive data acquisition (e.g., using mass spectrometry) but also informatics approaches via which to derive actionable information from large data sets. Here we review applications of proteomics to COVID-19 and SARS and outline how pipelines involving technologies such as artificial intelligence could be of value for research on these diseases.
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Affiliation(s)
- Anthony D. Whetton
- Stoller
Biomarker Discovery Centre, Faculty of Biology Medicine and Health
(FBMH), University of Manchester, Manchester M20 4GJ, United Kingdom
- Stem
Cell and Leukaemia Proteomics Laboratory, Manchester Cancer Research
Centre, University of Manchester, Manchester M13 9PL, United Kingdom
- Manchester
National Institute for Health Biomedical Research Centre, Manchester M13 9WL, United Kingdom
| | - George W. Preston
- Stoller
Biomarker Discovery Centre, Faculty of Biology Medicine and Health
(FBMH), University of Manchester, Manchester M20 4GJ, United Kingdom
- Stem
Cell and Leukaemia Proteomics Laboratory, Manchester Cancer Research
Centre, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Semira Abubeker
- Stoller
Biomarker Discovery Centre, Faculty of Biology Medicine and Health
(FBMH), University of Manchester, Manchester M20 4GJ, United Kingdom
- Stem
Cell and Leukaemia Proteomics Laboratory, Manchester Cancer Research
Centre, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Nophar Geifman
- Centre
for Health Informatics, FBMH, University
of Manchester, Manchester M13 9PL, United Kingdom
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17
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Albahri OS, Al-Obaidi JR, Zaidan AA, Albahri AS, Zaidan BB, Salih MM, Qays A, Dawood KA, Mohammed RT, Abdulkareem KH, Aleesa AM, Alamoodi AH, Chyad MA, Zulkifli CZ. Helping doctors hasten COVID-19 treatment: Towards a rescue framework for the transfusion of best convalescent plasma to the most critical patients based on biological requirements via ml and novel MCDM methods. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 196:105617. [PMID: 32593060 PMCID: PMC7305916 DOI: 10.1016/j.cmpb.2020.105617] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/16/2020] [Indexed: 05/04/2023]
Abstract
CONTEXT People who have recently recovered from the threat of deteriorating coronavirus disease-2019 (COVID-19) have antibodies to the coronavirus circulating in their blood. Thus, the transfusion of these antibodies to deteriorating patients could theoretically help boost their immune system. Biologically, two challenges need to be surmounted to allow convalescent plasma (CP) transfusion to rescue the most severe COVID-19 patients. First, convalescent subjects must meet donor selection plasma criteria and comply with national health requirements and known standard routine procedures. Second, multi-criteria decision-making (MCDM) problems should be considered in the selection of the most suitable CP and the prioritisation of patients with COVID-19. OBJECTIVE This paper presents a rescue framework for the transfusion of the best CP to the most critical patients with COVID-19 on the basis of biological requirements by using machine learning and novel MCDM methods. METHOD The proposed framework is illustrated on the basis of two distinct and consecutive phases (i.e. testing and development). In testing, ABO compatibility is assessed after classifying donors into the four blood types, namely, A, B, AB and O, to indicate the suitability and safety of plasma for administration in order to refine the CP tested list repository. The development phase includes patient and donor sides. In the patient side, prioritisation is performed using a contracted patient decision matrix constructed between 'serological/protein biomarkers and the ratio of the partial pressure of oxygen in arterial blood to fractional inspired oxygen criteria' and 'patient list based on novel MCDM method known as subjective and objective decision by opinion score method'. Then, the patients with the most urgent need are classified into the four blood types and matched with a tested CP list from the test phase in the donor side. Thereafter, the prioritisation of CP tested list is performed using the contracted CP decision matrix. RESULT An intelligence-integrated concept is proposed to identify the most appropriate CP for corresponding prioritised patients with COVID-19 to help doctors hasten treatments. DISCUSSION The proposed framework implies the benefits of providing effective care and prevention of the extremely rapidly spreading COVID-19 from affecting patients and the medical sector.
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Affiliation(s)
- O S Albahri
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia
| | - Jameel R Al-Obaidi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, Tanjong Malim, Perak 35900, Malaysia
| | - A A Zaidan
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia.
| | - A S Albahri
- Informatics Institute for Postgraduate Studies (IIPS), Iraqi Commission for Computers and Informatics (ICCI), Baghdad, Iraq
| | - B B Zaidan
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia
| | - Mahmood M Salih
- Department of Computer Science, Computer Science and Mathematics College, Tikrit University, Tikrit 34001, Iraq
| | - Abdulhadi Qays
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia
| | - K A Dawood
- Faculty of Computer Science and Information Technology, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - R T Mohammed
- Faculty of Computer Science and Information Technology, Universiti Putra Malaysia, Seri Kembangan, Malaysia
| | - Karrar Hameed Abdulkareem
- Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, Parit Raja, Malaysia
| | - A M Aleesa
- Faculty of Electronic and Electrical Engineering, Universiti Tun Hussein Onn, Batu Pahat, Johor 86400, Malaysia
| | - A H Alamoodi
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia
| | - M A Chyad
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia
| | - Che Zalina Zulkifli
- Department of Computing, Faculty of Arts, Computing and Creative Industry, Universiti Pendidikan, Tanjung Malim 35900, Malaysia
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18
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Kumar R, Lee MH, Mickael C, Kassa B, Pasha Q, Tuder R, Graham B. Pathophysiology and potential future therapeutic targets using preclinical models of COVID-19. ERJ Open Res 2020; 6:00405-2020. [PMID: 33313306 PMCID: PMC7720688 DOI: 10.1183/23120541.00405-2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/27/2020] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) gains entry into the lung epithelial cells by binding to the surface protein angiotensin-converting enzyme 2. Severe SARS-CoV-2 infection, also known as coronavirus disease 2019 (COVID-19), can lead to death due to acute respiratory distress syndrome mediated by inflammatory immune cells and cytokines. In this review, we discuss the molecular and biochemical bases of the interaction between SARS-CoV-2 and human cells, and in doing so we highlight knowledge gaps currently precluding development of new effective therapies. In particular, discovery of novel treatment targets in COVID-19 will start from understanding pathologic changes based on a large number of autopsy lung tissue samples. Pathogenetic roles of potential molecular targets identified in human lung tissues must be validated in established animal models. Overall, this stepwise approach will enable appropriate selection of candidate therapeutic modalities targeting SARS-CoV2 and the host inflammatory response.
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Affiliation(s)
- Rahul Kumar
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael H. Lee
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Claudia Mickael
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Biruk Kassa
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Qadar Pasha
- Functional Genomics Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rubin Tuder
- Dept of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brian Graham
- Dept of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
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19
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Lo MW, Kemper C, Woodruff TM. COVID-19: Complement, Coagulation, and Collateral Damage. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:1488-1495. [PMID: 32699160 PMCID: PMC7484432 DOI: 10.4049/jimmunol.2000644] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus disease of 2019 (COVID-19) is a highly contagious respiratory infection that is caused by the severe acute respiratory syndrome coronavirus 2. Although most people are immunocompetent to the virus, a small group fail to mount an effective antiviral response and develop chronic infections that trigger hyperinflammation. This results in major complications, including acute respiratory distress syndrome, disseminated intravascular coagulation, and multiorgan failure, which all carry poor prognoses. Emerging evidence suggests that the complement system plays a key role in this inflammatory reaction. Indeed, patients with severe COVID-19 show prominent complement activation in their lung, skin, and sera, and those individuals who were treated with complement inhibitors all recovered with no adverse reactions. These and other studies hint at complement's therapeutic potential in these sequalae, and thus, to support drug development, in this review, we provide a summary of COVID-19 and review complement's role in COVID-19 acute respiratory distress syndrome and coagulopathy.
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Affiliation(s)
- Martin W Lo
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, Queensland 4072, Australia; and
| | - Claudia Kemper
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Trent M Woodruff
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, Queensland 4072, Australia; and
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20
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Bian J, Liang M, Ding S, Wang L, Ni W, Xiong S, Li W, Bao X, Gao X, Wang R. iTRAQ-based high-throughput proteomics analysis reveals alterations of plasma proteins in patients infected with human bocavirus. PLoS One 2019; 14:e0225261. [PMID: 31751365 PMCID: PMC6872134 DOI: 10.1371/journal.pone.0225261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/31/2019] [Indexed: 12/18/2022] Open
Abstract
Human bocavirus (HBoV) is a member of the genus Bocavirus, family Parvoviridae, and subfamily Parvovirus and was first identified in nasopharyngeal aspirates of Swedish children with acute respiratory tract infection (ARTI) in 2005. It is the causative agent of nasopharyngeal aspirate disease and death in children. The HboV genomic structure is a linear single-stranded DNA (ssDNA). Its clinical pathogenic characteristics have been extensively studied, however, at present the molecular mechanism underlying the pathogenesis of HBoV infection is not completely clear. In this study, a total of 293 differentially expressed proteins (DEPs) between ARTI cases and healthy plasma samples were characterized using isobaric tags for relative and absolute quantitation (iTRAQ)-coupled bioinformatics analysis, among which 148 were up-regulated and 135 were down-regulated. Gene Ontology (GO) and Cluster of Orthologous Groups of proteins (COG) annotated an enrichment of DEPs in complement activation and biological processes like immunity, inflammation, signal transduction, substance synthesis, and metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis enriched DEPs mainly in the Wnt signaling pathway (ko04310), PPAR signaling pathway (ko03320), intestinal immune network for IgA production (ko04672), complement and coagulation cascades (ko04610), Toll-like receptor signaling pathway (ko04620) and B cell receptor signaling pathway (ko04662). Further, expression levels of three candidate proteins (upregulated PPP2R1A and CUL1, and downregulated CETP) were validated using western blotting. Our investigation is the first analysis of the proteomic profile of HBoV-infected ARTI cases using the iTRAQ approach, providing a foundation for a better molecular understanding of the pathogenesis of ARTI in children.
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Affiliation(s)
- Junmei Bian
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Min Liang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Shuxian Ding
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Liyan Wang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Wenchang Ni
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Shisi Xiong
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Wan Li
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Xingxing Bao
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Xue Gao
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
| | - Rong Wang
- Tongren Hospital of Wuhan University (Wuhan Third Hospital), Wuhan, PR China
- * E-mail:
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21
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Borna H, Hosseini Qale Noe SH, Harchegani AB, Talatappe NR, Ghatrehsamani M, Ghanei M, Shahriary A. A review on proteomics analysis to reveal biological pathways and predictive proteins in sulfur mustard exposed patients: roles of inflammation and oxidative stress. Inhal Toxicol 2019; 31:3-11. [DOI: 10.1080/08958378.2018.1558316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hojat Borna
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Hojjat Hosseini Qale Noe
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Asghar Beigi Harchegani
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Nima Rahmani Talatappe
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdi Ghatrehsamani
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mostafa Ghanei
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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22
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Bortz E, Wu TT, Patel P, Whitelegge JP, Sun R. Proteomics of Bronchoalveolar Lavage Fluid Reveals a Lung Oxidative Stress Response in Murine Herpesvirus-68 Infection. Viruses 2018; 10:v10120670. [PMID: 30486363 PMCID: PMC6316452 DOI: 10.3390/v10120670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
Abstract
Murine herpesvirus-68 (MHV-68) productively infects mouse lungs, exhibiting a complex pathology characteristic of both acute viral infections and chronic respiratory diseases. We sought to discover proteins differentially expressed in bronchoalveolar lavage (BAL) from mice infected with MHV-68. Mice were infected intranasally with MHV-68. After nine days, as the lytic phase of infection resolved, differential BAL proteins were identified by two-dimensional (2D) electrophoresis and mass spectrometry. Of 23 unique proteins, acute phase proteins, vitamin A transport, and oxidative stress response factors Pdx6 and EC-SOD (Sod3) were enriched. Correspondingly, iNOS2 was induced in lung tissue by seven days post-infection. Oxidative stress was partly a direct result of MHV-68 infection, as reactive oxygen species (ROS) were induced in cultured murine NIH3T3 fibroblasts and human lung A549 cells infected with MHV-68. Finally, mice infected with a recombinant MHV-68 co-expressing inflammatory cytokine murine interleukin 6 (IL6) showed exacerbated oxidative stress and soluble type I collagen characteristic of tissue recovery. Thus, oxidative stress appears to be a salient feature of MHV-68 pathogenesis, in part caused by lytic replication of the virus and IL6. Proteins and small molecules in lung oxidative stress networks therefore may provide new therapeutic targets to ameliorate respiratory virus infections.
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Affiliation(s)
- Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Ting-Ting Wu
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Parthive Patel
- Center for Molecular Biology and German Cancer Research Center (DKFZ), University of Heidelberg (ZMBH), 69120 Heidelberg, Germany.
| | - Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory & the Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Ren Sun
- Department of Molecular & Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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23
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Akiba C, Nakajima M, Miyajima M, Ogino I, Miura M, Inoue R, Nakamura E, Kanai F, Tada N, Kunichika M, Yoshida M, Nishimura K, Kondo A, Sugano H, Arai H. Leucine-rich α2-glycoprotein overexpression in the brain contributes to memory impairment. Neurobiol Aging 2017; 60:11-19. [PMID: 28917663 DOI: 10.1016/j.neurobiolaging.2017.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/28/2017] [Accepted: 08/15/2017] [Indexed: 12/19/2022]
Abstract
We previously reported increase in leucine-rich α2-glycoprotein (LRG) concentration in cerebrospinal fluid is associated with cognitive decline in humans. To investigate relationship between LRG expression in the brain and memory impairment, we analyzed transgenic mice overexpressing LRG in the brain (LRG-Tg) focusing on hippocampus. Immunostaining and Western blotting revealed age-related increase in LRG expression in hippocampal neurons in 8-, 24-, and 48-week-old controls and LRG-Tg. Y-maze and Morris water maze tests indicated retained spatial memory in 8- and 24-week-old LRG-Tg, while deteriorated in 48-week-old LRG-Tg compared with age-matched controls. Field excitatory postsynaptic potentials declined with age in LRG-Tg compared with controls at 8, 24, and 48 weeks. Paired-pulse ratio decreased with age in LRG-Tg, while increased in controls. As a result, long-term potentiation was retained in 8- and 24-week-old LRG-Tg, whereas diminished in 48-week-old LRG-Tg compared with age-matched controls. Electron microscopy observations revealed fewer synaptic vesicles and junctions in LRG-Tg compared with age-matched controls, which became significant with age. Hippocampal LRG overexpression contributes to synaptic dysfunction, which leads to memory impairment with advance of age.
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Affiliation(s)
- Chihiro Akiba
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Madoka Nakajima
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masakazu Miyajima
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ikuko Ogino
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masami Miura
- Neurophysiology Research Group, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Ritsuko Inoue
- Neurophysiology Research Group, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Eri Nakamura
- Laboratory of Disease Model Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fumio Kanai
- Laboratory of Disease Model Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Norihiro Tada
- Laboratory of Disease Model Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miyuki Kunichika
- Laboratory of Morpheme Analysis Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mitsutaka Yoshida
- Laboratory of Morpheme Analysis Imaging Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kinya Nishimura
- Neurophysiology Research Group, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan; Department of Anesthesiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akihide Kondo
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hidenori Sugano
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hajime Arai
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
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24
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Yang S, Pei Y, Zhao A. iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus. Sci Rep 2017; 7:45922. [PMID: 28374783 PMCID: PMC5379687 DOI: 10.1038/srep45922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/03/2017] [Indexed: 12/18/2022] Open
Abstract
Pseudorabies virus (PRV) is one of the most important pathogens of swine, resulting in severe economic losses to the pig industry. To improve our understanding of the host responses to PRV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry to quantitatively identify the differentially expressed cellular proteins in PRV-infected PK15 cells. In total, relative quantitative data were identified for 4333 proteins in PRV and mock- infected PK15 cells, among which 466 cellular proteins were differentially expressed, including 234 upregulated proteins and 232 downregulated proteins. Bioinformatics analysis disclosed that most of these differentially expressed proteins were involved in metabolic processes, cellular growth and proliferation, endoplasmic reticulum (ER) stress response, cell adhesion and cytoskeleton. Moreover, expression levels of four representative proteins, beta-catenin, STAT1, GRB2 and PCNA, were further confirmed by western blot analysis. This is the first attempt to analyze the protein profile of PRV-infected PK15 cells using iTRAQ technology, and our findings may provide valuable information to help understand the host response to PRV infection.
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Affiliation(s)
- Songbai Yang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Yue Pei
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
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25
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Shimizu M, Nakagishi Y, Inoue N, Mizuta M, Yachie A. Leucine-rich α2-glycoprotein as the acute-phase reactant to detect systemic juvenile idiopathic arthritis disease activity during anti-interleukin-6 blockade therapy: A case series. Mod Rheumatol 2017; 27:833-837. [PMID: 28094589 DOI: 10.1080/14397595.2016.1270795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES To assess the role of leucine-rich α2-glycoprotein (LRG) as a biomarker for monitoring systemic juvenile idiopathic arthritis (s-JIA) disease activity during interleukin (IL)-6 blockade treatment. METHODS We serially measured serum LRG levels in four s-JIA patients treated with the anti-IL-6 receptor antibody tocilizumab and determined the correlation between clinical symptoms and other inflammatory biomarkers and proinflammatory cytokines, including IL-18, IL-6, neopterin, and tumor necrosis factor-α receptor type I and II. The serum levels of LRG and proinflammatory cytokines were determined using enzyme-linked immunosorbent assay. RESULTS Serum LRG levels increased concomitantly with s-JIA disease flare-up and macrophage activation syndrome development. Furthermore, even in the clinically inactive phase, serum LRG levels were well above normal values. There were no correlations between serum LRG levels and indicators of s-JIA disease activity other than aspartate aminotransferase. There were significant positive correlations between serum LRG levels and proinflammatory cytokines. CONCLUSIONS Serum LRG levels might be a unique and potential biomarker of s-JIA disease activity during IL-6 blockade treatment.
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Affiliation(s)
- Masaki Shimizu
- a Department of Pediatrics, School of Medicine , Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University , Kanazawa , Japan
| | - Yasuo Nakagishi
- b Department of Pediatric Rheumatology , Hyogo Prefectural Kobe Children's Hospital , Kobe , Japan
| | - Natsumi Inoue
- a Department of Pediatrics, School of Medicine , Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University , Kanazawa , Japan
| | - Mao Mizuta
- a Department of Pediatrics, School of Medicine , Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University , Kanazawa , Japan.,b Department of Pediatric Rheumatology , Hyogo Prefectural Kobe Children's Hospital , Kobe , Japan
| | - Akihiro Yachie
- a Department of Pediatrics, School of Medicine , Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University , Kanazawa , Japan
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26
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Park MH, Jo M, Kim YR, Lee CK, Hong JT. Roles of peroxiredoxins in cancer, neurodegenerative diseases and inflammatory diseases. Pharmacol Ther 2016; 163:1-23. [PMID: 27130805 PMCID: PMC7112520 DOI: 10.1016/j.pharmthera.2016.03.018] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/22/2016] [Indexed: 12/29/2022]
Abstract
Peroxiredoxins (PRDXs) are antioxidant enzymes, known to catalyze peroxide reduction to balance cellular hydrogen peroxide (H2O2) levels, which are essential for cell signaling and metabolism and act as a regulator of redox signaling. Redox signaling is a critical component of cell signaling pathways that are involved in the regulation of cell growth, metabolism, hormone signaling, immune regulation and variety of other physiological functions. Early studies demonstrated that PRDXs regulates cell growth, metabolism and immune regulation and therefore involved in the pathologic regulator or protectant of several cancers, neurodegenerative diseases and inflammatory diseases. Oxidative stress and antioxidant systems are important regulators of redox signaling regulated diseases. In addition, thiol-based redox systems through peroxiredoxins have been demonstrated to regulate several redox-dependent process related diseases. In this review article, we will discuss recent findings regarding PRDXs in the development of diseases and further discuss therapeutic approaches targeting PRDXs. Moreover, we will suggest that PRDXs could be targets of several diseases and the therapeutic agents for targeting PRDXs may have potential beneficial effects for the treatment of cancers, neurodegenerative diseases and inflammatory diseases. Future research should open new avenues for the design of novel therapeutic approaches targeting PRDXs.
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Affiliation(s)
- Mi Hee Park
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongwon-gun, Chungbuk, Republic of Korea, 361-951
| | - MiRan Jo
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongwon-gun, Chungbuk, Republic of Korea, 361-951
| | - Yu Ri Kim
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongwon-gun, Chungbuk, Republic of Korea, 361-951
| | - Chong-Kil Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, 12 Gaesin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Jin Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongwon-gun, Chungbuk, Republic of Korea, 361-951.
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Du J, Xing S, Tian Z, Gao S, Xie J, Chang H, Liu G, Luo J, Yin H. Proteomic analysis of sheep primary testicular cells infected with bluetongue virus. Proteomics 2016; 16:1499-514. [PMID: 26989863 PMCID: PMC7168089 DOI: 10.1002/pmic.201500275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 01/03/2016] [Accepted: 03/11/2016] [Indexed: 01/06/2023]
Abstract
Bluetongue virus (BTV) causes a non‐contagious, arthropod‐transmitted disease in wild and domestic ruminants, such as sheep. In this study, we used iTRAQ labeling coupled with LC‐MS/MS for quantitative identification of differentially expressed proteins in BTV‐infected sheep testicular (ST) cells. Relative quantitative data were obtained for 4455 proteins in BTV‐ and mock‐infected ST cells, among which 101 and 479 proteins were differentially expressed at 24 and 48 h post‐infection, respectively, indicating further proteomic changes during the later stages of infection. Ten corresponding genes of differentially expressed proteins were validated via real‐time RT‐PCR. Expression levels of three representative proteins, eIF4a1, STAT1 and HSP27, were further confirmed via western blot analysis. Bioinformatics analysis disclosed that the differentially expressed proteins are primarily involved in biological processes related to innate immune response, signal transduction, nucleocytoplasmic transport, transcription and apoptosis. Several upregulated proteins were associated with the RIG‐I‐like receptor signaling pathway and endocytosis. To our knowledge, this study represents the first attempt to investigate proteome‐wide dysregulation in BTV‐infected cells with the aid of quantitative proteomics. Our collective results not only enhance understanding of the host response to BTV infection but also highlight multiple potential targets for the development of antiviral agents.
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Affiliation(s)
- Junzheng Du
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Shanshan Xing
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Zhancheng Tian
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Shandian Gao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Junren Xie
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Huiyun Chang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P. R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, P. R. China
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Proteomic Analysis of the Vitreous following Experimental Retinal Detachment in Rabbits. J Ophthalmol 2015; 2015:583040. [PMID: 26664739 PMCID: PMC4667062 DOI: 10.1155/2015/583040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 10/17/2015] [Accepted: 10/19/2015] [Indexed: 01/04/2023] Open
Abstract
Purpose. The pathogenesis of rhegmatogenous retinal detachment (RRD) remains incompletely understood, with no clinically effective treatment for potentially severe complications such as photoreceptor cell death and proliferative vitreoretinopathy. Here we investigate the protein profile of the vitreous following experimental retinal detachment using a comparative proteomic based approach. Materials and Methods. Retinal detachment was created in the right eyes of six New Zealand red pigmented rabbits. Sham surgery was undertaken in five other rabbits that were used as controls. After seven days the eyes were enucleated and the vitreous was removed. The vitreous samples were evaluated with two-dimensional polyacrylamide gel electrophoresis and the differentially expressed proteins were identified with tandem mass spectrometry. Results. Ten protein spots were found to be at least twofold differentially expressed when comparing the vitreous samples of the sham and retinal detachment surgery groups. Protein spots that were upregulated in the vitreous following retinal detachment were identified as albumin fragments, and those downregulated were found to be peroxiredoxin 2, collagen-Iα1 fragment, and α-1-antiproteinase F. Conclusions. Proteomic investigation of the rabbit vitreous has identified a set of proteins that help further our understanding of the pathogenesis of rhegmatogenous retinal detachment and its complications.
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Acinetobacter baumannii Extracellular OXA-58 Is Primarily and Selectively Released via Outer Membrane Vesicles after Sec-Dependent Periplasmic Translocation. Antimicrob Agents Chemother 2015; 59:7346-54. [PMID: 26369971 DOI: 10.1128/aac.01343-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/09/2015] [Indexed: 12/21/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) shelter cohabiting carbapenem-susceptible bacteria from carbapenem killing via extracellular release of carbapenem-hydrolyzing class D β-lactamases, including OXA-58. However, the mechanism of the extracellular release of OXA-58 has not been elucidated. In silico analysis predicted OXA-58 to be translocated to the periplasm via the Sec system. Using cell fractionation and Western blotting, OXA-58 with the signal peptide and C terminus deleted was not detected in the periplasmic and extracellular fractions. Overexpression of enhanced green fluorescent protein fused to the OXA-58 signal peptide led to its periplasmic translocation but not extracellular release, suggesting that OXA-58 is selectively released. The majority of the extracellular OXA-58 was associated with outer membrane vesicles (OMVs). The OMV-associated OXA-58 was detected only in a strain overexpressing OXA-58. The presence of OXA-58 in OMVs was confirmed by a carbapenem inactivation bioassay, proteomic analysis, and transmission electron microscopy. Imipenem treatment increased OMV formation and caused cell lysis, resulting in an increase in the OMV-associated and OMV-independent release of extracellular OXA-58. OMV-independent OXA-58 hydrolyzed nitrocefin more rapidly than OMV-associated OXA-58 but was more susceptible to proteinase K degradation. Rose bengal, an SecA inhibitor, inhibited the periplasmic translocation and OMV-associated release of OXA-58 and abolished the sheltering effect of CRAb. This study demonstrated that the majority of the extracellular OXA-58 is selectively released via OMVs after Sec-dependent periplasmic translocation. Addition of imipenem increased both OMV-associated and OMV-independent OXA-58, which may have different biological roles. SecA inhibitor could abolish the carbapenem-sheltering effect of CRAb.
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Identification of host-immune response protein candidates in the sera of human oral squamous cell carcinoma patients. PLoS One 2014; 9:e109012. [PMID: 25272005 PMCID: PMC4182798 DOI: 10.1371/journal.pone.0109012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/06/2014] [Indexed: 12/13/2022] Open
Abstract
One of the most common cancers worldwide is oral squamous cell carcinoma (OSCC), which is associated with a significant death rate and has been linked to several risk factors. Notably, failure to detect these neoplasms at an early stage represents a fundamental barrier to improving the survival and quality of life of OSCC patients. In the present study, serum samples from OSCC patients (n = 25) and healthy controls (n = 25) were subjected to two-dimensional gel electrophoresis (2-DE) and silver staining in order to identify biomarkers that might allow early diagnosis. In this regard, 2-DE spots corresponding to various up- and down-regulated proteins were sequenced via high-resolution MALDI-TOF mass spectrometry and analyzed using the MASCOT database. We identified the following differentially expressed host-specific proteins within sera from OSCC patients: leucine-rich α2-glycoprotein (LRG), alpha-1-B-glycoprotein (ABG), clusterin (CLU), PRO2044, haptoglobin (HAP), complement C3c (C3), proapolipoprotein A1 (proapo-A1), and retinol-binding protein 4 precursor (RBP4). Moreover, five non-host factors were detected, including bacterial antigens from Acinetobacter lwoffii, Burkholderia multivorans, Myxococcus xanthus, Laribacter hongkongensis, and Streptococcus salivarius. Subsequently, we analyzed the immunogenicity of these proteins using pooled sera from OSCC patients. In this regard, five of these candidate biomarkers were found to be immunoreactive: CLU, HAP, C3, proapo-A1 and RBP4. Taken together, our immunoproteomics approach has identified various serum biomarkers that could facilitate the development of early diagnostic tools for OSCC.
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Gouthamchandra K, Kumar A, Shwetha S, Mukherjee A, Chandra M, Ravishankar B, Khaja MN, Sadhukhan PC, Das S. Serum proteomics of hepatitis C virus infection reveals retinol-binding protein 4 as a novel regulator. J Gen Virol 2014; 95:1654-1667. [PMID: 24784414 DOI: 10.1099/vir.0.062430-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Persistent infection of hepatitis C virus (HCV) can lead to liver cirrhosis and hepatocellular carcinoma, which are currently diagnosed by invasive liver biopsy. Approximately 15-20 % of cases of chronic liver diseases in India are caused by HCV infection. In North India, genotype 3 is predominant, whereas genotype 1 is predominant in southern parts of India. The aim of this study was to identify differentially regulated serum proteins in HCV-infected Indian patients (genotypes 1 and 3) using a two-dimensional electrophoresis approach. We identified eight differentially expressed proteins by MS. Expression levels of one of the highly upregulated proteins, retinol-binding protein 4 (RBP4), was validated by ELISA and Western blotting in two independent cohorts. We also confirmed our observation in the JFH1 infectious cell culture system. Interestingly, the HCV core protein enhanced RBP4 levels and partial knockdown of RBP4 had a positive impact on HCV replication, suggesting a possible role for this cellular protein in regulating HCV infection. Analysis of RBP4-interacting partners using a bioinformatic approach revealed novel insights into the possible involvement of RBP4 in HCV-induced pathogenesis. Taken together, this study provided information on the proteome profile of the HCV-infected Indian population, and revealed a link between HCV infection, RBP4 and insulin resistance.
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Affiliation(s)
- K Gouthamchandra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Anuj Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Shivaprasad Shwetha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Anirban Mukherjee
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, GB-4 (East Wing) 1st Floor, 57, Dr Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, India
| | - Madhavi Chandra
- Bioviz Technologies Pvt Ltd, Sagar Society, Road No. 2, Banjara Hills, Hyderabad 500 034, India
| | | | - M N Khaja
- Bioviz Technologies Pvt Ltd, Sagar Society, Road No. 2, Banjara Hills, Hyderabad 500 034, India
| | - Provash Chandra Sadhukhan
- ICMR Virus Unit, Kolkata, ID & BG Hospital Campus, GB-4 (East Wing) 1st Floor, 57, Dr Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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Zhang X, Liu F, Li Q, Jia H, Pan L, Xing A, Xu S, Zhang Z. A proteomics approach to the identification of plasma biomarkers for latent tuberculosis infection. Diagn Microbiol Infect Dis 2014; 79:432-7. [PMID: 24865408 PMCID: PMC7127109 DOI: 10.1016/j.diagmicrobio.2014.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 11/17/2022]
Abstract
A proteomic analysis was performed to screen the potential latent tuberculosis infection (LTBI) biomarkers. A training set of spectra was used to generate diagnostic models, and a blind testing set was used to determine the accuracy of the models. Candidate peptides were identified using nano-liquid chromatography-electrospray ionization–tandem mass spectrometry. Based on the training set results, 3 diagnostic models recognized LTBI subjects with good cross-validation accuracy. In the blind testing set, LTBI subjects could be identified with sensitivities and specificities of 85.20% to 88.90% and 85.7% to 100%, respectively. Additionally, 14 potential LTBI biomarkers were identified, and all proteins were identified for the first time through proteomics in the plasma of healthy, latently infected individuals. In all, proteomic pattern analyses can increase the accuracy of LTBI diagnosis, and the data presented here provide novel insights into potential mechanisms involved in LTBI.
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Affiliation(s)
- Xia Zhang
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Fei Liu
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qi Li
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hongyan Jia
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liping Pan
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Aiying Xing
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shaofa Xu
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Zongde Zhang
- Department of Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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Zhang CG, Chromy BA, McCutchen-Maloney SL. Host–pathogen interactions: a proteomic view. Expert Rev Proteomics 2014; 2:187-202. [PMID: 15892564 DOI: 10.1586/14789450.2.2.187] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Host-pathogen interactions reflect the balance of host defenses and pathogen virulence mechanisms. Advances in proteomic technologies now afford opportunities to compare protein content between complex biologic systems ranging from cells to animals and clinical samples. Thus, it is now possible to characterize host-pathogen interactions from a global proteomic view. Most reports to date focus on cataloging protein content of pathogens and identifying virulence-associated proteins or proteomic alterations in host response. A more in-depth understanding of host-pathogen interactions has the potential to improve our mechanistic understanding of pathogenicity and virulence, thereby defining novel therapeutic and vaccine targets. In addition, proteomic characterization of the host response can provide pathogen-specific host biomarkers for rapid pathogen detection and characterization, as well as for early and specific detection of infectious diseases. A review of host-pathogen interactions focusing on proteomic analyses of both pathogen and host will be presented. Relevant genomic studies and host model systems will be also be discussed.
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Affiliation(s)
- Celia G Zhang
- Lawrence Livermore National Laboratory, Biosciences Directorate, 7000 East Avenue, Livermore, CA 94550, USA.
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Ray S, Patel SK, Kumar V, Damahe J, Srivastava S. Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures. Proteomics Clin Appl 2013; 8:53-72. [PMID: 24293340 PMCID: PMC7168033 DOI: 10.1002/prca.201300074] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 01/26/2023]
Abstract
Apart from direct detection of the infecting organisms or biomarker of the pathogen itself, surrogate host markers are also useful for sensitive and early diagnosis of pathogenic infections. Early detection of pathogenic infections, discrimination among closely related diseases with overlapping clinical manifestations, and monitoring of disease progression can be achieved by analyzing blood biomarkers. Therefore, over the last decade large numbers of proteomics studies have been conducted to identify differentially expressed human serum/plasma proteins in different infectious diseases with the intent of discovering novel potential diagnostic/prognostic biomarkers. However, in-depth review of the literature indicates that many reported biomarkers are altered in the same way in multiple infectious diseases, regardless of the type of infection. This might be a consequence of generic acute phase reactions, while the uniquely modulated candidates in different pathogenic infections could be indicators of some specific responses. In this review article, we will provide a comprehensive analysis of differentially expressed serum/plasma proteins in various infectious diseases and categorize the protein markers associated with generic or specific responses. The challenges associated with the discovery, validation, and translational phases of serum/plasma biomarker establishment are also discussed.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Hanschmann EM, Godoy JR, Berndt C, Hudemann C, Lillig CH. Thioredoxins, glutaredoxins, and peroxiredoxins--molecular mechanisms and health significance: from cofactors to antioxidants to redox signaling. Antioxid Redox Signal 2013; 19:1539-605. [PMID: 23397885 PMCID: PMC3797455 DOI: 10.1089/ars.2012.4599] [Citation(s) in RCA: 496] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 02/01/2013] [Accepted: 02/07/2013] [Indexed: 12/19/2022]
Abstract
Thioredoxins (Trxs), glutaredoxins (Grxs), and peroxiredoxins (Prxs) have been characterized as electron donors, guards of the intracellular redox state, and "antioxidants". Today, these redox catalysts are increasingly recognized for their specific role in redox signaling. The number of publications published on the functions of these proteins continues to increase exponentially. The field is experiencing an exciting transformation, from looking at a general redox homeostasis and the pathological oxidative stress model to realizing redox changes as a part of localized, rapid, specific, and reversible redox-regulated signaling events. This review summarizes the almost 50 years of research on these proteins, focusing primarily on data from vertebrates and mammals. The role of Trx fold proteins in redox signaling is discussed by looking at reaction mechanisms, reversible oxidative post-translational modifications of proteins, and characterized interaction partners. On the basis of this analysis, the specific regulatory functions are exemplified for the cellular processes of apoptosis, proliferation, and iron metabolism. The importance of Trxs, Grxs, and Prxs for human health is addressed in the second part of this review, that is, their potential impact and functions in different cell types, tissues, and various pathological conditions.
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Affiliation(s)
- Eva-Maria Hanschmann
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, Ernst-Moritz Arndt University, Greifswald, Germany
| | - José Rodrigo Godoy
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Duesseldorf, Germany
| | - Christoph Hudemann
- Institute of Laboratory Medicine, Molecular Diagnostics, Philipps University, Marburg, Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, Ernst-Moritz Arndt University, Greifswald, Germany
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 986] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Nimse SB, Song KS, Kim J, Sayyed DR, Kim T. 9G DNAChip Technology: Self-Assembled Monolayer (SAM) of ssDNA for Ultra-Sensitive Detection of Biomarkers. Int J Mol Sci 2013; 14:5723-33. [PMID: 23481635 PMCID: PMC3634481 DOI: 10.3390/ijms14035723] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 02/01/2013] [Accepted: 03/04/2013] [Indexed: 11/16/2022] Open
Abstract
A 9G DNAChip obtained by allowing the formation of a self-assembled monolayer (SAM) of oligonucleotides appended with nine consecutive guanines on the chip surface has been applied in the detection of biomarkers. Using a 9G DNAChip, biomarker in the concentration range of 4 pg/mL to 40 fg/mL can be easily differentiated in the buffer matrix. Moreover, it is the first time that a biomarker with a concentration of 40 fg/mL has been detected in a mixture of proteins without use of any signal amplification technique.
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Affiliation(s)
- Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea; E-Mails: (S.B.N.); (D.R.S.)
| | - Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; E-Mails: (K.-S.S.); (J.K.)
| | - Junghoon Kim
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; E-Mails: (K.-S.S.); (J.K.)
| | - Danishmalik Rafiq Sayyed
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea; E-Mails: (S.B.N.); (D.R.S.)
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea; E-Mails: (S.B.N.); (D.R.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-33-248-2078 (ext. 123); Fax: +82-33-256-3421
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Protective effects of long pentraxin PTX3 on lung injury in a severe acute respiratory syndrome model in mice. J Transl Med 2012; 92:1285-96. [PMID: 22732935 PMCID: PMC3955193 DOI: 10.1038/labinvest.2012.92] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The outbreak of severe acute respiratory syndrome (SARS) in 2003 reinforces the potential of lethal pandemics of respiratory viral infections. The underlying mechanisms of SARS are still largely undefined. Long pentraxin PTX3, a humoral mediator of innate immunity, has been reported to have anti-viral effects. We examined the role of PTX3 in coronavirus murine hepatitis virus strain 1 (MHV-1)-induced acute lung injury, a previously reported animal model for SARS. PTX3-deficient mice (129/SvEv/C57BL6/J) and their wild-type (WT) littermates were intranasally infected MHV-1. These mice were also treated with recombinant PTX3. Effects of PTX3 on viral binding and infectivity were determined in vitro. Cytokine expression, severity of lung injury, leukocyte infiltration and inflammatory responses were examined in vivo. In PTX3 WT mice, MHV-1 induced PTX3 expression in the lung and serum in a time-dependent manner. MHV-1 infection led to acute lung injury with greater severity in PTX3-deficient mice than that in WT mice. PTX3 deficiency enhanced early infiltration of neutrophils and macrophages in the lung. PTX3 bound to MHV-1 and MHV-3 and reduced MHV-1 infectivity in vitro. Administration of recombinant PTX3 significantly accelerated viral clearance in the lung, attenuated MHV-1-induced lung injury, and reduced early neutrophil influx and elevation of inflammatory mediators in the lung. Results from this study indicate a protective role of PTX3 in coronaviral infection-induced acute lung injury.
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Ray S, Srivastava R, Tripathi K, Vaibhav V, Patankar S, Srivastava S. Serum proteome changes in dengue virus-infected patients from a dengue-endemic area of India: towards new molecular targets? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:527-36. [PMID: 22917478 DOI: 10.1089/omi.2012.0037] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The global burden of dengue continues to worsen, specifically in tropical and subtropical countries, and has evolved as a major public health problem. We investigated the changes in serum proteome in dengue fever (DF) patients from a dengue-endemic area of India to obtain mechanistic insights about the disease pathogenesis, the host immune response, and identification of potential serum protein biomarkers of this infectious disease. In this study, serum samples from DF patients, healthy subjects, and patients with falciparum malaria (an infectious disease control) were investigated by 2D-DIGE in combination with MALDI-TOF/TOF MS. The findings were validated with Western blotting. Functional clustering of the identified proteins was performed using PANTHER and DAVID tools. Compared to the healthy controls, we found significant changes in the expression levels of 48 protein spots corresponding to 18 unique proteins (7 downregulated and 11 upregulated) in DF patients (p<0.05). Among these differentially-expressed proteins, 11 candidates exhibited different trends in dengue fever compared to falciparum malaria. Importantly, our results suggest that dengue virus infection leads to alterations in expression levels of multiple serum proteins involved in diverse and vital physiological pathways, including acute phase response signaling, complement cascades, hemostasis, and blood coagulation. For the first time we report here that the serum levels of hemopexin, haptoglobin, serum amyloid P, and kininogen precursor, are altered in DF. This study informs the pathogenesis and host immune response to dengue virus infection, as well as the current search for new diagnostic and molecular drug targets.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Proteomic investigation of falciparum and vivax malaria for identification of surrogate protein markers. PLoS One 2012; 7:e41751. [PMID: 22912677 PMCID: PMC3415403 DOI: 10.1371/journal.pone.0041751] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/25/2012] [Indexed: 01/30/2023] Open
Abstract
This study was conducted to analyze alterations in the human serum proteome as a consequence of infection by malaria parasites Plasmodium falciparum and P. vivax to obtain mechanistic insights about disease pathogenesis, host immune response, and identification of potential protein markers. Serum samples from patients diagnosed with falciparum malaria (FM) (n = 20), vivax malaria (VM) (n = 17) and healthy controls (HC) (n = 20) were investigated using multiple proteomic techniques and results were validated by employing immunoassay-based approaches. Specificity of the identified malaria related serum markers was evaluated by means of analysis of leptospirosis as a febrile control (FC). Compared to HC, 30 and 31 differentially expressed and statistically significant (p<0.05) serum proteins were identified in FM and VM respectively, and almost half (46.2%) of these proteins were commonly modulated due to both of the plasmodial infections. 13 proteins were found to be differentially expressed in FM compared to VM. Functional pathway analysis involving the identified proteins revealed the modulation of different vital physiological pathways, including acute phase response signaling, chemokine and cytokine signaling, complement cascades and blood coagulation in malaria. A panel of identified proteins consists of six candidates; serum amyloid A, hemopexin, apolipoprotein E, haptoglobin, retinol-binding protein and apolipoprotein A-I was used to build statistical sample class prediction models. By employing PLS-DA and other classification methods the clinical phenotypic classes (FM, VM, FC and HC) were predicted with over 95% prediction accuracy. Individual performance of three classifier proteins; haptoglobin, apolipoprotein A-I and retinol-binding protein in diagnosis of malaria was analyzed using receiver operating characteristic (ROC) curves. The discrimination of FM, VM, FC and HC groups on the basis of differentially expressed serum proteins demonstrates the potential of this analytical approach for the detection of malaria as well as other human diseases.
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Lu Q, Bai J, Zhang L, Liu J, Jiang Z, Michal JJ, He Q, Jiang P. Two-Dimensional Liquid Chromatography–Tandem Mass Spectrometry Coupled with Isobaric Tags for Relative and Absolute Quantification (iTRAQ) Labeling Approach Revealed First Proteome Profiles of Pulmonary Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus. J Proteome Res 2012; 11:2890-903. [DOI: 10.1021/pr201266z] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Qi Lu
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Bai
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Lili Zhang
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Liu
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351,
United States
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351,
United States
| | - Qindong He
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Jiang
- Key Laboratory
of Animal Diseases
Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary
Medicine, Nanjing Agricultural University, Nanjing 210095, China
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Srivastava R, Ray S, Vaibhav V, Gollapalli K, Jhaveri T, Taur S, Dhali S, Gogtay N, Thatte U, Srikanth R, Srivastava S. Serum profiling of leptospirosis patients to investigate proteomic alterations. J Proteomics 2012; 76 Spec No.:56-68. [PMID: 22554907 PMCID: PMC7185557 DOI: 10.1016/j.jprot.2012.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/20/2012] [Accepted: 04/07/2012] [Indexed: 11/05/2022]
Abstract
Leptospirosis is a zoonotic infectious disease of tropical, subtropical and temperate zones, which is caused by the pathogenic spirochetes of genus Leptospira. Although this zoonosis is generally not considered as fatal, the pathogen can eventually cause severe infection with septic shock, multi-organ failure and lethal pulmonary hemorrhages leading to mortality. In this study, we have performed a proteomic analysis of serum samples from leptospirosis patients (n = 6), febrile controls (falciparum malaria) (n = 8) and healthy subjects (n = 18) to obtain an insight about disease pathogenesis and host immune responses in leptospiral infections. 2DE and 2D-DIGE analysis in combination with MALDI-TOF/TOF MS revealed differential expression of 22 serum proteins in leptospirosis patients compared to the healthy controls. Among the identified differentially expressed proteins, 8 candidates exhibited different trends compared to the febrile controls. Functional analysis suggested the involvement of differentially expressed proteins in vital physiological pathways, including acute phase response, complement and coagulation cascades and hemostasis. This is the first report of analysis of human serum proteome alterations in leptospirosis patients, which revealed several differentially expressed proteins, including α-1-antitrypsin, vitronectin, ceruloplasmin, G-protein signaling regulator, apolipoprotein A-IV, which have not been reported in context of leptospirosis previously. This study will enhance our understanding about leptospirosis pathogenesis and provide a glimpse of host immunological responses. Additionally, a few differentially expressed proteins identified in this study may further be investigated as diagnostic or prognostic serum biomarkers for leptospirosis. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Rajneesh Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Cao Z, Han Z, Shao Y, Liu X, Sun J, Yu D, Kong X, Liu S. Proteomics analysis of differentially expressed proteins in chicken trachea and kidney after infection with the highly virulent and attenuated coronavirus infectious bronchitis virus in vivo. Proteome Sci 2012; 10:24. [PMID: 22463732 PMCID: PMC3342233 DOI: 10.1186/1477-5956-10-24] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/31/2012] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Infectious bronchitis virus (IBV) is first to be discovered coronavirus which is probably endemic in all regions with intensive impact on poultry production. In this study, we used two-dimensional gel electrophoresis (2-DE) and two-dimensional fluorescence difference gel electrophoresis (2-DIGE), coupled with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS), to explore the global proteome profiles of trachea and kidney tissues from chicken at different stages infected in vivo with the highly virulent ck/CH/LDL/97I P5 strain of infectious bronchitis virus (IBV) and the embryo-passaged, attenuated ck/CH/LDL/97I P115 strain. RESULTS Fifty-eight differentially expressed proteins were identified. Results demonstrated that some proteins which had functions in cytoskeleton organization, anti-oxidative stress, and stress response, showed different change patterns in abundance from chicken infected with the highly virulent ck/CH/LDL/97I P5 strain and those given the embryo-passaged, attenuated P115 stain. In addition, the dynamic transcriptional alterations of 12 selected proteins were analyzed by the real-time RT-PCR, and western blot analysis confirmed the change in abundance of heat shock proteins (HSP) beta-1, annexin A2, and annexin A5. CONCLUSIONS The proteomic alterations described here may suggest that these changes to protein expression correlate with IBV virus' virulence in chicken, hence provides valuable insights into the interactions of IBV with its host and may also assist with investigations of the pathogenesis of IBV and other coronavirus infections.
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Affiliation(s)
- Zhongzan Cao
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China.
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Serum proteome analysis of vivax malaria: An insight into the disease pathogenesis and host immune response. J Proteomics 2011; 75:3063-80. [PMID: 22086083 DOI: 10.1016/j.jprot.2011.10.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/24/2011] [Accepted: 10/20/2011] [Indexed: 10/15/2022]
Abstract
Vivax malaria is the most widely distributed human malaria resulting in 80-300 million clinical cases every year. It causes severe infection and mortality but is generally regarded as a benign disease and has not been investigated in detail. The present study aimed to perform human serum proteome analysis in a malaria endemic area in India to identify potential serum biomarkers for vivax malaria and understand host response. The proteomic analysis was performed on 16 age and gender matched subjects (vivax patients and control) in duplicate. Protein extraction protocols were optimized for large coverage of the serum proteome and to obtain high-resolution data. Identification of 67 differentially expressed and statistically significant (Student's t-test; p<0.05) protein spots was established by MALDI-TOF/TOF mass spectrometry. Many of the identified proteins such as apolipoprotein A and E, serum amyloid A and P, haptoglobin, ceruloplasmin, and hemopexin are interesting from a diagnostic point of view and could further be studied as potential serum biomarkers. The differentially expressed serum proteins in vivax malaria identified in this study were subjected to functional pathway analysis using multiple software, including Ingenuity Pathway Analysis (IPA), Protein ANalysis THrough Evolutionary Relationships (PANTHER) and Database for Annotation, Visualization and Integrated Discovery (DAVID) functional annotation tool for better understanding of the biological context of the identified proteins, their involvement in various physiological pathways and association with disease pathogenesis. Functional pathway analysis of the differentially expressed proteins suggested the modulation of multiple vital physiological pathways, including acute phase response signaling, complement and coagulation cascades, hemostasis and vitamin D metabolism pathway due to this parasitic infection. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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Blais DR, Nasheri N, McKay CS, Legault MC, Pezacki JP. Activity-based protein profiling of host-virus interactions. Trends Biotechnol 2011; 30:89-99. [PMID: 21944551 PMCID: PMC7114118 DOI: 10.1016/j.tibtech.2011.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 02/08/2023]
Abstract
Virologists have benefited from large-scale profiling methods to discover new host–virus interactions and to learn about the mechanisms of pathogenesis. One such technique, referred to as activity-based protein profiling (ABPP), uses active site-directed probes to monitor the functional state of enzymes, taking into account post-translational interactions and modifications. ABPP gives insight into the catalytic activity of enzyme families that does not necessarily correlate with protein abundance. ABPP has been used to investigate several viruses and their interactions with their hosts. Differential enzymatic activity induced by viruses has been monitored using ABPP. In this review, we present recent advances and trends involving the use of ABPP methods in understanding host–virus interactions and in identifying novel targets for diagnostic and therapeutic applications.
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Affiliation(s)
- David R. Blais
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Neda Nasheri
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Craig S. McKay
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
| | - Marc C.B. Legault
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
| | - John Paul Pezacki
- Steacie Institute for Molecular Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie Curie Private, Ottawa, ON, K1N 6N5, Canada
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Nickel CH, Ruedinger J, Misch F, Blume K, Maile S, Schulte J, Köhrle J, Hartmann O, Giersdorf S, Bingisser R. Copeptin and peroxiredoxin-4 independently predict mortality in patients with nonspecific complaints presenting to the emergency department. Acad Emerg Med 2011; 18:851-9. [PMID: 21843221 DOI: 10.1111/j.1553-2712.2011.01126.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Patients presenting to emergency departments (ED) with nonspecific complaints (NSCs) such as "not feeling well,""feeling weak,""being tired,""general deterioration," or other similar chief complaints that do not have a readily identifiable probable etiology are a common patient group at risk for adverse outcomes. Certain biomarkers, which have not yet been tested for prognostic value when applied to ED patients with NSCs, have emerged as useful tools for predicting prognosis in patients with a variety of diseases. This study tested the hypothesis that two of these novel markers, copeptin (a C-terminal portion of provasopressin) and/or peroxiredoxin-4 (Prx4), an enzyme that degrades hydrogen peroxide, singly or together are helpful in predicting death in the near term among patients presenting to the ED with NSCs. METHODS The Basel Non-specific Complaints (BANC) study is a delayed type cross-sectional diagnostic study with a prospective 30-day follow-up. ED patients with NSCs were consecutively enrolled. Patients with vital parameters out of the normal range were excluded. The primary endpoint of this study was the predictive value of copeptin and Prx4 for 30-day mortality in patients with NSCs. Measurement of both copeptin and Prx4 was performed in serum samples with sandwich immunoluminometric assays. RESULTS On follow-up at 30 days after ED presentation, 28 of 438 patients with NSC had died. Copeptin and Prx4 concentrations were significantly higher in nonsurvivors than in survivors (Kruskal-Wallis test, p = 0.0001 and p < 0.0001, respectively). In univariate models, Prx4 (likelihood ratio [LR] χ(2) = 22.24, p < 0.00001, concordance index [C-index] = 0.749) and copeptin (LR χ(2) = 16.98, p = 0.00004, C-index = 0.724) were both predictive of 30-day mortality, and elevated levels were associated with an increased mortality. The bivariable model, which included both Prx4 and copeptin (LR χ(2) = 28.22, p < 0.00001, C-index = 0.783), allows a significantly better prediction than the univariate Prx4 (p = 0.00025) and copeptin models (p = 0.00099), respectively. Both biomarkers provided independent and additional information to clinical risk scores (Katz Activities of Daily Living [ADL] and Charlson Comorbidity Index [CCI], all p < 0.0005). CONCLUSIONS Copeptin and Prx4 are new prognostic markers in patients presenting to the ED with NSCs. Copeptin and Prx4 might be valuable tools for risk stratification and decision-making in this patient group.
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Ray S, Reddy PJ, Jain R, Gollapalli K, Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 2011; 11:2139-61. [PMID: 21548090 DOI: 10.1002/pmic.201000460] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 02/28/2011] [Accepted: 03/07/2011] [Indexed: 01/22/2023]
Abstract
Serum is an ideal biological sample that contains an archive of information due to the presence of a variety of proteins released by diseased tissue, and serum proteomics has gained considerable interest for the disease biomarker discovery. Easy accessibility and rapid protein changes in response to disease pathogenesis makes serum an attractive sample for clinical research. Despite these advantages, the analysis of serum proteome is very challenging due to the wide dynamic range of proteins, difficulty in finding low-abundance target analytes due to the presence of high-abundance serum proteins, high levels of salts and other interfering compounds, variations among individuals and paucity of reproducibility. Sample preparation introduces pre-analytical variations and poses major challenges to analyze the serum proteome. The label-free detection techniques such as surface plasmon resonance, microcantilever, few nanotechniques and different resonators are rapidly emerging for the analysis of serum proteome and they have exhibited potential to overcome few limitations of the conventional techniques. In this article, we will discuss the current status of serum proteome analysis for the biomarker discovery and address key technological advancements, with a focus on challenges and amenable solutions.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Chiou SH, Wu CY. Clinical proteomics: current status, challenges, and future perspectives. Kaohsiung J Med Sci 2011; 27:1-14. [PMID: 21329886 DOI: 10.1016/j.kjms.2010.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 09/06/2010] [Indexed: 12/20/2022] Open
Abstract
This account will give an overview and evaluation of the current advances in mass spectrometry (MS)-based proteomics platforms and technology. A general review of some background information concerning the application of these methods in the characterization of molecular sizes and related protein expression profiles associated with different types of cells under varied experimental conditions will be presented. It is intended to provide a concise and succinct overview to those clinical researchers first exposed to this foremost powerful methodology in modern life sciences of postgenomic era. Proteomic characterization using highly sophisticated and expensive instrumentation of MS has been used to characterize biological samples of complex protein mixtures with vastly different protein structure and composition. These systems are then used to highlight the versatility and potential of the MS-based proteomic strategies for facilitating protein expression analysis of various disease-related organisms or tissues of interest. Major MS-based strategies reviewed herein include (1) matrix-assisted laser desorption ionization-MS and electron-spray ionization proteomics; (2) one-dimensional or two-dimensional gel-based proteomics; (3) gel-free shotgun proteomics in conjunction with liquid chromatography/tandem MS; (4) Multiple reaction monitoring coupled tandem MS quantitative proteomics and; (5) Phosphoproteomics based on immobilized metal affinity chromatography and liquid chromatography-MS/MS.
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Affiliation(s)
- Shyh-Horng Chiou
- Graduate Institute of Medicine and Center for Research Resources and Development, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Mehrani H, Ghanei M, Aslani J, Tabatabaei Z. Plasma proteomic profile of sulfur mustard exposed lung diseases patients using 2-dimensional gel electrophoresis. Clin Proteomics 2011; 8:2. [PMID: 21906349 PMCID: PMC3167199 DOI: 10.1186/1559-0275-8-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 05/31/2011] [Indexed: 12/30/2022] Open
Abstract
Introduction Sulfur mustard "bis (2-chlroethyl) sulphide" (SM) is a chemical warfare agent that remains a threat to human health. The aim of this study was to identify protein expression signature or biomarkers that reflect chronic lung damages induced by SM exposure. Methods Prior to analysis, plasma was fractionated using ethanol precipitation. Using two dimensional SDS-PAGE; fractionated protein profiles of 20 healthy and 20 exposed patients with lung diseases were established. Selected protein spots were successfully identified with MALDI TOF MS/MS. Results The results show that α1 haptoglobin isoforms were detected in plasma of the all lung disease patients but none of the healthy controls. Amyloid A1 isoforms was also detected in plasma of the lung disease patients but none of the healthy controls. Moreover, low molecular weight proteins were enriched in ethanol supernatant compared to ethanol precipitate. Conclusion Our present results and previous studies suggest that ongoing tissue remodeling is involved in SM exposed lung damage patients. These finding might improve patient care and suitable therapies.
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Affiliation(s)
- Hossein Mehrani
- Laboratory of Proteomics, and Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Wang W, Gou L, Xie G, Tong A, He F, Lu Z, Yao Y, Liu K, Li J, Tang M, Chen L, Yang J, Hu H, Wei YQ. Proteomic analysis of interstitial fluid in bone marrow identified that peroxiredoxin 2 regulates H(2)O(2) level of bone marrow during aging. J Proteome Res 2010; 9:3812-9. [PMID: 20568815 DOI: 10.1021/pr901180w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hematopoiesis in bone marrow declines during aging owing to alteration of the hematopoietic niche. However, due to difficult accessibility and other complexities, senescence-related alteration of the hematopoietic niche is largely unknown. The interstitial fluid of bone marrow (IFBM), a pivotal component of the hematopoietic niche, includes soluble secretory factors that are present between bone marrow cells. To characterize the proteomic profile changes of IFBM during aging, we analyzed the IFBMs of young, adult, and senescent rats using 2-DE combined with ESI/MALDI-Q-TOF MS. Finally, 31 differentially expressed proteins involved in multiple biological functions were identified. Peroxiredoxin 2 (Prx2), down-regulated during aging, was further analyzed and demonstrated that it is produced by bone marrow stromal cells. Interestingly, higher levels of hydrogen peroxide (H(2)O(2)) were detected in the bone marrow with lower Prx2 expression. Moreover, exogenous Prx2 reduced the intracellular H(2)O(2) level in bone marrow stromal cells in vitro. Therefore, Prx2 is implied in the regulation of H(2)O(2) production in the bone marrow during aging. Our data characterized the dynamic protein profiles of the bone marrow microenvironment during aging and we provided clues to elucidate the mechanism of creating a low ROS level in the hematopoietic niche.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Biotherapy, West China Hospital and College of Life Sciences, Sichuan University, Chengdu, China
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