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Ghetia C, Bhatt P, Mukhopadhyay C. Association of dengue virus non-structural-1 protein with disease severity: a brief review. Trans R Soc Trop Med Hyg 2022; 116:986-995. [PMID: 36125197 DOI: 10.1093/trstmh/trac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/19/2021] [Accepted: 08/31/2022] [Indexed: 01/19/2023] Open
Abstract
Dengue virus (DENV) was discovered by P. M. Ashburn and Charles F. Craig in 1907. Evidence of dengue-like illness was observed before 1907 and DENV epidemics have been reported from different parts of the world since then, with increased morbidity rates every year. DENV typically causes a febrile illness that ranges from mild asymptomatic infection to fatal dengue haemorrhagic fever (DHF) and/or dengue shock syndrome (DSS). Host mechanisms through which mild infection progresses to the fatal forms are still unknown. Few factors have been associated to aid severe disease acquisition, DENV non-structural 1 (NS1) protein being one of them. NS1 is a highly conserved glycoprotein among the Flavivirus and is often used as a biomarker for dengue diagnosis. This review focuses on assessing the role of NS1 in severe dengue. In this review, hospital-based studies on the association of dengue NS1 with severe dengue from all over the world have been assessed and analysed and the majority of the studies positively correlate high NS1 levels with DHF/DSS acquisition. The review also discusses a few experimental studies on NS1 that have shown it contributes to dengue pathogenesis. This review assesses the role of NS1 and disease severity from hospital-based studies and aims to provide better insights on the kinetics and dynamics of DENV infection with respect to NS1 for a better understanding of the role of NS1 in dengue.
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Affiliation(s)
- Charmi Ghetia
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Puneet Bhatt
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
| | - Chiranjay Mukhopadhyay
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal-576104, Karnataka, India
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Hayati RF, Denis D, Tallo KT, Sirait T, Tukan J, Santoso MS, Yohan B, Haryanto S, Frost SDW, Stubbs SCB, Sasmono RT. Molecular epidemiology of dengue in a setting of low reported endemicity: Kupang, East Nusa Tenggara province, Indonesia. Trans R Soc Trop Med Hyg 2021; 115:1304-1316. [PMID: 34528099 DOI: 10.1093/trstmh/trab138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/17/2021] [Accepted: 08/23/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Most regions in Indonesia experience annual dengue epidemics. However, the province of East Nusa Tenggara has consistently reported low incidence. We conducted a dengue molecular epidemiology study in Kupang, the capital of the province. METHODS Dengue patients were recruited from May 2016 to September 2017. Dengue virus (DENV) screening was performed using NS1 and immunoglobulin G (IgG)/IgM detection. Serotype was determined using reverse transcription polymerase chain reaction and the envelope genes were sequenced to infer the genetic identity and phylogeny. RESULTS From 119 patients, dengue was confirmed in 62 (52%). Compared with official data, underreporting of dengue incidence was observed. The majority (36%) of patients were children <10 y of age. Most patients (80%) experienced mild fever. All serotypes were detected, with DENV-3 as the predominant (57%). Kupang DENV-1 isolate was classified as genotype IV, an old and endemic strain, DENV-2 as cosmopolitan, DENV-3 as genotype I and DENV-4 as genotype II. Most isolates showed relatively low evolutionary rates and are closely related with strains from Bali and Timor Leste. CONCLUSIONS The low dengue incidence was most likely caused by sustained local circulation of endemic viruses. This study provides information on the epidemiology of dengue in a low-endemicity setting that should help future mitigation and disease management.
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Affiliation(s)
- Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Tuppak Sirait
- SK Lerik Regional Public Hospital, Kupang, Indonesia
| | - Joanita Tukan
- SK Lerik Regional Public Hospital, Kupang, Indonesia
| | | | | | | | - Simon D W Frost
- London School of Hygiene and Tropical Medicine, London, UK.,Microsoft Research, Redmond, WA, USA
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Saviola AJ, Negrão F, Yates JR. Proteomics of Select Neglected Tropical Diseases. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:315-336. [PMID: 32109150 DOI: 10.1146/annurev-anchem-091619-093003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Technological advances in mass spectrometry have enabled the extensive identification, characterization, and quantification of proteins in any biological system. In disease processes proteins are often altered in response to external stimuli; therefore, proteomics, the large-scale study of proteins and their functions, represents an invaluable tool for understanding the molecular basis of disease. This review highlights the use of mass spectrometry-based proteomics to study the pathogenesis, etiology, and pathology of several neglected tropical diseases (NTDs), a diverse group of disabling diseases primarily associated with poverty in tropical and subtropical regions of the world. While numerous NTDs have been the subject of proteomic studies, this review focuses on Buruli ulcer, dengue, leishmaniasis, and snakebite envenoming. The proteomic studies highlighted provide substantial information on the pathogenic mechanisms driving these diseases; they also identify molecular targets for drug discovery and development and uncover promising biomarkers that can assist in early diagnosis.
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Affiliation(s)
- Anthony J Saviola
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA;
| | - Fernanda Negrão
- Department of Biosciences and Technology of Bioactive Products, Institute of Biology, University of Campinas, São Paulo 13083-862, Brazil
| | - John R Yates
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, California 92037, USA;
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Tan XT, Amran FB, Thayan R, Ahmad N, Jaafar R, Haron R, Abdullah R, bin Shamsuddin SR, Md. Riffin NSB, Abdul-Rahman PS. Potential serum biomarkers associated with mild and severe leptospirosis infection: A cohort study in the Malaysian population. Electrophoresis 2017; 38:2141-2149. [DOI: 10.1002/elps.201600471] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 04/22/2017] [Accepted: 05/12/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Xue Ting Tan
- Bacteriology Unit; Institute for Medical Research; Kuala Lumpur Malaysia
- Department of Molecular Medicine, Faculty of Medicine; University of Malaya; Kuala Lumpur Malaysia
| | - Fairuz binti Amran
- Bacteriology Unit; Institute for Medical Research; Kuala Lumpur Malaysia
| | - Ravindran Thayan
- Virology Unit; Institute for Medical Research; Kuala Lumpur Malaysia
| | - Norazah Ahmad
- Bacteriology Unit; Institute for Medical Research; Kuala Lumpur Malaysia
| | - Roslinda Jaafar
- Microbiology Unit; Hospital Sultan Haji Ahmad Shah; Pahang Malaysia
| | - Rahimah Haron
- Department of Anesthesiology; Hospital Sultan Haji Ahmad Shah; Pahang Malaysia
| | - Rafidah Abdullah
- Department of Medical; Hospital Sultan Haji Ahmad Shah; Pahang Malaysia
| | | | | | - Puteri Shafinaz Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine; University of Malaya; Kuala Lumpur Malaysia
- University of Malaya Centre for Proteomics Research; University of Malaya; Kuala Lumpur Malaysia
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Wiktorowicz JE, Soman KV. Discovery of Candidate Biomarkers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:443-462. [PMID: 27975230 DOI: 10.1007/978-3-319-41448-5_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Properly performed, biomarker discovery can lead to effective candidates that can ultimately serve as predictors of disease, medical condition, define therapeutic parameters, and many other applications in medicine. Preferably, biomarkers comprise a panel of indicators, e.g. proteins and/or peptides that can be predictive or diagnostic of the medical condition of interest. Emphasis here is placed on "panel," as single candidates are rarely sufficient to provide the necessary sensitivity and specificity. To develop an effective panel that survives the development process described in Chap. 19 , proper experimental design and attention to important statistical parameters are critical to ensure success. Errors in discovery can lead to an inefficient use of expensive resources, as these may not be uncovered until the latter stages in biomarker development. Hence, accuracy, precision, and an estimate of the power of the proposed analyses are critical in the discovery of the panel of candidate biomarkers by proteomic methods, as is the selection of statistical approaches to refine and appropriately reduce the dataset for subsequent confirmatory assays.
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Brasier AR, Zhao Y, Wiktorowicz JE, Spratt HM, Nascimento EJM, Cordeiro MT, Soman KV, Ju H, Recinos A, Stafford S, Wu Z, Marques ETA, Vasilakis N. Molecular classification of outcomes from dengue virus -3 infections. J Clin Virol 2015; 64:97-106. [PMID: 25728087 DOI: 10.1016/j.jcv.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/13/2015] [Accepted: 01/16/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Dengue virus (DENV) infection is a significant risk to over a third of the human population that causes a wide spectrum of illness, ranging from sub-clinical disease to intermediate syndrome of vascular complications called dengue fever complicated (DFC) and severe, dengue hemorrhagic fever (DHF). Methods for discriminating outcomes will impact clinical trials and understanding disease pathophysiology. STUDY DESIGN We integrated a proteomics discovery pipeline with a heuristics approach to develop a molecular classifier to identify an intermediate phenotype of DENV-3 infectious outcome. RESULTS 121 differentially expressed proteins were identified in plasma from DHF vs dengue fever (DF), and informative candidates were selected using nonparametric statistics. These were combined with markers that measure complement activation, acute phase response, cellular leak, granulocyte differentiation and viral load. From this, we applied quantitative proteomics to select a 15 member panel of proteins that accurately predicted DF, DHF, and DFC using a random forest classifier. The classifier primarily relied on acute phase (A2M), complement (CFD), platelet counts and cellular leak (TPM4) to produce an 86% accuracy of prediction with an area under the receiver operating curve of >0.9 for DHF and DFC vs DF. CONCLUSIONS Integrating discovery and heuristic approaches to sample distinct pathophysiological processes is a powerful approach in infectious disease. Early detection of intermediate outcomes of DENV-3 will speed clinical trials evaluating vaccines or drug interventions.
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Affiliation(s)
- Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States.
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States
| | - John E Wiktorowicz
- Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States; Department of Biochemistry and Molecular Biology, UTMB, United States
| | - Heidi M Spratt
- Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States; Department Preventive Medicine and Community Health, UTMB, United States
| | - Eduardo J M Nascimento
- Department of Infectious Diseases and Microbiology and Immunology, University of Pittsburgh, United States
| | - Marli T Cordeiro
- Laboratorio de Virologia e Terapie Experimental do Centro de Pesquisas Aggeu Magalhaes-CPqAM, Fiocruz, Recife, Pernambuco, Brazil
| | - Kizhake V Soman
- Sealy Center for Molecular Medicine, UTMB, United States; Department of Biochemistry and Molecular Biology, UTMB, United States
| | - Hyunsu Ju
- Department Preventive Medicine and Community Health, UTMB, United States
| | - Adrian Recinos
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | | | - Zheng Wu
- Biomolecular Resource Facility, UTMB, United States
| | - Ernesto T A Marques
- Laboratorio de Virologia e Terapie Experimental do Centro de Pesquisas Aggeu Magalhaes-CPqAM, Fiocruz, Recife, Pernambuco, Brazil; Department of Infectious Diseases and Microbiology and Immunology, University of Pittsburgh, United States
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, United States
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8
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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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Desoubeaux G, Jourdan ML, Valera L, Jardin B, Hem S, Caille A, Cormier B, Marchand-Adam S, Bailly É, Diot P, Chandenier J. Proteomic demonstration of the recurrent presence of inter-alpha-inhibitor H4 heavy-chain during aspergillosis induced in an animal model. Int J Med Microbiol 2013; 304:327-38. [PMID: 24360996 DOI: 10.1016/j.ijmm.2013.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022] Open
Abstract
Invasive pulmonary aspergillosis remains a matter of great concern in oncology/haematology, intensive care units and organ transplantation departments. Despite the availability of various diagnostic tools with attractive features, new markers of infection are required for better medical care. We therefore looked for potential pulmonary biomarkers of aspergillosis, by carrying out two-dimensional (2D) gel electrophoresis comparing the proteomes of bronchial-alveolar lavage fluids (BALF) from infected rats and from control rats presenting non-specific inflammation, both immunocompromised. A bioinformatic analysis of the 2D-maps revealed significant differences in the abundance of 20 protein spots (ANOVA P-value<0.01; q-value<0.03; power>0.8). One of these proteins, identified by mass spectrometry, was considered of potential interest: inter-alpha-inhibitor H4 heavy-chain (ITIH4), characterised for the first time in this infectious context. Western blotting confirmed its overabundance in all infected BALF, particularly at early stages of murine aspergillosis. Further investigations were carried on rat serum, and confirmed that ITIH4 levels increased during experimental aspergillosis. Preliminary results in human samples strengthened this trend. To our knowledge, this is the first description of the involvement of ITIH4 in aspergillosis.
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Affiliation(s)
- Guillaume Desoubeaux
- CHU de Tours, Service de Parasitologie - Mycologie - Médecine tropicale, Tours, France; Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France.
| | - Marie-Lise Jourdan
- CHU de Tours, Service d'Hématologie Biologique, Tours, France; Université François Rabelais, INSERM U1069/N2C, Faculté de Médecine, Tours, France
| | - Lionel Valera
- Sysdiag, CNRS UMR 3145 Bio-Rad, Cap Delta, Montpellier, France
| | | | - Sonia Hem
- Plateforme de spectrométrie de masse protéomique - MSPP, Laboratoire de Protéomique Fonctionnelle, INRA UR1199, Montpellier, France
| | - Agnès Caille
- CHU de Tours, Centre d'Investigation Clinique, Tours, France; Université François Rabelais, INSERM 202, Faculté de Médecine, Tours, France
| | - Bénédicte Cormier
- CHU de Tours, Service d'Anatomie et Cytologie Pathologiques, Tours, France
| | - Sylvain Marchand-Adam
- Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France; CHU de Tours, Service de Pneumologie, Tours, France
| | - Éric Bailly
- CHU de Tours, Service de Parasitologie - Mycologie - Médecine tropicale, Tours, France
| | - Patrice Diot
- Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France; CHU de Tours, Service de Pneumologie, Tours, France
| | - Jacques Chandenier
- CHU de Tours, Service de Parasitologie - Mycologie - Médecine tropicale, Tours, France; Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France
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de la Cruz-Hernández SI, Flores-Aguilar H, González-Mateos S, López-Martinez I, Alpuche-Aranda C, Ludert JE, del Angel RM. Determination of viremia and concentration of circulating nonstructural protein 1 in patients infected with dengue virus in Mexico. Am J Trop Med Hyg 2013; 88:446-54. [PMID: 23339203 DOI: 10.4269/ajtmh.12-0023] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Higher levels of viremia and circulating nonstructural protein 1 (NS1) have been associated with dengue disease severity. In this study, viremia and circulating NS1 levels were determined in 225 serum samples collected from patients in Mexico infected with dengue virus serotypes 1 and 2 (DENV-1 and DENV-2). Patients with dengue hemorrhagic fever (DHF) who were infected with DENV-1 showed higher levels of circulating NS1 than patients with dengue fever (DF) (P = 0.0175). Moreover, NS1 levels were higher in patients with primary infections with DENV-1 than in patient infected with DENV-2 (P < 0.0001) and in patients with primary infections with DENV-2 than in patients with secondary infections with DENV-2 (P = 0.0051). Unexpectedly, viremia levels were higher in patients with DF than in those with DHF infected with either DENV-1 or DENV-2 (P = 0.0019 and P = 0.001, respectively) and in patients with primary infections than those with secondary DENV-2 infections (P < 0.0001). Results indicate that levels of circulating NS1 vary according to the infecting serotype, immunologic status (primary or secondary infection), and dengue disease severity.
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Affiliation(s)
- Sergio I de la Cruz-Hernández
- Departament of Virology, Instituto de Diagnóstico y Referencia Epimiológicos, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico.
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Kumar Y, Liang C, Bo Z, Rajapakse JC, Ooi EE, Tannenbaum SR. Serum proteome and cytokine analysis in a longitudinal cohort of adults with primary dengue infection reveals predictive markers of DHF. PLoS Negl Trop Dis 2012; 6:e1887. [PMID: 23209847 PMCID: PMC3510095 DOI: 10.1371/journal.pntd.0001887] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 09/16/2012] [Indexed: 12/21/2022] Open
Abstract
Background Infections caused by dengue virus are a major cause of morbidity and mortality in tropical and subtropical regions of the world. Factors that control transition from mild forms of disease such as dengue fever (DF) to more life-threatening forms such as dengue hemorrhagic fever (DHF) are poorly understood. Consequently, there are no reliable methods currently available for early triage of DHF patients resulting in significant over-hospitalization. Methodology/Principal Findings We have systematically examined the proteome, cytokines and inflammatory markers in sera from 62 adult dengue patients (44 DF; 18 DHF) with primary DENV infection, at three different times of infection representing the early febrile, defervescence and convalescent stages. Using fluorescent bioplex assays, we measured 27 cytokines in these serum samples. Additionally, we used multiple mass spectrometry methods for iTRAQ-based comparative analysis of serum proteome as well as measurements of protein adducts- 3-nitrotyrosine and 3-chlorotyrosine as surrogate measures of free radical activity. Using multiple methods such as OPLS, MRMR and MSVM-RFE for multivariate feature selection and classification, we report molecular markers that allow prediction of primary DHF with sensitivity and specificity of >80%. Conclusions/Significance This report constitutes a comprehensive analysis of molecular signatures of dengue disease progression and will help unravel mechanisms of dengue disease progression. Our analysis resulted in the identification of markers that may be useful for early prediction of DHF during the febrile phase. The combination of highly sensitive analytical methods and novel statistical approaches described here forms a robust platform for biomarker discovery. While the majority of patients who exhibit febrile dengue infection recover within a week, a small proportion of the patients progress to develop severe symptoms that can be life-threatening if not managed in a hospital setting. Because there is no method to accurately identify this subgroup of patients, many dengue patients are hospitalized unnecessarily, which causes significant burden to the healthcare system. In our study, we have systematically measured a large number of molecules including cytokines and serum proteins in blood samples from a dengue patient cohort using highly sensitive mass spectrometry-based methods. We have further developed novel statistical methods that allow us to identify small panels of measureable blood markers, which can distinguish dengue patients that develop milder, self-limiting form of the disease from those that progress to develop severe symptoms. Because these markers can be applied within 48–72 hours of onset of febrile symptoms, we expect them to be useful for early classification of severe dengue disease.
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Affiliation(s)
- Yadunanda Kumar
- Interdisciplinary Research Group in Infectious diseases, Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
| | - Cui Liang
- Interdisciplinary Research Group in Infectious diseases, Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
| | - Zheng Bo
- School of Computer Engineering, Nanyang Technological University (NTU), Singapore, Singapore
| | - Jagath C. Rajapakse
- School of Computer Engineering, Nanyang Technological University (NTU), Singapore, Singapore
| | - Eng Eong Ooi
- DUKE-NUS Graduate Medical School, Singapore, Singapore
| | - Steven R. Tannenbaum
- Interdisciplinary Research Group in Infectious diseases, Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Fragnoud R, Yugueros-Marcos J, Pachot A, Bedin F. Isotope Coded Protein Labeling analysis of plasma specimens from acute severe dengue fever patients. Proteome Sci 2012; 10:60. [PMID: 23101585 PMCID: PMC3547721 DOI: 10.1186/1477-5956-10-60] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 10/23/2012] [Indexed: 11/16/2022] Open
Abstract
Background Dengue fever is the most important arthropod born viral disease of public health significance. Although most patients suffer only from flu-like symptoms, a small group of patient experiences more severe forms of the disease. To contribute to a better understanding of its pathogenesis this study aims to identify proteins differentially expressed in a pool of five viremic plasma from severe dengue patients relative to a pool of five non-severe dengue patients. Results The use of Isotope Coded Protein Labeling (ICPLTM) to analyze plasma depleted of twenty high-abundance proteins allowed for the identification of 51 differentially expressed proteins, which were characterized by mass spectrometry. Using quantitative ELISA, three of these proteins (Leucine-rich glycoprotein 1, Vitamin D binding-protein and Ferritin) were confirmed as having an increased expression in a panel of severe dengue plasma. The proteins identified as overexpressed by ICPLTM in severe dengue plasma involve in clear up action after cell injury, tissue coherence and immune defense. Conclusion This ICPLTM study evaluating differences between acute severe dengue plasmas and acute non-severe dengue plasmas suggests that the three proteins identified are overexpressed early in the course of the disease. Their possible use as biomarkers for the prognostic of disease severity is discussed.
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Affiliation(s)
- Romain Fragnoud
- BioMérieux SA, Chemin de l'Orme, 69280, Marcy l'Etoile, France.
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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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DIGE enables the detection of a putative serum biomarker of fungal origin in a mouse model of invasive aspergillosis. J Proteomics 2012; 75:2536-49. [DOI: 10.1016/j.jprot.2012.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/27/2012] [Accepted: 01/30/2012] [Indexed: 11/20/2022]
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Brasier AR, Garcia J, Wiktorowicz JE, Spratt HM, Comach G, Ju H, Recinos A, Soman K, Forshey BM, Halsey ES, Blair PJ, Rocha C, Bazan I, Victor SS, Wu Z, Stafford S, Watts D, Morrison AC, Scott TW, Kochel TJ. Discovery proteomics and nonparametric modeling pipeline in the development of a candidate biomarker panel for dengue hemorrhagic fever. Clin Transl Sci 2012; 5:8-20. [PMID: 22376251 PMCID: PMC3590808 DOI: 10.1111/j.1752-8062.2011.00377.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Secondary dengue viral infection can produce capillary leakage associated with increased mortality known as dengue hemorrhagic fever (DHF). Because the mortality of DHF can be reduced by early detection and intensive support, improved methods for its detection are needed. We applied multidimensional protein profiling to predict outcomes in a prospective dengue surveillance study in South America. Plasma samples taken from initial clinical presentation of acute dengue infection were subjected to proteomics analyses using ELISA and a recently developed biofluid analysis platform. Demographics, clinical laboratory measurements, nine cytokines, and 419 plasma proteins collected at the time of initial presentation were compared between the DF and DHF outcomes. Here, the subject's gender, clinical parameters, two cytokines, and 42 proteins discriminated between the outcomes. These factors were reduced by multivariate adaptive regression splines (MARS) that a highly accurate classification model based on eight discriminant features with an area under the receiver operator curve (AUC) of 0.999. Model analysis indicated that the feature-outcome relationship were nonlinear. Although this DHF risk model will need validation in a larger cohort, we conclude that approaches to develop predictive biomarker models for disease outcome will need to incorporate nonparametric modeling approaches.
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Affiliation(s)
- Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, USA.
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16
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Yeng C, Osman E, Mohamed Z, Noordin R. Detection of immunogenic parasite and host-specific proteins in the sera of active and chronic individuals infected with Toxoplasma gondii. Electrophoresis 2011; 31:3843-9. [PMID: 21080484 DOI: 10.1002/elps.201000038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Toxoplasma gondii infection in pregnant women may result in abortion and foetal abnormalities, and may be life-threatening in immunocompromised hosts. To identify the potential infection markers of this disease, 2-DE and Western blot methods were employed to study the parasite circulating antigens and host-specific proteins in the sera of T. gondii-infected individuals. The comparisons were made between serum protein profiles of infected (n=31) and normal (n=10) subjects. Antigenic proteins were identified by immunoblotting using pooled sera and monoclonal anti-human IgM-HRP. Selected protein spots were characterised using mass spectrometry. Prominent differences were observed when serum samples of T. gondii-infected individuals and normal controls were compared. A significant up-regulation of host-specific proteins, α(2)-HS glycoprotein and α(1)-B glycoprotein, was also observed in the silver-stained gels of both active and chronic infections. However, only α(2)-HS glycoprotein and α(1)-B glycoprotein in the active infection showed immunoreactivity in Western blots. In addition, three spots of T. gondii proteins were detected, namely (i) hypothetical protein chrXII: 3984434-3 TGME 49, (ii) dual specificity protein phosphatase, catalytic domain TGME 49 and (iii) NADPH-cytochrome p450 reductase TGME 49. Thus, 2-DE approach followed by Western blotting has enabled the identification of five potential infection markers for the diagnosis of toxoplasmosis: three are parasite-specific proteins and two are host-specific proteins.
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Affiliation(s)
- Chen Yeng
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
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18
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Albuquerque LM, Trugilho MRO, Chapeaurouge A, Jurgilas PB, Bozza PT, Bozza FA, Perales J, Neves-Ferreira AGC. Two-dimensional difference gel electrophoresis (DiGE) analysis of plasmas from dengue fever patients. J Proteome Res 2010; 8:5431-41. [PMID: 19845402 DOI: 10.1021/pr900236f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dengue fever is the world's most important arthropod-born viral disease affecting humans. To contribute to a better understanding of its pathogenesis, this study aims to identify proteins differentially expressed in plasmas from severe dengue fever patients relative to healthy donors. The use of 2-D Fluorescence Difference Gel Electrophoresis to analyze plasmas depleted of six high-abundance proteins (albumin, IgG, antitrypsin, IgA, transferrin and haptoglobin) allowed for the detection of 73 differentially expressed protein spots (n = 13, p < 0.01), of which 37 could be identified by mass spectrometry. These 37 spots comprised a total of 14 proteins, as follows: 7 had increased expression in plasmas from dengue fever patients (C1 inhibitor, alpha1-antichymotrypsin, vitamin D-binding protein, fibrinogen gamma-chain, alpha1-acid glycoprotein, apolipoprotein J and complement component C3c), while 7 others had decreased expression in the same samples (alpha-2 macroglobulin, prothrombin, histidine-rich glycoprotein, apolipoproteins A-IV and A-I, transthyretin and complement component C3b). The possible involvement of these proteins in the inflammatory process triggered by dengue virus infection and in the repair mechanisms of vascular damage occurring in this pathology is discussed in this study.
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Affiliation(s)
- Lidiane M Albuquerque
- Lab Toxinologia and Lab. Imunofarmacologia, Pavilhao Ozorio de Almeida, Instituto Oswaldo Cruz and Instituto de Pesquisa Clinica Evandro Chagas, Fiocruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, Brazil
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