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Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. Mol Cell Proteomics 2020; 19:916-927. [PMID: 32303587 PMCID: PMC7261817 DOI: 10.1074/mcp.r120.001936] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
Protein microarrays are crucial tools in the study of proteins in an unbiased, high-throughput manner, as they allow for characterization of up to thousands of individually purified proteins in parallel. The adaptability of this technology has enabled its use in a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. In addition, the technology has also been shown to be useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases and cancers. In this review, we will summarize the developments that have been made in protein microarray technology in both in basic and translational research over the past decade. We will also introduce a novel membrane protein array, the GPCR-VirD array, and discuss the future directions of functional protein microarrays.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan R.O.C..
| | - Jessica Dunn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231.
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2
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Li Z, Zhang F, Zhang C, Wang C, Lu P, Zhao X, Hao L, Ding J. Immunoinformatics prediction of OMP2b and BCSP31 for designing multi-epitope vaccine against Brucella. Mol Immunol 2019; 114:651-660. [PMID: 31557626 DOI: 10.1016/j.molimm.2019.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/31/2022]
Abstract
Brucella poses a serious threat to human health. High quality vaccines for Brucella are urgently needed to effectively reduce the incidence of brucellosis. OMP2b and BCSP31 are important component proteins of the Brucella outer membrane and are highly immunogenic. Here, we used the bioinformatics software ProtParam, SOPMA, SWISS-MODEL, Rasmol, BepiPred, SYFPEITHI and IEDB to analyze the structure of these two proteins and predict the epitopes of T cells and B cells. Through analysis, we predicted three Th cell epitopes, seven CTL epitopes, eight B cell epitopes, and one T-B combined epitope of OMP2b protein. Subsequently, we also obtained three Th cell epitopes, six CTL epitopes, nine B cell epitopes and one T-B combined epitope of BCSP31 protein. The T-B combined epitopes and CTL epitopes of OMP2b and those of BCSP31 were synthesized to detect their immunogenicity. The IFN-γ ELISPOT assay showed that the T-B combined epitope peptides of OMP2b and BCSP31 activated Th cell immune responses. ELISA analysis detected the specific antibodies against the T-B combined epitope peptide of OMP2b and BCSP31 in the serum of Brucellosis patients. Additionally, CTL epitope peptide of OMP2b and BCSP31 proteins promoted the secretion of soluble perforin and granzyme B in the culture supernatant. In conclusion, our study shows that the T-B combined epitopes and CTL epitopes of OMP2b and BCSP31 have immunogenicity and immunoreactivity. Our results may lay a theoretical foundation for the development of vaccines against Brucella.
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Affiliation(s)
- Zhiwei Li
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China; Clinical Laboratory Center, People's Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, PR China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Chuntao Zhang
- Department of Immunology, Basic Medical College of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Changmin Wang
- Clinical Laboratory Center, People's Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, PR China
| | - Peipei Lu
- Clinical Laboratory Center, People's Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, PR China
| | - Xiao Zhao
- Department of Immunology, Basic Medical College of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Lijun Hao
- Clinical Laboratory Center, People's Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, PR China
| | - Jianbing Ding
- Department of Immunology, Basic Medical College of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China.
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3
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Liu EW, Skinner J, Tran TM, Kumar K, Narum DL, Jain A, Ongoiba A, Traoré B, Felgner PL, Crompton PD. Protein-Specific Features Associated with Variability in Human Antibody Responses to Plasmodium falciparum Malaria Antigens. Am J Trop Med Hyg 2018; 98:57-66. [PMID: 29141757 PMCID: PMC5928716 DOI: 10.4269/ajtmh.17-0437] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The magnitude of antibody responses varies across the individual proteins that constitute any given microorganism, both in the context of natural infection and vaccination with attenuated or inactivated pathogens. The protein-specific factors underlying this variability are poorly understood. In 267 individuals exposed to intense seasonal malaria, we examined the relationship between immunoglobulin G (IgG) responses to 861 Plasmodium falciparum proteins and specific features of these proteins, including their subcellular location, relative abundance, degree of polymorphism, and whether they are predicted to have human orthologs. We found that IgG reactivity was significantly higher to extracellular and plasma membrane proteins and also correlated positively with both protein abundance and degree of protein polymorphism. Conversely, IgG reactivity was significantly lower to proteins predicted to have human orthologs. These findings provide insight into protein-specific factors that are associated with variability in the magnitude of antibody responses to natural P. falciparum infection-data that could inform vaccine strategies to optimize antibody-mediated immunity as well as the selection of antigens for sero-diagnostic purposes.
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Affiliation(s)
- Eugene W Liu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Tuan M Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Krishan Kumar
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - David L Narum
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aarti Jain
- University of California, Irvine, Irvine, California
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, University of Sciences,Techniques and Technologies of Bamako, Bamako, Mali
| | - Boubacar Traoré
- Mali International Center of Excellence in Research, University of Sciences,Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
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4
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Darton TC, Baker S, Randall A, Dongol S, Karkey A, Voysey M, Carter MJ, Jones C, Trappl K, Pablo J, Hung C, Teng A, Shandling A, Le T, Walker C, Molina D, Andrews J, Arjyal A, Basnyat B, Pollard AJ, Blohmke CJ. Identification of Novel Serodiagnostic Signatures of Typhoid Fever Using a Salmonella Proteome Array. Front Microbiol 2017; 8:1794. [PMID: 28970824 PMCID: PMC5609549 DOI: 10.3389/fmicb.2017.01794] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/05/2017] [Indexed: 11/26/2022] Open
Abstract
Current diagnostic tests for typhoid fever, the disease caused by Salmonella Typhi, are poor. We aimed to identify serodiagnostic signatures of typhoid fever by assessing microarray signals to 4,445 S. Typhi antigens in sera from 41 participants challenged with oral S. Typhi. We found broad, heterogeneous antibody responses with increasing IgM/IgA signals at diagnosis. In down-selected 250-antigen arrays we validated responses in a second challenge cohort (n = 30), and selected diagnostic signatures using machine learning and multivariable modeling. In four models containing responses to antigens including flagellin, OmpA, HlyE, sipC, and LPS, multi-antigen signatures discriminated typhoid (n = 100) from other febrile bacteremia (n = 52) in Nepal. These models contained combinatorial IgM, IgA, and IgG responses to 5 antigens (ROC AUC, 0.67 and 0.71) or 3 antigens (0.87), although IgA responses to LPS also performed well (0.88). Using a novel systematic approach we have identified and validated optimal serological diagnostic signatures of typhoid fever.
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Affiliation(s)
- Thomas C Darton
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, and the Oxford National Institutes for Health Research Biomedical Research Centre, University of OxfordOxford, United Kingdom.,The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh City, Vietnam.,Department of Infection, Immunity and Cardiovascular Disease, The University of SheffieldSheffield, United Kingdom
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh City, Vietnam
| | - Arlo Randall
- Antigen Discovery Incorporated, IrvineCA, United States
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health SciencesKathmandu, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health SciencesKathmandu, Nepal
| | - Merryn Voysey
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, and the Oxford National Institutes for Health Research Biomedical Research Centre, University of OxfordOxford, United Kingdom.,Nuffield Department of Primary Care Health Sciences, University of OxfordOxford, United Kingdom
| | - Michael J Carter
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, and the Oxford National Institutes for Health Research Biomedical Research Centre, University of OxfordOxford, United Kingdom
| | - Claire Jones
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, and the Oxford National Institutes for Health Research Biomedical Research Centre, University of OxfordOxford, United Kingdom
| | - Krista Trappl
- Antigen Discovery Incorporated, IrvineCA, United States
| | - Jozelyn Pablo
- Antigen Discovery Incorporated, IrvineCA, United States
| | - Chris Hung
- Antigen Discovery Incorporated, IrvineCA, United States
| | - Andy Teng
- Antigen Discovery Incorporated, IrvineCA, United States
| | | | - Tim Le
- Antigen Discovery Incorporated, IrvineCA, United States
| | | | | | - Jason Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, StanfordCA, United States
| | - Amit Arjyal
- Nuffield Department of Primary Care Health Sciences, University of OxfordOxford, United Kingdom
| | - Buddha Basnyat
- Nuffield Department of Primary Care Health Sciences, University of OxfordOxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, and the Oxford National Institutes for Health Research Biomedical Research Centre, University of OxfordOxford, United Kingdom
| | - Christoph J Blohmke
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, and the Oxford National Institutes for Health Research Biomedical Research Centre, University of OxfordOxford, United Kingdom
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5
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Felgner J, Jain A, Nakajima R, Liang L, Jasinskas A, Gotuzzo E, Vinetz JM, Miyajima F, Pirmohamed M, Hassan-Hanga F, Umoru D, Jibir BW, Gambo S, Olateju K, Felgner PL, Obaro S, Davies DH. Development of ELISAs for diagnosis of acute typhoid fever in Nigerian children. PLoS Negl Trop Dis 2017. [PMID: 28640809 PMCID: PMC5498068 DOI: 10.1371/journal.pntd.0005679] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Improved serodiagnostic tests for typhoid fever (TF) are needed for surveillance, to facilitate patient management, curb antibiotic resistance, and inform public health programs. To address this need, IgA, IgM and IgG ELISAs using Salmonella enterica serovar Typhi (S. Typhi) lipopolysaccharide (LPS) and hemolysin E (t1477) protein were conducted on 86 Nigerian pediatric TF and 29 non-typhoidal Salmonella (NTS) cases, 178 culture-negative febrile cases, 28 "other" (i.e., non-Salmonella) pediatric infections, and 48 healthy Nigerian children. The best discrimination was achieved between TF and healthy children. LPS-specific IgA and IgM provided receiver operator characteristic areas under the curve (ROC AUC) values of 0.963 and 0.968, respectively, and 0.978 for IgA+M combined. Similar performance was achieved with t1477-specific IgA and IgM (0.968 and 0.968, respectively; 0.976 combined). IgG against LPS and t1477 was less accurate for discriminating these groups, possibly as a consequence of previous exposure, although ROC AUC values were still high (0.928 and 0.932, respectively). Importantly, discrimination between TF and children with other infections was maintained by LPS-specific IgA and IgM (AUC = 0.903 and 0.934, respectively; 0.938 combined), and slightly reduced for IgG (0.909), while t1477-specific IgG performed best (0.914). A similar pattern was seen when comparing TF with other infections from outside Nigeria. The t1477 may be recognized by cross-reactive antibodies from other acute infections, although a robust IgG response may provide some diagnostic utility in populations where incidence of other infections is low, such as in children. The data are consistent with IgA and IgM against S. Typhi LPS being specific markers of acute TF.
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Affiliation(s)
- Jiin Felgner
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Aarti Jain
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Rie Nakajima
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Li Liang
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Algis Jasinskas
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Eduardo Gotuzzo
- Alexander von Humboldt Institute of Tropical Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
- Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Alexander von Humboldt Institute of Tropical Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Fabio Miyajima
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Safiya Gambo
- Department of Pediatrics, Murtala Specialist Hospital, Kano, Nigeria
| | | | - Philip L. Felgner
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Stephen Obaro
- Department of Pediatrics, Aminu Kano Teaching Hospital, Kano, Nigeria
- University of Abuja Teaching Hospital, Gwagwalada, Nigeria
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- International Foundation against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - D. Huw Davies
- Division of Infectious Diseases, School of Medicine, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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6
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Jain A, Taghavian O, Vallejo D, Dotsey E, Schwartz D, Bell FG, Greef C, Davies DH, Grudzien J, Lee AP, Felgner PL, Liang L. Evaluation of quantum dot immunofluorescence and a digital CMOS imaging system as an alternative to conventional organic fluorescence dyes and laser scanning for quantifying protein microarrays. Proteomics 2016; 16:1271-9. [PMID: 26842269 DOI: 10.1002/pmic.201500375] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 11/07/2022]
Abstract
Organic fluorescent dyes are widely used for the visualization of bound antibody in a variety of immunofluorescence assays. However, the detection equipment is often expensive, fragile, and hard to deploy widely. Quantum dots (Qdot) are nanocrystals made of semiconductor materials that emit light at different wavelengths according to the size of the crystal, with increased brightness and stability. Here, we have evaluated a small benchtop "personal" optical imager (ArrayCAM) developed for quantification of protein arrays probed by Qdot-based indirect immunofluorescence. The aim was to determine if the Qdot imager system provides equivalent data to the conventional organic dye-labeled antibody/laser scanner system. To do this, duplicate proteome microarrays of Vaccinia virus, Brucella melitensis and Plasmodium falciparum were probed with identical samples of immune sera, and IgG, IgA, and IgM profiles visualized using biotinylated secondary antibodies followed by a tertiary reagent of streptavidin coupled to either P3 (an organic cyanine dye typically used for microarrays) or Q800 (Qdot). The data show excellent correlation for all samples tested (R > 0.8) with no significant change of antibody reactivity profiles. We conclude that Qdot detection provides data equivalent to that obtained using conventional organic dye detection. The portable imager offers an economical, more robust, and deployable alternative to conventional laser array scanners.
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Affiliation(s)
- Aarti Jain
- Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Omid Taghavian
- Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Derek Vallejo
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
| | - Emmanuel Dotsey
- Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | | | | | - D Huw Davies
- Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Abraham P Lee
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA
| | - Philip L Felgner
- Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Li Liang
- Division of Infectious Diseases, Department of Medicine, University of California Irvine, Irvine, CA, USA
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7
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A systems biology approach for diagnostic and vaccine antigen discovery in tropical infectious diseases. Curr Opin Infect Dis 2016; 28:438-45. [PMID: 26237545 DOI: 10.1097/qco.0000000000000193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW There is a need for improved diagnosis and for more rapidly assessing the presence, prevalence, and spread of newly emerging or reemerging infectious diseases. An approach to the pathogen-detection strategy is based on analyzing host immune response to the infection. This review focuses on a protein microarray approach for this purpose. RECENT FINDINGS Here we take a protein microarray approach to profile the humoral immune response to numerous infectious agents, and to identify the complete antibody repertoire associated with each disease. The results of these studies lead to the identification of diagnostic markers and potential subunit vaccine candidates. These results from over 30 different organisms can also provide information about common trends in the humoral immune response. SUMMARY This review describes the implications of the findings for clinical practice or research. A systems biology approach to identify the antibody repertoire associated with infectious diseases challenge using protein microarray has become a powerful method in identifying diagnostic markers and potential subunit vaccine candidates, and moreover, in providing information on proteomic feature (functional and physically properties) of seroreactive and serodiagnostic antigens. Combining the detection of the pathogen with a comprehensive assessment of the host immune response will provide a new understanding of the correlations between specific causative agents, the host response, and the clinical manifestations of the disease.
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Perkins JR, Barrionuevo E, Ranea JA, Blanca M, Cornejo-Garcia JA. Systems biology approaches to enhance our understanding of drug hypersensitivity reactions. Clin Exp Allergy 2015; 44:1461-72. [PMID: 25040150 DOI: 10.1111/cea.12371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hypersensitivity drug reactions (HDRs) encompass a wide spectrum of unpredictable clinical entities. They represent an important health problem, affecting people of all ages, and lead to a large strain on the public health system. Here, we summarize experiments that use high-throughput genomics technologies to investigate HDRs. We also introduce the field of systems biology as a relatively recent discipline concerned with the integration and analysis of high-throughput data sets such as DNA microarrays and next-generation sequencing data. We describe previous studies that have applied systems biology techniques to related fields such as allergy and asthma. Finally, we present a number of potential applications of systems biology to the study of HDRs, in order to make the reader aware of the types of analyses that can be performed and the insights that can be gained through their application.
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Affiliation(s)
- J R Perkins
- Research Laboratory, IBIMA-Regional University Hospital of Malaga-UMA, Spain
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Olaya-Abril A, Jiménez-Munguía I, Gómez-Gascón L, Obando I, Rodríguez-Ortega MJ. A Pneumococcal Protein Array as a Platform to Discover Serodiagnostic Antigens Against Infection. Mol Cell Proteomics 2015; 14:2591-608. [PMID: 26183717 DOI: 10.1074/mcp.m115.049544] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 01/22/2023] Open
Abstract
Pneumonia is one of the most common and severe diseases associated with Streptococcus pneumoniae infections in children and adults. Etiological diagnosis of pneumococcal pneumonia in children is generally challenging because of limitations of diagnostic tests and interference with nasopharyngeal colonizing strains. Serological assays have recently gained interest to overcome some problems found with current diagnostic tests in pediatric pneumococcal pneumonia. To provide insight into this field, we have developed a protein array to screen the antibody response to many antigens simultaneously. Proteins were selected by experimental identification from a collection of 24 highly prevalent pediatric clinical isolates in Spain, using a proteomics approach consisting of "shaving" the cell surface with proteases and further LC/MS/MS analysis. Ninety-five proteins were recombinantly produced and printed on an array. We probed it with a collection of sera from children with pneumococcal pneumonia. From the set of the most seroprevalent antigens, we obtained a clear discriminant response for a group of three proteins (PblB, PulA, and PrtA) in children under 4 years old. We validated the results by ELISA and an immunostrip assay showed the translation to easy-to-use, affordable tests. Thus, the protein array here developed presents a tool for broad use in serodiagnostics.
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Affiliation(s)
- Alfonso Olaya-Abril
- From the ‡Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3; and Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Jiménez-Munguía
- From the ‡Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3; and Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Gómez-Gascón
- §Departamento de Sanidad Animal, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3, Córdoba, Spain
| | - Ignacio Obando
- ¶Sección de Enfermedades Infecciosas Pediátricas e Inmunopatología, Hospital Universitario Infantil Virgen del Rocío, Sevilla, Spain
| | - Manuel J Rodríguez-Ortega
- From the ‡Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba; Campus de Excelencia Internacional CeiA3; and Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain;
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10
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Carmona SJ, Nielsen M, Schafer-Nielsen C, Mucci J, Altcheh J, Balouz V, Tekiel V, Frasch AC, Campetella O, Buscaglia CA, Agüero F. Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants. Mol Cell Proteomics 2015; 14:1871-84. [PMID: 25922409 PMCID: PMC4587317 DOI: 10.1074/mcp.m114.045906] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Indexed: 01/09/2023] Open
Abstract
Complete characterization of antibody specificities associated to natural infections is expected to provide a rich source of serologic biomarkers with potential applications in molecular diagnosis, follow-up of chemotherapeutic treatments, and prioritization of targets for vaccine development. Here, we developed a highly-multiplexed platform based on next-generation high-density peptide microarrays to map these specificities in Chagas Disease, an exemplar of a human infectious disease caused by the protozoan Trypanosoma cruzi. We designed a high-density peptide microarray containing more than 175,000 overlapping 15mer peptides derived from T. cruzi proteins. Peptides were synthesized in situ on microarray slides, spanning the complete length of 457 parasite proteins with fully overlapped 15mers (1 residue shift). Screening of these slides with antibodies purified from infected patients and healthy donors demonstrated both a high technical reproducibility as well as epitope mapping consistency when compared with earlier low-throughput technologies. Using a conservative signal threshold to classify positive (reactive) peptides we identified 2,031 disease-specific peptides and 97 novel parasite antigens, effectively doubling the number of known antigens and providing a 10-fold increase in the number of fine mapped antigenic determinants for this disease. Finally, further analysis of the chip data showed that optimizing the amount of sequence overlap of displayed peptides can increase the protein space covered in a single chip by at least ∼threefold without sacrificing sensitivity. In conclusion, we show the power of high-density peptide chips for the discovery of pathogen-specific linear B-cell epitopes from clinical samples, thus setting the stage for high-throughput biomarker discovery screenings and proteome-wide studies of immune responses against pathogens.
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Affiliation(s)
- Santiago J Carmona
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Morten Nielsen
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina; §Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | | | - Juan Mucci
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Jaime Altcheh
- ‖Servicio de Parasitología y Chagas, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, Argentina
| | - Virginia Balouz
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Valeria Tekiel
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Alberto C Frasch
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Oscar Campetella
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Carlos A Buscaglia
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
| | - Fernán Agüero
- From the ‡Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús, Universidad de San Martín - CONICET, Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina;
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11
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Nayak K, Jing L, Russell RM, Davies DH, Hermanson G, Molina DM, Liang X, Sherman DR, Kwok WW, Yang J, Kenneth J, Ahamed SF, Chandele A, Murali-Krishna K, Koelle DM. Identification of novel Mycobacterium tuberculosis CD4 T-cell antigens via high throughput proteome screening. Tuberculosis (Edinb) 2015; 95:275-87. [PMID: 25857935 DOI: 10.1016/j.tube.2015.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/24/2015] [Accepted: 03/01/2015] [Indexed: 10/23/2022]
Abstract
Elicitation of CD4 IFN-gamma T cell responses to Mycobacterium tuberculosis (MTB) is a rational vaccine strategy to prevent clinical tuberculosis. Diagnosis of MTB infection is based on T-cell immune memory to MTB antigens. The MTB proteome contains over four thousand open reading frames (ORFs). We conducted a pilot antigen identification study using 164 MTB proteins and MTB-specific T-cells expanded in vitro from 12 persons with latent MTB infection. Enrichment of MTB-reactive T-cells from PBMC used cell sorting or an alternate system compatible with limited resources. MTB proteins were used as single antigens or combinatorial matrices in proliferation and cytokine secretion readouts. Overall, our study found that 44 MTB proteins were antigenic, including 27 not previously characterized as CD4 T-cell antigens. Antigen truncation, peptide, NTM homology, and HLA class II tetramer studies confirmed malate synthase G (encoded by gene Rv1837) as a CD4 T-cell antigen. This simple, scalable system has potential utility for the identification of candidate MTB vaccine and biomarker antigens.
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Affiliation(s)
- Kaustuv Nayak
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Lichen Jing
- Department of Medicine, Division of Infectious Diseases, University of Washington, Box 358061, Seattle, WA 98195, USA.
| | - Ronnie M Russell
- Department of Medicine, Division of Infectious Diseases, University of Washington, Box 358061, Seattle, WA 98195, USA.
| | - D Huw Davies
- Department of Medicine, Division of Infectious Diseases, University of California, Room 376D Med-Surg II, Irvine, CA 92697-4068, USA; Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - Gary Hermanson
- Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - Douglas M Molina
- Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - Xiaowu Liang
- Antigen Discovery, Inc., 1 Technology Drive Suite E309, Irvine, CA 92618, USA.
| | - David R Sherman
- Seattle Biomedical Research Institute, 307 Westlake Ave. North, No. 500, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Box 359931, Seattle, WA 98195, USA.
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, 1201 9th Ave., Seattle, WA, 98101, USA.
| | - Junbao Yang
- Benaroya Research Institute at Virginia Mason, 1201 9th Ave., Seattle, WA, 98101, USA.
| | - John Kenneth
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Koramangala 2 Block, Bangaluru, Karnataka 560034, India.
| | - Syed F Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Koramangala 2 Block, Bangaluru, Karnataka 560034, India.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; Emory Vaccine Center, 1510 Clifton Road, Atlanta, GA 30329, USA.
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; Emory Vaccine Center, 1510 Clifton Road, Atlanta, GA 30329, USA; Department of Pediatrics, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - David M Koelle
- Department of Medicine, Division of Infectious Diseases, University of Washington, Box 358061, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Box 359931, Seattle, WA 98195, USA; Benaroya Research Institute at Virginia Mason, 1201 9th Ave., Seattle, WA, 98101, USA; Department of Laboratory Medicine, University of Washington, Box 358070, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 1100 Eastlake Ave. East, Seattle, WA 98109, USA.
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12
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On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology. SYSTEMS AND SYNTHETIC BIOLOGY 2014; 9:73-5. [PMID: 25972991 DOI: 10.1007/s11693-014-9158-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/08/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
Brucellosis is a zoonotic infection transmitted to humans from infected animals and is one of the widely spread zoonoses. Recently, six species were recognized within the genus Brucella wherein B. melitensis, B. suis and B. abortus are considered virulent for humans. While these species differ phenotypically by their pattern of metabolic activities, there has been an imperative need to understand pathogenesis of Brucella species. It has been foreseen that creating a human vaccine for Brucellosis would entail decreased dose of antibiotics. However the emerging role of Brucella pathogenesis still centers on isolation of the organism and various diagnostic tests thereby leading to varying strategies of treatment cycle. In view of disease heterogeneity, we focus systems and synthetic biology challenges that might improve our understanding the Brucella pathogenesis.
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13
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Lessa-Aquino C, Wunder EA, Lindow JC, Rodrigues CB, Pablo J, Nakajima R, Jasinskas A, Liang L, Reis MG, Ko AI, Medeiros MA, Felgner PL. Proteomic features predict seroreactivity against leptospiral antigens in leptospirosis patients. J Proteome Res 2014; 14:549-56. [PMID: 25358092 PMCID: PMC4286151 DOI: 10.1021/pr500718t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
With
increasing efficiency, accuracy, and speed we can access complete
genome sequences from thousands of infectious microorganisms; however,
the ability to predict antigenic targets of the immune system based
on amino acid sequence alone is still needed. Here we use a Leptospira interrogans microarray expressing 91% (3359)
of all leptospiral predicted ORFs (3667) and make an empirical accounting
of all antibody reactive antigens recognized in sera from naturally
infected humans; 191 antigens elicited an IgM or IgG response, representing
5% of the whole proteome. We classified the reactive antigens into
26 annotated COGs (clusters of orthologous groups), 26 JCVI Mainrole
annotations, and 11 computationally predicted proteomic features.
Altogether, 14 significantly enriched categories were identified,
which are associated with immune recognition including mass spectrometry
evidence of in vitro expression and in vivo mRNA up-regulation. Together,
this group of 14 enriched categories accounts for just 25% of the
leptospiral proteome but contains 50% of the immunoreactive antigens.
These findings are consistent with our previous studies of other Gram-negative
bacteria. This genome-wide approach provides an empirical basis to
predict and classify antibody reactive antigens based on structural,
physical–chemical, and functional proteomic features and a
framework for understanding the breadth and specificity of the immune
response to L. interrogans.
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Affiliation(s)
- Carolina Lessa-Aquino
- Fiocruz, Bio-Manguinhos, Brazilian Ministry of Health , Avenida Brasil, 4365 - Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil
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14
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Pitarch A, Nombela C, Gil C. Serum antibody signature directed against Candida albicans Hsp90 and enolase detects invasive candidiasis in non-neutropenic patients. J Proteome Res 2014; 13:5165-84. [PMID: 25377742 DOI: 10.1021/pr500681x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Invasive candidiasis (IC) adds significantly to the morbidity and mortality of non-neutropenic patients if not diagnosed and treated early. To uncover serologic biomarkers that alone or in combination could reliably detect IC in this population, IgG antibody-reactivity profiles to the Candida albicans intracellular proteome were examined by serological proteome analysis (SERPA) and data mining procedures in a training set of 24 non-neutropenic patients. Despite the high interindividual molecular heterogeneity, unsupervised clustering analyses revealed that serum 22-IgG antibody-reactivity patterns differentiated IC from non-IC patients. Univariate analyses further highlighted that 15 out of the 22 SERPA-identified IgG antibodies could be useful candidate IC biomarkers. The diagnostic performance of one of these candidates (anti-Hsp90 IgG antibodies) was validated using an ELISA prototype in a test set of 59 non-neutropenic patients. We then formulated an IC discriminator based on the combined immunoproteomic fingerprints of this and another SERPA-detected and previously validated IC biomarker (anti-Eno1 IgG antibodies) in the training set. Its consistency was substantiated using their ELISA prototypes in the test set. Receiver-operating-characteristic curve analyses showed that this two-biomarker signature accurately identified IC in non-neutropenic patients and provided better IC diagnostic accuracy than the individual biomarkers alone. We conclude that this serum IgG antibody signature directed against C. albicans Hsp90 and Eno1, if confirmed prospectively, may be useful for IC diagnosis in non-neutropenic patients.
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Affiliation(s)
- Aida Pitarch
- Department of Microbiology II, Faculty of Pharmacy, Complutense University of Madrid and Ramón y Cajal Institute of Health Research (IRYCIS) , Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
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15
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The impact of "omic" and imaging technologies on assessing the host immune response to biodefence agents. J Immunol Res 2014; 2014:237043. [PMID: 25333059 PMCID: PMC4182007 DOI: 10.1155/2014/237043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/23/2014] [Accepted: 08/05/2014] [Indexed: 01/08/2023] Open
Abstract
Understanding the interactions between host and pathogen is important for the development and assessment of medical countermeasures to infectious agents, including potential biodefence pathogens such as Bacillus anthracis, Ebola virus, and Francisella tularensis. This review focuses on technological advances which allow this interaction to be studied in much greater detail. Namely, the use of “omic” technologies (next generation sequencing, DNA, and protein microarrays) for dissecting the underlying host response to infection at the molecular level; optical imaging techniques (flow cytometry and fluorescence microscopy) for assessing cellular responses to infection; and biophotonic imaging for visualising the infectious disease process. All of these technologies hold great promise for important breakthroughs in the rational development of vaccines and therapeutics for biodefence agents.
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Davies DH, Chun S, Hermanson G, Tucker JA, Jain A, Nakajima R, Pablo J, Felgner PL, Liang X. T cell antigen discovery using soluble vaccinia proteome reveals recognition of antigens with both virion and nonvirion association. THE JOURNAL OF IMMUNOLOGY 2014; 193:1812-27. [PMID: 25024392 DOI: 10.4049/jimmunol.1400663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Vaccinia virus (VACV) is a useful model system for understanding the immune response to a complex pathogen. Proteome-wide Ab profiling studies reveal the humoral response to be strongly biased toward virion-associated Ags, and several membrane proteins induce Ab-mediated protection against VACV challenge in mice. Some studies have indicated that the CD4 response is also skewed toward proteins with virion association, whereas the CD8 response is more biased toward proteins with early expression. In this study, we have leveraged a VACV strain Western Reserve (VACV-WR) plasmid expression library, produced previously for proteome microarrays for Ab profiling, to make a solubilized full VACV-WR proteome for T cell Ag profiling. Splenocytes from VACV-WR-infected mice were assayed without prior expansion against the soluble proteome in assays for Th1 and Th2 signature cytokines. The response to infection was polarized toward a Th1 response, with the distribution of reactive T cell Ags comprising both early and late VACV proteins. Interestingly, the proportions of different functional subsets were similar to that present in the whole proteome. In contrast, the targets of Abs from the same mice were enriched for membrane and other virion components, as described previously. We conclude that a "nonbiasing" approach to T cell Ag discovery reveals a T cell Ag profile in VACV that is broader and less skewed to virion association than the Ab profile. The T cell Ag mapping method developed in the present study should be applicable to other organisms where expressible "ORFeome" libraries are also available, and it is readily scalable for larger pathogens.
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Affiliation(s)
- D Huw Davies
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697; Antigen Discovery, Inc., Irvine, CA 92618; and
| | - Sookhee Chun
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | | | - Jo Anne Tucker
- Division of Hematology and Oncology, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | - Aarti Jain
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | - Rie Nakajima
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
| | - Jozelyn Pablo
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697; Antigen Discovery, Inc., Irvine, CA 92618; and
| | - Philip L Felgner
- Division of Infectious Diseases, School of Medicine, University of California, Irvine, Irvine, CA 92697
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17
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Patra KP, Saito M, Atluri VL, Rolán HG, Young B, Kerrinnes T, Smits H, Ricaldi JN, Gotuzzo E, Gilman RH, Tsolis RM, Vinetz JM. A protein-conjugate approach to develop a monoclonal antibody-based antigen detection test for the diagnosis of human brucellosis. PLoS Negl Trop Dis 2014; 8:e2926. [PMID: 24901521 PMCID: PMC4046965 DOI: 10.1371/journal.pntd.0002926] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 04/20/2014] [Indexed: 11/19/2022] Open
Abstract
Human brucellosis is most commonly diagnosed by serology based on agglutination of fixed Brucella abortus as antigen. Nucleic acid amplification techniques have not proven capable of reproducibly and sensitively demonstrating the presence of Brucella DNA in clinical specimens. We sought to optimize a monoclonal antibody-based assay to detect Brucella melitensis lipopolysaccharide in blood by conjugating B. melitensis LPS to keyhole limpet hemocyanin, an immunogenic protein carrier to maximize IgG affinity of monoclonal antibodies. A panel of specific of monoclonal antibodies was obtained that recognized both B. melitensis and B. abortus lipopolysaccharide epitopes. An antigen capture assay was developed that detected B. melitensis in the blood of experimentally infected mice and, in a pilot study, in naturally infected Peruvian subjects. As a proof of principle, a majority (7/10) of the patients with positive blood cultures had B. melitensis lipopolysaccharide detected in the initial blood specimen obtained. One of 10 patients with relapsed brucellosis and negative blood culture had a positive serum antigen test. No seronegative/blood culture negative patients had a positive serum antigen test. Analysis of the pair of monoclonal antibodies (2D1, 2E8) used in the capture ELISA for potential cross-reactivity in the detection of lipopolysaccharides of E. coli O157:H7 and Yersinia enterocolitica O9 showed specificity for Brucella lipopolysaccharide. This new approach to develop antigen-detection monoclonal antibodies against a T cell-independent polysaccharide antigen based on immunogenic protein conjugation may lead to the production of improved rapid point-of-care-deployable assays for the diagnosis of brucellosis and other infectious diseases.
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Affiliation(s)
- Kailash P. Patra
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Mayuko Saito
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Vidya L. Atluri
- Department of Medical Microbiology, University of California Davis, Davis, California, United States of America
| | - Hortensia G. Rolán
- Department of Medical Microbiology, University of California Davis, Davis, California, United States of America
| | - Briana Young
- Department of Medical Microbiology, University of California Davis, Davis, California, United States of America
| | - Tobias Kerrinnes
- Department of Medical Microbiology, University of California Davis, Davis, California, United States of America
| | - Henk Smits
- Department of Biomedical Research, Royal Tropical Institute, Amsterdam, the Netherlands
| | - Jessica N. Ricaldi
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gotuzzo
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Laboratory of Research and Development, and Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Renee M. Tsolis
- Department of Medical Microbiology, University of California Davis, Davis, California, United States of America
- * E-mail: (RMT); (JMV)
| | - Joseph M. Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratory of Research and Development, and Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail: (RMT); (JMV)
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18
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Pre-erythrocytic antibody profiles induced by controlled human malaria infections in healthy volunteers under chloroquine prophylaxis. Sci Rep 2013; 3:3549. [PMID: 24351974 PMCID: PMC4894385 DOI: 10.1038/srep03549] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 11/28/2013] [Indexed: 11/08/2022] Open
Abstract
Complete sterile protection to Plasmodium falciparum (Pf) infection mediated by pre-erythrocytic immunity can be experimentally induced under chloroquine prophylaxis, through immunization with sporozoites from infected mosquitoes' bites (CPS protocol). To characterize the profile of CPS induced antibody (Ab) responses, we developed a proteome microarray containing 809 Pf antigens showing a distinct Ab profile with recognition of antigens expressed in pre-erythrocytic life-cycle stages. In contrast, plasma from naturally exposed semi-immune individuals from Kenya was skewed toward antibody reactivity against asexual blood stage antigens. CPS-immunized and semi-immune individuals generated antibodies against 192 and 202 Pf antigens, respectively, but only 60 antigens overlapped between the two groups. Although the number of reactive antigens varied between the CPS-immunized individuals, all volunteers reacted strongly against the pre-erythrocytic antigens circumsporozoite protein (CSP) and liver stage antigen 1 (LSA1). Well classified merozoite and erythrocytic antigens were strongly reactive in semi-immune individuals but lacking in the CPS immunized group. These data show that the antibody profile of CPS-immunized and semi-immune groups have quite distinct profiles reflecting their protective immunity; antibodies from CPS immunized individuals react strongly against pre-erythrocytic while semi-immune individuals mainly react against erythrocytic antigens.
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Identification of seroreactive proteins of Leptospira interrogans serovar copenhageni using a high-density protein microarray approach. PLoS Negl Trop Dis 2013; 7:e2499. [PMID: 24147173 PMCID: PMC3798601 DOI: 10.1371/journal.pntd.0002499] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
Background Leptospirosis is a widespread zoonotic disease worldwide. The lack of an adequate laboratory test is a major barrier for diagnosis, especially during the early stages of illness, when antibiotic therapy is most effective. Therefore, there is a critical need for an efficient diagnostic test for this life threatening disease. Methodology In order to identify new targets that could be used as diagnostic makers for leptopirosis, we constructed a protein microarray chip comprising 61% of Leptospira interrogans proteome and investigated the IgG response from 274 individuals, including 80 acute-phase, 80 convalescent-phase patients and 114 healthy control subjects from regions with endemic, high endemic, and no endemic transmission of leptospirosis. A nitrocellulose line blot assay was performed to validate the accuracy of the protein microarray results. Principal findings We found 16 antigens that can discriminate between acute cases and healthy individuals from a region with high endemic transmission of leptospirosis, and 18 antigens that distinguish convalescent cases. Some of the antigens identified in this study, such as LipL32, the non-identical domains of the Lig proteins, GroEL, and Loa22 are already known to be recognized by sera from human patients, thus serving as proof-of-concept for the serodiagnostic antigen discovery approach. Several novel antigens were identified, including the hypothetical protein LIC10215 which showed good sensitivity and specificity rates for both acute- and convalescent-phase patients. Conclusions Our study is the first large-scale evaluation of immunodominant antigens associated with naturally acquired leptospiral infection, and novel as well as known serodiagnostic leptospiral antigens that are recognized by antibodies in the sera of leptospirosis cases were identified. The novel antigens identified here may have potential use in both the development of new tests and the improvement of currently available assays for diagnosing this neglected tropical disease. Further research is needed to assess the utility of these antigens in more deployable diagnostic platforms. Leptospirosis is an infectious zoonotic disease that causes non-specific signs and symptoms in humans, which hampers the clinical diagnosis and treatment by physicians. Complications can occur if the proper treatment is not initiated early in the course of illness. Although the early diagnosis is critical for preventing unnecessary complications, currently available tests do not exhibit sufficient diagnostic sensitivity in the beginning of disease. We took advantage of high throughput techniques to perform an embracing study of the humoral immune response to the bacteria in order to identify antigens that could be used in a new test for the diagnosis of leptospirosis. A protein microarray chip containing 2,241 leptospiral proteins was constructed and probed with serum samples from patients and healthy individuals. We identified 24 proteins that are recognized by patients' sera but not by healthy individuals. These proteins are potential diagnostic markers, especially the ones identified for acute-phase patients, which can discriminate between a positive and a negative leptospirosis case within a few days after onset of symptoms. This work establishes the protein microarray approach for improving our understanding of the serological response to leptospirosis. Further research is needed to assess the performance of these antigens in the clinical setting.
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20
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Brucella melitensis T cell epitope recognition in humans with brucellosis in Peru. Infect Immun 2013; 82:124-31. [PMID: 24126518 DOI: 10.1128/iai.00796-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Brucella melitensis, one of the causative agents of human brucellosis, causes acute, chronic, and relapsing infection. While T cell immunity in brucellosis has been extensively studied in mice, no recognized human T cell epitopes that might provide new approaches to classifying and prognosticating B. melitensis infection have ever been delineated. Twenty-seven pools of 500 major histocompatibility complex class II (MHC-II) restricted peptides were created by computational prediction of promiscuous MHC-II CD4(+) T cell derived from the top 50 proteins recognized by IgG in human sera on a genome level B. melitensis protein microarray. Gamma interferon (IFN-γ) and interleukin-5 (IL-5) enzyme-linked immunospot (ELISPOT) analyses were used to quantify and compare Th1 and Th2 responses of leukapheresis-obtained peripheral blood mononuclear cells from Peruvian subjects cured after acute infection (n = 9) and from patients who relapsed (n = 5). Four peptide epitopes derived from 3 B. melitensis proteins (BMEI 1330, a DegP/HtrA protease; BMEII 0029, type IV secretion system component VirB5; and BMEII 0691, a predicted periplasmic binding protein of a peptide transport system) were found repeatedly to produce significant IFN-γ ELISPOT responses in both acute-infection and relapsing patients; none of the peptides distinguished the patient groups. IL-5 responses against the panel of peptides were insignificant. These experiments are the first to systematically identify B. melitensis MHC-II-restricted CD4(+) T cell epitopes recognized by the human immune response, with the potential for new approaches to brucellosis diagnostics and understanding the immunopathogenesis related to this intracellular pathogen.
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Abstract
Protein microarray technology is an emerging field that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. Protein microarrays are composed of two major classes: analytical and functional. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. Applications of protein microarrays, especially functional protein microarrays, have flourished over the past decade as the fabrication technology has matured. In this unit, advances in protein microarray technologies are reviewed, and then a series of examples are presented to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. Relevant areas of research include the detection of various binding properties of proteins, the study of protein post-translational modifications, the analysis of host-microbe interactions, profiling antibody specificity, and the identification of biomarkers in autoimmune diseases.
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Affiliation(s)
- F X Reymond Sutandy
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
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22
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Pemphigus vulgaris autoantibody profiling by proteomic technique. PLoS One 2013; 8:e57587. [PMID: 23505434 PMCID: PMC3591405 DOI: 10.1371/journal.pone.0057587] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 01/23/2013] [Indexed: 11/24/2022] Open
Abstract
Pemphigus vulgaris (PV) is a mucocutaneous blistering disease characterized by IgG autoantibodies against the stratified squamous epithelium. Current understanding of PV pathophysiology does not explain the mechanism of acantholysis in patients lacking desmoglein antibodies, which justifies a search for novel targets of pemphigus autoimmunity. We tested 264 pemphigus and 138 normal control sera on the multiplexed protein array platform containing 701 human genes encompassing many known keratinocyte cell-surface molecules and members of protein families targeted by organ-non-specific PV antibodies. The top 10 antigens recognized by the majority of test patients’ sera were proteins encoded by the DSC1, DSC3, ATP2C1, PKP3, CHRM3, COL21A1, ANXA8L1, CD88 and CHRNE genes. The most common combinations of target antigens included at least one of the adhesion molecules DSC1, DSC3 or PKP3 and/or the acetylcholine receptor CHRM3 or CHRNE with or without the MHC class II antigen DRA. To identify the PV antibodies most specific to the disease process, we sorted the data based on the ratio of patient to control frequencies of antigen recognition. The frequency of antigen recognition by patients that exceeded that of control by 10 and more times were the molecules encoded by the CD33, GP1BA, CHRND, SLC36A4, CD1B, CD32, CDH8, CDH9, PMP22 and HLA-E genes as well as mitochondrial proteins encoded by the NDUFS1, CYB5B, SOD2, PDHA1 and FH genes. The highest specificity to PV showed combinations of autoantibodies to the calcium pump encoded by ATP2C1 with C5a receptor plus DSC1 or DSC3 or HLA-DRA. The results identified new targets of pemphigus autoimmunity. Novel autoantibody signatures may help explain individual variations in disease severity and treatment response, and serve as sensitive and specific biomarkers for new diagnostic assays in PV patients.
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Román K, Castillo R, Gilman RH, Calderón M, Vivar A, Céspedes M, Smits HL, Meléndez P, Gotuzzo E, Guerra H, Maves RC, Matthias MA, Vinetz JM, Saito M. A foodborne outbreak of brucellosis at a police station cafeteria, Lima, Peru. Am J Trop Med Hyg 2013; 88:552-8. [PMID: 23382164 DOI: 10.4269/ajtmh.12-0606] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Brucella melitensis is highly infectious for humans and can be transmitted to humans in a number of epidemiological contexts. Within the context of an ongoing brucellosis surveillance project, an outbreak at a Peruvian police officer cafeteria was discovered, which led to active surveillance (serology, blood culture) for additional cases among 49 police officers who had also eaten there. The cohort was followed up to 18 months regardless of treatment or symptoms. Active surveillance estimated the attack rate at 26.5% (13 of 49). Blood cultures from four cases were positive; these isolates were indistinguishable using multiple locus variable number tandem repeat analysis. This investigation indicates the importance of case tracking and active surveillance for brucellosis in the context of potential common source exposure. These results provide rationale for public health investigations of brucellosis index cases including the bioterrorism-related dissemination of Brucella.
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Affiliation(s)
- Karina Román
- Department of Molecular and Cellular Sciences, Faculty of Sciences, and Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Perú.
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24
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Immune profiling with a Salmonella Typhi antigen microarray identifies new diagnostic biomarkers of human typhoid. Sci Rep 2013; 3:1043. [PMID: 23304434 PMCID: PMC3540400 DOI: 10.1038/srep01043] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/07/2012] [Indexed: 11/08/2022] Open
Abstract
Current serological diagnostic assays for typhoid fever are based on detecting antibodies against Salmonella LPS or flagellum, resulting in a high false-positive rate. Here we used a protein microarray containing 2,724 Salmonella enterica serovar Typhi antigens (>63% of proteome) and identified antibodies against 16 IgG antigens and 77 IgM antigens that were differentially reactive among acute typhoid patients and healthy controls. The IgG target antigens produced a sensitivity of 97% and specificity of 80%, whereas the IgM target antigens produced 97% and 91% sensitivity and specificity, respectively. Our analyses indicated certain features such as membrane association, secretion, and protein expression were significant enriching features of the reactive antigens. About 72% of the serodiagnostic antigens were within the top 25% of the ranked antigen list using a Naïve bayes classifier. These data provide an important resource for improved diagnostics, therapeutics and vaccine development against an important human pathogen.
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25
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Smirnova EA, Vasin AV, Sandybaev NT, Klotchenko SA, Plotnikova MA, Chervyakova OV, Sansyzbay AR, Kiselev OI. Current Methods of Human and Animal Brucellosis Diagnostics. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aid.2013.33026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Diagnostic peptide discovery: prioritization of pathogen diagnostic markers using multiple features. PLoS One 2012; 7:e50748. [PMID: 23272069 PMCID: PMC3522711 DOI: 10.1371/journal.pone.0050748] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/23/2012] [Indexed: 11/27/2022] Open
Abstract
The availability of complete pathogen genomes has renewed interest in the development of diagnostics for infectious diseases. Synthetic peptide microarrays provide a rapid, high-throughput platform for immunological testing of potential B-cell epitopes. However, their current capacity prevent the experimental screening of complete “peptidomes”. Therefore, computational approaches for prediction and/or prioritization of diagnostically relevant peptides are required. In this work we describe a computational method to assess a defined set of molecular properties for each potential diagnostic target in a reference genome. Properties such as sub-cellular localization or expression level were evaluated for the whole protein. At a higher resolution (short peptides), we assessed a set of local properties, such as repetitive motifs, disorder (structured vs natively unstructured regions), trans-membrane spans, genetic polymorphisms (conserved vs. divergent regions), predicted B-cell epitopes, and sequence similarity against human proteins and other potential cross-reacting species (e.g. other pathogens endemic in overlapping geographical locations). A scoring function based on these different features was developed, and used to rank all peptides from a large eukaryotic pathogen proteome. We applied this method to the identification of candidate diagnostic peptides in the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We measured the performance of the method by analyzing the enrichment of validated antigens in the high-scoring top of the ranking. Based on this measure, our integrative method outperformed alternative prioritizations based on individual properties (such as B-cell epitope predictors alone). Using this method we ranked 10 million 12-mer overlapping peptides derived from the complete T. cruzi proteome. Experimental screening of 190 high-scoring peptides allowed the identification of 37 novel epitopes with diagnostic potential, while none of the low scoring peptides showed significant reactivity. Many of the metrics employed are dependent on standard bioinformatic tools and data, so the method can be easily extended to other pathogen genomes.
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27
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Sustained and differential antibody responses to virulence proteins of Brucella melitensis during acute and chronic infections in human brucellosis. Eur J Clin Microbiol Infect Dis 2012; 32:437-47. [DOI: 10.1007/s10096-012-1767-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/16/2012] [Indexed: 01/18/2023]
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28
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Zhu H, Cox E, Qian J. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Proteomics Clin Appl 2012; 6:548-62. [PMID: 23027439 PMCID: PMC3600421 DOI: 10.1002/prca.201200041] [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: 05/21/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
Abstract
Functional protein microarrays were developed as a high-throughput tool to overcome the limitations of DNA microarrays and to provide a versatile platform for protein functional analyses. Recent years have witnessed tremendous growth in the use of protein microarrays, particularly functional protein microarrays, to address important questions in the field of clinical proteomics. In this review, we will summarize some of the most innovative and exciting recent applications of protein microarrays in clinical proteomics, including biomarker identification, pathogen-host interactions, and cancer biology.
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Affiliation(s)
- Heng Zhu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, MD, USA.
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29
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Liang L, Felgner PL. Predicting antigenicity of proteins in a bacterial proteome; a protein microarray and naïve Bayes classification approach. Chem Biodivers 2012; 9:977-90. [PMID: 22589097 DOI: 10.1002/cbdv.201100360] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Discovery of novel antigens associated with infectious diseases is fundamental to the development of serodiagnostic tests and protein subunit vaccines against existing and emerging pathogens. Efforts to predict antigenicity have relied on a few computational algorithms predicting signal peptide sequences (SignalP), transmembrane domains, or subcellular localization (pSort). An empirical protein microarray approach was developed to scan the entire proteome of any infectious microorganism and empirically determine immunoglobulin reactivity against all the antigens from a microorganism in infected individuals. The current database from this activity contains quantitative antibody reactivity data against 35,000 proteins derived from 25 infectious microorganisms and more than 30 million data points derived from 15,000 patient sera. Interrogation of these data sets has revealed ten proteomic features that are associated with antigenicity, allowing an in silico protein sequence and functional annotation based approach to triage the least likely antigenic proteins from those that are more likely to be antigenic. The first iteration of this approach applied to Brucella melitensis predicted 37% of the bacterial proteome containing 91% of the antigens empirically identified by probing proteome microarrays. In this study, we describe a naïve Bayes classification approach that can be used to assign a relative score to the likelihood that an antigen will be immunoreactive and serodiagnostic in a bacterial proteome. This algorithm predicted 20% of the B. melitensis proteome including 91% of the serodiagnostic antigens, a nearly twofold improvement in specificity of the predictor. These results give us confidence that further development of this approach will lead to further improvements in the sensitivity and specificity of this in silico predictive algorithm.
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Affiliation(s)
- Li Liang
- Department of Medicine, Division of Infectious Diseases, University of California, Irvine, CA 92697, USA
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30
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Translational research in infectious disease: current paradigms and challenges ahead. Transl Res 2012; 159:430-53. [PMID: 22633095 PMCID: PMC3361696 DOI: 10.1016/j.trsl.2011.12.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/23/2011] [Accepted: 12/24/2012] [Indexed: 12/25/2022]
Abstract
In recent years, the biomedical community has witnessed a rapid scientific and technologic evolution after the development and refinement of high-throughput methodologies. Concurrently and consequentially, the scientific perspective has changed from the reductionist approach of meticulously analyzing the fine details of a single component of biology to the "holistic" approach of broadmindedly examining the globally interacting elements of biological systems. The emergence of this new way of thinking has brought about a scientific revolution in which genomics, proteomics, metabolomics, and other "omics" have become the predominant tools by which large amounts of data are amassed, analyzed, and applied to complex questions of biology that were previously unsolvable. This enormous transformation of basic science research and the ensuing plethora of promising data, especially in the realm of human health and disease, have unfortunately not been followed by a parallel increase in the clinical application of this information. On the contrary, the number of new potential drugs in development has been decreasing steadily, suggesting the existence of roadblocks that prevent the translation of promising research into medically relevant therapeutic or diagnostic application. In this article, we will review, in a noninclusive fashion, several recent scientific advancements in the field of translational research, with a specific focus on how they relate to infectious disease. We will also present a current picture of the limitations and challenges that exist for translational research, as well as ways that have been proposed by the National Institutes of Health to improve the state of this field.
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Key Words
- 2-de, 2-dimensional electrophoresis
- 2-d dige, 2-dimensional differential in-gel electrophoresis
- cf, cystic fibrosis
- ctsa, clinical and translational science awards program
- ebv, epstein-barr virus
- fda, u.s. food and drug administration
- gwas, genome-wide association studies
- hcv, hepatitis c virus
- hmp, human microbiome project
- hplc, high-pressure liquid chromatography
- lc, liquid chromatography
- lsb, laboratory of systems biology
- mab, monoclonal antibody
- mrm/srm, multiple reaction monitoring/selective reaction monitoring
- ms, mass spectrometry
- ms/ms, tandem mass spectrometry
- ncats, national center for advancing translational sciences
- ncrr, national center of research resources
- niaid, national institute of allergy and infectious disease
- nih, national institutes of health
- nme, new molecular entity
- nmr, nuclear magnetic resonance
- pbmc, peripheral blood mononuclear cell
- pcr, polymerase chain reaction
- prr, pathogen recognition receptor
- qqq, triple quadrupole mass spectrometry
- sars-cov, coronavirus associated with severe acute respiratory syndrome
- snp, single nucleotide polymorphism
- tb, tuberculosis
- uti, urinary tract infection
- yfv, yellow fever virus
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31
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He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Front Cell Infect Microbiol 2012; 2:2. [PMID: 22919594 PMCID: PMC3417401 DOI: 10.3389/fcimb.2012.00002] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 01/12/2012] [Indexed: 12/20/2022] Open
Abstract
Brucella is a Gram-negative, facultative intracellular bacterium that causes zoonotic brucellosis in humans and various animals. Out of 10 classified Brucella species, B. melitensis, B. abortus, B. suis, and B. canis are pathogenic to humans. In the past decade, the mechanisms of Brucella pathogenesis and host immunity have been extensively investigated using the cutting edge systems biology and bioinformatics approaches. This article provides a comprehensive review of the applications of Omics (including genomics, transcriptomics, and proteomics) and bioinformatics technologies for the analysis of Brucella pathogenesis, host immune responses, and vaccine targets. Based on more than 30 sequenced Brucella genomes, comparative genomics is able to identify gene variations among Brucella strains that help to explain host specificity and virulence differences among Brucella species. Diverse transcriptomics and proteomics gene expression studies have been conducted to analyze gene expression profiles of wild type Brucella strains and mutants under different laboratory conditions. High throughput Omics analyses of host responses to infections with virulent or attenuated Brucella strains have been focused on responses by mouse and cattle macrophages, bovine trophoblastic cells, mouse and boar splenocytes, and ram buffy coat. Differential serum responses in humans and rams to Brucella infections have been analyzed using high throughput serum antibody screening technology. The Vaxign reverse vaccinology has been used to predict many Brucella vaccine targets. More than 180 Brucella virulence factors and their gene interaction networks have been identified using advanced literature mining methods. The recent development of community-based Vaccine Ontology and Brucellosis Ontology provides an efficient way for Brucella data integration, exchange, and computer-assisted automated reasoning.
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Affiliation(s)
- Yongqun He
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan Medical School Ann Arbor, MI, USA.
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Cannella AP, Tsolis RM, Liang L, Felgner PL, Saito M, Sette A, Gotuzzo E, Vinetz JM. Antigen-specific acquired immunity in human brucellosis: implications for diagnosis, prognosis, and vaccine development. Front Cell Infect Microbiol 2012; 2:1. [PMID: 22919593 PMCID: PMC3417515 DOI: 10.3389/fcimb.2012.00001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 01/11/2012] [Indexed: 11/13/2022] Open
Abstract
Brucella spp., are Gram negative bacteria that cause disease by growing within monocyte/macrophage lineage cells. Clinical manifestations of brucellosis are immune mediated, not due to bacterial virulence factors. Acquired immunity to brucellosis has been studied through observations of naturally infected hosts (cattle, goats), mouse models (mice), and human infection. Even though Brucella spp. are known for producing mechanisms that evade the immune system, cell-mediated immune responses drive the clinical manifestations of human disease after exposure to Brucella species, as high antibody responses are not associated with protective immunity. The precise mechanisms by which cell-mediated immune responses confer protection or lead to disease manifestations remain undefined. Descriptive studies of immune responses in human brucellosis show that TH1 (interferon-γ-producing T cells) are associated with dominant immune responses, findings consistent with animal studies. Whether these T cell responses are protective, or determine the different clinical responses associated with brucellosis is unknown, especially with regard to undulant fever manifestations, relapsing disease, or are associated with responses to distinct sets of Brucella spp. antigens are unknown. Few data regarding T cell responses in terms of specific recognition of Brucella spp. protein antigens and peptidic epitopes, either by CD4+ or CD8+ T cells, have been identified in human brucellosis patients. Additionally because current attenuated Brucella vaccines used in animals cause human disease, there is a true need for a recombinant protein subunit vaccine for human brucellosis, as well as for improved diagnostics in terms of prognosis and identification of unusual forms of brucellosis. This review will focus on current understandings of antigen-specific immune responses induced Brucella peptidic epitopes that has promise for yielding new insights into vaccine and diagnostics development, and for understanding pathogenetic mechanisms of human brucellosis.
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Affiliation(s)
- Anthony P Cannella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego La Jolla, CA, USA
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33
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Serial kinetics of the antibody response against the complete Brucella melitensis ORFeome in focal vertebral brucellosis. J Clin Microbiol 2012; 50:922-6. [PMID: 22219303 DOI: 10.1128/jcm.05298-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Human brucellosis is a common zoonosis worldwide. Here we present a case of focal vertebral brucellosis in a 71-year-old Mexican-American woman who contracted infection from unpasteurized goat milk. Standard agglutination serology was negative; the diagnosis was established by the isolation of Brucella melitensis from abscess fluid. A B. melitensis protein microarray comprised of nearly all proteins encoded by the bacterial genome was used to determine the kinetics of this patient's antibody responses to the complete collection of open reading frames existing in the genome (ORFeome). Three patterns of antibody responses against B. melitensis antigens were seen for serum samples obtained on days 0 (pretreatment), 14, 49, 100, and 180: (i) stable titers over time, (ii) a steady fall in titers, and (iii) an initial rise in titers followed by declining titers. Sera from this patient with chronic brucellosis recognized some of the same B. melitensis proteins as those recognized by sera from acute/subacute, blood culture-positive brucellosis patients but also recognized a distinct set of proteins. This study is the first to determine the kinetics of the human antibody responses to the complete repertoire of proteins encoded by a bacterial genome and demonstrates fundamentally different immunopathogenetic mechanisms between acute human brucellosis and chronic human brucellosis. While an extension of these findings to a larger patient population is necessary, these findings have important clinical and diagnostic implications and lead toward new insights into the fundamental immunopathogenesis of brucellosis.
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