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Nabi B, Kumawat M, Ahlawat N, Ahlawat S. Molecular, Structural, and Functional Diversity of Universal Stress Proteins (USPs) in Bacteria, Plants, and Their Biotechnological Applications. Protein J 2024; 43:437-446. [PMID: 38492187 DOI: 10.1007/s10930-024-10192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Universal stress proteins (USPs) are widely distributed and play crucial roles in cellular responses to biotic and abiotic stresses. These roles include regulating cell growth and development, cell motility, hypoxia responses, and ion sequestration. With the increasing frequency and intensity of extreme weather events due to climate change, pathogens have developed different strategies to withstand environmental stresses, in which USPs play a significant role in their survival and virulence. In this study, we analyzed the importance of USPs in various organisms, such as archaea, plants, and fungi, as a parameter that influences their survival. We discussed the different types Of USPs and their role, aiming to carry out fundamental research in this field to identify significant constraints for better understanding of USP functions at molecular level. Additionally, we discussed concepts and research techniques that could help overcome these hurdles and facilitate new molecular approaches to better understand and target USPs as important stress adaptation and survival regulators. Although the precise characteristics of USPs are still unclear, numerous innovative uses have already been developed, tested, and implemented. Complementary approaches to basic research and applications, as well as new technology and analytical techniques, may offer insights into the cryptic but crucial activities of USPs in various living systems.
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Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India.
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Allahabad, 211007, India
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India.
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Chugh S, Bahal RK, Dhiman R, Singh R. Antigen identification strategies and preclinical evaluation models for advancing tuberculosis vaccine development. NPJ Vaccines 2024; 9:57. [PMID: 38461350 PMCID: PMC10924964 DOI: 10.1038/s41541-024-00834-y] [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: 09/06/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024] Open
Abstract
In its myriad devastating forms, Tuberculosis (TB) has existed for centuries, and humanity is still affected by it. Mycobacterium tuberculosis (M. tuberculosis), the causative agent of TB, was the foremost killer among infectious agents until the COVID-19 pandemic. One of the key healthcare strategies available to reduce the risk of TB is immunization with bacilli Calmette-Guerin (BCG). Although BCG has been widely used to protect against TB, reports show that BCG confers highly variable efficacy (0-80%) against adult pulmonary TB. Unwavering efforts have been made over the past 20 years to develop and evaluate new TB vaccine candidates. The failure of conventional preclinical animal models to fully recapitulate human response to TB, as also seen for the failure of MVA85A in clinical trials, signifies the need to develop better preclinical models for TB vaccine evaluation. In the present review article, we outline various approaches used to identify protective mycobacterial antigens and recent advancements in preclinical models for assessing the efficacy of candidate TB vaccines.
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Affiliation(s)
- Saurabh Chugh
- Centre for Tuberculosis Research, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India
| | - Ritika Kar Bahal
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Ramandeep Singh
- Centre for Tuberculosis Research, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, Faridabad, 121001, Haryana, India.
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3
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Jiang F, Han Y, Liu Y, Xue Y, Cheng P, Xiao L, Gong W. A comprehensive approach to developing a multi-epitope vaccine against Mycobacterium tuberculosis: from in silico design to in vitro immunization evaluation. Front Immunol 2023; 14:1280299. [PMID: 38022558 PMCID: PMC10652892 DOI: 10.3389/fimmu.2023.1280299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The Bacillus Calmette-Guérin (BCG) vaccine, currently used against tuberculosis (TB), exhibits inconsistent efficacy, highlighting the need for more potent TB vaccines. Materials and methods In this study, we employed reverse vaccinology techniques to develop a promising multi-epitope vaccine (MEV) candidate, called PP13138R, for TB prevention. PP13138R comprises 34 epitopes, including B-cell, cytotoxic T lymphocyte, and helper T lymphocyte epitopes. Using bioinformatics and immunoinformatics tools, we assessed the physicochemical properties, structural features, and immunological characteristics of PP13138R. Results The vaccine candidate demonstrated excellent antigenicity, immunogenicity, and solubility without any signs of toxicity or sensitization. In silico analyses revealed that PP13138R interacts strongly with Toll-like receptor 2 and 4, stimulating innate and adaptive immune cells to produce abundant antigen-specific antibodies and cytokines. In vitro experiments further supported the efficacy of PP13138R by significantly increasing the population of IFN-γ+ T lymphocytes and the production of IFN-γ, TNF-α, IL-6, and IL-10 cytokines in active tuberculosis patients, latent tuberculosis infection individuals, and healthy controls, revealing the immunological characteristics and compare the immune responses elicited by the PP13138R vaccine across different stages of Mycobacterium tuberculosis infection. Conclusion These findings highlight the potential of PP13138R as a promising MEV candidate, characterized by favorable antigenicity, immunogenicity, and solubility, without any toxicity or sensitization.
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Affiliation(s)
- Fan Jiang
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
- Respiratory Research Institute, Senior Department of Pulmonary & Critical Care Medicine, The Eighth Medical Center of PLA General Hospital, Beijing, China
- Section of Health, No. 94804 Unit of the Chinese People’s Liberation Army, Shanghai, China
- Resident standardization training cadet corps, Air Force Hospital of Eastern Theater, Nanjing, China
| | - Yong Han
- Respiratory Research Institute, Senior Department of Pulmonary & Critical Care Medicine, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Yinping Liu
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Yong Xue
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Peng Cheng
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Li Xiao
- Respiratory Research Institute, Senior Department of Pulmonary & Critical Care Medicine, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Wenping Gong
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
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4
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Zhang G, Han L, Li Z, Chen Y, Li Q, Wang S, Shi H. Screening of immunogenic proteins and evaluation of vaccine candidates against Mycoplasma synoviae. NPJ Vaccines 2023; 8:121. [PMID: 37582795 PMCID: PMC10427712 DOI: 10.1038/s41541-023-00721-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023] Open
Abstract
Mycoplasma synoviae (M. synoviae) is a serious avian pathogen that causes significant economic losses to chicken and turkey producers worldwide. The currently available live attenuated and inactivated vaccines provide limited protection. The objective of this study was to identify potential subunit vaccine candidates using immunoproteomics and reverse vaccinology analyses and to evaluate their preliminary protection. Twenty-four candidate antigens were identified, and five of them, namely RS01790 (a putative sugar ABC transporter lipoprotein), BMP (a substrate-binding protein of the BMP family ABC transporter), GrpE (a nucleotide exchange factor), RS00900 (a putative nuclease), and RS00275 (an uncharacterized protein), were selected to evaluate their immunogenicity and preliminary protection. The results showed that all five antigens had good immunogenicity, and they were localized on the M. synoviae cell membrane. The antigens induced specific humoral and cellular immune responses, and the vaccinated chickens exhibited significantly greater body weight gain and lower air sac lesion scores and tracheal mucosal thicknesses. Additionally, the vaccinated chickens had lower M. synoviae loads in throat swabs than non-vaccinated chickens. The protective effect of the RS01790, BMP, GrpE, and RS00900 vaccines was better than that of the RS00275 vaccine. In conclusion, our study demonstrates the potential of subunit vaccines as a new approach to developing M. synoviae vaccines, providing new ideas for controlling the spread of M. synoviae worldwide.
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Affiliation(s)
- Guihua Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Lejiabao Han
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Zewei Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yifei Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Shifeng Wang
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611-0880, USA
| | - Huoying Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University (JIRLAAPS), Yangzhou, China.
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Cheng P, Jiang F, Wang G, Wang J, Xue Y, Wang L, Gong W. Bioinformatics analysis and consistency verification of a novel tuberculosis vaccine candidate HP13138PB. Front Immunol 2023; 14:1102578. [PMID: 36825009 PMCID: PMC9942524 DOI: 10.3389/fimmu.2023.1102578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Background With the increasing incidence of tuberculosis (TB) and the shortcomings of existing TB vaccines to prevent TB in adults, new TB vaccines need to be developed to address the complex TB epidemic. Method The dominant epitopes were screened from antigens to construct a novel epitope vaccine termed HP13138PB. The immune properties, structure, and function of HP13138PB were predicted and analyzed with bioinformatics and immunoinformatics. Then, the immune responses induced by the HP13138PB were confirmed by enzyme-linked immunospot assay (ELISPOT) and Th1/Th2/Th17 multi-cytokine detection kit. Result The HP13138PB vaccine consisted of 13 helper T lymphocytes (HTL) epitopes, 13 cytotoxic T lymphocytes (CTL) epitopes, and 8 B-cell epitopes. It was found that the antigenicity, immunogenicity, and solubility index of the HP13138PB vaccine were 0.87, 2.79, and 0.55, respectively. The secondary structure prediction indicated that the HP13138PB vaccine had 31% of α-helix, 11% of β-strand, and 56% of coil. The tertiary structure analysis suggested that the Z-score and the Favored region of the HP13138PB vaccine were -4.47 88.22%, respectively. Furthermore, the binding energies of the HP13138PB to toll-like receptor 2 (TLR2) was -1224.7 kcal/mol. The immunoinformatics and real-world experiments showed that the HP13138PB vaccine could induce an innate and adaptive immune response characterized by significantly higher levels of cytokines such as interferon-gamma (IFN-γ), tumor necrosis factor-α (TNF-α), interleukin-4 (IL-4), and IL-10. Conclusion The HP13138PB is a potential vaccine candidate to prevent TB, and this study preliminarily evaluated the ability of the HP13138PB to generate an immune response, providing a precursor target for developing TB vaccines.
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Affiliation(s)
- Peng Cheng
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China.,Department of Geriatrics, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Fan Jiang
- The Second Brigade of Cadet, Basic Medical School, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Guiyuan Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China.,Hebei North University, Zhangjiakou, Hebei, China
| | - Jie Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Yong Xue
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Liang Wang
- Department of Geriatrics, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
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Prado LCDS, Giacchetto Felice A, Rodrigues TCV, Tiwari S, Andrade BS, Kato RB, Oliveira CJF, Silva MV, Barh D, Azevedo VADC, Jaiswal AK, Soares SDC. New putative therapeutic targets against Serratia marcescens using reverse vaccinology and subtractive genomics. J Biomol Struct Dyn 2022; 40:10106-10121. [PMID: 34192477 DOI: 10.1080/07391102.2021.1942211] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Gram-negative bacillus Serratia marcescens, a member of Enterobacteriaceae family, is an opportunistic nosocomial pathogen commonly found in hospital outbreaks that can cause infections in the urinary tract, bloodstream, central nervous system and pneumonia. Because S. marcescens strains are resistant to several antibiotics, it is critical the need for effective treatments, including new drugs and vaccines. Here, we applied reverse vaccinology and subtractive genomic approaches for the in silico prediction of potential vaccine and drug targets against 59 strains of S. marcescens. We found 759 core non-host homologous proteins, of which 87 are putative surface-exposed proteins, 183 secreted proteins, and 80 membrane proteins. From these proteins, we predicted seven candidates vaccine targets: a sn-glycerol-3-phosphate-binding periplasmic protein UgpB, a vitamin B12 TonB-dependent receptor, a ferrichrome porin FhuA, a divisome-associated lipoprotein YraP, a membrane-bound lytic murein transglycosylase A, a peptidoglycan lytic exotransglycosylase, and a DUF481 domain-containing protein. We also predicted two drug targets: a N(4)-acetylcytidine amidohydrolase, and a DUF1428 family protein. Using the molecular docking approach for each drug target, we identified and selected ZINC04259491 and ZINC04235390 molecules as the most favorable interactions with the target active site residues. Our findings may contribute to the development of vaccines and new drug targets against S. marcescens. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ligia Carolina da Silva Prado
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andrei Giacchetto Felice
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Thaís Cristina Vilela Rodrigues
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Bahia, Brazil
| | - Rodrigo Bentes Kato
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo José Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Marcos Vinicius Silva
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, West Bengal, India
| | - Vasco Ariston de Carvalho Azevedo
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Arun Kumar Jaiswal
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Siomar de Castro Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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Weng S, Zhang J, Ma H, Zhou J, Jia L, Wan Y, Cui P, Ruan Q, Shao L, Wu J, Wang H, Zhang W, Xu Y. B21 DNA vaccine expressing ag85b, rv2029c, and rv1738 confers a robust therapeutic effect against latent Mycobacterium tuberculosis infection. Front Immunol 2022; 13:1025931. [PMID: 36569899 PMCID: PMC9768437 DOI: 10.3389/fimmu.2022.1025931] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Latent tuberculosis infection (LTBI) treatment is known to accelerate the decline in TB incidence, especially in high-risk populations. Mycobacterium tuberculosis (M. tb) expression profiles differ at different growth periods, and vaccines protective and therapeutic effects may increase when they include antigenic compositions from different periods. To develop a post-exposure vaccine that targets LTBI, we constructed four therapeutic DNA vaccines (A39, B37, B31, and B21) using different combinations of antigens from the proliferation phase (Ag85A, Ag85B), PE/PPE family (Rv3425), and latent phase (Rv2029c, Rv1813c, Rv1738). We compared the immunogenicity of the four DNA vaccines in C57BL/6j mice. The B21 vaccine stimulated the strongest cellular immune responses, namely Th1/Th17 and CD8+ cytotoxic T lymphocyte responses. It also induced the generation of strengthened effector memory and central memory T cells. In latently infected mice, the B21 vaccine significantly reduced bacterial loads in the spleens and lungs and decreased lung pathology. In conclusion, the B21 DNA vaccine can enhance T cell responses and control the reactivation of LTBI.
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Affiliation(s)
- Shufeng Weng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Jinyi Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Huixia Ma
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Jingyu Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Liqiu Jia
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanmin Wan
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peng Cui
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiaoling Ruan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Lingyun Shao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Honghai Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China,*Correspondence: Ying Xu, ; Wenhong Zhang,
| | - Ying Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China,Shanghai Huashen Institute of Microbes and Infections, Shanghai, China,*Correspondence: Ying Xu, ; Wenhong Zhang,
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8
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Cheng P, Xue Y, Wang J, Jia Z, Wang L, Gong W. Evaluation of the consistence between the results of immunoinformatics predictions and real-world animal experiments of a new tuberculosis vaccine MP3RT. Front Cell Infect Microbiol 2022; 12:1047306. [PMID: 36405961 PMCID: PMC9666678 DOI: 10.3389/fcimb.2022.1047306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/17/2022] [Indexed: 01/24/2023] Open
Abstract
Background Our previous study developed a novel peptide-based vaccine, MP3RT, to fight against tuberculosis (TB) infection in a mouse model. However, the consistency between the immunoinformatics predictions and the results of real-world animal experiments on the MP3RT vaccine remains unclear. Method In this study, we predicted the antigenicity, immunogenicity, physicochemical parameters, secondary structure, and tertiary structure of MP3RT using bioinformatics technologies. The immune response properties of the MP3RT vaccine were then predicted using the C-ImmSim server. Finally, humanized mice were used to verify the characteristics of the humoral and cellular immune responses induced by the MP3RT vaccine. Results MP3RT is a non-toxic and non-allergenic vaccine with an antigenicity index of 0.88 and an immunogenicity index of 0.61, respectively. Our results showed that the MP3RT vaccine contained 53.36% α-helix in the secondary structure, and the favored region accounted for 98.22% in the optimized tertiary structure. The binding affinities of the MP3RT vaccine to the human leukocyte antigen (HLA)-DRB1*01:01 allele, toll-like receptor-2 (TLR-2), and TLR-4 receptors were -1234.1 kcal/mol, -1066.4 kcal/mol, and -1250.4 kcal/mol, respectively. The results of the C-ImmSim server showed that the MP3RT vaccine could stimulate T and B cells to produce immune responses, such as high levels of IgM and IgG antibodies, IFN-γ, TNF-α, and IL-2 cytokines. Results from real-world animal experiments showed that the MP3RT vaccine could stimulate the humanized mice to produce high levels of IgG and IgG2a antibodies and IFN-γ+ T lymphocytes. Furthermore, the levels of IFN-γ, IL-2, and IL-6 cytokines in mice immunized with the MP3RT vaccine were significantly higher than those in the control group. Conclusion MP3RT is a highly antigenic and immunogenic potential vaccine that can effectively induce Th1-type immune responses in silico analysis and animal experiments. This study lays the foundation for evaluating the value of computational tools and immunoinformatic techniques in reverse vaccinology research.
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Affiliation(s)
- Peng Cheng
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
- Hebei North University, Zhangjiakou, Hebei, China
| | - Yong Xue
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Jie Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Zaixing Jia
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
- Cangzhou Hospital of Integrated Traditional Chinese and Western Medicine, Cangzhou, Hebei, China
| | - Liang Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
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9
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Investigating a putative transcriptional regulatory protein encoded by Rv1719 gene of Mycobacterium tuberculosis. Protein J 2022; 41:424-433. [PMID: 35715720 DOI: 10.1007/s10930-022-10062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/18/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, demonstrates immense plasticity with which it adapts to a highly dynamic and hostile host environment. This is facilitated by a web of signalling pathways constantly modulated by a multitude of proteins that regulate the flow of genetic information inside the pathogen. Transcription factors (TFs) belongs to one such family of proteins that modulate the signalling by regulating the abundance of proteins at the transcript level. In the current study, we have characterized the putative transcriptional regulatory protein encoded by the Rv1719 gene of Mycobacterium tuberculosis. This TF belongs to the IclR family of proteins with orthologs found in both bacterial and archaeal species. We cloned the Rv1719 gene into the pET28a expression vector and performed heterologous expression of the recombinant protein with E coli as the host. Further, optimization of the purification protocol by affinity chromatography and characterization of proteins for their functional viability has been demonstrated using various biochemical and/or biophysical approaches. Scale-up of purification yielded approximately 30 mg of ~ 28 kDa protein per litre of culture. In-silico protein domain analysis of Rv1719 protein predicted the presence of the helix-turn-helix (HTH) domain suggesting its ability to bind DNA sequence and modulate transcription; a hallmark of a transcriptional regulatory protein. Further, by performing electrophoretic mobility shift assay (EMSA) we demonstrated that the protein binds to a specific DNA fragment harboring the probable binding site of one of the predicted promoters.
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10
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Gong W, Pan C, Cheng P, Wang J, Zhao G, Wu X. Peptide-Based Vaccines for Tuberculosis. Front Immunol 2022; 13:830497. [PMID: 35173740 PMCID: PMC8841753 DOI: 10.3389/fimmu.2022.830497] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis. As a result of the coronavirus disease 2019 (COVID-19) pandemic, the global TB mortality rate in 2020 is rising, making TB prevention and control more challenging. Vaccination has been considered the best approach to reduce the TB burden. Unfortunately, BCG, the only TB vaccine currently approved for use, offers some protection against childhood TB but is less effective in adults. Therefore, it is urgent to develop new TB vaccines that are more effective than BCG. Accumulating data indicated that peptides or epitopes play essential roles in bridging innate and adaptive immunity and triggering adaptive immunity. Furthermore, innovations in bioinformatics, immunoinformatics, synthetic technologies, new materials, and transgenic animal models have put wings on the research of peptide-based vaccines for TB. Hence, this review seeks to give an overview of current tools that can be used to design a peptide-based vaccine, the research status of peptide-based vaccines for TB, protein-based bacterial vaccine delivery systems, and animal models for the peptide-based vaccines. These explorations will provide approaches and strategies for developing safer and more effective peptide-based vaccines and contribute to achieving the WHO's End TB Strategy.
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Affiliation(s)
- Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Chao Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Peng Cheng
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
- Hebei North University, Zhangjiakou City, China
| | - Jie Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
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Medley J, Goff A, Bettencourt PJG, Dare M, Cole L, Cantillon D, Waddell SJ. Dissecting the Mycobacterium bovis BCG Response to Macrophage Infection to Help Prioritize Targets for Anti-Tuberculosis Drug and Vaccine Discovery. Vaccines (Basel) 2022; 10:vaccines10010113. [PMID: 35062774 PMCID: PMC8780277 DOI: 10.3390/vaccines10010113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
New strategies are required to reduce the worldwide burden of tuberculosis. Intracellular survival and replication of Mycobacterium tuberculosis after macrophage phagocytosis is a fundamental step in the complex host–pathogen interactions that lead to granuloma formation and disease. Greater understanding of how the bacterium survives and thrives in these environments will inform novel drug and vaccine discovery programs. Here, we use in-depth RNA sequencing of Mycobacterium bovis BCG from human THP-1 macrophages to describe the mycobacterial adaptations to the intracellular environment. We identify 329 significantly differentially regulated genes, highlighting cholesterol catabolism, the methylcitrate cycle and iron homeostasis as important for mycobacteria inside macrophages. Examination of multi-functional gene families revealed that 35 PE/PPE genes and five cytochrome P450 genes were upregulated 24 h after infection, highlighting pathways of potential significance. Comparison of the intracellular transcriptome to gene essentiality and immunogenicity studies identified 15 potential targets that are both required for intracellular survival and induced on infection, and eight upregulated genes that have been demonstrated to be immunogenic in TB patients. Further insight into these new and established targets will support drug and vaccine development efforts.
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Affiliation(s)
- Jamie Medley
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Aaron Goff
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Paulo J. G. Bettencourt
- Faculty of Medicine, Catholic University of Portugal, 1649-023 Lisbon, Portugal;
- Center for Interdisciplinary Research in Health, Catholic University of Portugal, 1649-023 Lisbon, Portugal
| | - Madelaine Dare
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Liam Cole
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Daire Cantillon
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
| | - Simon J. Waddell
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK; (J.M.); (A.G.); (M.D.); (L.C.); (D.C.)
- Correspondence:
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12
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Chiwala G, Liu Z, Mugweru JN, Wang B, Khan SA, Bate PNN, Yusuf B, Hameed HMA, Fang C, Tan Y, Guan P, Hu J, Tan S, Liu J, Zhong N, Zhang T. A recombinant selective drug-resistant M. bovis BCG enhances the bactericidal activity of a second-line anti-tuberculosis regimen. Biomed Pharmacother 2021; 142:112047. [PMID: 34426260 DOI: 10.1016/j.biopha.2021.112047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022] Open
Abstract
Drug-resistant tuberculosis (DR-TB) poses a new threat to global health; to improve the treatment outcome, therapeutic vaccines are considered the best chemotherapy adjuvants. Unfortunately, there is no therapeutic vaccine approved against DR-TB. Our study assessed the therapeutic efficacy of a recombinant drug-resistant BCG (RdrBCG) vaccine in DR-TB. We constructed the RdrBCG overexpressing Ag85B and Rv2628 by selecting drug-resistant BCG strains and transformed them with plasmid pEBCG or pIBCG to create RdrBCG-E and RdrBCG-I respectively. Following successful stability testing, we tested the vaccine's safety in severe combined immune deficient (SCID) mice that lack both T and B lymphocytes plus immunoglobulins. Finally, we evaluated the RdrBCG's therapeutic efficacy in BALB/c mice infected with rifampin-resistant M. tuberculosis and treated with a second-line anti-TB regimen. We obtained M. bovis strains which were resistant to several second-line drugs and M. tuberculosis resistant to rifampin. Notably, the exogenously inserted genes were lost in RdrBCG-E but remained stable in the RdrBCG-I both in vitro and in vivo. When administered adjunct to a second-line anti-TB regimen in a murine model of DR-TB, the RdrBCG-I lowered lung M. tuberculosis burden by 1 log10. Furthermore, vaccination with RdrBCG-I adjunct to chemotherapy minimized lung tissue pathology in mice. Most importantly, the RdrBCG-I showed almost the same virulence as its parent BCG Tice strain in SCID mice. Our findings suggested that the RdrBCG-I was stable, safe and effective as a therapeutic vaccine. Hence, the "recombinant" plus "drug-resistant" BCG strategy could be a useful concept for developing therapeutic vaccines against DR-TB.
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MESH Headings
- Amikacin/pharmacology
- Amikacin/therapeutic use
- Animals
- Antigens, Bacterial/biosynthesis
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Antitubercular Agents/pharmacology
- Antitubercular Agents/therapeutic use
- BCG Vaccine/biosynthesis
- BCG Vaccine/genetics
- BCG Vaccine/immunology
- BCG Vaccine/therapeutic use
- Disease Models, Animal
- Drug Resistance, Bacterial/genetics
- Levofloxacin/pharmacology
- Levofloxacin/therapeutic use
- Mice, Inbred BALB C
- Mice, SCID
- Mycobacterium bovis/chemistry
- Mycobacterium bovis/drug effects
- Mycobacterium bovis/genetics
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/pathogenicity
- Plasmids
- Prothionamide/pharmacology
- Prothionamide/therapeutic use
- Pyrazinamide/pharmacology
- Pyrazinamide/therapeutic use
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/pathology
- Tuberculosis, Pulmonary/prevention & control
- Vaccines, Synthetic/biosynthesis
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/therapeutic use
- Virulence
- Mice
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Affiliation(s)
- Gift Chiwala
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
| | - Julius N Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, Embu 60100, Kenya
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shahzad Akbar Khan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China
| | - Petuel Ndip Ndip Bate
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China
| | - Buhari Yusuf
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou 510530, China; Guangzhou National Laboratory, Guangzhou 510320, China.
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13
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Sharma S, Sharma M. Proline-Glutamate/Proline-Proline-Glutamate (PE/PPE) proteins of Mycobacterium tuberculosis: The multifaceted immune-modulators. Acta Trop 2021; 222:106035. [PMID: 34224720 DOI: 10.1016/j.actatropica.2021.106035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022]
Abstract
The PE/PPE proteins encoded by seven percent (7%) of Mycobacterium tuberculosis (Mtb) genome are the chief constituents to pathogen's virulence reservoir. The fact that these genes have evolved along ESX secretory system in pathogenic Mtb strains make their investigation very intriguing. There is lot of speculation about the prominent role of these proteins at host pathogen interface and in disease pathogenesis. Nevertheless, the exact function of PE/PPE proteins still remains a mystery which calls for further research targeting these proteins. This article is an effort to document all the facts known so far with regard to these unique proteins which involves their origin, evolution, transcriptional control, and most important their role as host immune-modulators. Our understanding strongly points towards the versatile nature of these PE/PPE proteins as Mtb's host immune sensors and as decisive factors in shaping the outcome of infection. Further investigation on these proteins will surely pave way for newer and effective vaccines and therapeutics to control Tuberculosis (TB).
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Affiliation(s)
- Sadhna Sharma
- DS Kothari Central Interdisciplinary Research Centre and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
| | - Monika Sharma
- DS Kothari Central Interdisciplinary Research Centre and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
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14
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Arega AM, Pattanaik KP, Nayak S, Mahapatra RK. Computational discovery and ex-vivo validation study of novel antigenic vaccine candidates against tuberculosis. Acta Trop 2021; 217:105870. [PMID: 33636152 DOI: 10.1016/j.actatropica.2021.105870] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 12/26/2022]
Abstract
Tuberculosis (TB) is a complex infectious bacterial disease, which has evolved with highly successful mechanisms to interfere with host defenses and existing classes of antibiotics to resist eradication. The single obtainable TB vaccine, Bacille Calmette-Guerin (BCG) has failed to provide regular defense for respiratory TB in adults. In this study, a bioinformatics and immunoinformatics approach was applied on Mycobacterium tuberculosis (Mtb) H37Rv proteomes to discover the potential subunit vaccine candidates that elicit both tuberculosis-specific T-cells and B-cell immune response. A total of 4049 proteins of MtbH37RvMtbH37Rv were retrieved and subjected to in silico sequence-based analysis. Finally, five (P9WL69 (Rv2599), P9WIG1 (Rv0747), P9WLQ1 (Rv1987), O53608 (Rv0063), O06624 (Rv1566c)) novel putative proteins were selected. Among the five putative antigenic vaccine candidates, P9WL69 protein was selected for the ex-vivo validation study. The P9WL69 protein encoding gene was amplified and cloned on pET21b vector. The success of the recombinant clone (pET21b-RV2599) was confirmed by colony PCR, insert release test and sequencing. Furthermore, the identified epitopes of the P9WL69 protein were considered for in silico docking and molecular dynamics simulation study using Toll-like Receptors (TLRs) (TLR-2, TLR-4, TLR-9), Mannose receptor, and Myeloid differentiation 88 (MYD88) to understand their binding affinity towards the development of immunogenic vaccines against tuberculosis.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, India; National Veterinary Institute, Debre Zeit, Ethiopia
| | | | - Sasmita Nayak
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, India
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15
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Gong W, Liang Y, Mi J, Jia Z, Xue Y, Wang J, Wang L, Zhou Y, Sun S, Wu X. Peptides-Based Vaccine MP3RT Induced Protective Immunity Against Mycobacterium Tuberculosis Infection in a Humanized Mouse Model. Front Immunol 2021; 12:666290. [PMID: 33981313 PMCID: PMC8108698 DOI: 10.3389/fimmu.2021.666290] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/06/2021] [Indexed: 12/25/2022] Open
Abstract
Background Tuberculosis (TB) is still a global infectious disease that seriously threatens human beings. The only licensed TB vaccine Bacille Calmette-Guérin (BCG)’s protective efficacy varies significantly among populations and regions. It is very urgent to develop more effective vaccines. Methods In this study, eleven candidate proteins of Mycobacterium tuberculosis were selected to predict peptides with high-affinity binding capacity for the HLA-DRB1*01:01 molecule. The immunodominant peptides were identified with the enzyme-linked immunospot assay (ELISPOT) and linked in silico to result in a novel polypeptide vaccine in Escherichia coli cells. The vaccine’s protective efficacy was evaluated in humanized and wild-type C57BL/6 mice. The potential immune protective mechanisms were explored with Enzyme-linked Immunosorbent Assay (ELISA), flow cytometry, and ELISPOT. Results Six immunodominant peptides screened from 50 predicted peptides were used to construct a new polypeptide vaccine named MP3RT. After challenge with M. tuberculosis, the colony-forming units (CFUs), lung lesion area, and the number of inflammatory cells in humanized mice rather than wild-type mice vaccinated with MP3RT were significantly lower than these in mice immunized with PBS. The humanized mice vaccinated with MP3RT revealed significant increases in IFN-γ cytokine production, IFN-γ+ T lymphocytes, CD3+IFN-γ+ T lymphocytes, and the MP3RT-specific IgG antibody. Conclusions Taken together, MP3RT is a promising peptides-based TB vaccine characterized by inducing high levels of IFN-γ and CD3+IFN-γ+ T lymphocytes in humanized mice. These new findings will lay a foundation for the development of peptides-based vaccines against TB.
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Affiliation(s)
- Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yan Liang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jie Mi
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Zaixing Jia
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China.,Graduate School, Hebei North University, Zhangjiakou, China
| | - Yong Xue
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jie Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Lan Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute for Tuberculosis Research, 8th Medical Center, Chinese People's Liberation Army General Hospital, Beijing, China
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16
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Sundar S, Thangamani L, Piramanayagam S. Computational identification of significant immunogenic epitopes of the putative outer membrane proteins from Mycobacterium tuberculosis. J Genet Eng Biotechnol 2021; 19:48. [PMID: 33779881 PMCID: PMC8006519 DOI: 10.1186/s43141-021-00148-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/15/2021] [Indexed: 12/20/2022]
Abstract
Novel vaccines are required to effectively combat the epidemic spread of tuberculosis. Using in silico approaches, this study focuses on prediction of potential B cell and T cell binding immunogenic epitopes for 30 putative outer membrane proteins of Mtb. Among these, certain immunodominant epitopes of Rv0172, Rv0295c, Rv1006, Rv2264c, and Rv2525c were found, which are capable of binding B-cell and a maximum number of MHC alleles. The selected immunodominant epitopes were screened for their allergenic and antigenic properties, their percentage identity against the human proteome and their structural properties. Further, the binding efficacy of the immunodominant epitopes of Rv0295c and Rv1006 with HLA-DRB1*04:01 was analyzed using molecular docking and molecular dynamics studies. Hence, the in silico-derived immunogenic peptides (epitopes) could potentially be used for the design of subunit vaccines against tuberculosis.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India.
| | - Lokesh Thangamani
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
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Systematic Evaluation of Mycobacterium tuberculosis Proteins for Antigenic Properties Identifies Rv1485 and Rv1705c as Potential Protective Subunit Vaccine Candidates. Infect Immun 2021; 89:IAI.00585-20. [PMID: 33318140 PMCID: PMC8097267 DOI: 10.1128/iai.00585-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/27/2020] [Indexed: 01/07/2023] Open
Abstract
The lack of efficacious vaccines against Mycobacterium tuberculosis (MTB) infection is a limiting factor in the prevention and control of tuberculosis (TB), the leading cause of death from an infectious agent. Improvement or replacement of the BCG vaccine with one that reliably protects all age groups is urgent. The lack of efficacious vaccines against Mycobacterium tuberculosis (MTB) infection is a limiting factor in the prevention and control of tuberculosis (TB), the leading cause of death from an infectious agent. Improvement or replacement of the BCG vaccine with one that reliably protects all age groups is urgent. Concerns exist that antigens currently being evaluated are too homogeneous. To identify new protective antigens, we screened 1,781 proteins from a high-throughput proteome-wide protein purification study for antigenic activity. Forty-nine antigens (34 previously unreported) induced antigen-specific gamma interferon (IFN-γ) release from peripheral blood mononuclear cells (PBMCs) derived from 4,452 TB and suspected TB patients and 167 healthy donors. Three (Rv1485, Rv1705c, and Rv1802) of the 20 antigens evaluated in a BALB/c mouse challenge model showed protective efficacy, reducing lung CFU counts by 66.2%, 75.8%, and 60%, respectively. Evaluation of IgG2a/IgG1 ratios and cytokine release indicated that Rv1485 and Rv1705c induce a protective Th1 immune response. Epitope analysis of PE/PPE protein Rv1705c, the strongest candidate, identified a dominant epitope in its extreme N-terminal domain accounting for 90% of its immune response. Systematic preclinical assessment of antigens Rv1485 and Rv1705c is warranted.
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18
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Jagadeb M, Pattanaik KP, Rath SN, Sonawane A. Identification and evaluation of immunogenic MHC-I and MHC-II binding peptides from Mycobacterium tuberculosis. Comput Biol Med 2020; 130:104203. [PMID: 33450502 DOI: 10.1016/j.compbiomed.2020.104203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022]
Abstract
Due to several limitations of the only available BCG vaccine, to generate adequate protective immune responses, it is important to develop potent and cost-effective vaccines against tuberculosis (TB). In this study, we have used an immune-informatics approach to identify potential peptide based vaccine targets against TB. The proteome of Mycobacterium tuberculosis (Mtb), the causative agent of TB, was analyzed for secretory or surface localized antigenic proteins as potential vaccine candidates. The T- and B-cell epitopes as well as MHC molecule binding efficiency were identified and mapped in the modelled structures of the selected proteins. Based on antigenicity score and molecular dynamic simulation (MD) studies two peptides namely Pep-9 and Pep-15 were analyzed, modelled and docked with MHC-I and MHC-II structures. Both peptides exhibited no cytotoxicity and were able to induce proinflammatory cytokine secretion in stimulated macrophages. The molecular docking, MD and in-vitro studies of the predicted B and T-cell epitopes of Pep-9 and Pep-15 peptides with the modelled MHC structures exhibited strong binding affinity and antigenic properties, suggesting that the complex is stable, and that these peptides can be considered as a potential candidates for the development of vaccine against TB.
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Affiliation(s)
- Manaswini Jagadeb
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India.
| | | | - Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.
| | - Avinash Sonawane
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India; Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore (IIT Indore), Simrol, Madhya Pradesh, India.
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19
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Identification and in silico functional prediction of lineage-specific SNPs distributed in DosR-related proteins and resuscitation-promoting factor proteins of Mycobacterium tuberculosis. Heliyon 2020; 6:e05744. [PMID: 33364506 PMCID: PMC7753917 DOI: 10.1016/j.heliyon.2020.e05744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/21/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
One-third of the world population is infected by Mycobacterium tuberculosis, which may persist in the latent or dormant state. Bacteria can shift to dormancy when encountering harsh conditions such as low oxygen, nutrient starvation, high acidity and host immune defenses. Genes related to the dormancy survival regulator (DosR) regulon are responsible for the inhibition of aerobic respiration and replication, which is required to enter dormancy. Conversely, resuscitation-promoting factor (rpf) proteins participate in reactivation from dormancy and the development of active tuberculosis (TB). Many DosR regulon and rpf proteins are immunodominant T cell antigens that are highly expressed in latent TB infection. They could serve as TB vaccine candidates and be used for diagnostic development. We explored the genetic polymorphisms of 50 DosR-related genes and 5 rpf genes among 1,170 previously sequenced clinical M. tuberculosis genomes. Forty-three lineage- or sublineage-specific nonsynonymous single nucleotide polymorphisms (nsSNPs) were identified. Ten nsSNPs were specific to all Mtb isolates belonging to lineage 1 (L1). Two common sublineages, the Beijing family (L2.2) and EAI2 (L1.2.1), differed at as many as 26 lineage- or sublineage-specific SNPs. DosR regulon genes related to membrane proteins and the rpf family possessed mean dN/dS ratios greater than one, suggesting that they are under positive selection. Although the T cell epitope regions of DosR-related and rpf antigens were quite conserved, we found that the epitopes in L1 had higher rates of genetic polymorphisms than the other lineages. Some mutations in immunogenic epitopes of the antigens were specific to particular M. tuberculosis lineages. Therefore, the genetic diversity of the DosR regulon and rpf proteins might impact the adaptation of M. tuberculosis to the dormant state and the immunogenicity of latency antigens, which warrants further investigation.
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Sefidi-Heris Y, Jahangiri A, Mokhtarzadeh A, Shahbazi MA, Khalili S, Baradaran B, Mosafer J, Baghbanzadeh A, Hejazi M, Hashemzaei M, Hamblin MR, Santos HA. Recent progress in the design of DNA vaccines against tuberculosis. Drug Discov Today 2020; 25:S1359-6446(20)30345-7. [PMID: 32927065 DOI: 10.1016/j.drudis.2020.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/31/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022]
Abstract
Current tuberculosis (TB) vaccines have some disadvantages and many efforts have been undertaken to produce effective TB vaccines. As a result of their advantages, DNA vaccines are promising future vaccine candidates. This review focuses on the design and delivery of novel DNA-based vaccines against TB.
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Affiliation(s)
- Youssof Sefidi-Heris
- Department of Biology, College of Sciences, Shiraz University, 7146713565, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, 193955487, Tehran, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran.
| | - Mohammad-Ali Shahbazi
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland; Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC), Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran.
| | - Saeed Khalili
- Department of Biology Sciences, Faculty of Sciences, Shahid Rajaee Teacher Training University, 1678815811, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran
| | - Jafar Mosafer
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, 9516915169, Torbat Heydariyeh, Iran; Nanotechnology Research Center, School of Pharmacy, Mashhad University of Medical Sciences, 9196773117, Mashhad, Iran
| | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran
| | - Maryam Hejazi
- Immunology Research Center, Tabriz University of Medical Sciences, 5166614731, Tabriz, Iran
| | - Mahmoud Hashemzaei
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Zabol University of Medical Sciences, 9861615881, Zabol, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa.
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland; Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki FI-00014, Finland.
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21
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Narvskaya O, Starkova D, Levi D, Alexandrova N, Molchanov V, Chernyaeva E, Vyazovaya A, Mushkin A, Zhuravlev V, Solovieva N, Vishnevskiy B, Mokrousov I. First insight into the whole-genome sequence variations in Mycobacterium bovis BCG-1 (Russia) vaccine seed lots and their progeny clinical isolates from children with BCG-induced adverse events. BMC Genomics 2020; 21:567. [PMID: 32811436 PMCID: PMC7437937 DOI: 10.1186/s12864-020-06973-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background The only licensed live Bacille Calmette-Guérin (BCG) vaccine used to prevent severe childhood tuberculosis comprises genetically divergent strains with variable protective efficacy and rates of BCG-induced adverse events. The whole-genome sequencing (WGS) allowed evaluating the genome stability of BCG strains and the impact of spontaneous heterogeneity in seed and commercial lots on the efficacy of BCG-vaccines in different countries. Our study aimed to assess sequence variations and their putative effects on genes and protein functions in the BCG-1 (Russia) seed lots compared to their progeny isolates available from immunocompetent children with BCG-induced disease (mainly, osteitis). Results Based on the WGS data, we analyzed the links between seed lots 361, 367, and 368 used for vaccine manufacture in Russia in different periods, and their nine progeny isolates recovered from immunocompetent children with BCG-induced disease. The complete catalog of variants in genes relative to the reference genome (GenBank: CP013741) included 4 synonymous and 8 nonsynonymous single nucleotide polymorphisms, and 3 frameshift deletions. Seed lot 361 shared variants with 2 of 6 descendant isolates that had higher proportions of such polymorphisms in several genes, including ppsC, eccD5, and eccA5 involved in metabolism and cell wall processes and reportedly associated with virulence in mycobacteria. One isolate preserved variants of its parent seed lot 361 without gain of further changes in the sequence profile within 14 years. Conclusions The background genomic information allowed us for the first time to follow the BCG diversity starting from the freeze-dried seed lots to descendant clinical isolates. Sequence variations in several genes of seed lot 361 did not alter the genomic stability and viability of the vaccine and appeared accumulated in isolates during the survival in the human organism. The impact of the observed variations in the context of association with the development of BCG-induced disease should be evaluated in parallel with the immune status and host genetics. Comparative genomic studies of BCG seed lots and their descendant clinical isolates represent a beneficial approach to better understand the molecular bases of efficacy and adverse events during the long-term survival of BCG in the host organism.
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Affiliation(s)
- Olga Narvskaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia. .,St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, 191036, Russia.
| | - Daria Starkova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia
| | - Diana Levi
- Scientific Center for Expert Evaluation of Medical Products, Moscow, 127051, Russia
| | - Natalia Alexandrova
- Scientific Center for Expert Evaluation of Medical Products, Moscow, 127051, Russia
| | - Vladimir Molchanov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia. .,Present address: Van Andel Institute, Grand Rapids, MI, 49503-2518, USA.
| | | | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia
| | - Alexander Mushkin
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, 191036, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, 191036, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, 191036, Russia
| | - Boris Vishnevskiy
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, 191036, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia
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22
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Coskun FS, Srivastava S, Raj P, Dozmorov I, Belkaya S, Mehra S, Golden NA, Bucsan AN, Chapagain ML, Wakeland EK, Kaushal D, Gumbo T, van Oers NSC. sncRNA-1 Is a Small Noncoding RNA Produced by Mycobacterium tuberculosis in Infected Cells That Positively Regulates Genes Coupled to Oleic Acid Biosynthesis. Front Microbiol 2020; 11:1631. [PMID: 32849337 PMCID: PMC7399025 DOI: 10.3389/fmicb.2020.01631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Nearly one third of the world’s population is infected with Mycobacterium tuberculosis (Mtb). While much work has focused on the role of different Mtb encoded proteins in pathogenesis, recent studies have revealed that Mtb also transcribes many noncoding RNAs whose functions remain poorly characterized. We performed RNA sequencing and identified a subset of Mtb H37Rv-encoded small RNAs (<30 nts in length) that were produced in infected macrophages. Designated as smaller noncoding RNAs (sncRNAs), three of these predominated the read counts. Each of the three, sncRNA-1, sncRNA-6, and sncRNA-8 had surrounding sequences with predicted stable secondary RNA stem loops. Site-directed mutagenesis of the precursor sequences suggest the existence of a hairpin loop dependent RNA processing mechanism. A functional assessment of sncRNA-1 suggested that it positively regulated two mycobacterial transcripts involved in oleic acid biosynthesis. Complementary loss- and gain- of-function approaches revealed that sncRNA-1 positively supports Mtb growth and survival in nutrient-depleted cultures as well as in infected macrophages. Overall, the findings reveal that Mtb produces sncRNAs in infected cells, with sncRNA-1 modulating mycobacterial gene expression including genes coupled to oleic acid biogenesis.
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Affiliation(s)
- Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Serkan Belkaya
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Smriti Mehra
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Nadia A Golden
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Allison N Bucsan
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Moti L Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Deepak Kaushal
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States.,Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Nicolai S C van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, United States
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23
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Mycobacterium tuberculosis Rv2005c Induces Dendritic Cell Maturation and Th1 Responses and Exhibits Immunotherapeutic Activity by Fusion with the Rv2882c Protein. Vaccines (Basel) 2020; 8:vaccines8030370. [PMID: 32664238 PMCID: PMC7564171 DOI: 10.3390/vaccines8030370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
Immunotherapy represents a promising approach for improving current antibiotic treatments through the engagement of the host’s immune system. Latency-associated antigens have been included as components of multistage subunit tuberculosis vaccines. We first identified Rv2005c, a DosR regulon-encoded protein, as a seroreactive protein. In this study, we found that Rv2005c induced dendritic cell (DC) maturation and Th1 responses, and its expression by Mycobacterium tuberculosis (Mtb) within macrophages was enhanced by treatment with CoCl2, a hypoxia-mimetic agent. T cells activated by Rv2005c-matured DCs induced antimycobacterial activity in macrophages under hypoxic conditions but not under normoxic conditions. However, Rv2005c alone did not exhibit any significant vaccine efficacy in our mouse model. The fusion of Rv2005c to the macrophage-activating protein Rv2882c resulted in significant activation of DCs and antimycobacterial activity in macrophages, which were enhanced under hypoxic conditions. Furthermore, the Rv2882c-Rv2005c fusion protein showed significant adjunctive immunotherapeutic effects and led to the generation of long-lasting, antigen-specific, multifunctional CD4+ T cells that coproduced TNF-α, IFN-γ and IL-2 in the lungs of our established mouse model. Overall, these results provide a novel fusion protein with immunotherapeutic potential as adjunctive chemotherapy for tuberculosis.
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24
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Vierboom MPM, Chenine AL, Darrah PA, Vervenne RAW, Boot C, Hofman SO, Sombroek CC, Dijkman K, Khayum MA, Stammes MA, Haanstra KG, Hoffmann C, Schmitt D, Silvestre N, White AG, Borish HJ, Seder RA, Ouaked N, Leung-Theung-Long S, Inchauspé G, Anantha R, Limbach M, Evans TG, Casimiro D, Lempicki M, Laddy DJ, Bonavia A, Verreck FAW. Evaluation of heterologous prime-boost vaccination strategies using chimpanzee adenovirus and modified vaccinia virus for TB subunit vaccination in rhesus macaques. NPJ Vaccines 2020; 5:39. [PMID: 32435513 PMCID: PMC7224290 DOI: 10.1038/s41541-020-0189-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/08/2020] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis (TB) still is the principal cause of death from infectious disease and improved vaccination strategies are required to reduce the disease burden and break TB transmission. Here, we investigated different routes of administration of vectored subunit vaccines based on chimpanzee-derived adenovirus serotype-3 (ChAd3) for homologous prime-boosting and modified vaccinia virus Ankara (MVA) for heterologous boosting with both vaccine vectors expressing the same antigens from Mycobacterium tuberculosis (Ag85B, ESAT6, Rv2626, Rv1733, RpfD). Prime-boost strategies were evaluated for immunogenicity and protective efficacy in highly susceptible rhesus macaques. A fully parenteral administration regimen was compared to exclusive respiratory mucosal administration, while parenteral ChAd3-5Ag prime-boosting and mucosal MVA-5Ag boosting were applied as a push-and-pull strategy from the periphery to the lung. Immune analyses corroborated compartmentalized responses induced by parenteral versus mucosal vaccination. Despite eliciting TB-specific immune responses, none of the investigational regimes conferred a protective effect by standard readouts of TB compared to non-vaccinated controls, while lack of protection by BCG underpinned the stringency of this non-human primate test modality. Yet, TB manifestation after full parenteral vaccination was significantly less compared to exclusive mucosal vaccination.
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Affiliation(s)
- Michel P M Vierboom
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | - Patricia A Darrah
- 3Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Richard A W Vervenne
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Charelle Boot
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Sam O Hofman
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Claudia C Sombroek
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Karin Dijkman
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Mohamed A Khayum
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Marieke A Stammes
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Krista G Haanstra
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Chantal Hoffmann
- 4Infectious Diseases Department, Transgene SA, ABL Europe Building, Lyon, France
| | - Doris Schmitt
- 4Infectious Diseases Department, Transgene SA, ABL Europe Building, Lyon, France
| | - Nathalie Silvestre
- 4Infectious Diseases Department, Transgene SA, ABL Europe Building, Lyon, France
| | - Alexander G White
- 5Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - H Jacob Borish
- 5Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Robert A Seder
- 3Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | | | | | - Geneviève Inchauspé
- 4Infectious Diseases Department, Transgene SA, ABL Europe Building, Lyon, France
| | | | | | | | | | - Maria Lempicki
- 7International AIDS Vaccine Initiative, New York, NY USA
| | | | | | - Frank A W Verreck
- 1Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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25
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Potential Genes Related to Levofloxacin Resistance in Mycobacterium tuberculosis Based on Transcriptome and Methylome Overlap Analysis. J Mol Evol 2020; 88:202-209. [PMID: 31919584 PMCID: PMC6989609 DOI: 10.1007/s00239-019-09926-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023]
Abstract
Drug-resistant Mycobacterium tuberculosis (M. tuberculosis) has become an increasingly serious public health problem and has complicated tuberculosis (TB) treatment. Levofloxacin (LOF) is an ideal anti-tuberculosis drug in clinical applications. However, the detailed molecular mechanisms of LOF-resistant M. tuberculosis in TB treatment have not been revealed. Our study performed transcriptome and methylome sequencing to investigate the potential biological characteristics of LOF resistance in M. tuberculosis H37Rv. In the transcriptome analysis, 953 differentially expressed genes (DEGs) were identified; 514 and 439 DEGs were significantly downregulated and upregulated in the LOF-resistant group and control group, respectively. The KEGG pathway analysis revealed that 97 pathways were enriched in this study. In the methylome analysis, 239 differentially methylated genes (DMGs) were identified; 150 and 89 DMGs were hypomethylated and hypermethylated in the LOF-resistant group and control group, respectively. The KEGG pathway analysis revealed that 74 pathways were enriched in this study. The overlap study suggested that 25 genes were obtained. It was notable that nine genes expressed downregulated mRNA and upregulated methylated levels, including pgi, fadE4, php, cyp132, pckA, rpmB1, pfkB, acg, and ctpF, especially cyp132, pckA, and pfkB, which were vital in LOF-resistant M. tuberculosis H37Rv. The overlapping genes between transcriptome and methylome could be essential for studying the molecular mechanisms of LOF-resistant M. tuberculosis H37Rv. These results may provide informative evidence for TB treatment with LOF.
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Tuberculosis diagnosis: algorithm that May discriminate latent from active tuberculosis. Heliyon 2019; 5:e02559. [PMID: 31692671 PMCID: PMC6806400 DOI: 10.1016/j.heliyon.2019.e02559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/08/2019] [Accepted: 09/27/2019] [Indexed: 01/26/2023] Open
Abstract
Diagnosis of tuberculosis still faces a lot of challenges and is one of the priorities in the field of tuberculosis management. Deciphering the complex tuberculosis pathogenicity network could provide biomarkers for diagnosis. We discussed the distribution of HLA-B17, -DQB and -DRB together with QuantiFERON test results in tuberculosis infection. A case control study was done during which a total of 337 subjects were enrolled comprising 227 active tuberculosis (ATB), 46 latent tuberculosis infection (LTBI) and 64 healthy controls (HC). Sequence-specific primer polymerase chain reaction and immune epitope database were used to genotype samples and determine the epitope binding ability of the over-represented alleles respectively. QuantiFERON test was done according to manufacturer's instructions. The peptides HLA-B*5801 and HLA-DRB1*12 and the peptides HLA-B*5802 and HLA-DQB1*03 were found to be associated with latent tuberculosis while the haplotypes DRB1*10-DQB1*02 and DRB1*13-DQB1*06 were found to be associated with active tuberculosis (All p-values≤0.05). The association of HLA-B*5801 and HLA-B*5802 with latent tuberculosis was linked to their ability to bind or not mycobacterial antigens. DRB1*10-DQB1*02 haplotype was found to be over-represented in LTBI compared to ATB (p-value = 0.0015) while DRB1*13-DQB1*06 was found to be under-represented in LTBI compared to ATB (p-value = 0.0335). The DRB1*10-DQB1*02 haplotype was only found in the LTBI when compared with the ATB group. The present study suggests the following algorithm to discriminate LTBI from ATB: QuantiFERON+ and DRB1*10-DQB1*02 haplotype + may indicate LTBI; QuantiFERON+ and DRB1*10-DQB1*02 haplotype - may indicate ATB.
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27
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Van Dis E, Sogi KM, Rae CS, Sivick KE, Surh NH, Leong ML, Kanne DB, Metchette K, Leong JJ, Bruml JR, Chen V, Heydari K, Cadieux N, Evans T, McWhirter SM, Dubensky TW, Portnoy DA, Stanley SA. STING-Activating Adjuvants Elicit a Th17 Immune Response and Protect against Mycobacterium tuberculosis Infection. Cell Rep 2019; 23:1435-1447. [PMID: 29719256 DOI: 10.1016/j.celrep.2018.04.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/09/2018] [Accepted: 03/30/2018] [Indexed: 01/04/2023] Open
Abstract
There are a limited number of adjuvants that elicit effective cell-based immunity required for protection against intracellular bacterial pathogens. Here, we report that STING-activating cyclic dinucleotides (CDNs) formulated in a protein subunit vaccine elicit long-lasting protective immunity to Mycobacterium tuberculosis in the mouse model. Subcutaneous administration of this vaccine provides equivalent protection to that of the live attenuated vaccine strain Bacille Calmette-Guérin (BCG). Protection is STING dependent but type I IFN independent and correlates with an increased frequency of a recently described subset of CXCR3-expressing T cells that localize to the lung parenchyma. Intranasal delivery results in superior protection compared with BCG, significantly boosts BCG-based immunity, and elicits both Th1 and Th17 immune responses, the latter of which correlates with enhanced protection. Thus, a CDN-adjuvanted protein subunit vaccine has the capability of eliciting a multi-faceted immune response that results in protection from infection by an intracellular pathogen.
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Affiliation(s)
- Erik Van Dis
- Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kimberly M Sogi
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chris S Rae
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | - Kelsey E Sivick
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | - Natalie H Surh
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | | | - David B Kanne
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | - Ken Metchette
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | - Justin J Leong
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | - Jacob R Bruml
- Aduro Biotech, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA
| | - Vivian Chen
- School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kartoosh Heydari
- LKS Flow Cytometry Core, Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Tom Evans
- Vaccitech Limited, King Charles House, Park End Street, Oxford OX1 1JD, UK
| | | | | | - Daniel A Portnoy
- Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, CA 94720, USA; School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sarah A Stanley
- Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, CA 94720, USA; School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, Berkeley, CA 94720, USA.
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28
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Fihiruddin, Artama WT, Wibawa T, Mertaniasih NM. EXPRESSION OF IMMUNOGLOBULIN, GRANZYME-B AND PERFORIN AGAINST Ag85A AND Ag85B PROTEINS OF MYCOBACTERIUM TUBERCULOSIS IN BALB/C MICE. Afr J Infect Dis 2019; 13:13-20. [PMID: 31384722 PMCID: PMC6675963 DOI: 10.21010/ajid.v13i2.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/21/2019] [Accepted: 07/03/2019] [Indexed: 11/24/2022] Open
Abstract
Background: Ag85 is a protein that may maintain survival of M. tuberculosis in intracellular parts of host cells and is considered as a virulence factor. The expression of Ag85 protein can stimulate proliferation and differentiation of B- cells and T-cells in patients with tuberculosis. This research aimed to determine the ability of Ag85A and Ag85B proteins in activating the response of antibodies, granzyme-B and perforin in Balb/c mice. Materials and Methods: Twenty-five male Balb/c mice were assigned into five groups. Group I was treated with adjuvant, group II with Bacillus Calmette-Guerin (BCG) vaccine, group III with a combination of BCG and Ag85A, group IV with a combination of BCG and Ag85B and group V with a combination of BCG, Ag85A and Ag85B. Concentrations of immunoglobulin G, granzyme-B and perforin were examined using ELISA and the number of CD8+ T-cells and NK T-cells were checked by flow cytometry. Results: The highest concentration of immunoglobulin G was found in group V with 62.49±5.4327 ng/ml. The highest mean number of CD8+ T-cells, NK T-cells, granzyme-B and perforin was found in group IV with 4.32%, 1.03%, 35.11±1.7789 pg/ml and 6.19±0.2235 pg/ml, respectively. The results of One-Way ANOVA test showed that there were significant differences in immunoglobulin responses, with p<0.05. The expressions of granzyme-B and perforin were higher in mice treated with combination of BCG and recombinant proteins. Conclusions: Ag85 protein can be combined with the BCG vaccine to improve protection against M. tuberculosis infection.
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Affiliation(s)
- Fihiruddin
- Doctoral Program, Research Center of Biotechnology, Universitas Gadjah Mada, Yogyakarta. Indonesia.,Department of Medical Laboratory Technology, Politeknik Kesehatan Mataram, Indonesia
| | - Wayan Tunas Artama
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta. Indonesia.,One Health/Ecohealth Resource Center, Universitas Gadjah Mada, Yogyakarta. Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta. Indonesia
| | - Ni Made Mertaniasih
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya. Indonesia
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Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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30
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Kyeong HH, Choi Y, Kim HS. GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking. Bioinformatics 2018; 34:469-476. [PMID: 28968726 DOI: 10.1093/bioinformatics/btx589] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 09/15/2017] [Indexed: 01/16/2023] Open
Abstract
Motivation The identification of T-cell epitopes has many profound translational applications in the areas of transplantation, disease diagnosis, vaccine/therapeutic protein development and personalized immunotherapy. While data-driven methods have been widely used for the prediction of peptide binders with notable successes, the structural modeling of peptide binding to MHC molecules is crucial for understanding the underlying molecular mechanism of the immunological processes. Results We developed GradDock, a structure-based method for the rapid and accurate modeling of peptide binding to MHC Class I (pMHC-I). GradDock explicitly models diverse unbound peptides in vacuo and inserts them into the MHC-I groove through a steered gradient descent with a topological correction process. The simulation process yields diverse structural conformations including native-like peptides. We completely revised the Rosetta score terms and developed a new ranking function specifically for pMHC-I. Using the diverse peptides, a linear programming approach is applied to find the optimal weights for the individual Rosetta score terms. Our examination revealed that a refinement of the dihedral angles and a modification of the repulsion can dramatically improve the modeling quality. GradDock is five-times faster than a Rosetta-based docking approach for pMHC-I. We also demonstrate that the predictive capability of GradDock with the re-weighted Rosetta ranking function is consistently more accurate than the Rosetta-based method with the standard Rosetta score (approximately three-times better for a cross-docking set). Availability and implementation GradDock is freely available for academic purposes. The program and the ranking score weights for Rosetta are available at http://bel.kaist.ac.kr/research/GradDock. Contact hskim76@kaist.ac.kr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hyun-Ho Kyeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yoonjoo Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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31
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Meier NR, Jacobsen M, Ottenhoff THM, Ritz N. A Systematic Review on Novel Mycobacterium tuberculosis Antigens and Their Discriminatory Potential for the Diagnosis of Latent and Active Tuberculosis. Front Immunol 2018; 9:2476. [PMID: 30473692 PMCID: PMC6237970 DOI: 10.3389/fimmu.2018.02476] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023] Open
Abstract
Background: Current immunodiagnostic tests for tuberculosis (TB) are based on the detection of an immune response toward mycobacterial antigens injected into the skin or following an in-vitro simulation in interferon gamma-release assays. Both tests have limited sensitivity and are unable to differentiate between tuberculosis infection (LTBI) and active tuberculosis disease (aTB). To overcome this, the use of novel Mycobacterium tuberculosis (M. tuberculosis) stage-specific antigens for the diagnosis of LTBI and aTB has gained interest in recent years. This review summarizes current evidence on novel antigens used for the immunodiagnosis of tuberculosis and discrimination of LTBI and aTB. In addition, results on measured biomarkers after stimulation with novel M. tuberculosis antigens were also reviewed. Methods: A systematic literature review was performed in Pubmed, EMBASE and web of science searching articles from 2000 up until December 2017. Only articles reporting studies in humans using novel antigens were included. Results: Of 1,533 articles screened 34 were included in the final analysis. A wide range of novel antigens expressed during different stages and types of LTBI and aTB have been assessed. M. tuberculosis antigens Rv0081, Rv1733c, Rv1737c, Rv2029c, Rv2031 and Rv2628, all encoded by the dormancy of survival regulon, were among the most widely studied antigens and showed the most promising results. These antigens have been shown to have best potential for differentiating LTBI from aTB. In addition, several studies have shown that the inclusion of cytokines other than IFN-γ can improve sensitivity. Conclusion: There is limited evidence that the inclusion of novel antigens as well as the measurement of other biomarkers than IFN-γ may improve sensitivity and may lead to a discrimination of LTBI from aTB.
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Affiliation(s)
- Noëmi R Meier
- University of Basel Children's Hospital, Mycobacterial Research, Basel, Switzerland.,University of Basel, Faculty of Medicine, Basel, Switzerland
| | - Marc Jacobsen
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Nicole Ritz
- University of Basel Children's Hospital, Mycobacterial Research, Basel, Switzerland.,University of Basel, Faculty of Medicine, Basel, Switzerland.,The Royal Children's Hospital Melbourne, Infectious Disease Unit, Melbourne, VIC, Australia
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32
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Kim WS, Kim JS, Kim HM, Kwon KW, Eum SY, Shin SJ. Comparison of immunogenicity and vaccine efficacy between heat-shock proteins, HSP70 and GrpE, in the DnaK operon of Mycobacterium tuberculosis. Sci Rep 2018; 8:14411. [PMID: 30258084 PMCID: PMC6158166 DOI: 10.1038/s41598-018-32799-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
Antigens (Ags) in Mycobacterium tuberculosis (Mtb) that are constitutively expressed, overexpressed during growth, essential for survival, and highly conserved may be good vaccine targets if they induce the appropriate anti-Mtb Th1 immune response. In this context, stress response-related antigens of Mtb might serve as attractive targets for vaccine development as they are rapidly expressed and are up-regulated during Mtb infection in vivo. Our group recently demonstrated that GrpE, encoded by rv0351 as a cofactor of heat-shock protein 70 (HSP70) in the DnaK operon, is a novel immune activator that interacts with DCs to generate Th1-biased memory T cells in an antigen-specific manner. In this study, GrpE was evaluated as a subunit vaccine in comparison with the well-known HSP70 against the hyper-virulent Mtb Beijing K-strain. Both HSP70- and GrpE-specific effector/memory T cells expanded to a similar extent as those stimulated with ESAT-6 in the lung and spleen of Mtb-infected mice, but GrpE only produced a similar level of IFN-γ to that produced by ESAT-6 stimulation during the late phase and the early phase of Mtb K infection, indicating that GrpE is highly-well recognised by the host immune system as a T cell antigen. Mice immunised with the GrpE subunit vaccine displayed enhanced antigen-specific IFN-γ and serum IgG2c responses along with antigen-specific effector/memory T cell expansion in the lungs. In addition, GrpE-immunisation markedly induced multifunctional Th1-type CD4+ T cells co-expressing IFN-γ, TNF-α, and IL-2 in the lungs of Mtb K-infected mice, whereas HSP70-immunisation induced mixed Th1/Th2 immune responses. GrpE-immunisation conferred a more significant protective effect than that of HSP70-immunisation in terms of bacterial reduction and improved inflammation, accompanied by the remarkable persistence of GrpE-specific multifunctional CD4+ T cells. These results suggest that GrpE is an excellent vaccine antigen component for the development of a multi-antigenic Mtb subunit vaccine by generating Th1-biased memory T cells with multifunctional capacity, and confers durable protection against the highly virulent Mtb K.
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Affiliation(s)
- Woo Sik Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Jong-Seok Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon, South Korea
| | - Hong Min Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Kee Woong Kwon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok-Yong Eum
- Division of Immunopathology and Cellular Immunology, International Tuberculosis Research Center, Changwon, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
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33
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Coler RN, Day TA, Ellis R, Piazza FM, Beckmann AM, Vergara J, Rolf T, Lu L, Alter G, Hokey D, Jayashankar L, Walker R, Snowden MA, Evans T, Ginsberg A, Reed SG. The TLR-4 agonist adjuvant, GLA-SE, improves magnitude and quality of immune responses elicited by the ID93 tuberculosis vaccine: first-in-human trial. NPJ Vaccines 2018; 3:34. [PMID: 30210819 PMCID: PMC6123489 DOI: 10.1038/s41541-018-0057-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/20/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of infectious death worldwide. Development of improved TB vaccines that boost or replace BCG is a major global health goal. ID93 + GLA-SE is a fusion protein TB vaccine candidate combined with the Toll-like Receptor 4 agonist adjuvant, GLA-SE. We conducted a phase 1, randomized, double-blind, dose-escalation clinical trial to evaluate two dose levels of the ID93 antigen, administered intramuscularly alone or in combination with two dose levels of the GLA-SE adjuvant, in 60 BCG-naive, QuantiFERON-negative, healthy adults in the US (ClinicalTrials.gov identifier: NCT01599897). When administered as 3 injections, 28 days apart, all dose levels of ID93 alone and ID93 + GLA-SE demonstrated an acceptable safety profile. All regimens elicited vaccine-specific humoral and cellular responses. Compared with ID93 alone, vaccination with ID93 + GLA-SE elicited higher titers of ID93-specific antibodies, a preferential increase in IgG1 and IgG3 subclasses, and a multifaceted Fc-mediated effector function response. The addition of GLA-SE also enhanced the magnitude and polyfunctional cytokine profile of CD4+ T cells. The data demonstrate an acceptable safety profile and indicate that the GLA-SE adjuvant drives a functional humoral and T-helper 1 type cellular response. A tuberculosis vaccine containing an immunity-potentiating agent stimulated strong immune responses in a first-in-human trial. Tuberculosis (TB) is the world’s foremost cause of infectious disease deaths, yet lacks an effective vaccine for adult humans. Rhea Coler, of the Infectious Disease Research Institute, Seattle, and a team from the United States and South Africa, tested their prophylactic on 60 healthy US adults. The vaccine consisted of ID93, a fusion of TB therapeutic target proteins, and GLA-SE—a supplement to boost immune responses. The candidate proved safe in all participants, with mild-to-moderate adverse effects, and provoked promising immune responses. The formulation was significantly more effective with GLA-SE than without. Further studies will elucidate the therapeutic benefit of this formulation and its ability to combat the pathogenicity of TB.
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Affiliation(s)
- Rhea N Coler
- 1Infectious Disease Research Institute, Seattle, WA 98102 USA.,2Department of Global Health, University of Washington, Seattle, WA 98195 USA.,3PAI Life Sciences, Seattle, WA 98102 USA
| | - Tracey A Day
- 1Infectious Disease Research Institute, Seattle, WA 98102 USA
| | | | - Franco M Piazza
- 1Infectious Disease Research Institute, Seattle, WA 98102 USA
| | | | - Julie Vergara
- 1Infectious Disease Research Institute, Seattle, WA 98102 USA
| | - Tom Rolf
- 1Infectious Disease Research Institute, Seattle, WA 98102 USA
| | - Lenette Lu
- 5Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Boston, MA 02139 USA
| | - Galit Alter
- 5Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Boston, MA 02139 USA
| | | | | | | | | | | | | | - Steven G Reed
- 1Infectious Disease Research Institute, Seattle, WA 98102 USA
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34
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In silico design of Mycobacterium tuberculosis epitope ensemble vaccines. Mol Immunol 2018; 97:56-62. [DOI: 10.1016/j.molimm.2018.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 02/08/2023]
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35
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Pathakumari B, Devasundaram S, Maddineni P, Raja A. Rv2204c, Rv0753c and Rv0009 antigens specific T cell responses in latent and active TB – a flow cytometry-based analysis. Int J Med Microbiol 2018; 308:297-305. [DOI: 10.1016/j.ijmm.2017.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 10/17/2017] [Accepted: 12/04/2017] [Indexed: 12/17/2022] Open
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36
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Hussain OA, Junejo KN. Predicting treatment outcome of drug-susceptible tuberculosis patients using machine-learning models. Inform Health Soc Care 2018; 44:135-151. [PMID: 29461901 DOI: 10.1080/17538157.2018.1433676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tuberculosis (TB) is a deadly contagious disease and a serious global health problem. It is curable but due to its lengthy treatment process, a patient is likely to leave the treatment incomplete, leading to a more lethal, drug resistant form of disease. The World Health Organization (WHO) propagates Directly Observed Therapy Short-course (DOTS) as an effective way to stop the spread of TB in communities with a high burden. But DOTS also adds a significant burden on the financial feasibility of the program. We aim to facilitate TB programs by predicting the outcome of the treatment of a particular patient at the start of treatment so that their health workers can be utilized in a targeted and cost-effective way. The problem was modeled as a classification problem, and the outcome of treatment was predicted using state-of-art implementations of 3 machine learning algorithms. 4213 patients were evaluated, out of which 64.37% completed their treatment. Results were evaluated using 4 performance measures; accuracy, precision, sensitivity, and specificity. The models offer an improvement of more than 12% accuracy over the baseline prediction. Empirical results also revealed some insights to improve TB programs. Overall, our proposed methodology will may help teams running TB programs manage their human resources more effectively, thus saving more lives.
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Affiliation(s)
- Owais A Hussain
- a Graduate School of Science and Engineering , Karachi Institute of Economics and Technology , Karachi , Pakistan
| | - Khurum N Junejo
- a Graduate School of Science and Engineering , Karachi Institute of Economics and Technology , Karachi , Pakistan
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37
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Rastogi R, Kumar A, Kaur J, Saini V, Kaur J, Bhatnagar A. Rv0646c, an esterase from M. tuberculosis, up-regulates the host immune response in THP-1 macrophages cells. Mol Cell Biochem 2018; 447:189-202. [DOI: 10.1007/s11010-018-3303-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022]
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38
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Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine. Nat Med 2018; 24:130-143. [PMID: 29334373 DOI: 10.1038/nm.4473] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
Despite widespread use of the bacille Calmette-Guérin (BCG) vaccine, tuberculosis (TB) remains a leading cause of global mortality from a single infectious agent (Mycobacterium tuberculosis or Mtb). Here, over two independent Mtb challenge studies, we demonstrate that subcutaneous vaccination of rhesus macaques (RMs) with rhesus cytomegalovirus vectors encoding Mtb antigen inserts (hereafter referred to as RhCMV/TB)-which elicit and maintain highly effector-differentiated, circulating and tissue-resident Mtb-specific CD4+ and CD8+ memory T cell responses-can reduce the overall (pulmonary and extrapulmonary) extent of Mtb infection and disease by 68%, as compared to that in unvaccinated controls, after intrabronchial challenge with the Erdman strain of Mtb at ∼1 year after the first vaccination. Fourteen of 34 RhCMV/TB-vaccinated RMs (41%) across both studies showed no TB disease by computed tomography scans or at necropsy after challenge (as compared to 0 of 17 unvaccinated controls), and ten of these RMs were Mtb-culture-negative for all tissues, an exceptional long-term vaccine effect in the RM challenge model with the Erdman strain of Mtb. These results suggest that complete vaccine-mediated immune control of highly pathogenic Mtb is possible if immune effector responses can intercept Mtb infection at its earliest stages.
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39
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Hadizadeh M, Tabatabaiepour SN, Tabatabaiepour SZ, Hosseini Nave H, Mohammadi M, Sohrabi SM. Genome-Wide Identification of Potential Drug Target in Enterobacteriaceae Family: A Homology-Based Method. Microb Drug Resist 2018; 24:8-17. [DOI: 10.1089/mdr.2016.0259] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Morteza Hadizadeh
- Department of Agriculture, Payame Noor University (PNU), Tehran, Iran
| | | | | | - Hossein Hosseini Nave
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Mohammadi
- Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, Lorestan University of Medical Sciences, Khorramabad, Iran
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40
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Su H, Zhu S, Zhu L, Kong C, Huang Q, Zhang Z, Wang H, Xu Y. Mycobacterium tuberculosis Latent Antigen Rv2029c from the Multistage DNA Vaccine A39 Drives TH1 Responses via TLR-mediated Macrophage Activation. Front Microbiol 2017; 8:2266. [PMID: 29204139 PMCID: PMC5698697 DOI: 10.3389/fmicb.2017.02266] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/02/2017] [Indexed: 01/13/2023] Open
Abstract
Targeting of Mycobacterium tuberculosis (MTB) latent antigens comprises a crucial strategy for the development of alternative tuberculosis (TB) vaccine(s) that protects against TB reactivation. Here, we generated a multistage DNA vaccine, A39, containing the early antigens Ag85A and Rv3425 as well as the latency-associated protein Rv2029c, which conferred protective immunity in a pre-exposure mouse model. Moreover, administration of the A39 vaccination after MTB exposure inhibited reactivation and resulted in significantly lower bacterial loads in the lungs and spleen of mice, compared to those in the control population. Subsequently, we investigated the effect of Rv2029c on innate immunity and characterized the molecular details of the interaction of this protein with the host via iTRAQ proteomic and biochemical assay analyses. Rv2029c activated macrophages, triggered the production of pro-inflammatory cytokines, and promoted toll-like receptor/mitogen-activated protein kinase (TLR/MAPK)-dependent macrophage apoptosis. Furthermore, Rv2029c treatment enhanced the ability of Mycobacterium bovis Bacillus Calmette-Guérin (BCG)-infected macrophages to present antigens to CD4+ T cells in vitro, which correlated with an increase in MHC-II expression. Lastly, Rv2029c-treated macrophages activated T cells, effectively polarized CD4+ and CD8+ T cells to secrete IFN-γ and IL-2, and specifically expanded a population of CD44highCD62LlowCD4+/CD8+ effector/memory cells, indicating that Rv2029c, as a specific recall antigen, contributes to Th1 polarization in T cell immunity. These results suggest that Rv2029c and A39 comprise promising targets for the development of next-generation clinical TB therapeutic vaccines.
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Affiliation(s)
- Haibo Su
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China.,GMU-GIBH Joint School of Life Science, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The Second People's Hospital of Guangdong Province, Guangzhou, China
| | - Shengling Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lin Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Cong Kong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Qi Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Zhi Zhang
- The Second People's Hospital of Guangdong Province, Guangzhou, China
| | - Honghai Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
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41
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Vollmer AC, Bark SJ. Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications. ADVANCES IN APPLIED MICROBIOLOGY 2017; 102:1-36. [PMID: 29680123 DOI: 10.1016/bs.aambs.2017.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified the conservation of Usp-like proteins across bacteria, archaea, plants, and even some invertebrate animals. Regulation of these proteins under diverse stresses has been associated with different stress-response genes including spoT and relA in the stringent response and the dosR two-component signaling pathways. These and other foundational studies suggest Usps serve regulatory and protective roles to enable adaptation and survival under external stresses. Despite these foundational studies, many bacterial species have multiple paralogs of genes encoding these proteins and ablation of the genes does not provide a distinct phenotype. This outcome has limited our understanding of the biochemical functions of these proteins. Here, we summarize the current knowledge of Usps in general and UspA in particular across different genera as well as conclusions about their functions from seminal studies in diverse organisms. Our objective has been to organize the foundational studies in this field to identify the significant impediments to further understanding of Usp functions at the molecular level. We propose ideas and experimental approaches that may overcome these impediments and drive future development of molecular approaches to understand and target Usps as central regulators of stress adaptation and survival. Despite the fact that the full functions of Usps are still not known, creative many applications have already been proposed, tested, and used. The complementary approaches of basic research and applications, along with new technology and analytic tools, may yield the elusive yet critical functions of universal stress proteins in diverse systems.
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42
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Garcia-Morales L, Leon-Solis L, Monroy-Muñoz IE, Talavera-Paulin M, Serafin-López J, Estrada-Garcia I, Rivera-Gutierrez S, Cerna-Cortes JF, Helguera-Repetto AC, Gonzalez-Y-Merchand JA. Comparative proteomic profiles reveal characteristic Mycobacterium tuberculosis proteins induced by cholesterol during dormancy conditions. MICROBIOLOGY-SGM 2017; 163:1237-1247. [PMID: 28771131 DOI: 10.1099/mic.0.000512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cholesterol has been reported to play an important role during Mycobacterium tuberculosis infection and during its dormant state inside the host. We present the determination of proteomic profiles of M. tuberculosis H37Rv in the presence of cholesterol as the sole carbon source under exponential growth and in two in vitro dormancy phases (NRP1 and NRP2). Using 2D-PAGE, we detected that M. tuberculosis expressed a high diversity of proteins in both exponential and non-replicative phases. We also found that cholesterol was involved in the overexpression of some proteins related to sulfur metabolism (CysA2), electron transport (FixB), cell wall synthesis (Ald), iron storage (BfrB), protein synthesis (Tig and EF-Tu) and dormancy maintenance (HspX and TB 31.7). According to our results we propose that proteins Ald, BfrB, FadA5 and TB31.7 are likely to play a fundamental role during in vitro dormancy of M. tuberculosis in the presence of cholesterol, helping to counteract its intracellular hostile microenvironment.
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Affiliation(s)
- Lazaro Garcia-Morales
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Lizbel Leon-Solis
- Laboratorios de Biologicos y Reactivos de México S.A. de C.V., Birmex. Instituto Nacional de Virologia. Prolongacion Manuel Carpio No. 492, Delegacion Miguel Hidalgo 11340, Ciudad de Mexico, Mexico
| | - Irma E Monroy-Muñoz
- Departamento de Genetica y Genomica Humana, Torre de Investigacion, Instituto Nacional de Perinatologia Isidro Espinosa de los Reyes, SSA. Montes Urales 800, Lomas de Chapultepec, Ciudad de Mexico, 11000, Mexico
| | - Moises Talavera-Paulin
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Jeanet Serafin-López
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Iris Estrada-Garcia
- Departamento de Inmunologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Sandra Rivera-Gutierrez
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Jorge F Cerna-Cortes
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
| | - Addy C Helguera-Repetto
- Departamento de Inmunobioquimica, Torre de Investigacion, Instituto Nacional de Perinatologia Isidro Espinosa de los Reyes, SSA. Montes Urales 800, Lomas de Chapultepec, Ciudad de Mexico, 11000, Mexico
| | - Jorge A Gonzalez-Y-Merchand
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas (ENCB), Instituto Politecnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de Mexico, 11340, Mexico
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Ashayeri-Panah M, Eftekhar F, Kazemi B, Joseph J. Cloning, optimization of induction conditions and purification of Mycobacterium tuberculosis Rv1733c protein expressed in Escherichia coli. IRANIAN JOURNAL OF MICROBIOLOGY 2017; 9:64-73. [PMID: 29213997 PMCID: PMC5715279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND AND OBJECTIVES Rv1733c is a latency antigen from Mycobacterium tuberculosis, a probable integral-membrane protein with promiscuous T-cell and B-cell epitopes, making it a potential vaccine candidate against tuberculosis. This study aimed to clone and optimize the expression of recombinant Rv1733c in Escherichia coli for purification. MATERIALS AND METHODS Chemically synthesized rv1733c coding sequence was cloned in pET-23a(+) followed by transforming E. coli BL21 (DE3) cells. To evaluate the induction conditions for optimized expression, factorial design of experiments was employed using four different media as well as four levels of isopropyl-b-D-thiogalactopyranosid [IPTG] concentration and duration of induction. The recombinant protein was then purified using a His-tag purification kit and detected through western blotting. RESULTS Recombinant Rv1733c (> 24 kDa) was expressed and accumulated in the cytoplasm of the E. coli cells. Medium composition showed the most significant effect on the yield of the recombinant protein (P = 0.000). The highest yield of recombinant Rv1733c occurred in the presence of 0.4 mM of IPTG in Terrific Broth medium (containing 1.2% tryptone, 2.4% yeast extract, 72 mM K 2 HPO 4 , 17 mM KH 2 PO 4 and 0.4% glycerol) after 10 h at 37°C. Under these conditions, the expression level was around 0.5 g/L of culture medium. Purified Rv1733c was detected by an anti-polyhistidine antibody and a tuberculosis patient's serum. Systematic optimization of induction conditions gave us high yield of recombinant polyhistidine-tagged Rv1733c in E. coli which was successfuly purified. CONCLUSION We believe that the purified Rv1733c recombinant protein from M. tuberculosis might be a good candidate for vaccine production against tuberculosis.
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Affiliation(s)
- Mitra Ashayeri-Panah
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran, Iran
| | - Fereshteh Eftekhar
- Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran, Iran,Corresponding author: Feresteh Eftekhar, PhD, Department of Microbiology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran, Iran. Tel: +98-21-29903208, Fax: +98-21-22431664,
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Joan Joseph
- Hospital Clinic/HIVACAT, School of Medicine, University of Barcelona, Barcelona, Spain
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Novel vaccine potential of Rv3131, a DosR regulon-encoded putative nitroreductase, against hyper-virulent Mycobacterium tuberculosis strain K. Sci Rep 2017; 7:44151. [PMID: 28272457 PMCID: PMC5341159 DOI: 10.1038/srep44151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating evidence indicates that latency-associated Mycobacterium tuberculosis (Mtb)-specific antigens from the dormancy survival regulator regulon (DosR) may be promising novel vaccine target antigens for the development of an improved tuberculosis vaccine. After transcriptional profiling of DosR-related genes in the hyper-virulent Beijing Mtb strain K and the reference Mtb strain H37Rv, we selected Rv3131, a hypothetical nitroreductase, as a vaccine antigen and evaluated its vaccine efficacy against Mtb K. Mtb K exhibited stable and constitutive up-regulation of rv3131 relative to Mtb H37Rv under three different growth conditions (at least 2-fold induction) including exponential growth in normal culture conditions, hypoxia, and inside macrophages. Mice immunised with Rv3131 formulated in GLA-SE, a well-defined TLR4 adjuvant, displayed enhanced Rv3131-specific IFN-γ and serum IgG2c responses along with effector/memory T cell expansion and remarkable generation of Rv3131-specific multifunctional CD4+ T cells co-producing TNF-α, IFN-γ and IL-2 in both spleen and lung. Following challenge with Mtb K, the Rv3131/GLA-SE-immunised group exhibited a significant reduction in bacterial number and less extensive lung inflammation accompanied by the obvious persistence of Rv3131-specific multifunctional CD4+ T cells. These results suggest that Rv3131 could be an excellent candidate for potential use in a multi-antigenic Mtb subunit vaccine, especially against Mtb Beijing strains.
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Nikitushkin VD, Demina GR, Kaprelyants AS. Rpf proteins are the factors of reactivation of the dormant forms of actinobacteria. BIOCHEMISTRY (MOSCOW) 2017; 81:1719-1734. [DOI: 10.1134/s0006297916130095] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rationale for selection of developmentally regulated genes as vaccine candidates against Leishmania infantum infection. Vaccine 2016; 34:5474-5478. [DOI: 10.1016/j.vaccine.2016.08.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 01/20/2023]
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Awoniyi DO, Teuchert A, Sutherland JS, Mayanja-Kizza H, Howe R, Mihret A, Loxton AG, Sheehama J, Kassa D, Crampin AC, Dockrell HM, Kidd M, Rosenkrands I, Geluk A, Ottenhoff THM, Corstjens PLAM, Chegou NN, Walzl G. Evaluation of cytokine responses against novel Mtb antigens as diagnostic markers for TB disease. J Infect 2016; 73:219-30. [PMID: 27311746 DOI: 10.1016/j.jinf.2016.04.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 11/27/2022]
Abstract
OBJECTIVE We investigated the accuracy of host markers detected in Mtb antigen-stimulated whole blood culture supernatant in the diagnosis of TB. METHODS Prospectively, blood from 322 individuals with presumed TB disease from six African sites was stimulated with four different Mtb antigens (Rv0081, Rv1284, ESAT-6/CFP-10, and Rv2034) in a 24 h whole blood stimulation assay (WBA). The concentrations of 42 host markers in the supernatants were measured using the Luminex multiplex platform. Diagnostic biosignatures were investigated through the use of multivariate analysis techniques. RESULTS 17% of the participants were HIV infected, 106 had active TB disease and in 216 TB was excluded. Unstimulated concentrations of CRP, SAA, ferritin and IP-10 had better discriminating ability than markers from stimulated samples. Accuracy of marker combinations by general discriminant analysis (GDA) identified a six analyte model with 77% accuracy for TB cases and 84% for non TB cases, with a better performance in HIV uninfected patients. CONCLUSIONS A biosignature of 6 cytokines obtained after stimulation with four Mtb antigens has moderate potential as a diagnostic tool for pulmonary TB disease individuals and stimulated marker expression had no added value to unstimulated marker performance.
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Affiliation(s)
- Dolapo O Awoniyi
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, Cape Town, South Africa
| | - Andrea Teuchert
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, Cape Town, South Africa
| | | | | | - Rawleigh Howe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Andre G Loxton
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, Cape Town, South Africa
| | - Jacob Sheehama
- University of Namibia, Faculty of Health Sciences, School of Medicine, Namibia
| | - Desta Kassa
- Ethiopian Health and Nutrition Research Institute, Addis Ababa, Ethiopia
| | - Amelia C Crampin
- Karonga Prevention Study, Chilumba, Malawi; London School of Hygiene and Tropical Medicine, London, UK
| | | | - Martin Kidd
- Centre for Statistical Analysis, Stellenbosch University, South Africa
| | | | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - P L A M Corstjens
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Novel N Chegou
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, Cape Town, South Africa
| | - Gerhard Walzl
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, Cape Town, South Africa.
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Farrell D, Jones G, Pirson C, Malone K, Rue-Albrecht K, Chubb AJ, Vordermeier M, Gordon SV. Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis. Microb Genom 2016; 2:e000071. [PMID: 28348866 PMCID: PMC5320590 DOI: 10.1099/mgen.0.000071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/26/2016] [Indexed: 11/18/2022] Open
Abstract
The discovery of novel antigens is an essential requirement in devising new diagnostics or vaccines for use in control programmes against human tuberculosis (TB) and bovine tuberculosis (bTB). Identification of potential epitopes recognised by CD4+ T cells requires prediction of peptide binding to MHC class-II, an obligatory prerequisite for T cell recognition. To comprehensively prioritise potential MHC-II-binding epitopes from Mycobacterium bovis, the agent of bTB and zoonotic TB in humans, we integrated three binding prediction methods with the M. bovisproteome using a subset of human HLA alleles to approximate the binding of epitope-containing peptides to the bovine MHC class II molecule BoLA-DRB3. Two parallel strategies were then applied to filter the resulting set of binders: identification of the top-scoring binders or clusters of binders. Our approach was tested experimentally by assessing the capacity of predicted promiscuous peptides to drive interferon-γ secretion from T cells of M. bovis infected cattle. Thus, 376 20-mer peptides, were synthesised (270 predicted epitopes, 94 random peptides with low predictive scores and 12 positive controls of known epitopes). The results of this validation demonstrated significant enrichment (>24 %) of promiscuously recognised peptides predicted in our selection strategies, compared with randomly selected peptides with low prediction scores. Our strategy offers a general approach to the identification of promiscuous epitopes tailored to target populations where there is limited knowledge of MHC allelic diversity.
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Affiliation(s)
- Damien Farrell
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Gareth Jones
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Christopher Pirson
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Kerri Malone
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Kevin Rue-Albrecht
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,3School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Anthony J Chubb
- 4School of Medicine, University College Dublin, Dublin D4, Ireland
| | - Martin Vordermeier
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Stephen V Gordon
- 6School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.,5Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin D4, Ireland.,1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,4School of Medicine, University College Dublin, Dublin D4, Ireland
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Gupta D, Banerjee S, Pailan S, Saha P. In silico identification and characterization of a hypothetical protein of Mycobacterium tuberculosis EAI5 as a potential virulent factor. Bioinformation 2016; 12:182-191. [PMID: 28149053 PMCID: PMC5267962 DOI: 10.6026/97320630012182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 05/27/2016] [Accepted: 05/28/2016] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis, a life threatening disease caused by different strains of Mycobacterium tuberculosis is creating an alarming condition due to the emergence of increasing multi drug resistance (MDR) trait. In this study, in silico approach was used for the identification of a conserved novel virulent factor in Mycobacterium tuberculosis EAI5 (Accession no.CP006578) which can also act as potential therapeutic target. Systematic comparative search of genes that are common to strain EAI5 and other human pathogenic strains of M. tuberculosis enlisted 408 genes. These were absent in the non-pathogenic Mycobacterium smegmatis MC2155 and in the human genome. Among those genes, only the protein coding hypothetical genes (97 out of 408) and their corresponding products were selected for further exploration. Of these, 11 proteins were found to have notable conserved domains, of which one hypothetical protein (NCBI Acc No. AGQ35418.1) was selected for further in silico exploration which was found to have two functional domains, one having phosphatidylinositol specific phospholipase C (PI-PLC) activity while the other short domain with weak lectin binding activity. As PI-PLC contributes virulence property in some pathogenic bacteria with a broad range of activities, different bioinformatic tools were used to explore its physicochemical and other important properties which indicated its secretary nature. This PI-PLC was previously not reported as drug/vaccine target to the best of our knowledge. Its predicted 3D structure can be explored for development of inhibitor for novel therapeutic strategies against MDR-TB.
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Affiliation(s)
- Debdoot Gupta
- Department of Microbiology, Burdwan University, Golapbag, Burdwan - 713104, West Bengal, India
| | - Samiddha Banerjee
- Department of Microbiology, Burdwan University, Golapbag, Burdwan - 713104, West Bengal, India
| | - Santanu Pailan
- Department of Microbiology, Burdwan University, Golapbag, Burdwan - 713104, West Bengal, India
| | - Pradipta Saha
- Department of Microbiology, Burdwan University, Golapbag, Burdwan - 713104, West Bengal, India
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Gcebe N, Michel A, Gey van Pittius NC, Rutten V. Comparative Genomics and Proteomic Analysis of Four Non-tuberculous Mycobacterium Species and Mycobacterium tuberculosis Complex: Occurrence of Shared Immunogenic Proteins. Front Microbiol 2016; 7:795. [PMID: 27375559 PMCID: PMC4894912 DOI: 10.3389/fmicb.2016.00795] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 05/11/2016] [Indexed: 01/15/2023] Open
Abstract
The Esx and PE/PPE families of proteins are among the most immunodominant mycobacterial antigens and have thus been the focus of research to develop vaccines and immunological tests for diagnosis of bovine and human tuberculosis, mainly caused by Mycobacterium bovis and Mycobacterium tuberculosis, respectively. In non-tuberculous mycobacteria (NTM), multiple copies of genes encoding homologous proteins have mainly been identified in pathogenic Mycobacterium species phylogenically related to Mycobacterium tuberculosis and Mycobacterium bovis. Only ancestral copies of these genes have been identified in nonpathogenic NTM species like Mycobacterium smegmatis, Mycobacterium sp. KMS, Mycobacterium sp. MCS, and Mycobacterium sp. JLS. In this study we elucidated the genomes of four nonpathogenic NTM species, viz Mycobacterium komanii sp. nov., Mycobacterium malmesburii sp. nov., Mycobacterium nonchromogenicum, and Mycobacterium fortuitum ATCC 6841. These genomes were investigated for genes encoding for the Esx and PE/PPE (situated in the esx cluster) family of proteins as well as adjacent genes situated in the ESX-1 to ESX-5 regions. To identify proteins actually expressed, comparative proteomic analyses of purified protein derivatives from three of the NTM as well as Mycobacterium kansasii ATCC 12478 and the commercially available purified protein derivatives from Mycobacterium bovis and Mycobacterium avium was performed. The genomic analysis revealed the occurrence in each of the four NTM, orthologs of the genes encoding for the Esx family, the PE and PPE family proteins in M. bovis and M. tuberculosis. The identification of genes of the ESX-1, ESX-3, and ESX-4 region including esxA, esxB, ppe68, pe5, and pe35 adds to earlier reports of these genes in nonpathogenic NTM like M. smegmatis, Mycobacterium sp. JLS and Mycobacterium KMS. This report is also the first to identify esxN gene situated within the ESX-5 locus in M. nonchromogenicum. Our proteomics analysis identified a total of 609 proteins in the six PPDs and 22 of these were identified as shared between PPD of M.bovis and one or more of the NTM PPDs. Previously characterized M tuberculosis/M. bovis homologous immunogenic proteins detected in one or more of the nonpathogenic NTM in this study included CFP-10 (detected in M. malmesburii sp. nov. PPD), GroES (detected in all NTM PPDs but M. malmesburii sp. nov.), DnaK (detected in all NTM PPDs), and GroEL (detected in all NTM PPDs). This study confirms reports that the ESX-1, ESX-3, and ESX-4 regions are ancestral regions and thus found in the genomes of most mycobacteria. Identification of NTM homologs of immunogenic proteins warrants further investigation of their ability to cause cross-reactive immune responses with MTBC antigens.
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Affiliation(s)
- Nomakorinte Gcebe
- Tuberculosis Laboratory, Agricultural Research Council - Onderstepoort Veterinary InstituteOnderstepoort, South Africa; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of PretoriaOnderstepoort, South Africa
| | - Anita Michel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria Onderstepoort, South Africa
| | - Nicolaas C Gey van Pittius
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University Tygerberg, South Africa
| | - Victor Rutten
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of PretoriaOnderstepoort, South Africa; Division of Immunology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht UniversityUtrecht, Netherlands
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