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D'Souza C, Kishore U, Tsolaki AG. The PE-PPE Family of Mycobacterium tuberculosis: Proteins in Disguise. Immunobiology 2023; 228:152321. [PMID: 36805109 DOI: 10.1016/j.imbio.2022.152321] [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: 06/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis has thrived in parallel with humans for millennia, and despite our efforts, M. tuberculosis continues to plague us, currently infecting a third of the world's population. The success of M. tuberculosis has recently been attributed, in part, to the PE-PPE family; a unique collection of 168 proteins fundamentally involved in the pathogenesis of M. tuberculosis. The PE-PPE family proteins have been at the forefront of intense research efforts since their discovery in 1998 and whilst our knowledge and understanding has significantly advanced over the last two decades, many important questions remain to be elucidated. This review consolidates and examines the vast body of existing literature regarding the PE-PPE family proteins, with respect to the latest developments in elucidating their evolution, structure, subcellular localisation, function, and immunogenicity. This review also highlights significant inconsistencies and contradictions within the field. Additionally, possible explanations for these knowledge gaps are explored. Lastly, this review poses many important questions, which need to be addressed to complete our understanding of the PE-PPE family, as well as highlighting the challenges associated with studying this enigmatic family of proteins. Further research into the PE-PPE family, together with technological advancements in genomics and proteomics, will undoubtedly improve our understanding of the pathogenesis of M. tuberculosis, as well as identify key targets/candidates for the development of novel drugs, diagnostics, and vaccines.
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Affiliation(s)
- Christopher D'Souza
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom
| | - Uday Kishore
- Department of Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anthony G Tsolaki
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom.
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2
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Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T. Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information. Front Med (Lausanne) 2022; 9:1008527. [PMID: 36405591 PMCID: PMC9669072 DOI: 10.3389/fmed.2022.1008527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2023] Open
Abstract
Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial outbreaks in healthcare associated settings. It is known to cause infection in all age groups and exhibits multi-drug resistance with high potential for horizontal transmission. Because of this reason combined with limited therapeutic choices available, C. auris infection has been acknowledged as a potential risk for causing a future pandemic, and thus seeking a promising strategy for its treatment is imperative. Here, we combined evolutionary information with reverse vaccinology approach to identify novel epitopes for vaccine design that could elicit CD4+ T-cell responses against C. auris. To this end, we extensively scanned the family of proteins encoded by C. auris genome. In addition, a pathogen may acquire substitutions in epitopes over a period of time which could cause its escape from the immune response thus rendering the vaccine ineffective. To lower this possibility in our design, we eliminated all rapidly evolving genes of C. auris with positive selection. We further employed highly conserved regions of multiple C. auris strains and identified two immunogenic and antigenic T-cell epitopes that could generate the most effective immune response against C. auris. The antigenicity scores of our predicted vaccine candidates were calculated as 0.85 and 1.88 where 0.5 is the threshold for prediction of fungal antigenic sequences. Based on our results, we conclude that our vaccine candidates have the potential to be successfully employed for the treatment of C. auris infection. However, in vivo experiments are imperative to further demonstrate the efficacy of our design.
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Affiliation(s)
- Shishir K. Gupta
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Özge Osmanoglu
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Rashmi Minocha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sourish Reddy Bandi
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Functional Genomics and Systems Biology Group, University of Würzburg, Würzburg, Germany
- BioComputing Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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3
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Dhasmana A, Dhasmana S, Alsulimani A, Kotnala S, Kashyap VK, Haque S, Jaggi M, Yallapu MM, Chauhan SC. In silico CD4 + T-cell multiepitope prediction and HLA distribution analysis for Marburg Virus-A strategy for vaccine designing. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:101751. [PMID: 38881729 PMCID: PMC11178283 DOI: 10.1016/j.jksus.2021.101751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Marburg, a RNA virus (MRV), is responsible for causing hemorrhagic fever that affects humans and non-human primates. World Health Organization (WHO), National Institutes of Health (NIH) and Centre of Disease Control and Prevention (CDC) considered this as an extremely dangerous virus, thus categorised as risk group 4, category A priority pathogen and category "A" bioterrorism agent, respectively. Despite of all these alarming concerns, no prophylaxis arrangements are available against this virus till date. In fact, the construction of immunogenic vaccine candidates by traditional molecular immunology methods is time consuming and very expensive. Considering these concerns, herein, we have designed CD4 + T Cell multiepitopes against MRV using in silico approach. The pin-point criteria of the screening and selection of potential epitopes are, non-mutagenic, antigenic, large HLAs coverage, non-toxic and high world population coverage. This kind of methodology and investigations can precisely reduce the expenditure and valuable time for experimental planning in development of vaccines in laboratories. In current scenario, researchers are frequently using in silico approaches to speed up their vaccine-based lab studies. The computational studies are highly valuable for the screening of large epitope dataset into smaller one prior to in vitro and in vivo confirmatory analyses.
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Affiliation(s)
- Anupam Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
- Department of Biosciences, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India
| | - Swati Dhasmana
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sudhir Kotnala
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Vivek Kumar Kashyap
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Meena Jaggi
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX, USA
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4
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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: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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
- *Correspondence: Xueqiong Wu, ; Guangyu Zhao,
| | - 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
- *Correspondence: Xueqiong Wu, ; Guangyu Zhao,
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Ortega-Tirado D, Arvizu-Flores AA, Velazquez C, Garibay-Escobar A. The role of immunoinformatics in the development of T-cell peptide-based vaccines against Mycobacterium tuberculosis. Expert Rev Vaccines 2020; 19:831-841. [PMID: 32945209 DOI: 10.1080/14760584.2020.1825950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is a major health problem worldwide. The BCG, the only authorized vaccine to fight TB, shows a variable protection in the adult population highlighting the need of a new vaccine. Immunoinformatics offers a variety of tools that can predict immunogenic T-cell peptides of Mycobacterium tuberculosis (Mtb) that can be used to create a new vaccine. Immunoinformatics has made possible the identification of immunogenic T-cell peptides of Mtb that have been tested in vitro showing a potential for using these molecules as part of a new TB vaccine. AREAS COVERED This review summarizes the most common immunoinformatics tools to identify immunogenic T-cell peptides and presents a compilation about research studies that have identified T-cell peptides of Mtb by using immunoinformatics. Also, it is provided a summary of the TB vaccines undergoing clinical trials. EXPERT OPINION In the next few years, the field of peptide-based vaccines will keep growing along with the development of more efficient and sophisticated immunoinformatic tools to identify immunogenic peptides with a greater accuracy.
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Affiliation(s)
- David Ortega-Tirado
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
| | - Aldo A Arvizu-Flores
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
| | - Carlos Velazquez
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento De Ciencias Químico Biológicas Universidad De Sonora , Hermosillo, Sonora, México
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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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7
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Ortega-Tirado D, Niño-Padilla EI, Arvizu-Flores AA, Velazquez C, Espitia C, Serrano CJ, Enciso-Moreno JA, Sumoza-Toledo A, Garibay-Escobar A. Identification of immunogenic T-cell peptides of Mycobacterium tuberculosis PE_PGRS33 protein. Mol Immunol 2020; 125:123-130. [PMID: 32659597 DOI: 10.1016/j.molimm.2020.06.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/02/2020] [Accepted: 06/24/2020] [Indexed: 12/11/2022]
Abstract
The development of a more efficient vaccine is needed to improve tuberculosis control. One of the current approaches is to identify immunogenic T-cell peptides that can elicit a protective and specific immune response. These peptides come from immunogenic proteins of the pathogen. The PE_PGRS33 protein of Mycobacterium tuberculosis has been proved immunogenic. However, little is known about immunogenic T-cell peptides of PE_PGRS33 and their interactions with MHC-II molecules. Therefore, we used the SYFPHEITHI database to determine the immunogenic PE_PGRS33 T-cell peptides. Next, we built homology models by using MOE v2018.1 software in order to obtain information about the specific interactions between the peptides and I-Ak. The AlgPred server was employed to look for allergenic sites in PE_PGRS33. We developed a sequence alignment between PE_PGRS33 and all the human proteins by using BLAST. Three peptides were commercially synthesized, and their activity was evaluated in vitro by the stimulation of PBMC from household contacts of TB patients. Our in silico results showed five immunogenic T-cell peptides. BLAST analysis showed low homology of PE_PGRS33 with human proteins and AlgPred did not reveal allergenic sites in PE_PGRS33. The three peptides triggered the activation of CD4+ T cells from the households contacts, showed by the production of IFN-γ. We identified three immunogenic peptides of PE_PGRS33 that demonstrated activity in vitro which allows to deepen into the immune response towards mycobacterial antigens, moving forward to the identification of new vaccine candidates.
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Affiliation(s)
- David Ortega-Tirado
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, México
| | - Esmeralda Ivonne Niño-Padilla
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, México
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, México
| | - Carlos Velazquez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, México
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Coyoacán Ciudad de México, México
| | - Carmen J Serrano
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Interior Alameda #45, 98000, Zacatecas, Zacatecas, México
| | - José Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Interior Alameda #45, 98000, Zacatecas, Zacatecas, México
| | - Adriana Sumoza-Toledo
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Agustín de Iturbide s/n, 91700, Veracruz, Veracruz, México
| | - Adriana Garibay-Escobar
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, México.
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Kwon KW, Choi HH, Han SJ, Kim JS, Kim WS, Kim H, Kim LH, Kang SM, Park J, Shin SJ. Vaccine efficacy of a Mycobacterium tuberculosis Beijing-specific proline-glutamic acid (PE) antigen against highly virulent outbreak isolates. FASEB J 2019; 33:6483-6496. [PMID: 30753099 DOI: 10.1096/fj.201802604r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus Calmette-Guerin vaccine confers insufficient pulmonary protection against tuberculosis (TB), particularly the Mycobacterium tuberculosis (Mtb) Beijing strain infection. Identification of vaccine antigens (Ags) by considering Mtb genetic diversity is crucial for the development of improved TB vaccine. MTBK_20640, a new Beijing genotype-specific proline-glutamic acid-family Ag, was identified by comparative genomic analysis. Its immunologic features were characterized by evaluating interactions with dendritic cells (DCs), and immunogenicity and vaccine efficacy were determined against highly virulent Mtb Beijing outbreak Korean Beijing (K) strain and HN878 strain in murine infection model. MTBK_20640 induced DCs via TLR2 and downstream MAPK and NF-κB signaling pathways, effectively promoting naive CD4-positive (CD4+) T-cell proliferation and IFN-γ production. Different IFN-γ response was observed in mice infected with Mtb K or reference H37Rv strain. Significant induction of T helper type 1 cell-polarized Ag-specific multifunctional CD4+ T cells and a marked Ag-specific IgG2c response were observed in mice immunized with MTBK_20640/glucopyranosyl lipid adjuvant-stable emulsion. The immunization conferred long-term protection against 2 Mtb Beijing outbreak strains, as evidenced by a significant reduction in colony-forming units in the lung and spleen and reduced lung inflammation. MTBK_20640 vaccination conferred long-term protection against highly virulent Mtb Beijing strains. MTBK_20640 may be developed into a novel Ag component in multisubunit TB vaccines in the future.-Kwon, K. W., Choi, H.-H., Han, S. J., Kim, J.-S., Kim, W. S., Kim, H., Kim, L.-H., Kang, S. M., Park, J., Shin, S. J. Vaccine efficacy of a Mycobacterium tuberculosis Beijing-specific proline-glutamic acid (PE) antigen against highly virulent outbreak isolates.
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Affiliation(s)
- Kee Woong Kwon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Hong-Hee Choi
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung Jung Han
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong-Seok Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (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
| | - Woo Sik Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (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
| | - Hongmin Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Lee-Han Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon Myung Kang
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jaehun Park
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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9
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Mohareer K, Asalla S, Banerjee S. Cell death at the cross roads of host-pathogen interaction in Mycobacterium tuberculosis infection. Tuberculosis (Edinb) 2018; 113:99-121. [PMID: 30514519 DOI: 10.1016/j.tube.2018.09.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/13/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) continues to be the leading cause of death by any single infectious agent, accounting for around 1.7 million annual deaths globally, despite several interventions and support programs by national and international agencies. With the development of drug resistance in Mycobacterium tuberculosis (M. tb), there has been a paradigm shift in TB research towards host-directed therapy. The potential targets include the interactions between host and bacterial proteins that are crucial for pathogenesis. Hence, collective efforts are being made to understand the molecular details of host-pathogen interaction for possible translation into host-directed therapy. The present review focuses on 'host cell death modalities' of host-pathogen interaction, which play a crucial role in determining the outcome of TB disease progression. Several cell death modalities that occur in response to mycobacterial infection have been identified in human macrophages either as host defences for bacterial clearance or as pathogen strategies for multiplication and dissemination. These cell death modalities include apoptosis, necrosis, pyroptosis, necroptosis, pyronecrosis, NETosis, and autophagy. These processes are highly overlapping with several mycobacterial proteins participating in more than one cell death pathway. Until now, reviews in M. tb and host cell death have discussed either focusing on host evasion strategies, apoptosis, autophagy, and necrosis or describing all these forms with limited discussions of their role in host-pathogen interactions. Here, we present a comprehensive review of various mycobacterial factors modulating host cell death pathways and the cross-talk between them. Besides this, we have discussed the networking of host cell death pathways including the interference of host miRNA during M. tb infection with their respective targets. Through this review, we present the host targets that overlap across several cell death modalities and the technical limitations of methodology in cell death research. Given the compelling need to discover alternative drug target(s), this review identifies these overlapping cell death factors as potential targets for host-directed therapy.
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Affiliation(s)
- Krishnaveni Mohareer
- Molecular Pathogenesis Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India-500046
| | - Suman Asalla
- Molecular Pathogenesis Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India-500046
| | - Sharmistha Banerjee
- Molecular Pathogenesis Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India-500046.
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10
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Protective Vaccine Efficacy of the Complete Form of PPE39 Protein from Mycobacterium tuberculosis Beijing/K Strain in Mice. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00219-17. [PMID: 28877927 DOI: 10.1128/cvi.00219-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/24/2017] [Indexed: 11/20/2022]
Abstract
The aim of this study was to evaluate the protective efficacy of MTBK_24820, a complete form of PPE39 protein derived from a predominant Beijing/K strain of Mycobacterium tuberculosis in South Korea. Mice were immunized with MTKB_24820, M. bovis Bacilli Calmette-Guérin (BCG), or adjuvant prior to a high-dosed Beijing/K strain aerosol infection. After 4 and 9 weeks, bacterial loads were determined and histopathologic and immunologic features in the lungs and spleens of the M. tuberculosis-infected mice were analyzed. Putative immunogenic T-cell epitopes were examined using synthetic overlapping peptides. Successful immunization of MTBK_24820 in mice was confirmed by increased IgG responses (P < 0.05) and recalled gamma interferon (IFN-γ), interleukin-2 (IL-2), IL-6, and IL-17 responses (P < 0.05 or P < 0.01) to MTBK_24820. After challenge with the Beijing/K strain, an approximately 0.5 to 1.0 log10 reduction in CFU in lungs and fewer lung inflammation lesions were observed in MTBK_24820-immunized mice compared to those for control mice. Moreover, MTBK_24820 immunization elicited significantly higher numbers of CD4+ T cells producing protective cytokines, such as IFN-γ and IL-17, in lungs and spleens (P < 0.01) and CD4+ multifunctional T cells producing IFN-γ, tumor necrosis factor alpha (TNF-α), and/or IL-17 (P < 0.01) than in control mice, suggesting protection comparable to that of BCG against the hypervirulent Beijing/K strain. The dominant immunogenic T-cell epitopes that induced IFN-γ production were at the N terminus (amino acids 85 to 102 and 217 to 234). Its vaccine potential, along with protective immune responses in vivo, may be informative for vaccine development, particularly in regions where the M. tuberculosis Beijing/K-strain is frequently isolated from TB patients.
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Predicting promiscuous antigenic T cell epitopes of Mycobacterium tuberculosis mymA operon proteins binding to MHC Class I and Class II molecules. INFECTION GENETICS AND EVOLUTION 2016; 44:182-189. [DOI: 10.1016/j.meegid.2016.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/24/2016] [Accepted: 07/03/2016] [Indexed: 11/21/2022]
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12
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Pandey K, Sharma M, Saarav I, Singh S, Dutta P, Bhardwaj A, Sharma S. Analysis of the DosR regulon genes to select cytotoxic T lymphocyte epitope specific vaccine candidates using a reverse vaccinology approach. Int J Mycobacteriol 2016; 5:34-43. [DOI: 10.1016/j.ijmyco.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 10/22/2022] Open
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Deng W, Zeng J, Xiang X, Li P, Xie J. PE11 (Rv1169c) selectively alters fatty acid components of Mycobacterium smegmatis and host cell interleukin-6 level accompanied with cell death. Front Microbiol 2015; 6:613. [PMID: 26157429 PMCID: PMC4477156 DOI: 10.3389/fmicb.2015.00613] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/02/2015] [Indexed: 11/26/2022] Open
Abstract
PE/PPE family proteins, named after their conserved PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains of N-terminal, are most intriguing aspects of pathologic mycobacterial genome. The roles of most members of this family remain unknown, although selected genes of this family are related to the virulence of Mycobacterium tuberculosis. In order to decipher the role of Rv1169c, the Mycobacterium smegmatis strain heterologous expressed this ORF was constructed and identified that Rv1169c was a cell wall associated protein with a novel function in modifying the cell wall fatty acids. The growth of Rv1169c expressing strain was affected under surface stress, acidic condition and antibiotics treatment. M. smegmatis expressing Rv1169c induced necrotic cell death of macrophage after infection and significantly decreased interlukin-6 production compared to controls. In general, these results underscore a proposing role of Rv1169c in virulence of M. tuberculosis, as it's role in the susceptibility of anti-mycobacteria factors caused by modified cell wall fatty acid, and the induced necrotic cell death by Rv1169c is crucial for M. tuberculosis virulence during infection.
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Affiliation(s)
- Wanyan Deng
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Jie Zeng
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Xiaohong Xiang
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Ping Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University Chongqing, China
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Gastelum-Aviña P, Velazquez C, Espitia C, Lares-Villa F, Garibay-Escobar A. A PE_PGRS33 protein ofMycobacterium tuberculosis: an ideal target for future tuberculosis vaccine design. Expert Rev Vaccines 2015; 14:699-711. [DOI: 10.1586/14760584.2015.1015995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014; 26:431-44. [PMID: 25453224 PMCID: PMC4314449 DOI: 10.1016/j.smim.2014.09.012] [Citation(s) in RCA: 278] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Abstract
The causative agent of human tuberculosis, Mycobacterium tuberculosis complex (MTBC), comprises seven phylogenetically distinct lineages associated with different geographical regions. Here we review the latest findings on the nature and amount of genomic diversity within and between MTBC lineages. We then review recent evidence for the effect of this genomic diversity on mycobacterial phenotypes measured experimentally and in clinical settings. We conclude that overall, the most geographically widespread Lineage 2 (includes Beijing) and Lineage 4 (also known as Euro-American) are more virulent than other lineages that are more geographically restricted. This increased virulence is associated with delayed or reduced pro-inflammatory host immune responses, greater severity of disease, and enhanced transmission. Future work should focus on the interaction between MTBC and human genetic diversity, as well as on the environmental factors that modulate these interactions.
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Affiliation(s)
- Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
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Teh-Poot C, Tzec-Arjona E, Martínez-Vega P, Ramirez-Sierra MJ, Rosado-Vallado M, Dumonteil E. From genome screening to creation of vaccine against Trypanosoma cruzi by use of immunoinformatics. J Infect Dis 2014; 211:258-66. [PMID: 25070943 DOI: 10.1093/infdis/jiu418] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, and activation of CD8(+) T cells is crucial for a protective immune response. Therefore, the identification of antigens with major histocompatibility complex class I epitopes is a crucial step for vaccine development against T. cruzi. Our aim was to identify novel antigens and epitopes by immunoinformatics analysis of the parasite proteome (12 969 proteins) and to validate their immunotherapeutic potential in infected mice. We identified 172 predicted epitopes, using NetMHC and RANKPEP. The corresponding protein sequences were reanalyzed to generate a consensus prediction, and 26 epitopes were selected for in vivo validation. The interferon γ (IFN-γ) recall response of splenocytes from T. cruzi-infected mice confirmed that 10 of 26 epitopes (38%) induced IFN-γ production. The immunotherapeutic potential of a mixture of all 10 peptides was evaluated in infected mice. The therapeutic vaccine was able to control T. cruzi infection, as evidenced by reduced parasitemia, cardiac tissue inflammation, and parasite burden and increased survival. These findings illustrate the benefits of this approach for the rapid development of a vaccine against pathogens with large genomes. The identified peptides and the proteins from which they are derived are excellent candidates for the development of a vaccine against T. cruzi.
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Affiliation(s)
- Christian Teh-Poot
- Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Evelyn Tzec-Arjona
- Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Pedro Martínez-Vega
- Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Maria Jesus Ramirez-Sierra
- Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Miguel Rosado-Vallado
- Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Eric Dumonteil
- Laboratorio de Parasitología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
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17
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Kerns PW, Ackhart DF, Basaraba RJ, Leid JG, Shirtliff ME. Mycobacterium tuberculosis pellicles express unique proteins recognized by the host humoral response. Pathog Dis 2014; 70:347-58. [PMID: 24453174 DOI: 10.1111/2049-632x.12142] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) causes both acute and chronic infections in humans characterized by tolerance to antibiotics and reactivation to cause secondary tuberculosis. These characteristics have led to renewed interest in the in vitro pellicle, or biofilm mode of growth, where bacteria grow to produce a thick aggregate at the air-liquid interface and exhibit increased phenotypic resistance to antibiotics. We infected guinea pigs with the virulent H37Rv strain of MTB for 60 days at which point we collected blood. To identify antigenic proteins, membrane protein extracts of MTB H37Ra pellicles and shaken cultures grown for 3, 5, or 7 weeks were probed with the infected animals' sera after the proteins were separated by two-dimensional gel electrophoresis (2DGE). Antigenic proteins were then identified using MALDI-TOF/TOF mass spectrometry peptide mass fingerprinting. Antigenic pellicle proteins were compared across the three timepoints to identify those that were produced consistently during pellicle growth. They were also compared to those membrane proteins identified from harvested shaken cultures to determine pellicle-specific vs. universally expressed proteins. Using this technique, we identified 44 distinct antigenic proteins, nine of which were pellicle-specific. The sequence of antigenic pellicle-specific proteins was checked for sequence conservation across 15 sequenced MTB clinical isolates, three other members of the MTB complex, as well as M. avium and M. smegmatis. The antigenic pellicle-specific protein Rv0097 was found to have very high sequence conservation within the MTB complex but not with related mycobacteria, while FabG4 was highly conserved in all mycobacteria analyzed. These conserved pellicle-specific proteins represent targets for the development of future diagnostic tests and vaccines.
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Affiliation(s)
- Patrick W Kerns
- Graduate Program in Molecular Microbiology and Immunology, University of Maryland, Baltimore, Baltimore, MD, USA
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18
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Rokicki J, Knox D, Dowell RD, Copley SD. CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics 2014; 15:65. [PMID: 24460813 PMCID: PMC3908345 DOI: 10.1186/1471-2164-15-65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 01/11/2014] [Indexed: 02/08/2023] Open
Abstract
Background The relationships between bacterial genomes are complicated by rampant horizontal gene transfer, varied selection pressures, acquisition of new genes, loss of genes, and divergence of genes, even in closely related lineages. As more and more bacterial genomes are sequenced, organizing and interpreting the incredible amount of relational information that connects them becomes increasingly difficult. Results We have developed CodaChrome (http://www.sourceforge.com/p/codachrome), a one-versus-all proteome comparison tool that allows the user to visually investigate the relationship between a bacterial proteome of interest and the proteomes encoded by every other bacterial genome recorded in GenBank in a massive interactive heat map. This tool has allowed us to rapidly identify the most highly conserved proteins encoded in the bacterial pan-genome, fast-clock genes useful for subtyping of bacterial species, the evolutionary history of an indel in the Sphingobium lineage, and an example of horizontal gene transfer from a member of the genus Enterococcus to a recent ancestor of Helicobacter pylori. Conclusion CodaChrome is a user-friendly and powerful tool for simultaneously visualizing relationships between thousands of proteomes.
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Affiliation(s)
| | | | - Robin D Dowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder CO, USA.
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19
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Vani J, Shaila MS, Trinath J, Balaji KN, Kaveri SV, Bayry J. Mycobacterium tuberculosis Cell Wall–Associated Rv3812 Protein Induces Strong Dendritic Cell–Mediated Interferon γ Responses and Exhibits Vaccine Potential. J Infect Dis 2013; 208:1034-6. [DOI: 10.1093/infdis/jit281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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20
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Tiwari BM, Kannan N, Vemu L, Raghunand TR. The Mycobacterium tuberculosis PE proteins Rv0285 and Rv1386 modulate innate immunity and mediate bacillary survival in macrophages. PLoS One 2012; 7:e51686. [PMID: 23284742 PMCID: PMC3524191 DOI: 10.1371/journal.pone.0051686] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/05/2012] [Indexed: 12/04/2022] Open
Abstract
The unique PE/PPE multigene family of proteins occupies almost 10% of the coding sequence of Mycobacterium tuberculosis (M.tb), the causative agent of human tuberculosis. Although some members of this family have been shown to be involved in pathways essential to M.tb pathogenesis, their precise physiological functions remain largely undefined. Here, we investigate the roles of the conserved members of the ‘PE only’ subfamily Rv0285 (PE5) and Rv1386 (PE15) in mediating host-pathogen interactions. Recombinant Mycobacterium smegmatis strains expressing PE5 and PE15 showed enhanced survival vs controls in J774.1 and THP-1 macrophages - this increase in viable counts was correlated with a reduction in transcript levels of inducible nitric oxide synthase. An up-regulation of anti- and down-regulation of pro-inflammatory cytokine levels was also observed in infected macrophages implying an immuno-modulatory function for these proteins. Induction of IL-10 production upon infection of THP-1 macrophages was associated with increased phosphorylation of the MAP Kinases p38 and ERK1/2, which was abolished in the presence of the pharmacological inhibitors SB203580 and PD98059. The PE5-PPE4 and PE15-PPE20 gene pairs were observed to be co-operonic in M.tb, hinting at an additional level of complexity in the functioning of these proteins. We conclude that M.tb exploits the PE proteins to evade the host immune response by altering the Th1 and Th2 type balance thereby favouring in vivo bacillary survival.
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Affiliation(s)
| | - Nisha Kannan
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Lakshmi Vemu
- Nizam’s Institute of Medical Sciences, Hyderabad, India
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McEvoy CRE, Cloete R, Müller B, Schürch AC, van Helden PD, Gagneux S, Warren RM, Gey van Pittius NC. Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS One 2012; 7:e30593. [PMID: 22496726 PMCID: PMC3319526 DOI: 10.1371/journal.pone.0030593] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/19/2011] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis complex (MTBC) genomes contain 2 large gene families termed pe and ppe. The function of pe/ppe proteins remains enigmatic but studies suggest that they are secreted or cell surface associated and are involved in bacterial virulence. Previous studies have also shown that some pe/ppe genes are polymorphic, a finding that suggests involvement in antigenic variation. Using comparative sequence analysis of 18 publicly available MTBC whole genome sequences, we have performed alignments of 33 pe (excluding pe_pgrs) and 66 ppe genes in order to detect the frequency and nature of genetic variation. This work has been supplemented by whole gene sequencing of 14 pe/ppe (including 5 pe_pgrs) genes in a cohort of 40 diverse and well defined clinical isolates covering all the main lineages of the M. tuberculosis phylogenetic tree. We show that nsSNP's in pe (excluding pgrs) and ppe genes are 3.0 and 3.3 times higher than in non-pe/ppe genes respectively and that numerous other mutation types are also present at a high frequency. It has previously been shown that non-pe/ppe M. tuberculosis genes display a remarkably low level of purifying selection. Here, we also show that compared to these genes those of the pe/ppe families show a further reduction of selection pressure that suggests neutral evolution. This is inconsistent with the positive selection pressure of "classical" antigenic variation. Finally, by analyzing such a large number of genes we were able to detect large differences in mutation type and frequency between both individual genes and gene sub-families. The high variation rates and absence of selective constraints provides valuable insights into potential pe/ppe function. Since pe/ppe proteins are highly antigenic and have been studied as potential vaccine components these results should also prove informative for aspects of M. tuberculosis vaccine design.
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Affiliation(s)
- Christopher R E McEvoy
- Department of Science and Technology, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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Akhter Y, Ehebauer MT, Mukhopadhyay S, Hasnain SE. The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: Perhaps more? Biochimie 2012; 94:110-6. [DOI: 10.1016/j.biochi.2011.09.026] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/27/2011] [Indexed: 02/03/2023]
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Wang J, Huang Y, Zhang A, Zhu C, Yang Z, Xu H. DNA polymorphism of Mycobacterium tuberculosis PE_PGRS33 gene among clinical isolates of pediatric TB patients and its associations with clinical presentation. Tuberculosis (Edinb) 2011; 91:287-92. [PMID: 21664871 DOI: 10.1016/j.tube.2011.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 04/26/2011] [Accepted: 05/09/2011] [Indexed: 11/16/2022]
Abstract
In vitro and in animal studies have suggested an important role for the Mycobacterium tuberculosis PE_PGRS33 protein in the pathogenesis of TB. A significant level of PE_PGRS33 gene DNA polymorphism among clinical isolates from adult tuberculosis (TB) patients and its association with clinical and epidemiological phenotypes of the disease has been found. To better understand the role of PE_PGRS33 protein in the pathogenesis pediatric TB, we investigated DNA polymorphism of the PE_PGRS33 gene among 101 of pediatric TB patients' isolates and assessed the relationship between the PE_PGRS33 sequence variation and clinical characteristics of TB. Twelve different PE_PGRS33 sequence variations representing 12 different alleles were observed among the 101 M. tuberculosis clinical isolates investigated. Of these 101 isolates, 62(59.41%) had PE_PGRS33 alleles that would result in a change in the amino acid sequence of the PE_PGRS33 protein. The degree of DNA polymorphism within individual M. tuberculosis isolates from pediatric TB patients was remarkably lower than that previously found in M. tuberculosis isolates from adults TB patients. The frequency distribution of isolates having PE_PGRS33 gene sequence variations was similar between Beijing and non-Beijing families of the pathogen. Patients having TB meningitis and negative PPD skin test results appeared to be more likely to be infected by isolates having a mutant type of the PE_PGRS33 gene than patients who had no TB meningitis (OR 2.54, 95% CI [1.11-5.84]) and patients who had positive PPD-skin test results (OR 4.26, 95% CI [1.14-12.86]), respectively. This study provides new insight into the molecular pathogenesis of pediatric TB.
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Affiliation(s)
- Jun Wang
- Department of Infection and Digestion, Children's Hospital of Chongqing Medical University, No. 136 Zhongshan Er Road, Yuzhong District, Chongqing 400014, PR China
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Expression and Purification of Isotopically Enriched MHC Binding Immunogenic Peptides for NMR Studies. Int J Pept Res Ther 2011. [DOI: 10.1007/s10989-011-9251-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Mycobacterial PE/PPE proteins at the host-pathogen interface. Clin Dev Immunol 2011; 2011:497203. [PMID: 21318182 PMCID: PMC3034920 DOI: 10.1155/2011/497203] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/23/2010] [Indexed: 11/17/2022]
Abstract
The mycobacterial PE/PPE proteins have attracted much interest since their formal identification just over a decade ago. It has been widely speculated that these proteins may play a role in evasion of host immune responses, possibly via antigenic variation. Although a cohesive understanding of their function(s) has yet to be established, emerging data increasingly supports a role for the PE/PPE proteins at multiple levels of the infectious process. This paper will delineate salient features of the families revealed by comparative genomics, bioinformatic analyses and genome-wide screening approaches and will summarise existing knowledge of subcellular localization, secretion pathways, and protein structure. These characteristics will be considered in light of findings on innate and adaptive host responses to PE/PPE proteins, and we will review the increasing body of data on B and T cell recognition of these proteins. Finally, we will consider how current knowledge and future explorations may contribute to a more comprehensive understanding of these intriguing proteins and their involvement in host pathogen interactions. Ultimately this information could underpin future intervention strategies, for example, in the area of new and improved diagnostic tools and vaccine candidates.
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In silico proteomic characterization of human epidermal growth factor receptor 2 (HER-2) for the mapping of high affinity antigenic determinants against breast cancer. Amino Acids 2011; 42:1349-60. [DOI: 10.1007/s00726-010-0830-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 12/23/2010] [Indexed: 10/18/2022]
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27
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Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK. Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase. INFECTION GENETICS AND EVOLUTION 2010; 11:308-19. [PMID: 21094280 DOI: 10.1016/j.meegid.2010.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/15/2010] [Accepted: 10/18/2010] [Indexed: 02/01/2023]
Abstract
Antigenic drift is the ability of the swine influenza virus to undergo continuous and progressive changes in response to the host immune system. These changes dictate influenza vaccine updates annually to ensure inclusion of antigens of the most current strains. The identification of those peptides that stimulate T-cell responses, termed T-cell epitopes, is essential for the development of successful vaccines. In this study, the highly conserved and specific epitopes from neuraminidase of globally distributed H1N1 strains were predicted so that these potential vaccine candidates may escape with antigenic drift. A total of nine novel CD8(+) T-cell epitopes for MHC class-I and eight novel CD4(+) T-cell epitopes for MHC class-II alleles were proposed as novel epitope based vaccine candidates. Additionally, the epitope FSYKYGNGV was identified as a highly conserved, immunogenic and potential vaccine candidate, capable for generating both CD8(+) and CD4(+) responses.
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Affiliation(s)
- Shishir K Gupta
- Society for Biological Research & Rural Development, Lucknow, UP, India.
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Gupta SK, Smita S, Sarangi AN, Srivastava M, Akhoon BA, Rahman Q, Gupta SK. In silico CD4+ T-cell epitope prediction and HLA distribution analysis for the potential proteins of Neisseria meningitidis Serogroup B—A clue for vaccine development. Vaccine 2010; 28:7092-7. [DOI: 10.1016/j.vaccine.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 07/22/2010] [Accepted: 08/02/2010] [Indexed: 01/11/2023]
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29
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Expression of PE_PGRS 62 protein in Mycobacterium smegmatis decrease mRNA expression of proinflammatory cytokines IL-1β, IL-6 in macrophages. Mol Cell Biochem 2010; 340:223-9. [DOI: 10.1007/s11010-010-0421-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 02/10/2010] [Indexed: 12/30/2022]
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Nagata R, Kawaji S, Minakawa Y, Wang X, Yanaka T, Mori Y. A specific induction of interleukin-10 by the Map41 recombinant PPE antigen of Mycobacterium avium subsp. paratuberculosis. Vet Immunol Immunopathol 2009; 135:71-78. [PMID: 20018382 DOI: 10.1016/j.vetimm.2009.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 10/29/2009] [Accepted: 11/06/2009] [Indexed: 10/20/2022]
Abstract
Interleukin-10 (IL-10) is not only an essential immunoregulator in host immunity, but also it accounts for the intracellular survival of mycobacteria because of its inhibitory activity against anti-mycobacterial functions of macrophage. It has been also indicated that blood cells from calves infected with Mycobacterium avium subsp. paratuberculosis (Map) produce a large amount of IL-10 after stimulation with Map antigen, and it leads to suppression of Interferon-gamma (IFN-gamma) production in T-cells. This characteristic expression of IL-10 in Map-infected cattle seems to be playing important roles in the pathogenesis of Johne's disease caused by Map, and could be an important diagnostic indicator. The aim of this study was to investigate the diagnostic significance of IL-10 production from blood cells stimulated by a PPE (Proline-Proline-Glutamic acid) protein family of Map. The recombinant PPE protein, Map41, which has been reported as one of the IFN-gamma inducing antigens of Map, also strongly induced IL-10 from macrophages obtained from infected calves. The elicited IL-10 production in response to Map41 from experimentally infected calves was as early as 2 weeks after the inoculation of Map, and the IL-10 production was detected earlier than that of IFN-gamma. The blood cells from calves immunized with Map produced higher amounts of IL-10 against Map41 stimulation than those of calves immunized with various Mycobacterium species. Furthermore, this IL-10 induction also showed high specificity to Map in guinea pigs experimentally infected with various Mycobacterium species. These observations suggest that IL-10 assay is a useful diagnostic method in the early stage of Johne's disease.
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Affiliation(s)
- Reiko Nagata
- Research Team for Paratuberculosis, National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Satoko Kawaji
- Faculty of Veterinary Science, University of Sydney, Australia
| | - Yuu Minakawa
- Research Team for Paratuberculosis, National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Xuebo Wang
- Advanced Technology Development Center, Kyoritsu Seiyaku Corporation, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Tadashi Yanaka
- Advanced Technology Development Center, Kyoritsu Seiyaku Corporation, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Yasuyuki Mori
- Research Team for Paratuberculosis, National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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McEvoy CRE, van Helden PD, Warren RM, van Pittius NCG. Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene region. BMC Evol Biol 2009; 9:237. [PMID: 19769792 PMCID: PMC2758852 DOI: 10.1186/1471-2148-9-237] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 09/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PPE38 (Rv2352c) is a member of the large PPE gene family of Mycobacterium tuberculosis and related mycobacteria. The function of PPE proteins is unknown but evidence suggests that many are cell-surface associated and recognised by the host immune system. Previous studies targeting other PPE gene members suggest that some display high levels of polymorphism and it is thought that this might represent a means of providing antigenic variation. We have analysed the genetic variability of the PPE38 genomic region on a cohort of M. tuberculosis clinical isolates representing all of the major phylogenetic lineages, along with the ancestral M. tuberculosis complex (MTBC) member M. canettii, and supplemented this with analysis of publicly available whole genome sequences representing additional M. tuberculosis clinical isolates, other MTBC members and non tuberculous mycobacteria (NTM). Where possible we have extended this analysis to include the adjacent plcABC and PPE39/40 genomic regions. RESULTS We show that the ancestral MTBC PPE38 region comprises 2 homologous PPE genes (PPE38 and PPE71), separated by 2 esat-6 (esx)-like genes and that this structure derives from an esx/esx/PPE duplication in the common ancestor of M. tuberculosis and M. marinum. We also demonstrate that this region of the genome is hypervariable due to frequent IS6110 integration, IS6110-associated recombination, and homologous recombination and gene conversion events between PPE38 and PPE71. These mutations result in combinations of gene deletion, gene truncation and gene disruption in the majority of clinical isolates. These mutations were generally found to be IS6110 strain lineage-specific, although examples of additional within-lineage and even within-cluster mutations were observed. Furthermore, we provide evidence that the published M. tuberculosis H37Rv whole genome sequence is inaccurate regarding this region. CONCLUSION Our results show that this antigen-encoding region of the M. tuberculosis genome is hypervariable. The observation that numerous different mutations have become fixed within specific lineages demonstrates that this genomic region is undergoing rapid molecular evolution and that further lineage-specific evolutionary expansion and diversification has occurred subsequent to the lineage-defining mutational events. We predict that functional loss of these genes could aid immune evasion. Finally, we also show that the PPE38 region of the published M. tuberculosis H37Rv whole genome sequence is not representative of the ATCC H37Rv reference strain.
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Affiliation(s)
- Christopher RE McEvoy
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
| | - Nicolaas C Gey van Pittius
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, South Africa
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Analysis of predicted CD8+ T cell epitopes from proteins encoded by the specific RD regions of Mycobacterium tuberculosis for vaccine development and specific diagnosis. Mol Biol Rep 2009; 37:1793-9. [PMID: 19609720 DOI: 10.1007/s11033-009-9613-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2008] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
A number of regions designated as RD1-RD16 (region of difference) and encompassing 129 open reading frames have been identified between Mycobacterium tuberculosis and Mycobacterium bovis on the one hand and Bacillus Calmette-Guérin on the other. Identification of T cell epitopes from this set of proteins may serve to define candidate antigens with potentials in specific diagnosis and development of new vaccines against TB. All possible nonameric peptide sequences from proteins of these M. tuberculosis specific regions were analyzed in silico for the ability to bind to 33 alleles of class I HLA. These results reveal that of all RD proteins, a significant number of these peptides are predicted to be high-affinity HLA binders (T (1/2) >or= 100 min), irrespective of the length of the protein, and 67% of the peptides predicted to bind are mono-allelic in their binding. Pathogen peptides that could behave as self- or partially self-peptides in the host were eliminated using a comparative study with the human proteome, thus the number of peptides for analysis was reduced. The predicted epitopes can be tested experimentally for their inclusion in a potential vaccine against tuberculosis and specific diagnosis.
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33
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Design of immunogenic peptides from Mycobacterium tuberculosis genes expressed during macrophage infection. Tuberculosis (Edinb) 2009; 89:210-7. [DOI: 10.1016/j.tube.2009.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 11/21/2022]
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Chaitra MG, Shaila MS, Nayak R. Characterization of T-cell immunogenicity of two PE/PPE proteins of Mycobacterium tuberculosis. J Med Microbiol 2008; 57:1079-1086. [PMID: 18719176 DOI: 10.1099/jmm.0.47565-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The PE and PPE proteins of Mycobacterium tuberculosis form a source of antigenic variation among different strains of this bacterium. Two of the PE_PGRS protein-encoding genes, rv3812 and rv3018c, are expressed in pathogenic mycobacteria and are implicated, respectively, in the persistence of the organism in macrophages and in virulence. Peptides derived from these proteins have been predicted to bind major histocompatibility complex (MHC) class I with high affinity on the basis of immunoinformatics analysis, suggesting a possible role for these proteins in antimycobacterial immunity. In the present work, using DNA constructs containing the rv3812 and rv3018c genes of M. tuberculosis, the immunogenicity of these proteins was demonstrated in BALB/c mice. Immunization with either DNA construct induced a significant number of CD8+-type T cells and a strong Th1-type response, with high gamma interferon (IFN-gamma) and low interleukin-4 responses. Three nonameric peptides of Rv3812 and two of Rv3018c elicited a strong T-cell response in an MHC-restricted manner. An epitope-specific response was demonstrated by the lysis of peptide-pulsed antigen-presenting cells, release of perforin and IFN-gamma production. Experimentally, these peptides bound with high affinity to MHC H-2Kd and showed low dissociation rates of peptide-MHC complexes. This study suggests that the identified T-cell epitopes may contribute to immunity against tuberculosis if included in a vaccine.
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Affiliation(s)
- M G Chaitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - M S Shaila
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - R Nayak
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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Frequent homologous recombination events in Mycobacterium tuberculosis PE/PPE multigene families: potential role in antigenic variability. J Bacteriol 2008; 190:7838-46. [PMID: 18820012 DOI: 10.1128/jb.00827-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PE and PPE (PE/PPE) multigene families of Mycobacterium tuberculosis are particularly GC-rich and share extensive homologous repetitive sequences. We hypothesized that they may undergo homologous recombination events, a mechanism rarely described in the natural evolution of mycobacteria. To test our hypothesis, we developed a specific oligonucleotide-based microarray targeting nearly all of the PE/PPE genes, aimed at detecting signals for homologous recombination. Such a microarray has never before been reported due to the multiplicity and highly repetitive and homologous nature of these sequences. Application of the microarray to a collection of M. tuberculosis clinical isolates (n = 33) representing prevalent spoligotype strain families in Tunisia allowed successful detection of six deleted genomic regions involving a total of two PE and seven PPE genes. Some of these deleted genes are known to be immunodominant or involved in virulence. The four precisely determined deletions were flanked by 400- to 500-bp stretches of nearly identical sequences lying mainly at the conserved N-terminal region of the PE/PPE genes. These highly homologous sequences thus serve as substrates to mediate both intergenic and intragenic homologous recombination events, indicating an important function in generating strain variation. Importantly, all recombination events yielded a new in-frame fusion chimeric gene. Hence, homologous recombination within and between PE/PPE genes likely increased their antigenic variability, which may have profound implications in pathogenicity and/or host adaptation. The finding of high prevalence (approximately 45% and approximately 58%) for at least two of the genomic deletions suggests that they likely confer advantageous biological attributes.
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36
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Lin MY, Ottenhoff TH. Not to wake a sleeping giant: new insights into host-pathogen interactions identify new targets for vaccination against latent Mycobacterium tuberculosis infection. Biol Chem 2008; 389:497-511. [DOI: 10.1515/bc.2008.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AbstractMycobacterium tuberculosisis one of the worlds' most successful and sophisticated pathogens. It is estimated that over 2 billion people today harbour latentM. tuberculosisinfection without any clinical symptoms. As most new cases of active tuberculosis (TB) arise from this (growing) number of latently infected individuals, urgent measures to control TB reactivation are required, including post-exposure/therapeutic vaccines. The current bacille Calmette-Guérin (BCG) vaccine and all new generation TB vaccines being developed and tested are essentially designed as prophylactic vaccines. Unfortunately, these vaccines are unlikely to be effective in individuals already latently infected withM. tuberculosis. Here, we argue that detailed analysis ofM. tuberculosisgenes that are switched on predominantly during latent stage infection may lead to the identification of new antigenic targets for anti-TB strategies. We will describe essential host-pathogen interactions in TB with particular emphasis on TB latency and persistent infection. Subsequently, we will focus on novel groups of late-stage specific genes, encoded amongst others by theM. tuberculosisdormancy (dosR) regulon, and summarise recent studies describing human T-cell recognition of these dormancy antigens in relation to (latent)M. tuberculosisinfection. We will discuss the possible relevance of these new classes of antigens for vaccine development against TB.
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37
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Chaitra MG, Shaila MS, Chandra NR, Nayak R. HLA-A*0201-restricted cytotoxic T-cell epitopes in three PE/PPE family proteins of Mycobacterium tuberculosis. Scand J Immunol 2008; 67:411-7. [PMID: 18248530 DOI: 10.1111/j.1365-3083.2008.02078.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CD8+ T cells are thought to play an important role in protective immunity against tuberculosis. We report the identification of three peptides derived from Rv1818c, Rv3812 and Rv3018c proteins of Mycobacterium tuberculosis that bound to HLA-A*0201 molecules and their ability to induce in vitro T-cell response in peripheral blood lymphocytes from HLA-A*0201-positive healthy individuals (PPD+) and patients with TB. The peptide-specific cytotoxic T lymphocytes (CTL) generated were capable of recognizing peptide pulsed targets. Three 9-mer peptides bound with high affinity to HLA-A*0201 and displayed low dissociation rates of the bound peptide from HLA. Epitope-specific recognition was demonstrated by the release of perforin and gamma-interferon. Overall, our results demonstrate the presence of HLA class I-restricted CD8+ CTL against proteins from PE and PPE proteins of M. tuberculosis and identify epitopes that are strongly recognized by HLA-A*0201-restricted CD8+ T cells in humans. These epitopes thus represent potential subunit components for the design of vaccines against tuberculosis.
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Affiliation(s)
- M G Chaitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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38
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Parida R, Shaila MS, Mukherjee S, Chandra NR, Nayak R. Computational analysis of proteome of H5N1 avian influenza virus to define T cell epitopes with vaccine potential. Vaccine 2007; 25:7530-9. [PMID: 17900763 DOI: 10.1016/j.vaccine.2007.08.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2007] [Revised: 08/16/2007] [Accepted: 08/19/2007] [Indexed: 01/10/2023]
Abstract
The existing vaccines against influenza are based on the generation of neutralizing antibody primarily directed against surface proteins - hemagglutinin and neuraminidase. In this work, we have computationally defined conserved T cell epitopes of proteins of influenza virus H5N1 to help in the design of a vaccine with haplotype specificity for a target population. The peptides from the proteome of H5N1 virus which are predicted to bind to different HLAs, do not show similarity with peptides of human proteome and are also identified to be generated by proteolytic cleavage. These peptides could be made use of in the design of either a DNA vaccine or a subunit vaccine against influenza.
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Affiliation(s)
- R Parida
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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39
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Chaitra MG, Nayak R, Shaila MS. Modulation of immune responses in mice to recombinant antigens from PE and PPE families of proteins of Mycobacterium tuberculosis by the Ribi adjuvant. Vaccine 2007; 25:7168-76. [PMID: 17709160 DOI: 10.1016/j.vaccine.2007.07.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 07/14/2007] [Accepted: 07/16/2007] [Indexed: 11/25/2022]
Abstract
Three proteins of PE and PPE families of Mycobacterium tuberculosis were evaluated for their ability to induce T cell responses in mice. To enhance immunity induced by protein immunization, we tested the efficacy of adjuvant Ribi (monophosphoryl lipid A+TDM), along with three proteins of the PE/PPE family. Balb/c mice were subcutaneously injected with recombinant proteins, encoded by Rv1818c, Rv3018c and Rv3812 genes of M. tuberculosis H37Rv, formulated with Ribi or IFA for comparative study. Sera from mice immunized with Ribi revealed an increase in the specific immunoglobulin G titers by twofold against Ribi than in mice immunized with IFA. Ribi also elicited stronger delayed-type hypersensitivity and cytotoxic T-lymphocyte activity against the recombinant proteins when compared with IFA. Antigen specific IgG subclass analysis showed that Ribi tends to facilitate IgG2a production, suggesting enhancement of predominant Th1 response which in turn may facilitate increased production of protective IFN-gamma. Furthermore, Ribi preparation increased the number of T cells secreting IFN-gamma. These results indicate that Ribi acts as an effective adjuvant for immune response to antigens of M. tuberculosis. For the first time, we demonstrate that Rv3018c, Rv1818c and Rv3812 proteins of PE/PPE family are T cell antigens with vaccine potential.
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MESH Headings
- Adjuvants, Immunologic
- Animals
- Antibodies, Bacterial/blood
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Cell Wall Skeleton/immunology
- Cord Factors/immunology
- Cytotoxicity, Immunologic
- Female
- Freund's Adjuvant/immunology
- Hypersensitivity, Delayed
- Immunoglobulin G/blood
- Injections, Subcutaneous
- Interferon-gamma/biosynthesis
- Lipid A/analogs & derivatives
- Lipid A/immunology
- Mice
- Mice, Inbred BALB C
- Mycobacterium tuberculosis/immunology
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- T-Lymphocytes/immunology
- Tuberculosis Vaccines/genetics
- Tuberculosis Vaccines/immunology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
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Affiliation(s)
- M G Chaitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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40
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Chaitra MG, Shaila MS, Nayak R. Evaluation of T-cell responses to peptides with MHC class I-binding motifs derived from PE_PGRS 33 protein of Mycobacterium tuberculosis. J Med Microbiol 2007; 56:466-474. [PMID: 17374885 DOI: 10.1099/jmm.0.46928-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The PE and PPE proteins of Mycobacterium tuberculosis form a source of antigenic variation among different strains of M. tuberculosis. One of the PE_PGRS proteins, Rv1818c, plays a role in the pathogenesis of mycobacterial infection and specifically influences host-cell responses to tuberculosis infection. Although little is known about these two classes of protein, an immunoinformatics approach has indicated the possibility of their participation in eliciting a major histocompatibility complex (MHC) class I-mediated immune response against tuberculosis, as peptides derived from Rv1818c are predicted to bind to MHC class I molecules with high affinity. In the present work, a DNA vaccine was constructed encoding the full-length Rv1818c protein of M. tuberculosis and its immunogenicity was analysed in BALB/c mice. Immunization with Rv1818c DNA induced a strong CD8+ cytotoxic lymphocyte and Th1-type response, with high levels of gamma interferon (IFN-gamma) and low levels of interleukin-4. Two nonameric peptides (Peptide(6-14) and Peptide(385-393)) from Rv1818c were identified by their ability to induce the production of IFN-gamma by CD8+ T cells in mice immunized with Rv1818c DNA. An epitope-specific response was demonstrated by the lysis of peptide-pulsed antigen-presenting cells, release of cytotoxic granules and IFN-gamma production. These peptides bound with high affinity to MHC H-2K(d) and showed low dissociation rates of peptide-MHC complexes. These results could form the basis for testing the identified T-cell epitopes of PE_PGRS proteins in the induction of protective immunity against M. tuberculosis challenge in the mouse model.
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Affiliation(s)
- M G Chaitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - M S Shaila
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - R Nayak
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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41
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Shaila MS, Nayak R, Prakash SS, Georgousakis M, Brandt E, McMillan DJ, Batzloff MR, Pruksakorn S, Good MF, Sriprakash KS. Comparative in silico analysis of two vaccine candidates for group A streptococcus predicts that they both may have similar safety profiles. Vaccine 2007; 25:3567-73. [PMID: 17293014 DOI: 10.1016/j.vaccine.2007.01.079] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 12/20/2006] [Accepted: 01/16/2007] [Indexed: 10/23/2022]
Abstract
BACKGROUND Concerns of immune cross-reactivity, between epitopes of the group A streptococcal (GAS) M-proteins and host proteins have hindered the progress of an effective GAS vaccine. An ideal M-protein based subunit vaccine should not elicit heart tissue cross-reactive antibody responses and should not activate M-protein specific CD4+ T-cells. In the current study we used a bioinformatic and immunoinformatic approach to assess the safety of J8 and J14, chimeric vaccine constructs containing a GAS derived M-protein epitope embedded in flanking GCN4 region. We demonstrate that at the primary amino acid level J8 and J14 show very little homology to human proteins. ProPred, RANKPEP and HLABIND algorithms failed to predict significant binding between the M-protein specific regions of J8 and J14 and class II binding alleles. A single peptide was predicted to bind to HLA class I allele B_2705. This data was supported by cellular proliferation assays demonstrating few peripheral blood mononuclear cells (PBMCs) from donors respond to J8 and J14. Reassuringly, there was no correlation between proliferation to these peptides, and proliferation to host proteins. This data suggests that J8 and J14 are unlikely to induce cross-reactive immune responses, and will be safe for use in humans.
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Affiliation(s)
- Melkote S Shaila
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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42
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Mishra S, Sinha S. Prediction and molecular modeling of T-cell epitopes derived from placental alkaline phosphatase for use in cancer immunotherapy. J Biomol Struct Dyn 2006; 24:109-21. [PMID: 16928134 DOI: 10.1080/07391102.2006.10507104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In our ongoing efforts to combat cancer, peptide-based tumor vaccines are promising as one of the several alternatives used for cancer immunotherapy and immunoprevention. We have attempted to identify T-cell epitopes suitable for the development of a peptide-based cancer vaccine directed towards placental isozyme of alkaline phosphatase (PLAP), an oncofetal antigen. After identifying amino acid residues specific to PLAP and distinct from other close PLAP homologs, we have used sequence-based immunoinformatics tools (BIMAS and SYFPEITHI) and conducted molecular modeling studies using InsightII to investigate the binding affinity of the epitopes containing the unique residues with respective MHC class I molecules. Promiscuous epitopes binding to different alleles of different class I HLA loci were analyzed to get a population coverage that is widespread. Binding affinity deduced from the modeling studies corroborated the status of most of the epitopes scoring high in BIMAS and SYFPEITHI. We have thus identified specific epitopes from PLAP that have a potential for binding to their respective MHC class I alleles with high affinity. These peptides would be analysed in experiments to demonstrate their involvement in the induction of primary cytotoxic T-cell responses in vitro, using respective HLA-restricted T-cells in our way towards the development of an effective anti-cancer vaccine in a background of diverse MHC haplotypes.
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Affiliation(s)
- Seema Mishra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029 India
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43
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Insights into the evolutionary history of tubercle bacilli as disclosed by genetic rearrangements within a PE_PGRS duplicated gene pair. BMC Evol Biol 2006; 6:107. [PMID: 17163995 PMCID: PMC1762029 DOI: 10.1186/1471-2148-6-107] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 12/12/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The highly homologous PE_PGRS (Proline-glutamic acid_polymorphic GC-rich repetitive sequence) genes are members of the PE multigene family which is found only in mycobacteria. PE genes are particularly abundant within the genomes of pathogenic mycobacteria where they seem to have expanded as a result of gene duplication events. PE_PGRS genes are characterized by their high GC content and extensive repetitive sequences, making them prone to recombination events and genetic variability. RESULTS Comparative sequence analysis of Mycobacterium tuberculosis genes PE_PGRS17 (Rv0978c) and PE_PGRS18 (Rv0980c) revealed a striking genetic variation associated with this typical tandem duplicate. In comparison to the M. tuberculosis reference strain H37Rv, the variation (named the 12/40 polymorphism) consists of an in-frame 12-bp insertion invariably accompanied by a set of 40 single nucleotide polymorphisms (SNPs) that occurs either in PE_PGRS17 or in both genes. Sequence analysis of the paralogous genes in a representative set of worldwide distributed tubercle bacilli isolates revealed data which supported previously proposed evolutionary scenarios for the M. tuberculosis complex (MTBC) and confirmed the very ancient origin of "M. canettii" and other smooth tubercle bacilli. Strikingly, the identified polymorphism appears to be coincident with the emergence of the post-bottleneck successful clone from which the MTBC expanded. Furthermore, the findings provide direct and clear evidence for the natural occurrence of gene conversion in mycobacteria, which appears to be restricted to modern M. tuberculosis strains. CONCLUSION This study provides a new perspective to explore the molecular events that accompanied the evolution, clonal expansion, and recent diversification of tubercle bacilli.
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de Jonge MI, Brosch R, Brodin P, Demangel C, Cole ST. Tuberculosis: from genome to vaccine. Expert Rev Vaccines 2006; 4:541-51. [PMID: 16117711 DOI: 10.1586/14760584.4.4.541] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The availability of mycobacterial genome sequences has paved the way to identifying potential tuberculosis vaccine candidates in order to replace the currently used bacillus Calmette-Guérin (BCG) vaccines that show variable protective efficacy in adults. Genomics provides the basis for bioinformatic, transcriptomic and proteomic analysis, increases screening efficiency and enables valuable information concerning the biology and virulence of the mycobacterial species to be extracted by comparative genomics. Although in silico results must be confirmed in vitro and in vivo, bioinformatic analysis of the genomes is highlighting candidates for testing. For designing subunit vaccines, attenuated or improved recombinant whole-cell live vaccines, information from the genomes of the human host and pathogenic mycobacterial species is of great help.
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Affiliation(s)
- Marien I de Jonge
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 Rue du Docteur Roux 75724 Paris, France.
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45
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Vani J, Shaila MS, Chandra NR, Nayak R. A combined immuno-informatics and structure-based modeling approach for prediction of T cell epitopes of secretory proteins of Mycobacterium tuberculosis. Microbes Infect 2006; 8:738-46. [PMID: 16476561 DOI: 10.1016/j.micinf.2005.09.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2005] [Revised: 09/06/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
The role of secretory proteins of Mycobacterium tuberculosis in pathogenesis and stimulation of specific host responses is well documented. They are also shown to activate different cell types, which subsequently present mycobacterial antigens to T cells. Therefore identification of T cell epitopes from this set of proteins may serve to define candidate antigens with vaccine potential. Fifty-two secretory proteins of M. tuberculosis H37Rv were analyzed computationally for the presence of HLA class I binding nonameric peptides. All possible overlapping nonameric peptide sequences from 52 secretory proteins were generated in silico and analyzed for their ability to bind to 33 alleles belonging to A, B and C loci of HLA class I. Fifteen percent of generated peptides are predicted to bind to HLA with halftime of dissociation T(1/2) >or=100 min and 73% of the peptides predicted to bind are mono-allelic in their binding. The structural basis for recognition of no-namers by different HLA molecules was studied employing structural modeling of HLA class I-peptide complexes and there exists a good correlation between structural analysis and binding prediction. Pathogen peptides that could behave as self- or partially self-peptides in the host were eliminated using a comparative study with the human proteome, thus reducing the number of peptides for analysis. The implications of the finding for vaccine development are discussed vis-à-vis the limitations of the use of subunit vaccine and DNA vaccine.
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Affiliation(s)
- J Vani
- Department of Microbiology & Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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Sánchez FO, Rodríguez JI, Agudelo G, García LF. Immune responsiveness and lymphokine production in patients with tuberculosis and healthy controls. Infect Immun 1994; 10:858-67. [PMID: 7960152 DOI: 10.1016/j.micinf.2008.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 04/05/2008] [Accepted: 04/26/2008] [Indexed: 01/13/2023] Open
Abstract
The aim of the present study was to determine the profile of immune responsiveness that differentiates patients with tuberculosis (TB) from healthy tuberculin-positive controls. Forty-five patients with pulmonary TB and 16 healthy tuberculin-positive controls, all human immunodeficiency virus negative, were studied. Patients had decreased reactivity to tuberculin, diminished proliferative response to purified protein derivative (PPD), lower concentrations of interleukin-2 (IL-2) and gamma interferon in PPD-stimulated cultures, no increase in the percentage of gamma/delta cells in PPD-stimulated cultures, and higher immunoglobulin G antimycobacterial antibodies compared with control subjects. Furthermore, controls exhibited decreased production of IL-4 by PPD-stimulated cells. Multivariate discriminant and factor analyses demonstrated divergent patterns of immune reactivity against mycobacterial antigens. The association of IL-4 and immunoglobulin G antibody levels in patients, in contrast to the high reactivity to tuberculin, increased proliferation to PPD, and higher levels of IL-2 and gamma interferon observed in healthy controls suggested that most TB patients exhibit a TH2 pattern of immune responsiveness while tuberculin-positive healthy individuals have a TH1 pattern.
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Affiliation(s)
- F O Sánchez
- Laboratorio Central de Investigaciones, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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