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P M, Ahmad J, Samal J, Sheikh JA, Arora SK, Khubaib M, Aggarwal H, Kumari I, Luthra K, Rahman SA, Hasnain SE, Ehtesham NZ. Mycobacterium tuberculosis Specific Protein Rv1509 Evokes Efficient Innate and Adaptive Immune Response Indicative of Protective Th1 Immune Signature. Front Immunol 2021; 12:706081. [PMID: 34386011 PMCID: PMC8354026 DOI: 10.3389/fimmu.2021.706081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022] Open
Abstract
Dissecting the function(s) of proteins present exclusively in Mycobacterium tuberculosis (M.tb) will provide important clues regarding the role of these proteins in mycobacterial pathogenesis. Using extensive computational approaches, we shortlisted ORFs/proteins unique to M.tb among 13 different species of mycobacteria and identified a hypothetical protein Rv1509 as a ‘signature protein’ of M.tb. This unique protein was found to be present only in M.tb and absent in all other mycobacterial species, including BCG. In silico analysis identified numerous putative T cell and B cell epitopes in Rv1509. Initial in vitro experiments using innate immune cells demonstrated Rv1509 to be immunogenic with potential to modulate innate immune responses. Macrophages treated with Rv1509 exhibited higher activation status along with substantial release of pro-inflammatory cytokines. Besides, Rv1509 protein boosts dendritic cell maturation by increasing the expression of activation markers such as CD80, HLA-DR and decreasing DC-SIGN expression and this interaction was mediated by innate immune receptor TLR2. Further, in vivo experiments in mice demonstrated that Rv1509 protein promotes the expansion of multifunctional CD4+ and CD8+T cells and induces effector memory response along with evoking a canonical Th1 type of immune response. Rv1509 also induces substantial B cell response as revealed by increased IgG reactivity in sera of immunized animals. This allowed us to demonstrate the diagnostic efficacy of this protein in sera of human TB patients compared to the healthy controls. Taken together, our results reveal that Rv1509 signature protein has immunomodulatory functions evoking immunological memory response with possible implications in serodiagnosis and TB vaccine development.
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Affiliation(s)
- Manjunath P
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Javeed Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
| | | | - Simran Kaur Arora
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Mohd Khubaib
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Heena Aggarwal
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Seyed E Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India.,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India
| | - Nasreen Z Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology, New Delhi, India
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Rana A, Thakur S, Bhardwaj N, Kumar D, Akhter Y. Excavating the surface-associated and secretory proteome of Mycobacterium leprae for identifying vaccines and diagnostic markers relevant immunodominant epitopes. Pathog Dis 2016; 74:ftw110. [PMID: 27856491 DOI: 10.1093/femspd/ftw110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/13/2016] [Accepted: 11/13/2016] [Indexed: 02/03/2023] Open
Abstract
For centuries, Mycobacterium leprae, etiological agent of leprosy, has been afflicting mankind regardless of extensive use of live-attenuated vaccines and antibiotics. Surface-associated and secretory proteins (SASPs) are attractive targets against bacteria. We have integrated biological knowledge with computational approaches and present a proteome-wide identification of SASPs. We also performed computational assignment of immunodominant epitopes as coordinates of prospective antigenic candidates in most important class of SASPs, the outer membrane proteins (OMPs). Exploiting the known protein sequence and structural characteristics shared by the SASPs from bacteria, 17 lipoproteins, 11 secretory and 19 novel OMPs (including 4 essential proteins) were identified in M. leprae As OMPs represent the most exposed antigens on the cell surface, their immunoinformatics analysis showed that the identified 19 OMPs harbor T-cell MHC class I epitopes and class II epitopes against HLA-DR alleles (54), while 15 OMPs present potential T-cell class II epitopes against HLA-DQ alleles (6) and 7 OMPs possess T-cell class II epitopes against HLA-DP alleles (5) of humans. Additionally, 11 M. leprae OMPs were found to have B-cell epitopes and these may be considered as prime candidates for the development of new immunotherapeutics against M. leprae.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh-176206, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh-176206, India
| | - Nupur Bhardwaj
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh-176206, India
| | - Devender Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh-176206, India
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh-176206, India
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Harvey MJ, Mason NJ, McLean A, Murray-Rust P, Rzepa HS, Stewart JJP. Standards-based curation of a decade-old digital repository dataset of molecular information. J Cheminform 2015; 7:43. [PMID: 26322133 PMCID: PMC4550659 DOI: 10.1186/s13321-015-0093-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/02/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. RESULTS The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. CONCLUSIONS We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the "supporting information") should be conducted in a manner that facilitates automatic periodic curation. Graphical abstractStandards and metadata-based curation of a decade-old digital repository dataset of molecular information.
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Affiliation(s)
- Matthew J Harvey
- />High Performance Computing Service, Imperial College London, London, SW7 2AZ UK
| | - Nicholas J Mason
- />Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
| | - Andrew McLean
- />High Performance Computing Service, Imperial College London, London, SW7 2AZ UK
| | - Peter Murray-Rust
- />Department of Chemistry, Centre for Molecular Informatics, Lensfield Road, Cambridge, CB2 1EW UK
| | - Henry S Rzepa
- />Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
| | - James J P Stewart
- />Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO 80921 USA
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Harvey MJ, Mason NJ, McLean A, Rzepa HS. Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers. J Cheminform 2015; 7:37. [PMID: 26257829 PMCID: PMC4528360 DOI: 10.1186/s13321-015-0081-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the persistent identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. RESULTS The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. CONCLUSIONS Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data. Graphical abstract.
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Affiliation(s)
- Matthew J Harvey
- />High Performance Computing Service, Imperial College London, London, UK
| | - Nicholas J Mason
- />Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
| | - Andrew McLean
- />High Performance Computing Service, Imperial College London, London, UK
| | - Henry S Rzepa
- />Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ UK
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Harvey MJ, Mason NJ, Rzepa HS. Digital data repositories in chemistry and their integration with journals and electronic notebooks. J Chem Inf Model 2014; 54:2627-35. [PMID: 25171653 DOI: 10.1021/ci500302p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We discuss the concept of recasting the data-rich scientific journal article into two components, a narrative and separate data components, each of which is assigned a persistent digital object identifier. Doing so allows each of these components to exist in an environment optimized for purpose. We make use of a poorly-known feature of the handle system for assigning persistent identifiers that allows an individual data file from a larger file set to be retrieved according to its file name or its MIME type. The data objects allow facile visualization and retrieval for reuse of the data and facilitates other operations such as data mining. Examples from five recently published articles illustrate these concepts.
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Affiliation(s)
- Matthew J Harvey
- High Performance Computing Unit, ICT Division, Imperial College London , South Kensington Campus, London SW7 2AZ, United Kingdom
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Rzepa HS, Wentrup C. Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO2 Extrusions from Five-Membered Rings. J Org Chem 2013; 78:7565-74. [DOI: 10.1021/jo401146k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henry S. Rzepa
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW2 2AZ, U.K
| | - Curt Wentrup
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland
4072, Australia
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