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Neto TAP, Sidney J, Grifoni A, Sette A. Correlative CD4 and CD8 T-cell immunodominance in humans and mice: Implications for preclinical testing. Cell Mol Immunol 2023; 20:1328-1338. [PMID: 37726420 PMCID: PMC10616275 DOI: 10.1038/s41423-023-01083-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
Antigen-specific T-cell recognition is restricted by Major Histocompatibility Complex (MHC) molecules, and differences between CD4 and CD8 immunogenicity in humans and animal species used in preclinical vaccine testing are yet to be fully understood. In this study, we addressed this matter by analyzing experimentally identified epitopes based on published data curated in the Immune Epitopes DataBase (IEDB) database. We first analyzed SARS-CoV-2 spike (S) and nucleoprotein (N), which are two common targets of the immune response and well studied in both human and mouse systems. We observed a weak but statistically significant correlation between human and H-2b mouse T-cell responses (CD8 S specific (r = 0.206, p = 1.37 × 10-13); CD4 S specific (r = 0.118, p = 2.63 × 10-5) and N specific (r = 0.179, p = 2.55 × 10-4)). Due to intrinsic differences in MHC molecules across species, we also investigated the association between the immunodominance of common Human Leukocyte Antigen (HLA) alleles for which HLA transgenic mice are available, namely, A*02:01, B*07:02, DRB1*01:01, and DRB1*04:01, and found higher significant correlations for both CD8 and CD4 (maximum r = 0.702, p = 1.36 × 10-31 and r = 0.594, p = 3.04-122, respectively). Our results further indicated that some regions are commonly immunogenic between humans and mice (either H-2b or HLA transgenic) but that others are human specific. Finally, we noted a significant correlation between CD8 and CD4 S- (r = 0.258, p = 7.33 × 1021) and N-specific (r = 0.369, p = 2.43 × 1014) responses, suggesting that discrete protein subregions can be simultaneously recognized by T cells. These findings were confirmed in other viral systems, providing general guidance for the use of murine models to test T-cell immunogenicity of viral antigens destined for human use.
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Affiliation(s)
- Tertuliano Alves Pereira Neto
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA
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Abstract
Background Ebolavirus (EBOV) is responsible for one of the most fatal diseases encountered by mankind. Cellular T-cell responses have been implicated to be important in providing protection against the virus. Antigenic variation can result in viral escape from immune recognition. Mapping targets of immune responses among the sequence of viral proteins is, thus, an important first step towards understanding the immune responses to viral variants and can aid in the identification of vaccine targets. Herein, we performed a large-scale, proteome-wide mapping and diversity analyses of putative HLA supertype-restricted T-cell epitopes of Zaire ebolavirus (ZEBOV), the most pathogenic species among the EBOV family. Methods All publicly available ZEBOV sequences (14,098) for each of the nine viral proteins were retrieved, removed of irrelevant and duplicate sequences, and aligned. The overall proteome diversity of the non-redundant sequences was studied by use of Shannon’s entropy. The sequences were predicted, by use of the NetCTLpan server, for HLA-A2, -A3, and -B7 supertype-restricted epitopes, which are relevant to African and other ethnicities and provide for large (~86%) population coverage. The predicted epitopes were mapped to the alignment of each protein for analyses of antigenic sequence diversity and relevance to structure and function. The putative epitopes were validated by comparison with experimentally confirmed epitopes. Results & discussion ZEBOV proteome was generally conserved, with an average entropy of 0.16. The 185 HLA supertype-restricted T-cell epitopes predicted (82 (A2), 37 (A3) and 66 (B7)) mapped to 125 alignment positions and covered ~24% of the proteome length. Many of the epitopes showed a propensity to co-localize at select positions of the alignment. Thirty (30) of the mapped positions were completely conserved and may be attractive for vaccine design. The remaining (95) positions had one or more epitopes, with or without non-epitope variants. A significant number (24) of the putative epitopes matched reported experimentally validated HLA ligands/T-cell epitopes of A2, A3 and/or B7 supertype representative allele restrictions. The epitopes generally corresponded to functional motifs/domains and there was no correlation to localization on the protein 3D structure. These data and the epitope map provide important insights into the interaction between EBOV and the host immune system. Electronic supplementary material The online version of this article (10.1186/s12864-017-4328-8) contains supplementary material, which is available to authorized users.
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Khan AM, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Abd Raman HS, Brusic V, Tan TW, Thomas August J. Analysis of viral diversity for vaccine target discovery. BMC Med Genomics 2017; 10:78. [PMID: 29322922 PMCID: PMC5763473 DOI: 10.1186/s12920-017-0301-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples. Our methodology has been implemented as an analytical pipeline that brings significant advancement to the field of reverse vaccinology, enabling systematic screening of known sequence data in nature for identification of vaccine targets. This includes key steps (i) comprehensive and extensive collection of sequence data of viral proteomes (the virome), (ii) data cleaning, (iii) large-scale sequence alignments, (iv) peptide entropy analysis, (v) intra- and inter-species variation analysis of conserved sequences, including human homology analysis, and (vi) functional and immunological relevance analysis. CONCLUSION These steps are combined into the pipeline ensuring that a more refined process, as compared to a simple evolutionary conservation analysis, will facilitate a better selection of vaccine targets and their prioritization for subsequent experimental validation.
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Affiliation(s)
- Asif M. Khan
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Jalan MAEPS Perdana, Serdang, Selangor Darul Ehsan 43400 Malaysia
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 USA
| | - Yongli Hu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597 Singapore
| | - Olivo Miotto
- Centre for Genomics and Global Health, University of Oxford, Oxford, UK
- Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Rajthevee, Bangkok, Thailand
| | - Natascha M. Thevasagayam
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597 Singapore
| | - Rashmi Sukumaran
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597 Singapore
| | - Hadia Syahirah Abd Raman
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Jalan MAEPS Perdana, Serdang, Selangor Darul Ehsan 43400 Malaysia
| | - Vladimir Brusic
- Menzies Health Institute Queensland, Griffith University, Parklands Dr, Southport, 4215 QLD Australia
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597 Singapore
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 USA
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Kumar S, Thangakani AM, Nagarajan R, Singh SK, Velmurugan D, Gromiha MM. Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions. Sci Rep 2016; 6:22258. [PMID: 26924748 PMCID: PMC4770294 DOI: 10.1038/srep22258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
Why do patients suffering from neurodegenerative diseases generate autoantibodies that selectively bind soluble aggregates of amyloidogenic proteins? Presently, molecular basis of interactions between the soluble aggregates and human immune system is unknown. By analyzing sequences of experimentally validated T-cell autoimmune epitopes, aggregating peptides, amyloidogenic proteins and randomly generated peptides, here we report overlapping regions that likely drive aggregation as well as generate autoantibodies against the aggregates. Sequence features, that make short peptides susceptible to aggregation, increase their incidence in human T-cell autoimmune epitopes by 4–6 times. Many epitopes are predicted to be significantly aggregation prone (aggregation propensities ≥10%) and the ones containing experimentally validated aggregating regions are enriched in hydrophobicity by 10–20%. Aggregate morphologies also influence Human Leukocyte Antigen (HLA) - types recognized by the aggregating regions containing epitopes. Most (88%) epitopes that contain amyloid fibril forming regions bind HLA-DR, while majority (63%) of those containing amorphous β-aggregating regions bind HLA-DQ. More than two-thirds (70%) of human amyloidogenic proteins contain overlapping regions that are simultaneously aggregation prone and auto-immunogenic. Such regions help clear soluble aggregates by generating selective autoantibodies against them. This can be harnessed for early diagnosis of proteinopathies and for drug/vaccine design against them.
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Affiliation(s)
- Sandeep Kumar
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield MO 63017, USA
| | - A Mary Thangakani
- Center for Advanced Studies in Crystallography and Biophysics and Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - R Nagarajan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Satish K Singh
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield MO 63017, USA
| | - D Velmurugan
- Center for Advanced Studies in Crystallography and Biophysics and Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Brusic V, Petrovsky N. Immunoinformatics and its relevance to understanding human immune disease. Expert Rev Clin Immunol 2014; 1:145-57. [DOI: 10.1586/1744666x.1.1.145] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Huang J, Cao Y, Bu X, Wu C. Residue analysis of a CTL epitope of SARS-CoV spike protein by IFN-gamma production and bioinformatics prediction. BMC Immunol 2012; 13:50. [PMID: 22963340 PMCID: PMC3575293 DOI: 10.1186/1471-2172-13-50] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/31/2012] [Indexed: 01/15/2023] Open
Abstract
Background Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by the novel coronavirus SARS-CoV. The T cell epitopes of the SARS CoV spike protein are well known, but no systematic evaluation of the functional and structural roles of each residue has been reported for these antigenic epitopes. Analysis of the functional importance of side-chains by mutational study may exaggerate the effect by imposing a structural disturbance or an unusual steric, electrostatic or hydrophobic interaction. Results We demonstrated that N50 could induce significant IFN-gamma response from SARS-CoV S DNA immunized mice splenocytes by the means of ELISA, ELISPOT and FACS. Moreover, S366-374 was predicted to be an optimal epitope by bioinformatics tools: ANN, SMM, ARB and BIMAS, and confirmed by IFN-gamma response induced by a series of S358-374-derived peptides. Furthermore, each of S366-374 was replaced by alanine (A), lysine (K) or aspartic acid (D), respectively. ANN was used to estimate the binding affinity of single S366-374 mutants to H-2 Kd. Y367 and L374 were predicated to possess the most important role in peptide binding. Additionally, these one residue mutated peptides were synthesized, and IFN-gamma production induced by G368, V369, A371, T372 and K373 mutated S366-374 were decreased obviously. Conclusions We demonstrated that S366-374 is an optimal H-2 Kd CTL epitope in the SARS CoV S protein. Moreover, Y367, S370, and L374 are anchors in the epitope, while C366, G368, V369, A371, T372, and K373 may directly interact with TCR on the surface of CD8-T cells.
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Affiliation(s)
- Jun Huang
- Institute of Immunology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control Research of Ministry of Education, Sun Yat-sen University, Guangzhou, China
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Atanasova M, Dimitrov I, Flower DR, Doytchinova I. MHC Class II Binding Prediction by Molecular Docking. Mol Inform 2011; 30:368-75. [PMID: 27466953 DOI: 10.1002/minf.201000132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/01/2010] [Indexed: 01/08/2023]
Abstract
Proteins of the Major Histocompatibility Complex (MHC) bind self and nonself peptide antigens or epitopes within the cell and present them at the cell surface for recognition by T cells. All T-cell epitopes are MHC binders but not all MCH binders are T-cell epitopes. The MHC class II proteins are extremely polymorphic. Polymorphic residues cluster in the peptide-binding region and largely determine the MHC's peptide selectivity. The peptide binding site on MHC class II proteins consist of five binding pockets. Using molecular docking, we have modelled the interactions between peptide and MHC class II proteins from locus DRB1. A combinatorial peptide library was generated by mutation of residues at peptide positions which correspond to binding pockets (so called anchor positions). The binding affinities were assessed using different scoring functions. The normalized scoring functions for each amino acid at each anchor position were used to construct quantitative matrices (QM) for MHC class II binding prediction. Models were validated by external test sets comprising 4540 known binders. Eighty percent of the known binders are identified in the best predicted 15 % of all overlapping peptides, originating from one protein.
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Affiliation(s)
- M Atanasova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str, 1000 Sofia, Bulgaria phone: +359 2 9236599; fax: +359 2 9879874.
| | - I Dimitrov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str, 1000 Sofia, Bulgaria phone: +359 2 9236599; fax: +359 2 9879874
| | - D R Flower
- Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - I Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str, 1000 Sofia, Bulgaria phone: +359 2 9236599; fax: +359 2 9879874
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Khan JM, Ranganathan S. pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. Immunome Res 2010; 6 Suppl 1:S2. [PMID: 20875153 PMCID: PMC2946780 DOI: 10.1186/1745-7580-6-s1-s2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Identification of antigenic peptide epitopes is an essential prerequisite in T cell-based molecular vaccine design. Computational (sequence-based and structure-based) methods are inexpensive and efficient compared to experimental approaches in screening numerous peptides against their cognate MHC alleles. In structure-based protocols, suited to alleles with limited epitope data, the first step is to identify high-binding peptides using docking techniques, which need improvement in speed and efficiency to be useful in large-scale screening studies. We present pDOCK: a new computational technique for rapid and accurate docking of flexible peptides to MHC receptors and primarily apply it on a non-redundant dataset of 186 pMHC (MHC-I and MHC-II) complexes with X-ray crystal structures. Results We have compared our docked structures with experimental crystallographic structures for the immunologically relevant nonameric core of the bound peptide for MHC-I and MHC-II complexes. Primary testing for re-docking of peptides into their respective MHC grooves generated 159 out of 186 peptides with Cα RMSD of less than 1.00 Å, with a mean of 0.56 Å. Amongst the 25 peptides used for single and variant template docking, the Cα RMSD values were below 1.00 Å for 23 peptides. Compared to our earlier docking methodology, pDOCK shows upto 2.5 fold improvement in the accuracy and is ~60% faster. Results of validation against previously published studies represent a seven-fold increase in pDOCK accuracy. Conclusions The limitations of our previous methodology have been addressed in the new docking protocol making it a rapid and accurate method to evaluate pMHC binding. pDOCK is a generic method and although benchmarks against experimental structures, it can be applied to alleles with no structural data using sequence information. Our outcomes establish the efficacy of our procedure to predict highly accurate peptide structures permitting conformational sampling of the peptide in MHC binding groove. Our results also support the applicability of pDOCK for in silico identification of promiscuous peptide epitopes that are relevant to higher proportions of human population with greater propensity to activate T cells making them key targets for the design of vaccines and immunotherapies.
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Affiliation(s)
- Javed Mohammed Khan
- Department of Chemistry and Biomolecular Sciences and ARC Center of Excellence in Bioinformatics, Macquarie University, NSW 2109, Australia.
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Saffari B, Mohabatkar H. Computational analysis of cysteine proteases (Clan CA, Family Cl) of Leishmania major to find potential epitopic regions. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 7:87-95. [PMID: 19944381 PMCID: PMC5054412 DOI: 10.1016/s1672-0229(08)60037-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Leishmania is associated with a broad spectrum of diseases, ranging from simple cutaneous to invasive visceral leishmaniasis. Here, the sequences of ten cysteine proteases of types A, B and C of Leishmania major were obtained from GeneDB database. Prediction of MHC class I epitopes of these cysteine proteases was performed by NetCTL program version 1.2. In addition, by using BcePred server, different structural properties of the proteins were predicted to find out their potential B cell epitopes. According to this computational analysis, nine regions were predicted as B cell epitopes. The results provide useful information for designing peptide-based vaccines.
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Affiliation(s)
- Babak Saffari
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
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Abstract
Recent years have witnessed an explosive growth in available biological data pertaining to autoimmunity research. This includes a tremendous quantity of sequence data (biological structures, genetic and physical maps, pathways, etc.) generated by genome and proteome projects plus extensive clinical and epidemiological data. Autoimmunity research stands to greatly benefit from this data so long as appropriate strategies are available to enable full access to and utilization of this data. The quantity and complexity of this biological data necessitates use of advanced bioinformatics strategies for its efficient retrieval, analysis and interpretation. Major progress has been made in development of specialized tools for storage, analysis and modeling of immunological data, and this has led to development of a whole new field know as immunoinformatics. With advances in novel high-throughput immunology technologies immunoinformatics is transforming understanding of how the immune system functions. This paper reviews advances in the field of immunoinformatics pertinent to autoimmunity research including databases, tools in genomics and proteomics, tools for study of B- and T-cell epitopes, integrative approaches, and web servers.
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Affiliation(s)
- Nikolai Petrovsky
- Flinders Medical Centre/Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
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Tong JC, Sinha AA. Immunological hotspots analyzed by docking simulations: evidence for a general mechanism in pemphigus vulgaris pathology and transformation. BMC Immunol 2008; 9:30. [PMID: 18564435 PMCID: PMC2440363 DOI: 10.1186/1471-2172-9-30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 06/19/2008] [Indexed: 01/23/2023] Open
Abstract
Background Pemphigus vulgaris (PV) is an acquired autoimmune blistering disorder in which greater than 80% of active patients produce autoantibodies to the desmosomal protein desmogelin 3 (Dsg3). As the disease progresses, 40–50% of patients may also develop reactivity to a second component of the desmosomal complex, desmogelin 1 (Dsg1). T cells are clearly required for the production of autoantibodies in PV. However, few T-cell specificities within Dsg3 or Dsg1 have been reported to date, and the precise role of T-cells in disease pathogenesis and evolution remains poorly understood. In particular, no studies have addressed the immunological mechanisms that underlie the observed clinical heterogeneity in pemphigus. We report here a structure-based technique for the screening of DRB1*0402-specific immunological (T-cell epitope) hotspots in both Dsg3 and Dsg1 glycoproteins. Results High predictivity was obtained for DRB1*0402 (r2 = 0.90, s = 1.20 kJ/mol, q2 = 0.82, spress = 1.61 kJ/mol) predictive model, compared to experimental data. In silico mapping of the T-cell epitope repertoires in Dsg3 and Dsg1 glycoproteins revealed that the potential immunological hotspots of both target autoantigens are highly conserved, despite limited sequence identity (54% identical, 72% similar). A similar number of well-conserved (18%) high-affinity binders were predicted to exist within both Dsg3 and Dsg1, with analogous distribution of binding registers. Conclusion This study provides interesting new insights into the possible mechanism for PV disease progression. Our data suggests that the potential T-cell epitope repertoires encoded in Dsg1 and Dsg3 is substantially overlapping, and it may be possible to apply a common, antigen-specific therapeutic strategy with efficacy across distinct clinical phases of disease.
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Affiliation(s)
- Joo Chuan Tong
- Data Mining Department, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore.
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Zhang GL, Khan AM, Srinivasan KN, Heiny AT, Lee KX, Kwoh CK, August JT, Brusic V. Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics 2008; 9 Suppl 1:S19. [PMID: 18315850 PMCID: PMC2259420 DOI: 10.1186/1471-2105-9-s1-s19] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunological hotspots, has been observed in several antigens. These clusters may be exploited to facilitate the development of epitope-based vaccines by selecting a small number of hotspots that can elicit all of the required T-cell activation functions. Given the large size of pathogen proteomes, including of variant strains, computational tools are necessary for automated screening and selection of immunological hotspots. RESULTS Hotspot Hunter is a web-based computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes through analysis of antigenic diversity. It allows screening and selection of hotspots specific to four common HLA supertypes, namely HLA class I A2, A3, B7 and class II DR. The system uses Artificial Neural Network and Support Vector Machine methods as predictive engines. Soft computing principles were employed to integrate the prediction results produced by both methods for robust prediction performance. Experimental validation of the predictions showed that Hotspot Hunter can successfully identify majority of the real hotspots. Users can predict hotspots from a single protein sequence, or from a set of aligned protein sequences representing pathogen proteome. The latter feature provides a global view of the localizations of the hotspots in the proteome set, enabling analysis of antigenic diversity and shift of hotspots across protein variants. The system also allows the integration of prediction results of the four supertypes for identification of hotspots common across multiple supertypes. The target selection feature of the system shortlists candidate peptide hotspots for the formulation of an epitope-based vaccine that could be effective against multiple variants of the pathogen and applicable to a large proportion of the human population. CONCLUSION Hotspot Hunter is publicly accessible at http://antigen.i2r.a-star.edu.sg/hh/. It is a new generation computational tool aiding in epitope-based vaccine design.
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Affiliation(s)
- Guang Lan Zhang
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
- School of Computer Engineering, Nanyang Technological University, Singapore 639798
| | - Asif M Khan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Kellathur N Srinivasan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Product Evaluation and Registration Division, Centre for Drug Administration, Health Sciences Authority, 11 Biopolis Way, #011-03 Helios, Singapore 138667
| | - AT Heiny
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - KX Lee
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, Singapore 639798
| | - J Thomas August
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- School of Land, Crop, and Food Sciences, University of Queensland, Brisbame 4072, Australia
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Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One 2007; 2:e796. [PMID: 17726526 PMCID: PMC1949492 DOI: 10.1371/journal.pone.0000796] [Citation(s) in RCA: 465] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/29/2007] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Binding of peptides to Major Histocompatibility Complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular immune system. The human MHC class I system (HLA-I) is extremely polymorphic. The number of registered HLA-I molecules has now surpassed 1500. Characterizing the specificity of each separately would be a major undertaking. PRINCIPAL FINDINGS Here, we have drawn on a large database of known peptide-HLA-I interactions to develop a bioinformatics method, which takes both peptide and HLA sequence information into account, and generates quantitative predictions of the affinity of any peptide-HLA-I interaction. Prospective experimental validation of peptides predicted to bind to previously untested HLA-I molecules, cross-validation, and retrospective prediction of known HIV immune epitopes and endogenous presented peptides, all successfully validate this method. We further demonstrate that the method can be applied to perform a clustering analysis of MHC specificities and suggest using this clustering to select particularly informative novel MHC molecules for future biochemical and functional analysis. CONCLUSIONS Encompassing all HLA molecules, this high-throughput computational method lends itself to epitope searches that are not only genome- and pathogen-wide, but also HLA-wide. Thus, it offers a truly global analysis of immune responses supporting rational development of vaccines and immunotherapy. It also promises to provide new basic insights into HLA structure-function relationships. The method is available at http://www.cbs.dtu.dk/services/NetMHCpan.
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Affiliation(s)
- Morten Nielsen
- Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark.
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Tong JC, Zhang ZH, August JT, Brusic V, Tan TW, Ranganathan S. In silico characterization of immunogenic epitopes presented by HLA-Cw*0401. Immunome Res 2007; 3:7. [PMID: 17705876 PMCID: PMC2040137 DOI: 10.1186/1745-7580-3-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 08/20/2007] [Indexed: 11/13/2022] Open
Abstract
Background HLA-C locus products are poorly understood in part due to their low expression at the cell surface. Recent data indicate that these molecules serve as major restriction elements for human immunodeficiency virus type 1 (HIV-1) cytotoxic T lymphocyte (CTL) epitopes. We report here a structure-based technique for the prediction of peptides binding to Cw*0401. The models were rigorously trained, tested and validated using experimentally verified Cw*0401 binding and non-binding peptides obtained from biochemical studies. A new scoring scheme facilitates the identification of immunological hot spots within antigens, based on the sum of predicted binding energies of the top four binders within a window of 30 amino acids. Results High predictivity is achieved when tested on the training (r2 = 0.88, s = 3.56 kJ/mol, q2 = 0.84, spress = 5.18 kJ/mol) and test (AROC = 0.93) datasets. Characterization of the predicted Cw*0401 binding sequences indicate that amino acids at key anchor positions share common physico-chemical properties which correlate well with existing experimental studies. Conclusion The analysis of predicted Cw*0401-binding peptides showed that anchor residues may not be restrictive and the Cw*0401 binding pockets may possibly accommodate a wide variety of peptides with common physico-chemical properties. The potential Cw*0401-specific T-cell epitope repertoires for HIV-1 p24gag and gp160gag glycoproteins are well distributed throughout both glycoproteins, with thirteen and nine immunological hot spots for HIV-1 p24gag and gp160gag glycoproteins respectively. These findings provide new insights into HLA-C peptide selectivity, indicating that pre-selection of candidate HLA-C peptides may occur at the TAP level, prior to peptide loading in the endoplasmic reticulum.
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Affiliation(s)
- Joo Chuan Tong
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore
| | - Zong Hong Zhang
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore
| | - J Thomas August
- Department of Pharmacology and Molecular Sciences, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
| | - Shoba Ranganathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- Department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute, Macquarie University, NSW 2109, Australia
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15
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Trost B, Bickis M, Kusalik A. Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools. Immunome Res 2007; 3:5. [PMID: 17381846 PMCID: PMC1847428 DOI: 10.1186/1745-7580-3-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 03/24/2007] [Indexed: 11/10/2022] Open
Abstract
Background Peptides derived from endogenous antigens can bind to MHC class I molecules. Those which bind with high affinity can invoke a CD8+ immune response, resulting in the destruction of infected cells. Much work in immunoinformatics has involved the algorithmic prediction of peptide binding affinity to various MHC-I alleles. A number of tools for MHC-I binding prediction have been developed, many of which are available on the web. Results We hypothesize that peptides predicted by a number of tools are more likely to bind than those predicted by just one tool, and that the likelihood of a particular peptide being a binder is related to the number of tools that predict it, as well as the accuracy of those tools. To this end, we have built and tested a heuristic-based method of making MHC-binding predictions by combining the results from multiple tools. The predictive performance of each individual tool is first ascertained. These performance data are used to derive weights such that the predictions of tools with better accuracy are given greater credence. The combined tool was evaluated using ten-fold cross-validation and was found to signicantly outperform the individual tools when a high specificity threshold is used. It performs comparably well to the best-performing individual tools at lower specificity thresholds. Finally, it also outperforms the combination of the tools resulting from linear discriminant analysis. Conclusion A heuristic-based method of combining the results of the individual tools better facilitates the scanning of large proteomes for potential epitopes, yielding more actual high-affinity binders while reporting very few false positives.
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Affiliation(s)
- Brett Trost
- Departments of Computer Science and Mathematics & Statistics, University of Saskatchewan, Saskatchewan, Canada
| | - Mik Bickis
- Departments of Computer Science and Mathematics & Statistics, University of Saskatchewan, Saskatchewan, Canada
| | - Anthony Kusalik
- Departments of Computer Science and Mathematics & Statistics, University of Saskatchewan, Saskatchewan, Canada
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16
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Li S, Yao X, Liu H, Li J, Fan B. Prediction of T-cell epitopes based on least squares support vector machines and amino acid properties. Anal Chim Acta 2007; 584:37-42. [PMID: 17386582 DOI: 10.1016/j.aca.2006.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/07/2006] [Accepted: 11/08/2006] [Indexed: 10/23/2022]
Abstract
T-lymphocyte (T-cell) is a very important component in human immune system. It possesses a receptor (TCR) that is specific for the foreign epitopes which are in a form of short peptides bound to the major histocompatibility complex (MHC). When T-cell receives the message about the peptides bound to MHC, it makes the immune system active and results in the disposal of the immunogen. The antigenic determinants recognized and bound by the T-cell receptor is known as T-cell epitope. The accurate prediction of T-cell epitopes is crucial for vaccine development and clinical immunology. For the first time we developed new models using least squares support vector machine (LSSVM) and amino acid properties for T-cell epitopes prediction. A dataset including 203 short peptides (167 non-epitopes and 36 epitopes) was used as the input dataset and it was randomly divided into a training set and a test set. The models based on LSSVM and amino acid properties were evaluated using leave-one-out cross-validation method and the predictive ability of the test set, and obtained the results of 0.9875 and 0.9734 under the ROC curves, respectively. This result is more satisfactory than that were reported before. Especially, the accuracy of true positive gets a marked enhancement.
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Affiliation(s)
- Shuyan Li
- Department of Chemistry, Lanzhou University, Lanzhou 730000, China
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Zhang GL, Bozic I, Kwoh CK, August JT, Brusic V. Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods 2007; 320:143-54. [PMID: 17303158 PMCID: PMC2806231 DOI: 10.1016/j.jim.2006.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 12/20/2006] [Indexed: 12/13/2022]
Abstract
Experimental approaches for identifying T-cell epitopes are time-consuming, costly and not applicable to the large scale screening. Computer modeling methods can help to minimize the number of experiments required, enable a systematic scanning for candidate major histocompatibility complex (MHC) binding peptides and thus speed up vaccine development. We developed a prediction system based on a novel data representation of peptide/MHC interaction and support vector machines (SVM) for prediction of peptides that promiscuously bind to multiple Human Leukocyte Antigen (HLA, human MHC) alleles belonging to a HLA supertype. Ten-fold cross-validation results showed that the overall performance of SVM models is improved in comparison to our previously published methods based on hidden Markov models (HMM) and artificial neural networks (ANN), also confirmed by blind testing. At specificity 0.90, sensitivity values of SVM models were 0.90 and 0.92 for HLA-A2 and -A3 dataset respectively. Average area under the receiver operating curve (A(ROC)) of SVM models in blind testing are 0.89 and 0.92 for HLA-A2 and -A3 datasets. A(ROC) of HLA-A2 and -A3 SVM models were 0.94 and 0.95, validated using a full overlapping study of 9-mer peptides from human papillomavirus type 16 E6 and E7 proteins. In addition, a large-scale experimental dataset has been used to validate HLA-A2 and -A3 SVM models. The SVM prediction models were integrated into a web-based computational system MULTIPRED1, accessible at antigen.i2r.a-star.edu.sg/multipred1/.
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Affiliation(s)
- Guang Lan Zhang
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
- School of Computer Engineering, Nanyang Technological University, Block N4, Nanyang Avenue, Singapore 639798, Singapore
| | - Ivana Bozic
- Faculty of Mathematics, University of Belgrade, Belgrade, Serbia and Montenegro
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, Block N4, Nanyang Avenue, Singapore 639798, Singapore
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Corresponding author. Tel.: +1 617 632 3824; fax: +1 617 632 3351. (V. Brusic)
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18
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Tong JC, Tan TW, Sinha AA, Ranganathan S. Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris. BMC Bioinformatics 2006; 7 Suppl 5:S7. [PMID: 17254312 PMCID: PMC1764484 DOI: 10.1186/1471-2105-7-s5-s7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The target antigen of PV, desmoglein 3 (Dsg3), is crucial for initiating T-cell response in early disease. Although a number of T-cell specificities within Dsg3 have been reported, the number is limited and the role of T-cells in the pathogenesis of PV remains poorly understood. We report here a structure-based model for the prediction of peptide binding to DRB1*0402 and DQB1*0503. The scoring functions were rigorously trained, tested and validated using experimentally verified peptide sequences. Results High predictivity is obtained for both DRB1*0402 (r2 = 0.90, s = 1.20 kJ/mol, q2 = 0.82, spress = 1.61 kJ/mol) and DQB1*0503 (r2 = 0.95, s = 1.20 kJ/mol, q2 = 0.75, spress = 2.15 kJ/mol) models, compared to experimental data. We investigated the binding patterns of Dsg3 peptides and illustrate the existence of multiple immunodominant epitopes that may be responsible for both disease initiation and propagation in PV. Further analysis reveals that DRB1*0402 and DQB1*0503 may share similar specificities by binding peptides at different binding registers, thus providing a molecular mechanism for the dual HLA association observed in PV. Conclusion Collectively, the results of this study provide interesting new insights into the pathology of PV. This is the first report illustrating high-level of cross-reactivity between both PV-implicated alleles, DRB1*0402 and DQB1*0503, as well as the existence of a potentially large number of T-cell epitopes throughout the entire Dsg3 extracellular domain (ECD) and transmembrane region. Our results reveal that DR4 and DR6 PV may initiate in the ECD and transmembrane region respectively, with implications for immunotherapeutic strategies for the treatment of this autoimmune disease.
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Affiliation(s)
- Joo Chuan Tong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Animesh A Sinha
- Center for Investigative Dermatology, Division of Dermatology and Cutaneous Sciences, College of Human Medicine, Michigan State University, 4120 Biomedical and Physical Sciences Building, East Lansing, MI 48824, USA
| | - Shoba Ranganathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute, Macquarie University, Sydney NSW 2109, Australia
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19
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Khan AM, Heiny AT, Lee KX, Srinivasan KN, Tan TW, August JT, Brusic V. Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinformatics 2006; 7 Suppl 5:S4. [PMID: 17254309 PMCID: PMC1764481 DOI: 10.1186/1471-2105-7-s5-s4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. We also studied the effects of sequence determinants on viral antigenic diversity. Short peptides, principally 9-mers were studied because they represent the predominant length of binding cores of T-cell epitopes, which are important for formulation of vaccines. Results Our analysis showed that the number of unique protein sequences required to represent complete antigenic diversity of short peptides in dengue virus is significantly smaller than that required to represent complete protein sequence diversity. Short-peptide antigenic diversity shows an asymptotic relationship to the number of unique protein sequences, indicating that for large sequence sets (~200) the addition of new protein sequences has marginal effect to increasing antigenic diversity. A near-linear relationship was observed between the extent of antigenic diversity and the length of protein sequences, suggesting that, for the practical purpose of vaccine development, antigenic diversity of short peptides from dengue virus can be represented by short regions of sequences (~<100 aa) within viral antigens that are specific targets of immune responses (such as T-cell epitopes specific to particular human leukocyte antigen alleles). Conclusion This study provides evidence that there are limited numbers of antigenic combinations in protein sequence variants of a viral species and that short regions of the viral protein are sufficient to capture antigenic diversity of T-cell epitopes. The approach described herein has direct application to the analysis of other viruses, in particular those that show high diversity and/or rapid evolution, such as influenza A virus and human immunodeficiency virus (HIV).
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Affiliation(s)
- Asif M Khan
- The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Microbiology, The Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
| | - AT Heiny
- The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Biochemistry, The Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
| | - Kenneth X Lee
- The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Microbiology, The Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
| | - KN Srinivasan
- The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Tin Wee Tan
- Department of Biochemistry, The Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
| | - J Thomas August
- The Division of Biomedical Sciences, Johns Hopkins Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Vladimir Brusic
- Department of Microbiology, The Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
- School of Land and Food Sciences, and Institute for Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
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20
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Khan AM, Miotto O, Heiny A, Salmon J, Srinivasan K, Nascimento E, Marques ET, Brusic V, Tan TW, August JT. A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol 2006; 244:141-7. [PMID: 17434154 PMCID: PMC2041846 DOI: 10.1016/j.cellimm.2007.02.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 02/06/2007] [Indexed: 11/24/2022]
Abstract
Epitope-based vaccines provide a new strategy for prophylactic and therapeutic application of pathogen-specific immunity. A critical requirement of this strategy is the identification and selection of T-cell epitopes that act as vaccine targets. This study describes current methodologies for the selection process, with dengue virus as a model system. A combination of publicly available bioinformatics algorithms and computational tools are used to screen and select antigen sequences as potential T-cell epitopes of supertype human leukocyte antigen (HLA) alleles. The selected sequences are tested for biological function by their activation of T-cells of HLA transgenic mice and of pathogen infected subjects. This approach provides an experimental basis for the design of pathogen specific, T-cell epitope-based vaccines that are targeted to majority of the genetic variants of the pathogen, and are effective for a broad range of differences in human leukocyte antigens among the global human population.
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Affiliation(s)
- Asif M. Khan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Olivo Miotto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Institute of Systems Science, National University of Singapore, 25 Heng Mui Keng Terrace, Singapore 119615, Singapore
| | - A.T. Heiny
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Jerome Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
| | - K.N. Srinivasan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
- Product Evaluation & Registration Division, Centre for Drug Administration, Health Sciences Authority, 11 Biopolis Way, Singapore 138667, Singapore
| | - Eduardo Nascimento
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
| | - Ernesto T. Marques
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
| | - Vladimir Brusic
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
- School of Land and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, United States of America
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21
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Braga-Neto UM, Marques ETA. From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol 2006; 2:e81. [PMID: 16863395 PMCID: PMC1523295 DOI: 10.1371/journal.pcbi.0020081] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The development of DNA microarray technology a decade ago led to the establishment of functional genomics as one of the most active and successful scientific disciplines today. With the ongoing development of immunomic microarray technology—a spatially addressable, large-scale technology for measurement of specific immunological response—the new challenge of functional immunomics is emerging, which bears similarities to but is also significantly different from functional genomics. Immunonic data has been successfully used to identify biological markers involved in autoimmune diseases, allergies, viral infections such as human immunodeficiency virus (HIV), influenza, diabetes, and responses to cancer vaccines. This review intends to provide a coherent vision of this nascent scientific field, and speculate on future research directions. We discuss at some length issues such as epitope prediction, immunomic microarray technology and its applications, and computation and statistical challenges related to functional immunomics. Based on the recent discovery of regulation mechanisms in T cell responses, we envision the use of immunomic microarrays as a tool for advances in systems biology of cellular immune responses, by means of immunomic regulatory network models.
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Affiliation(s)
- Ulisses M Braga-Neto
- Experimental Therapy Laboratory, Aggeu Magalhães Research Center - CPqAM/FIOCRUZ, Recife, Brazil.
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Zhu S, Udaka K, Sidney J, Sette A, Aoki-Kinoshita KF, Mamitsuka H. Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics 2006; 22:1648-55. [PMID: 16613909 DOI: 10.1093/bioinformatics/btl141] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that MHC molecules can be classified into supertypes in terms of peptide-binding specificities. Therefore, we first give a method for reducing the redundancy in a given dataset based on information entropy, then present a novel approach for prediction by learning a predictive model from a dataset of binders for not only the molecule of interest but also for other MHC molecules. RESULTS We experimented on the HLA-A family with the binding nonamers of A1 supertype (HLA-A*0101, A*2601, A*2902, A*3002), A2 supertype (A*0201, A*0202, A*0203, A*0206, A*6802), A3 supertype (A*0301, A*1101, A*3101, A*3301, A*6801) and A24 supertype (A*2301 and A*2402), whose data were collected from six publicly available peptide databases and two private sources. The results show that our approach significantly improves the prediction accuracy of peptides that bind a specific HLA molecule when we combine binding data of HLA molecules in the same supertype. Our approach can thus be used to help find new binders for MHC molecules.
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Affiliation(s)
- Shanfeng Zhu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji 611-0011, Japan
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Gupta V, Tabiin TM, Sun K, Chandrasekaran A, Anwar A, Yang K, Chikhlikar P, Salmon J, Brusic V, Marques ET, Kellathur SN, August TJ. SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens. Virology 2006; 347:127-39. [PMID: 16387339 PMCID: PMC7111852 DOI: 10.1016/j.virol.2005.11.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 09/22/2005] [Accepted: 11/22/2005] [Indexed: 01/12/2023]
Abstract
Correspondence between the T-cell epitope responses of vaccine immunogens and those of pathogen antigens is critical to vaccine efficacy. In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund's adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). Lysosomal trafficking of the LAMP/N chimera in transfected cells was documented by both confocal and immunoelectron microscopy. The responses of the immunized mice differed markedly. The strongest T-cell IFN-γ and CTL responses were to the LAMP-N chimera followed by the pN immunogen. In contrast, N-GST elicited strong T cell IL-4 but minimal IFN-γ responses and a much greater antibody response. Despite these differences, however, the immunodominant T-cell ELISpot responses to each of the three immunogens were elicited by the same N peptides, with the greatest responses being generated by a cluster of five overlapping peptides, N76–114, each of which contained nonameric H2d binding domains with high binding scores for both class I and, except for N76–93, class II alleles. These results demonstrate that processing and presentation of N, whether exogenously or endogenously derived, resulted in common immunodominant epitopes, supporting the usefulness of modified antigen delivery and trafficking forms and, in particular, LAMP chimeras as vaccine candidates. Nevertheless, the profiles of T-cell responses were distinctly different. The pronounced Th-2 and humoral response to N protein plus adjuvant are in contrast to the balanced IFN-γ and IL-4 responses and strong memory CTL responses to the LAMP-N chimera.
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Affiliation(s)
- Vandana Gupta
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Tani M. Tabiin
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Kai Sun
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Ananth Chandrasekaran
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Azlinda Anwar
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
| | - Kun Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Priya Chikhlikar
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Jerome Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Vladimir Brusic
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
- School of Land and Food Sciences and the Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia
| | - Ernesto T.A. Marques
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
- Department of Medicine, Division of Infectious Diseases, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21218, USA
- Virology and Experimental Therapy Laboratory, Aggeu Magalhaes Research Center, Recife, PE 50670-420, Brazil
| | - Srinivasan N. Kellathur
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Thomas J. August
- Division of Biomedical Sciences, Johns Hopkins in Singapore, 31 Biopolis Way, #02-01 The Nanos, Singapore 138669, Singapore
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
- Corresponding author. Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA. Fax: +1 410 502 3066.
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Abstract
The immune system is concerned with the recognition and disposal of foreign or "non self" molecules or cells that enter the body of an immunologically competent individual. The generation of an immune response depends on the interaction of components, namely, the immunogen (nonself or foreign cell or molecule), antibody producing humoral immune system, and sensitized lymphocyte producing cellular immune system. An immunogen possesses surface structures referred to as epitopes; the precise pattern of each epitope enables an individual's immune system to recognize cells or molecules as self or immunogens. During the recognition process, the specific cells known as macrophages identify the epitope structures on the immunogen and save them in the form of short peptides 10-18 amino-acids-long known as immune dominant peptides (IDPs). IDPs are then bound with surface proteins on macrophages known as MHC protein complexes. The macrophages then present this IDP-MHC complex to a T cell that possesses a specific receptor that is specific for the foreign epitope on the IDP bound to MHC complex. This initiates an immune system cascade that results in the disposal of the immunogen. The study and accurate prediction of T-cell epitopes is, thus, very important for designing vaccines against pathogenic diseases. The present study applied the newly developed biosupport vector machine to the T-cell epitope data. This new algorithm introduces a biobasis function into the conventional support vector machines so that the nonnumerical attributes (amino acids) in protein sequences can be recognized without a feature extraction process, which often fails to properly code the biological content in protein sequences. The prediction accuracy of a 10-fold cross validation is 90.31%, compared with 87.86% using support vector machines reported as the best compared with other algorithms in an earlier study.
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Affiliation(s)
- Zheng Rong Yang
- Department of Computer Science, University of Exeter, United Kingdom.
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25
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Tongchusak S, Chaiyaroj SC, Veeramani A, Koh JLY, Brusic V. CandiVF – Candida albicans Virulence Factor Database. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-005-9268-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zhang GL, Khan AM, Srinivasan KN, August JT, Brusic V. MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res 2005; 33:W172-9. [PMID: 15980449 PMCID: PMC1160213 DOI: 10.1093/nar/gki452] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MULTIPRED is a web-based computational system for the prediction of peptide binding to multiple molecules (proteins) belonging to human leukocyte antigens (HLA) class I A2, A3 and class II DR supertypes. It uses hidden Markov models and artificial neural network methods as predictive engines. A novel data representation method enables MULTIPRED to predict peptides that promiscuously bind multiple HLA alleles within one HLA supertype. Extensive testing was performed for validation of the prediction models. Testing results show that MULTIPRED is both sensitive and specific and it has good predictive ability (area under the receiver operating characteristic curve AROC > 0.80). MULTIPRED can be used for the mapping of promiscuous T-cell epitopes as well as the regions of high concentration of these targets—termed T-cell epitope hotspots. MULTIPRED is available at .
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Affiliation(s)
- Guang Lan Zhang
- Institute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
- School of Computer Engineering, Nanyang Technological UniversitySingapore 639798
| | - Asif M. Khan
- Institute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
- Department of Biochemistry, National University of SingaporeSingapore 117597
| | - Kellathur N. Srinivasan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of MedicineBaltimore, MD 21205, USA
- Division of Biomedical SciencesJohns Hopkins in Singapore, #02-01 The Nanos, 31 Biopolis Way, Singapore 138669
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of MedicineBaltimore, MD 21205, USA
- Division of Biomedical SciencesJohns Hopkins in Singapore, #02-01 The Nanos, 31 Biopolis Way, Singapore 138669
| | - Vladimir Brusic
- Institute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
- School of Land and Food Sciences and the Institute for Molecular Bioscience, University of QueenslandBrisbane QLD 4072, Australia
- To whom correspondence should be addressed. Tel: +65 96212 415; Fax: +65 6774 8056;
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27
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Abstract
An improved understanding of the human immune system and the genetic make-up of pathogens, together with advances in instrumentation and bioinformatics, have provided new insights into the variation of immune responses to vaccines within the human population. Pathogen variation and the diversity of the immune system components within the human population make the design of universal vaccines difficult. New subunit vaccines that target immunologically similar subgroups of the human population and representative pathogen variants are emerging from research that combines immunomics, pathogen genomics, and high-throughput instrumentation.
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Affiliation(s)
- Vladimir Brusic
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613.
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