1
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Ma J, Tian Z, Shi Q, Dong X, Sun Y. Affinity chromatography for virus-like particle manufacturing: Challenges, solutions, and perspectives. J Chromatogr A 2024; 1721:464851. [PMID: 38574547 DOI: 10.1016/j.chroma.2024.464851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
The increasing medical application of virus-like particles (VLPs), notably vaccines and viral vectors, has increased the demand for commercial VLP production. However, VLP manufacturing has not yet reached the efficiency level achieved for recombinant protein therapeutics, especially in downstream processing. This review provides a comprehensive analysis of the challenges associated with affinity chromatography for VLP purification with respect to the diversity and complexity of VLPs and the associated upstream and downstream processes. The use of engineered affinity ligands and matrices for affinity chromatography is first discussed. Although several representative affinity ligands are currently available for VLP purification, most of them have difficulty in balancing ligand universality, ligand selectivity and mild operation conditions. Then, phage display technology and computer-assisted design are discussed as efficient methods for the rapid discovery of high-affinity peptide ligands. Finally, the VLP purification by affinity chromatography is analyzed. The process is significantly influenced by virus size and variation, ligand type and chromatographic mode. To address the updated regulatory requirements and epidemic outbreaks, technical innovations in affinity chromatography and process intensification and standardization in VLP purification should be promoted to achieve rapid process development and highly efficient VLP manufacturing, and emphasis is given to the discovery of universal ligands, applications of gigaporous matrices and platform technology. It is expected that the information in this review can provide a better understanding of the affinity chromatography methods available for VLP purification and offer useful guidance for the development of affinity chromatography for VLP manufacturing in the decades to come.
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Affiliation(s)
- Jing Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Zengquan Tian
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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2
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Bruno PM, Timms RT, Abdelfattah NS, Leng Y, Lelis FJN, Wesemann DR, Yu XG, Elledge SJ. High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform. Nat Biotechnol 2023; 41:980-992. [PMID: 36593401 PMCID: PMC10314971 DOI: 10.1038/s41587-022-01566-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Identification of CD8+ T cell epitopes is critical for the development of immunotherapeutics. Existing methods for major histocompatibility complex class I (MHC class I) ligand discovery are time intensive, specialized and unable to interrogate specific proteins on a large scale. Here, we present EpiScan, which uses surface MHC class I levels as a readout for whether a genetically encoded peptide is an MHC class I ligand. Predetermined starting pools composed of >100,000 peptides can be designed using oligonucleotide synthesis, permitting large-scale MHC class I screening. We exploit this programmability of EpiScan to uncover an unappreciated role for cysteine that increases the number of predicted ligands by 9-21%, reveal affinity hierarchies by analysis of biased anchor peptide libraries and screen viral proteomes for MHC class I ligands. Using these data, we generate and iteratively refine peptide binding predictions to create EpiScan Predictor. EpiScan Predictor performs comparably to other state-of-the-art MHC class I peptide binding prediction algorithms without suffering from underrepresentation of cysteine-containing peptides. Thus, targeted immunopeptidomics using EpiScan will accelerate CD8+ T cell epitope discovery toward the goal of individual-specific immunotherapeutics.
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Affiliation(s)
- Peter M Bruno
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Richard T Timms
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Nouran S Abdelfattah
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Felipe J N Lelis
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Lim CP, Kok BH, Lim HT, Chuah C, Abdul Rahman B, Abdul Majeed AB, Wykes M, Leow CH, Leow CY. Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design. Pathog Glob Health 2023; 117:134-151. [PMID: 35550001 PMCID: PMC9970233 DOI: 10.1080/20477724.2022.2072456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.
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Affiliation(s)
- Chin Peng Lim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia.,Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Candy Chuah
- Faculty of Health Sciences, Universiti Teknologi MARA, Penang, Malaysia
| | | | | | - Michelle Wykes
- Molecular Immunology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Malaysia
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4
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Nilsson JB, Grifoni A, Tarke A, Sette A, Nielsen M. PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage. Front Immunol 2021; 12:728936. [PMID: 34484239 PMCID: PMC8416060 DOI: 10.3389/fimmu.2021.728936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
The use of minimal peptide sets offers an appealing alternative for design of vaccines and T cell diagnostics compared to conventional whole protein approaches. T cell immunogenicity towards peptides is contingent on binding to human leukocyte antigen (HLA) molecules of the given individual. HLA is highly polymorphic, and each variant typically presents a different repertoire of peptides. This polymorphism combined with pathogen diversity challenges the rational selection of peptide sets with broad immunogenic potential and population coverage. Here we propose PopCover-2.0, a simple yet highly effective method, for resolving this challenge. The method takes as input a set of (predicted) CD8 and/or CD4 T cell epitopes with associated HLA restriction and pathogen strain annotation together with information on HLA allele frequencies, and identifies peptide sets with optimal pathogen and HLA (class I and II) coverage. PopCover-2.0 was benchmarked on historic data in the context of HIV and SARS-CoV-2. Further, the immunogenicity of the selected SARS-CoV-2 peptides was confirmed by experimentally validating the peptide pools for T cell responses in a panel of SARS-CoV-2 infected individuals. In summary, PopCover-2.0 is an effective method for rational selection of peptide subsets with broad HLA and pathogen coverage. The tool is available at https://services.healthtech.dtu.dk/service.php?PopCover-2.0.
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Affiliation(s)
- Jonas Birkelund Nilsson
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Internal Medicine, University of Genoa, Genoa, Italy
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
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5
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Boniolo F, Dorigatti E, Ohnmacht AJ, Saur D, Schubert B, Menden MP. Artificial intelligence in early drug discovery enabling precision medicine. Expert Opin Drug Discov 2021; 16:991-1007. [PMID: 34075855 DOI: 10.1080/17460441.2021.1918096] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Precision medicine is the concept of treating diseases based on environmental factors, lifestyles, and molecular profiles of patients. This approach has been found to increase success rates of clinical trials and accelerate drug approvals. However, current precision medicine applications in early drug discovery use only a handful of molecular biomarkers to make decisions, whilst clinics gear up to capture the full molecular landscape of patients in the near future. This deep multi-omics characterization demands new analysis strategies to identify appropriate treatment regimens, which we envision will be pioneered by artificial intelligence.Areas covered: In this review, the authors discuss the current state of drug discovery in precision medicine and present our vision of how artificial intelligence will impact biomarker discovery and drug design.Expert opinion: Precision medicine is expected to revolutionize modern medicine; however, its traditional form is focusing on a few biomarkers, thus not equipped to leverage the full power of molecular landscapes. For learning how the development of drugs can be tailored to the heterogeneity of patients across their molecular profiles, artificial intelligence algorithms are the next frontier in precision medicine and will enable a fully personalized approach in drug design, and thus ultimately impacting clinical practice.
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Affiliation(s)
- Fabio Boniolo
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany.,School of Medicine, Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Emilio Dorigatti
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany.,Statistical Learning and Data Science, Department of Statistics, Ludwig Maximilian Universität München, Munich, Germany
| | - Alexander J Ohnmacht
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany.,Department of Biology, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Dieter Saur
- School of Medicine, Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Benjamin Schubert
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany.,Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Michael P Menden
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Munich, Germany.,Department of Biology, Ludwig-Maximilians University Munich, Martinsried, Germany.,German Centre for Diabetes Research (DZD e.V.), Neuherberg, Germany
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6
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Azim KF, Lasker T, Akter R, Hia MM, Bhuiyan OF, Hasan M, Hossain MN. Combination of highly antigenic nucleoproteins to inaugurate a cross-reactive next generation vaccine candidate against Arenaviridae family. Heliyon 2021; 7:e07022. [PMID: 34041391 PMCID: PMC8144012 DOI: 10.1016/j.heliyon.2021.e07022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/09/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
Arenaviral infections often result lethal hemorrhagic fevers, affecting primarily in African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapy. Hence, the study was employed to design a highly immunogenic cross-reactive vaccine against Arenaviridae family using reverse vaccinology approach. The whole proteome of Lassa virus (LASV), Lymphocytic Choriomeningitis virus (LCMV), Lujo virus and Guanarito virus were retrieved and assessed to determine the most antigenic viral proteins. Both T-cell and B-cell epitopes were predicted and screened based on transmembrane topology, antigenicity, allergenicity, toxicity and molecular docking analysis. The final constructs were designed using different adjuvants, top epitopes, PADRE sequence and respective linkers and were assessed for the efficacy, safety, stability and molecular cloning purposes. The proposed epitopes were highly conserved (84%–100%) and showed greater cumulative population coverage. Moreover, T cell epitope GWPYIGSRS was conserved in Junin virus (Argentine mammarenavirus) and Sabia virus (Brazilian mammarenavirus), while B cell epitope NLLYKICLSG was conserved in Machupo virus (Bolivian mammarenavirus) and Sabia virus, indicating the possibility of final vaccine construct to confer a broad range immunity in the host. Docking analysis of the refined vaccine with different MHC molecules and human immune receptors were biologically significant. The vaccine-receptor (V1-TLR3) complex showed minimal deformability at molecular level and was compatible for cloning into pET28a(+) vector of E. coli strain K12. The study could be helpful in developing vaccine to combat arenaviral infections in the future. However, further in vitro and in vivo trials using model animals are highly recommended for the experimental validation of our findings.
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Affiliation(s)
- Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tahera Lasker
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Rahima Akter
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mantasha Mahmud Hia
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Omar Faruk Bhuiyan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Nazmul Hossain
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh.,Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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7
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Abstract
MOTIVATION Conceptually, epitope-based vaccine design poses two distinct problems: (i) selecting the best epitopes to elicit the strongest possible immune response and (ii) arranging and linking them through short spacer sequences to string-of-beads vaccines, so that their recovery likelihood during antigen processing is maximized. Current state-of-the-art approaches solve this design problem sequentially. Consequently, such approaches are unable to capture the inter-dependencies between the two design steps, usually emphasizing theoretical immunogenicity over correct vaccine processing, thus resulting in vaccines with less effective immunogenicity in vivo. RESULTS In this work, we present a computational approach based on linear programming, called JessEV, that solves both design steps simultaneously, allowing to weigh the selection of a set of epitopes that have great immunogenic potential against their assembly into a string-of-beads construct that provides a high chance of recovery. We conducted Monte Carlo cleavage simulations to show that a fixed set of epitopes often cannot be assembled adequately, whereas selecting epitopes to accommodate proper cleavage requirements substantially improves their recovery probability and thus the effective immunogenicity, pathogen and population coverage of the resulting vaccines by at least 2-fold. AVAILABILITY AND IMPLEMENTATION The software and the data analyzed are available at https://github.com/SchubertLab/JessEV. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emilio Dorigatti
- Faculty of Mathematics Informatics and Statistics, Ludwig Maximilian Universität, München 80333, Germany.,Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Benjamin Schubert
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany.,Department of Mathematics, Technical University of Munich, Garching bei München 85748, Germany
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8
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Robleda-Castillo R, Ros-Lucas A, Martinez-Peinado N, Alonso-Padilla J. An Overview of Current Uses and Future Opportunities for Computer-Assisted Design of Vaccines for Neglected Tropical Diseases. Adv Appl Bioinform Chem 2021; 14:25-47. [PMID: 33623396 PMCID: PMC7894434 DOI: 10.2147/aabc.s258759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022] Open
Abstract
Neglected tropical diseases are infectious diseases that impose high morbidity and mortality rates over 1.5 billion people worldwide. Originally restricted to tropical and subtropical regions, changing climate conditions have increased their potential to emerge elsewhere. Control of their impact suffers from shortages like poor epidemiological surveillance or irregular drug distribution, and some NTDs still lack of appropriate diagnostics and/or efficient therapeutics. For these, availability of vaccines to prevent new infections, or the worsening of those already established, would mean a major breakthrough. However, only dengue and rabies count with approved vaccines at present. Herein, we review the state-of-the-art of vaccination strategies for NTDs, setting the focus on third generation vaccines and the concept of reverse vaccinology. Its capability to address pathogens´ biological complexity, likely contributing to save developmental costs is discussed. The use of computational tools is a fundamental aid to analyze increasingly large datasets aimed at designing vaccine candidates with the highest, possibly, opportunities to succeed. Ultimately, we identify and analyze those studies that took an in silico approach to find vaccine candidates, and experimentally assessed their immunogenicity and/or protection capabilities.
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Affiliation(s)
- Raquel Robleda-Castillo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - University of Barcelona, Barcelona, 08036, Spain
| | - Albert Ros-Lucas
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - University of Barcelona, Barcelona, 08036, Spain
| | - Nieves Martinez-Peinado
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - University of Barcelona, Barcelona, 08036, Spain
| | - Julio Alonso-Padilla
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - University of Barcelona, Barcelona, 08036, Spain
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9
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Computational Analysis of African Swine Fever Virus Protein Space for the Design of an Epitope-Based Vaccine Ensemble. Pathogens 2020; 9:pathogens9121078. [PMID: 33371523 PMCID: PMC7767518 DOI: 10.3390/pathogens9121078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/12/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
African swine fever virus is the etiological agent of African swine fever, a transmissible severe hemorrhagic disease that affects pigs, causing massive economic losses. There is neither a treatment nor a vaccine available, and the only method to control its spread is by extensive culling of pigs. So far, classical vaccine development approaches have not yielded sufficiently good results in terms of concomitant safety and efficacy. Nowadays, thanks to advances in genomic and proteomic techniques, a reverse vaccinology strategy can be explored to design alternative vaccine formulations. In this study, ASFV protein sequences were analyzed using an in-house pipeline based on publicly available immunoinformatic tools to identify epitopes of interest for a prospective vaccine ensemble. These included experimentally validated sequences from the Immune Epitope Database, as well as de novo predicted sequences. Experimentally validated and predicted epitopes were prioritized following a series of criteria that included evolutionary conservation, presence in the virulent and currently circulating variant Georgia 2007/1, and lack of identity to either the pig proteome or putative proteins from pig gut microbiota. Following this strategy, 29 B-cell, 14 CD4+ T-cell and 6 CD8+ T-cell epitopes were selected, which represent a starting point to investigating the protective capacity of ASFV epitope-based vaccines.
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10
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Dorigatti E, Schubert B. Graph-theoretical formulation of the generalized epitope-based vaccine design problem. PLoS Comput Biol 2020; 16:e1008237. [PMID: 33095790 PMCID: PMC7652351 DOI: 10.1371/journal.pcbi.1008237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 11/09/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Epitope-based vaccines have revolutionized vaccine research in the last decades. Due to their complex nature, bioinformatics plays a pivotal role in their development. However, existing algorithms address only specific parts of the design process or are unable to provide formal guarantees on the quality of the solution. We present a unifying formalism of the general epitope vaccine design problem that tackles all phases of the design process simultaneously and combines all prevalent design principles. We then demonstrate how to formulate the developed formalism as an integer linear program, which guarantees optimality of the designs. This makes it possible to explore new regions of the vaccine design space, analyze the trade-offs between the design phases, and balance the many requirements of vaccines.
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Affiliation(s)
- Emilio Dorigatti
- Department of Statistics, Ludwig Maximilian Universität, München, Germany
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Schubert
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching bei München, Germany
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11
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Estrada E. COVID-19 and SARS-CoV-2. Modeling the present, looking at the future. PHYSICS REPORTS 2020; 869:1-51. [PMID: 32834430 PMCID: PMC7386394 DOI: 10.1016/j.physrep.2020.07.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 05/21/2023]
Abstract
Since December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has produced an outbreak of pulmonary disease which has soon become a global pandemic, known as COronaVIrus Disease-19 (COVID-19). The new coronavirus shares about 82% of its genome with the one which produced the 2003 outbreak (SARS CoV-1). Both coronaviruses also share the same cellular receptor, which is the angiotensin-converting enzyme 2 (ACE2) one. In spite of these similarities, the new coronavirus has expanded more widely, more faster and more lethally than the previous one. Many researchers across the disciplines have used diverse modeling tools to analyze the impact of this pandemic at global and local scales. This includes a wide range of approaches - deterministic, data-driven, stochastic, agent-based, and their combinations - to forecast the progression of the epidemic as well as the effects of non-pharmaceutical interventions to stop or mitigate its impact on the world population. The physical complexities of modern society need to be captured by these models. This includes the many ways of social contacts - (multiplex) social contact networks, (multilayers) transport systems, metapopulations, etc. - that may act as a framework for the virus propagation. But modeling not only plays a fundamental role in analyzing and forecasting epidemiological variables, but it also plays an important role in helping to find cures for the disease and in preventing contagion by means of new vaccines. The necessity for answering swiftly and effectively the questions: could existing drugs work against SARS CoV-2? and can new vaccines be developed in time? demands the use of physical modeling of proteins, protein-inhibitors interactions, virtual screening of drugs against virus targets, predicting immunogenicity of small peptides, modeling vaccinomics and vaccine design, to mention just a few. Here, we review these three main areas of modeling research against SARS CoV-2 and COVID-19: (1) epidemiology; (2) drug repurposing; and (3) vaccine design. Therefore, we compile the most relevant existing literature about modeling strategies against the virus to help modelers to navigate this fast-growing literature. We also keep an eye on future outbreaks, where the modelers can find the most relevant strategies used in an emergency situation as the current one to help in fighting future pandemics.
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Affiliation(s)
- Ernesto Estrada
- Instituto Universitario de Matemáticas y Aplicaciones, Universidad de Zaragoza, 50009 Zaragoza, Spain
- ARAID Foundation, Government of Aragón, 50018 Zaragoza, Spain
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12
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Michel-Todó L, Reche PA, Bigey P, Pinazo MJ, Gascón J, Alonso-Padilla J. In silico Design of an Epitope-Based Vaccine Ensemble for Chagas Disease. Front Immunol 2019; 10:2698. [PMID: 31824493 PMCID: PMC6882931 DOI: 10.3389/fimmu.2019.02698] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/01/2019] [Indexed: 01/21/2023] Open
Abstract
Trypanosoma cruzi infection causes Chagas disease, which affects 7 million people worldwide. Two drugs are available to treat it: benznidazole and nifurtimox. Although both are efficacious against the acute stage of the disease, this is usually asymptomatic and goes undiagnosed and untreated. Diagnosis is achieved at the chronic stage, when life-threatening heart and/or gut tissue disruptions occur in ~30% of those chronically infected. By then, the drugs' efficacy is reduced, but not their associated high toxicity. Given current deficiencies in diagnosis and treatment, a vaccine to prevent infection and/or the development of symptoms would be a breakthrough in the management of the disease. Current vaccine candidates are mostly based on the delivery of single antigens or a few different antigens. Nevertheless, due to the high biological complexity of the parasite, targeting as many antigens as possible would be desirable. In this regard, an epitope-based vaccine design could be a well-suited approach. With this aim, we have gone through publicly available databases to identify T. cruzi epitopes from several antigens. By means of a computer-aided strategy, we have prioritized a set of epitopes based on sequence conservation criteria, projected population coverage of Latin American population, and biological features of their antigens of origin. Fruit of this analysis, we provide a selection of CD8+ T cell, CD4+ T cell, and B cell epitopes that have <70% identity to human or human microbiome protein sequences and represent the basis toward the development of an epitope-based vaccine against T. cruzi.
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Affiliation(s)
- Lucas Michel-Todó
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Pedro Antonio Reche
- Laboratory of Immunomedicine, Faculty of Medicine, University Complutense of Madrid, Madrid, Spain
| | - Pascal Bigey
- Université de Paris, UTCBS, CNRS, INSERM, Paris, France.,PSL University, ChimieParisTech, Paris, France
| | - Maria-Jesus Pinazo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Joaquim Gascón
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Julio Alonso-Padilla
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic, University of Barcelona, Barcelona, Spain
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13
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Raoufi E, Hemmati M, Eftekhari S, Khaksaran K, Mahmodi Z, Farajollahi MM, Mohsenzadegan M. Epitope Prediction by Novel Immunoinformatics Approach: A State-of-the-art Review. Int J Pept Res Ther 2019; 26:1155-1163. [PMID: 32435171 PMCID: PMC7224030 DOI: 10.1007/s10989-019-09918-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/21/2022]
Abstract
Immunoinformatics is a science that helps to create significant immunological information using bioinformatics softwares and applications. One of the most important applications of immunoinformatics is the prediction of a variety of specific epitopes for B cell recognition and T cell through MHC class I and II molecules. This method reduces costs and time compared to laboratory tests. In this state-of-the-art review, we review about 50 papers to find the latest and most used immunoinformatic tools as well as their applications for predicting the viral, bacterial and tumoral structural and linear epitopes of B and T cells. In the clinic, the main application of prediction of epitopes is for designing peptide-based vaccines. Peptide-based vaccines are a considerably potential alternative to low-cost vaccines that may reduce the risks related to the production of common vaccines.
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Affiliation(s)
- Ehsan Raoufi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Hemmati
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samane Eftekhari
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kamal Khaksaran
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Mahmodi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad M. Farajollahi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, Iran University of Medical Sciences (IUMS), Hemmat Highway, Tehran, Iran
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14
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Dewi SK, Ali S, Prasasty VD. Broad Spectrum Peptide Vaccine Design Against Hepatitis C Virus. Curr Comput Aided Drug Des 2019; 15:120-135. [PMID: 30280672 DOI: 10.2174/1573409914666181003151222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 08/12/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a global burden. There is no peptide vaccine found as modality to cure the disease is available due to the weak cellular immune response and the limitation to induce humoral immune response. METHODS Five predominated HCV subtypes in Indonesia (1a, 1b, 1c, 3a, and 3k) were aligned and the conserved regions were selected. Twenty alleles of class I MHC including HLA-A, HLA-B, and HLAC types were used to predict the potential epitopes by using NetMHCPan and IEDB. Eight alleles of HLA-DRB1, together with a combination of 3 alleles of HLA-DQA1 and 5 alleles of HLA-DQB1 were utilized for Class II MHC epitopes prediction using NetMHCIIPan and IEDB. LBtope and Ig- Pred were used to predict B cells epitopes. Moreover, proteasome analysis was performed by NetCTL and the stability of the epitopes in HLA was calculated using NetMHCStabPan for Class I. All predicted epitopes were analyzed for its antigenicity, toxicity, and stability. Population coverage, molecular docking and molecular dynamics were performed for several best epitopes. RESULTS The results showed that two best epitopes from envelop protein, GHRMAWDMMMNWSP (E1) and PALSTGLIHLHQN (E2) were selected as promising B cell and CD8+ T cell inducers. Other two peptides, LGIGTVLDQAETAG and VLVLNPSVAATLGF, taken from NS3 protein were selected as CD4+ T cell inducer. CONCLUSION This study suggested the utilization of all four peptides to make a combinational peptide vaccine for in vivo study to prove its ability in inducing secondary response toward HCV.
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Affiliation(s)
- Sherly Kurnia Dewi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Soegianto Ali
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia.,Faculty of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
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15
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Induction of neoantigen-reactive T cells from healthy donors. Nat Protoc 2019; 14:1926-1943. [DOI: 10.1038/s41596-019-0170-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/21/2019] [Indexed: 12/21/2022]
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16
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Mohammed AA, ALnaby AM, Sabeel SM, AbdElmarouf FM, Dirar AI, Ali MM, Khandgawi MA, Yousif AM, Abdulgadir EM, Sabahalkhair MA, Abbas AE, Hassan MA. Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches. Bioinform Biol Insights 2018; 12:1177932218809703. [PMID: 30542244 PMCID: PMC6236636 DOI: 10.1177/1177932218809703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/06/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Mycetoma is a distinct body tissue destructive and neglected tropical
disease. It is endemic in many tropical and subtropical countries. Mycetoma
is caused by bacterial infections (actinomycetoma) such as
Streptomyces somaliensis and Nocardiae or true fungi
(eumycetoma) such as Madurella
mycetomatis. To date, treatments fail to cure the infection and
the available marketed drugs are expensive and toxic upon prolonged usage.
Moreover, no vaccine was prepared yet against mycetoma. Aim: The aim of this study is to predict effective epitope-based vaccine against
fructose-bisphosphate aldolase enzymes of M. mycetomatis
using immunoinformatics approaches. Methods and materials: Fructose-bisphosphate aldolase of M. mycetomatis sequence
was retrieved from NCBI. Different prediction tools were used to analyze the
nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class
II and class I. Then the proposed peptides were docked using Autodock 4.0
software program. Results and conclusions: The proposed and promising peptides KYLQ show a potent binding affinity to
B-cell, FEYARKHAF with a very strong binding affinity to MHC I alleles and
FFKEHGVPL that shows a very strong binding affinity to MHC II and MHC I
alleles. This indicates a strong potential to formulate a new vaccine,
especially with the peptide FFKEHGVPL which is likely to be the first
proposed epitope-based vaccine against fructose-bisphosphate aldolase of
M. mycetomatis. This study recommends an in vivo
assessment for the most promising peptides especially FFKEHGVPL.
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Affiliation(s)
- Arwa A Mohammed
- Department of Pharmacy, Sudan Medical Council, Khartoum, Sudan.,Department of Biotechnology, Africa City of Technology, Khartoum, Sudan
| | - Ayman Mh ALnaby
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan
| | - Solima M Sabeel
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Fagr M AbdElmarouf
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Amina I Dirar
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Mostafa M Ali
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Medical Laboratory, University of Sciences and Technology, Omdurman, Sudan
| | - Mustafa A Khandgawi
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | | | - Eman M Abdulgadir
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan
| | - Magdi A Sabahalkhair
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Pharmacy, The National Ribat University, Khartoum, Sudan
| | - Ayman E Abbas
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan.,Faculty of Medicine and Health Sciences, Omdurman Islamic University, Omdurman, Sudan
| | - Mohammed A Hassan
- Department of Biotechnology, Africa City of Technology, Khartoum, Sudan
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17
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Oyarzún P, Kobe B. Recombinant and epitope-based vaccines on the road to the market and implications for vaccine design and production. Hum Vaccin Immunother 2017; 12:763-7. [PMID: 26430814 DOI: 10.1080/21645515.2015.1094595] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Novel vaccination approaches based on rational design of B- and T-cell epitopes - epitope-based vaccines - are making progress in the clinical trial pipeline. The epitope-focused recombinant protein-based malaria vaccine (termed RTS,S) is a next-generation approach that successfully reached phase-III trials, and will potentially become the first commercial vaccine against a human parasitic disease. Progress made on methods such as recombinant DNA technology, advanced cell-culture techniques, immunoinformatics and rational design of immunogens are driving the development of these novel concepts. Synthetic recombinant proteins comprising both B- and T-cell epitopes can be efficiently produced through modern biotechnology and bioprocessing methods, and can enable the induction of large repertoires of immune specificities. In particular, the inclusion of appropriate CD4+ T-cell epitopes is increasingly considered a key vaccine component to elicit robust immune responses, as suggested by results coming from HIV-1 clinical trials. In silico strategies for vaccine design are under active development to address genetic variation in pathogens and several broadly protective "universal" influenza and HIV-1 vaccines are currently at different stages of clinical trials. Other methods focus on improving population coverage in target populations by rationally considering specificity and prevalence of the HLA proteins, though a proof-of-concept in humans has not been demonstrated yet. Overall, we expect immunoinformatics and bioprocessing methods to become a central part of the next-generation epitope-based vaccine development and production process.
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Affiliation(s)
- Patricio Oyarzún
- a Biotechnology Center, Facultad de Ingeniería y Tecnología, Universidad San Sebastián , Concepción , Chile
| | - Bostjan Kobe
- b School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Center, University of Queensland , Brisbane , Australia
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18
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Abdulaziz S, Halabi H, Omair MA, Attar S, Alghamdi A, Shabrawishi M, Neyazi A, Alnazzawi H, Meraiani N, Almoallim H. Biological therapy in arthritis patients with hepatitis B or C infection: a multicenter retrospective case series. Eur J Rheumatol 2017; 4:194-199. [PMID: 29164002 PMCID: PMC5685275 DOI: 10.5152/eurjrheum.2017.17003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/10/2017] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Reactivation of viral hepatitis B (HBV) and C (HCV) has been reported in various case reports of patients with arthritis on biological therapy. The objective of this study was to describe the clinical characteristics and outcomes of arthritis patients with HBV or HCV treated with biological therapy. MATERIAL AND METHODS This is a retrospective case series including all patients above 13 years of age with arthritis patients from four centers in Saudi Arabia with concurrent chronic viral hepatitis infection (HBV or HCV) who received biological agents in the rheumatology clinics during their course of their disease from duration of the disease onset until last outpatient visit up to November 2015. Demographic information, full details about the hepatitis status of each patient, rheumatic disease diagnosis and different therapies used were reviewed. RESULTS We identified 10 cases each with HBV and HCV on biological therapy. The mean age in the HBV group was 51 (34-85) years and 80% were females. Eight patients had rheumatoid arthritis (RA), one patient had RA/systemic lupus erythematosus, and one had human immunodeficiency virus related-arthritis. Seven were chronic inactive HBsAg carriers and three had chronic active HBV. Nine HBV patients received prophylactic antiviral therapy. Two cases with chronic HBV had reactivation with no elevation of the transaminases.The mean age in the HCV group was 54 (23-79) years and all were female RA patients. Three had detectable hepatitis C virus-ribonuecleic acid (HCV-RNA) before the start of biological therapy. Nine HCV patients received antiviral treatment and seven had a sustained virologic response (SVR) before start of biological treatment. Three patients had detectable HCV-RNA during the course of biological therapy. One of the three was a non-responder and two were relapsers. One of the patients with HCV relapse was started on sofosbuvir plus ribavirin and achieved SVR on follow-up. CONCLUSION We report the successful use of biological therapy in arthritis patients with hepatitis B infection with antiviral therapy with no detoriation of their viral status. Due to the lack of sufficient prospective studies demonstrating the rate of HCV flare on biological therapy, caution should be exercised and careful monitoring with liver enzymes and viral load is mandated in vulnerable HCV RNA patients. Treatment should be individualized by the rheumatologist in collaboration with the hepatologist to minimize complications.
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Affiliation(s)
- Sultana Abdulaziz
- Unit of Rheumatology, Department of Medicine, King Fahd Hospital, Jeddah, Saudi Arabia
| | - Hussein Halabi
- Department of Medicine, King Faisal Specialist Hospital, Jeddah, Saudi Arabia
| | - Mohammed A. Omair
- Division of Rheumatology, Department of Medicine, King Saud University College of Medicine, Riyadh, Saudi Arabia
| | - Suzan Attar
- Department of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah Alghamdi
- Unit of Gastroenterology, Department of Medicine, King Fahd Hospital, Jeddah, Saudi Arabia
| | | | - Abdulwahab Neyazi
- Department of Medicine, Umm Alqura University School of Medicine, Makkah, Saudi Arabia
| | - Haneen Alnazzawi
- Department of Medicine, Umm Alqura University School of Medicine, Makkah, Saudi Arabia
| | - Nuha Meraiani
- Department of Medicine, King Faisal Specialist Hospital, Jeddah, Saudi Arabia
| | - Hani Almoallim
- Department of Medicine, Umm Alqura University School of Medicine, Makkah, Saudi Arabia
- Department of Medicine, Dr. Soliman Fakeeh Hospital, Jeddah, Saudi Arabia
- Alzaidi Chair of Research Diseases, Umm Alqura University School of Medicine, Makkah, Saudi Arabia
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19
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Schubert B, de la Garza L, Mohr C, Walzer M, Kohlbacher O. ImmunoNodes - graphical development of complex immunoinformatics workflows. BMC Bioinformatics 2017; 18:242. [PMID: 28482806 PMCID: PMC5422934 DOI: 10.1186/s12859-017-1667-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/30/2017] [Indexed: 11/10/2022] Open
Abstract
Background Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the other hand, are difficult to integrate with other tools, which is typically required for the complex analysis and prediction pipelines required for advanced applications. Result We present ImmunoNodes, an immunoinformatics toolbox that is fully integrated into the visual workflow environment KNIME. By dragging and dropping tools and connecting them to indicate the data flow through the pipeline, it is possible to construct very complex workflows without the need for coding. Conclusion ImmunoNodes allows users to build complex workflows with an easy to use and intuitive interface with a few clicks on any desktop computer.
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Affiliation(s)
- Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany. .,Applied Bioinformatics, Dept. of Computer Science, Tübingen, 72076, Germany. .,Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, 02115, USA.
| | - Luis de la Garza
- Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.,Applied Bioinformatics, Dept. of Computer Science, Tübingen, 72076, Germany
| | - Christopher Mohr
- Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.,Applied Bioinformatics, Dept. of Computer Science, Tübingen, 72076, Germany
| | - Mathias Walzer
- Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.,Applied Bioinformatics, Dept. of Computer Science, Tübingen, 72076, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.,Applied Bioinformatics, Dept. of Computer Science, Tübingen, 72076, Germany.,Quantitative Biology Center (QBiC), Tübingen, 72076, Germany.,Faculty of Medicine, University of Tübingen, Tübingen, 72076, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
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20
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21
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Schubert B, Walzer M, Brachvogel HP, Szolek A, Mohr C, Kohlbacher O. FRED 2: an immunoinformatics framework for Python. Bioinformatics 2016; 32:2044-6. [PMID: 27153717 PMCID: PMC4920123 DOI: 10.1093/bioinformatics/btw113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/23/2016] [Indexed: 12/22/2022] Open
Abstract
Summary: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications. Availability and implementation: FRED 2 is available at http://fred-2.github.io Contact:schubert@informatik.uni-tuebingen.de Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany
| | - Mathias Walzer
- Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany
| | | | - András Szolek
- Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany
| | - Christopher Mohr
- Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany Quantitative Biology Center, Tübingen 72076, Germany Faculty of Medicine, University of Tübingen, Tübingen 72076, Germany Max Planck Institute for Developmental Biology, Biomolecular Interactions, Tübingen 72076, Germany
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22
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Abstract
String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers.
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23
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Abstract
Immunoinformatics involves the application of computational methods to immunological problems. Prediction of B- and T-cell epitopes has long been the focus of immunoinformatics, given the potential translational implications, and many tools have been developed. With the advent of next-generation sequencing (NGS) methods, an unprecedented wealth of information has become available that requires more-advanced immunoinformatics tools. Based on information from whole-genome sequencing, exome sequencing and RNA sequencing, it is possible to characterize with high accuracy an individual’s human leukocyte antigen (HLA) allotype (i.e., the individual set of HLA alleles of the patient), as well as changes arising in the HLA ligandome (the collection of peptides presented by the HLA) owing to genomic variation. This has allowed new opportunities for translational applications of epitope prediction, such as epitope-based design of prophylactic and therapeutic vaccines, and personalized cancer immunotherapies. Here, we review a wide range of immunoinformatics tools, with a focus on B- and T-cell epitope prediction. We also highlight fundamental differences in the underlying algorithms and discuss the various metrics employed to assess prediction quality, comparing their strengths and weaknesses. Finally, we discuss the new challenges and opportunities presented by high-throughput data-sets for the field of epitope prediction.
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Affiliation(s)
- Linus Backert
- Applied Bioinformatics, Center of Bioinformatics and Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center of Bioinformatics and Department of Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
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24
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Oyarzun P, Kobe B. Computer-aided design of T-cell epitope-based vaccines: addressing population coverage. Int J Immunogenet 2015. [PMID: 26211755 DOI: 10.1111/iji.12214] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Epitope-based vaccines (EVs) make use of short antigen-derived peptides corresponding to immune epitopes, which are administered to trigger a protective humoral and/or cellular immune response. EVs potentially allow for precise control over the immune response activation by focusing on the most relevant - immunogenic and conserved - antigen regions. Experimental screening of large sets of peptides is time-consuming and costly; therefore, in silico methods that facilitate T-cell epitope mapping of protein antigens are paramount for EV development. The prediction of T-cell epitopes focuses on the peptide presentation process by proteins encoded by the major histocompatibility complex (MHC). Because different MHCs have different specificities and T-cell epitope repertoires, individuals are likely to respond to a different set of peptides from a given pathogen in genetically heterogeneous human populations. In addition, protective immune responses are only expected if T-cell epitopes are restricted by MHC proteins expressed at high frequencies in the target population. Therefore, without careful consideration of the specificity and prevalence of the MHC proteins, EVs could fail to adequately cover the target population. This article reviews state-of-the-art algorithms and computational tools to guide EV design through all the stages of the process: epitope prediction, epitope selection and vaccine assembly, while optimizing vaccine immunogenicity and coping with genetic variation in humans and pathogens.
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Affiliation(s)
- P Oyarzun
- Biotechnology Centre, Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción, Chile
| | - B Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
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25
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Schubert B, Brachvogel HP, Jürges C, Kohlbacher O. EpiToolKit--a web-based workbench for vaccine design. ACTA ACUST UNITED AC 2015; 31:2211-3. [PMID: 25712691 PMCID: PMC4481845 DOI: 10.1093/bioinformatics/btv116] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/18/2015] [Indexed: 11/13/2022]
Abstract
UNLABELLED EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets. AVAILABILITY AND IMPLEMENTATION http://www.epitoolkit.de CONTACT schubert@informatik.uni-tuebingen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Philipp Brachvogel
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Christopher Jürges
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany, Applied Bioinformatics, Department of Computer Science, 72076 Tübingen, Germany, Quantitative Biology Center, 72076 Tübingen, Germany and Faculty of Medicine, University of Tübingen, 72076 Tübingen, Germany
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26
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Soria-Guerra RE, Nieto-Gomez R, Govea-Alonso DO, Rosales-Mendoza S. An overview of bioinformatics tools for epitope prediction: implications on vaccine development. J Biomed Inform 2014; 53:405-14. [PMID: 25464113 DOI: 10.1016/j.jbi.2014.11.003] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 09/16/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Exploitation of recombinant DNA and sequencing technologies has led to a new concept in vaccination in which isolated epitopes, capable of stimulating a specific immune response, have been identified and used to achieve advanced vaccine formulations; replacing those constituted by whole pathogen-formulations. In this context, bioinformatics approaches play a critical role on analyzing multiple genomes to select the protective epitopes in silico. It is conceived that cocktails of defined epitopes or chimeric protein arrangements, including the target epitopes, may provide a rationale design capable to elicit convenient humoral or cellular immune responses. This review presents a comprehensive compilation of the most advantageous online immunological software and searchable, in order to facilitate the design and development of vaccines. An outlook on how these tools are supporting vaccine development is presented. HIV and influenza have been taken as examples of promising developments on vaccination against hypervariable viruses. Perspectives in this field are also envisioned.
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Affiliation(s)
- Ruth E Soria-Guerra
- Laboratorio de Ingeniería de Biorreactores, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico
| | - Ricardo Nieto-Gomez
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico
| | - Dania O Govea-Alonso
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico
| | - Sergio Rosales-Mendoza
- Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, Mexico.
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Rosendahl Huber S, van Beek J, de Jonge J, Luytjes W, van Baarle D. T cell responses to viral infections - opportunities for Peptide vaccination. Front Immunol 2014; 5:171. [PMID: 24795718 PMCID: PMC3997009 DOI: 10.3389/fimmu.2014.00171] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/31/2014] [Indexed: 12/22/2022] Open
Abstract
An effective immune response against viral infections depends on the activation of cytotoxic T cells that can clear infection by killing virus-infected cells. Proper activation of these T cells depends on professional antigen-presenting cells, such as dendritic cells (DCs). In this review, we will discuss the potential of peptide-based vaccines for prevention and treatment of viral diseases. We will describe features of an effective response against both acute and chronic infections, such as an appropriate magnitude, breadth, and quality and discuss requirements for inducing such an effective antiviral immune response. We will address modifications that affect presentation of vaccine components by DCs, including choice of antigen, adjuvants, and formulation. Furthermore, we will describe differences in design between preventive and therapeutic peptide-based vaccines. The ultimate goal in the design of preventive vaccines is to develop a universal vaccine that cross-protects against multiple strains of the virus. For therapeutic vaccines, cross-protection is of less importance, but enhancing existing T cell responses is essential. Although peptide vaccination is successful in inducing responses in human papillomavirus (HPV) infected patients, there are still several challenges such as choosing the right target epitopes, choosing safe adjuvants that improve immunogenicity of these epitopes, and steering the immune response in the desired direction. We will conclude with an overview of the current status of peptide vaccination, hurdles to overcome, and prospects for the future.
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Affiliation(s)
- Sietske Rosendahl Huber
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Josine van Beek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Jørgen de Jonge
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Willem Luytjes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Debbie van Baarle
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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Schubert B, Lund O, Nielsen M. Evaluation of peptide selection approaches for epitope-based vaccine design. ACTA ACUST UNITED AC 2013; 82:243-51. [DOI: 10.1111/tan.12199] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/11/2013] [Accepted: 08/14/2013] [Indexed: 12/01/2022]
Affiliation(s)
- B. Schubert
- Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science; University of Tübingen; 72076 Tübingen Germany
| | - O. Lund
- CBS, Department of Systems Biology; Technical University of Denmark DTU; 2800 Lyngby Denmark
| | - M. Nielsen
- CBS, Department of Systems Biology; Technical University of Denmark DTU; 2800 Lyngby Denmark
- Instituto de Investigaciones Biotecnológicas; Universidad Nacional de San Martín; San Martín Argentina
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Ferri C, Sebastiani M, Antonelli A, Colaci M, Manfredi A, Giuggioli D. Current treatment of hepatitis C-associated rheumatic diseases. Arthritis Res Ther 2012; 14:215. [PMID: 22731694 PMCID: PMC3446515 DOI: 10.1186/ar3865] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The hepatitis C virus (HCV) is both hepatotropic and lymphotropic, responsible for a great number of hepatic and extrahepatic immune-system disorders that comprise the so-called HCV syndrome. HCV-associated rheumatic diseases are characterized by frequent clinico-serological overlap; therefore, correct classification of individual patients is necessary before therapeutic decisions are made. This is particularly difficult to do, however, because of the coexistence of viral infection and complex autoimmune alterations. In this context, mixed cryoglobulinemia syndrome (MCs) represents the prototype of virus-related autoimmune-lymphoproliferative diseases. MCs can be treated at different levels by means of etiological treatment with antivirals (peg-interferon-alpha plus ribavirin) aimed at HCV eradication and/or pathogenetic/symptomatic treatments directed to both immune-system alterations and the vasculitic process (rituximab, cyclophosphamide, steroids, plasmapheresis, and so on). In clinical practice, the therapeutic strategy should be modulated according to severity/activity of the MCs and possibly tailored to each individual patient's conditions. Cryoglobulinemic skin ulcers may represent a therapeutic challenge, which should be managed by means of both local and systemic treatments. HCV-associated arthritis should be differentiated from the simple comorbidity of HCV infection and classical rheumatoid arthritis. It may be treated with low doses of steroids and/or hydroxychloroquine; the use of biologics (rituximab) may be considered in more severe cases. Primary Sjögren's syndrome is rarely associated with HCV infection, while sicca syndrome and myalgia are frequently detectable in hepatitis C patients, with or without cryoglobulinemic vasculitis. Other autoimmune rheumatic disorders (poly/dermatomyositis, polyarteritis nodosa, osteosclerosis, fibromyalgia, and so on) have been reported as potentially associated with HCV infection in patient populations from different countries, suggesting the role of genetic and/or environmental co-factors. The therapeutic approach to these disorders should be decided according to each individual patient's evaluation, including hepatic, virological, and immunological findings.
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Affiliation(s)
- Clodoveo Ferri
- Rheumatology Unit, University of Modena and Reggio Emilia School of Medicine, 41100 Modena, Italy.
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Roohvand F, Kossari N. Advances in hepatitis C virus vaccines, part two: advances in hepatitis C virus vaccine formulations and modalities. Expert Opin Ther Pat 2012; 22:391-415. [PMID: 22455502 DOI: 10.1517/13543776.2012.673589] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Developing a vaccine against HCV is an important medical and global priority. Unavailability and potential dangers associated with using attenuated HCV viral particles for vaccine preparation have resulted in the use of HCV genes and proteins formulated in novel vaccine modalities. AREAS COVERED In part one of this review, advances in basic knowledge for HCV vaccine design were provided. Herein, a detailed and correlated patents (searched by Espacenet) and literatures (searched by Pubmed) review on HCV vaccine formulations and modalities is provided, including: subunit, DNA, epitopic-peptide/polytopic, live vector- and whole yeast-based vaccines. Less-touched areas in vaccine studies such as mucosal, plant-based, and chimeric HBV/HCV vaccines are also discussed. Furthermore, results of preclinical/clinical studies on selected HCV vaccines as well as pros and cons of different strategies are reviewed. Finally, potential strategies for creation and/or improvement of HCV vaccine formulations are discussed. EXPERT OPINION Promising outcomes of a few HCV vaccine modalities in phase I/II clinical trials predict the accessibility of at least partially effective vaccines to inhibit or treat the chronic state of HCV infection (specially in combination with standard antiviral therapy). ChronVac-C (plasmid DNA), TG4040 (MVA-based), and GI-5005 (whole yeast-based) might be the most obvious HCV vaccine candidates to be approved in the near future.
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Affiliation(s)
- Farzin Roohvand
- Hepatitis & AIDS Department, Pasteur Institute of Iran, Tehran, Iran.
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