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Magazine N, Zhang T, Bungwon AD, McGee MC, Wu Y, Veggiani G, Huang W. Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development. Immunohorizons 2024; 8:214-226. [PMID: 38427047 PMCID: PMC10985062 DOI: 10.4049/immunohorizons.2400003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and virus immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination in humans. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the TLRs, B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.
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Affiliation(s)
- Nicholas Magazine
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Anang D. Bungwon
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Michael C. McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
| | - Yingying Wu
- Department of Mathematics, University of Houston, Houston, TX
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
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2
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Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T, Munthe LA. Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Front Immunol 2023; 14:1265044. [PMID: 38045681 PMCID: PMC10691274 DOI: 10.3389/fimmu.2023.1265044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/01/2023] [Indexed: 12/05/2023] Open
Abstract
During the COVID-19 pandemic we utilized an AI-driven T cell epitope prediction tool, the NEC Immune Profiler (NIP) to scrutinize and predict regions of T cell immunogenicity (hotspots) from the entire SARS-CoV-2 viral proteome. These immunogenic regions offer potential for the development of universally protective T cell vaccine candidates. Here, we validated and characterized T cell responses to a set of minimal epitopes from these AI-identified universal hotspots. Utilizing a flow cytometry-based T cell activation-induced marker (AIM) assay, we identified 59 validated screening hits, of which 56% (33 peptides) have not been previously reported. Notably, we found that most of these novel epitopes were derived from the non-spike regions of SARS-CoV-2 (Orf1ab, Orf3a, and E). In addition, ex vivo stimulation with NIP-predicted peptides from the spike protein elicited CD8+ T cell response in PBMC isolated from most vaccinated donors. Our data confirm the predictive accuracy of AI platforms modelling bona fide immunogenicity and provide a novel framework for the evaluation of vaccine-induced T cell responses.
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Affiliation(s)
- Lorenzo Federico
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Viktoriia Chaban
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Julie Røkke Osen
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Murat Gainullin
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Smorodina
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Hassen Kared
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Oslo University Hospital, Oslo, Norway
| | | | | | - Ludvig Andre Munthe
- Department of Immunology, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for B cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Magazine N, Zhang T, Bungwon AD, McGee MC, Wu Y, Veggiani G, Huang W. Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564184. [PMID: 37961687 PMCID: PMC10634854 DOI: 10.1101/2023.10.26.564184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the toll-like receptors (TLRs), B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.
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Affiliation(s)
- Nicholas Magazine
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tianyi Zhang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Anang D. Bungwon
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michael C. McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yingying Wu
- Department of Mathematics, University of Houston, Houston, TX 77204, USA
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Fletcher P, O'Donnell KL, Doratt BM, Malherbe DC, Clancy CS, Rhoderick JF, Feldmann F, Hanley PW, Ksiazek TG, Geisbert TW, Messaoudi I, Marzi A. Single-dose VSV-based vaccine protects cynomolgus macaques from disease after Taï Forest virus infection. Emerg Microbes Infect 2023:2239950. [PMID: 37470396 PMCID: PMC10392270 DOI: 10.1080/22221751.2023.2239950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Taï Forest virus (TAFV) is a lesser-known ebolavirus that causes lethal infections in chimpanzees and is responsible for a single human case. Limited research has been done on this human pathogen; however, with the recent emergence of filoviruses in West Africa, further investigation and countermeasure development against this virus is warranted.We developed a vesicular stomatitis virus (VSV)-based vaccine expressing the TAFV glycoprotein as the viral antigen and assessed it for protective efficacy in nonhuman primates (NHPs). Following a single high-dose vaccination, NHPs developed antigen-specific binding and neutralizing antibodies as well as modest T cell responses. Importantly, all vaccinated NHPs were uniformly protected from disease after lethal TAFV challenge while the naïve control group succumbed to the disease. Histopathologic lesions consistent with filovirus disease were present in control NHPs but were not observed in vaccinated NHPs. Transcriptional analysis of whole blood samples obtained after vaccination and challenge was performed to gain insight into molecular underpinnings conferring protection. Differentially expressed genes (DEG) detected 7 days post-vaccination were enriched to processes associated with innate immunity and antiviral responses. Only a small number of DEG was detected in vaccinated NHPs post-challenge while over 1,000 DEG were detected in control NHPs at end-stage disease which mapped to gene ontology terms indicative of defense responses and inflammation. Taken together, this data demonstrates the effective single-dose protection of the VSV-TAFV vaccine, and its potential for use in outbreaks.
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Affiliation(s)
- Paige Fletcher
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kyle L O'Donnell
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Brianna M Doratt
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Delphine C Malherbe
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Chad S Clancy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Joseph F Rhoderick
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas G Ksiazek
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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Chen CB, Hung WK, Wang CW, Lee CC, Hung SI, Chung WH. Advances in understanding of the pathogenesis and therapeutic implications of drug reaction with eosinophilia and systemic symptoms: an updated review. Front Med (Lausanne) 2023; 10:1187937. [PMID: 37457584 PMCID: PMC10338933 DOI: 10.3389/fmed.2023.1187937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Drug reaction with eosinophilia and systemic symptoms or drug-induced hypersensitivity syndrome (DRESS/DIHS) is one type of severe cutaneous adverse reaction (SCAR). It is featured by fever, widespread skin lesions, protracted clinical course, internal organ involvement, and possibly long-term autoimmune sequelae. The presence of high-risk human leukocyte antigen (HLA) alleles, hypersensitivity reaction after culprit drug ingestion, and human herpesvirus reactivation may all contribute to its complex clinical manifestations. Some recent studies focusing on the roles of involved cytokines/chemokines and T cells co-signaling pathways in DRESS/DIHS were conducted. In addition, some predictors of disease severity and prognosis were also reported. In this review, we provided an update on the current understanding of the pathogenesis, potential biomarkers, and the relevant therapeutic rationales of DRESS/DIHS.
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Affiliation(s)
- Chun-Bing Chen
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou, Taiwan
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
- Xiamen Chang Gung Allergology Consortium, Xiamen Chang Gung Hospital, Xiamen, China
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wei-Kai Hung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chuang-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou, Taiwan
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
- Xiamen Chang Gung Allergology Consortium, Xiamen Chang Gung Hospital, Xiamen, China
| | - Chih-Chun Lee
- Department of Medical Education, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Shuen-Iu Hung
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou, Taiwan
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
- Xiamen Chang Gung Allergology Consortium, Xiamen Chang Gung Hospital, Xiamen, China
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou, Taiwan
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
- Department of Dermatology, Beijing Tsinghua Chang Gung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
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6
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Gouttefangeas C, Klein R, Maia A. The good and the bad of T cell cross-reactivity: challenges and opportunities for novel therapeutics in autoimmunity and cancer. Front Immunol 2023; 14:1212546. [PMID: 37409132 PMCID: PMC10319254 DOI: 10.3389/fimmu.2023.1212546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/24/2023] [Indexed: 07/07/2023] Open
Abstract
T cells are main actors of the immune system with an essential role in protection against pathogens and cancer. The molecular key event involved in this absolutely central task is the interaction of membrane-bound specific T cell receptors with peptide-MHC complexes which initiates T cell priming, activation and recall, and thus controls a range of downstream functions. While textbooks teach us that the repertoire of mature T cells is highly diverse, it is clear that this diversity cannot possibly cover all potential foreign peptides that might be encountered during life. TCR cross-reactivity, i.e. the ability of a single TCR to recognise different peptides, offers the best solution to this biological challenge. Reports have shown that indeed, TCR cross-reactivity is surprisingly high. Hence, the T cell dilemma is the following: be as specific as possible to target foreign danger and spare self, while being able to react to a large spectrum of body-threatening situations. This has major consequences for both autoimmune diseases and cancer, and significant implications for the development of T cell-based therapies. In this review, we will present essential experimental evidence of T cell cross-reactivity, implications for two opposite immune conditions, i.e. autoimmunity vs cancer, and how this can be differently exploited for immunotherapy approaches. Finally, we will discuss the tools available for predicting cross-reactivity and how improvements in this field might boost translational approaches.
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Affiliation(s)
- Cécile Gouttefangeas
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Ana Maia
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
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Moustakas AK, Nguyen H, James EA, Papadopoulos GK. Autoimmune susceptible HLA class II motifs facilitate the presentation of modified neoepitopes to potentially autoreactive T cells. Cell Immunol 2023; 390:104729. [PMID: 37301094 DOI: 10.1016/j.cellimm.2023.104729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
Rheumatoid arthritis (RA), multiple sclerosis (MS), type 1 diabetes (T1D), and celiac disease (CD), are strongly associated with susceptible HLA class II haplotypes. The peptide-binding pockets of these molecules are polymorphic, thus each HLA class II protein presents a distinct set of peptides to CD4+ T cells. Peptide diversity is increased through post-translational modifications, generating non-templated sequences that enhance HLA binding and/or T cell recognition. The high-risk HLA-DR alleles that confer susceptibility to RA are notable for their ability to accommodate citrulline, promoting responses to citrullinated self-antigens. Likewise, HLA-DQ alleles associated with T1D and CD favor the binding of deamidated peptides. In this review, we discuss structural features that promote modified self-epitope presentation, provide evidence supporting the relevance of T cell recognition of such antigens in disease processes, and make a case that interrupting the pathways that generate such epitopes and reprogramming neoepitope-specific T cells are key strategies for effective therapeutic intervention.
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Affiliation(s)
- Antonis K Moustakas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, GR26100 Argostoli, Cephalonia, Greece
| | - Hai Nguyen
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Eddie A James
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Bioprocessing and Bioproducts, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, GR47100 Arta, Greece
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8
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Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine. Diagnostics (Basel) 2022; 12:diagnostics12122981. [PMID: 36552988 PMCID: PMC9777080 DOI: 10.3390/diagnostics12122981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Vaccines are an upcoming medical intervention for breast cancer. By targeting the tumor antigen, cancer vaccines can be designed to train the immune system to recognize tumor cells. Therefore, along with technological advances, the vaccine design process is now starting to be carried out with more rational methods such as designing epitope-based peptide vaccines using immunoinformatics methods. Immunoinformatics methods can assist vaccine design in terms of antigenicity and safety. Common protocols used to design epitope-based peptide vaccines include tumor antigen identification, protein structure analysis, T cell epitope prediction, epitope characterization, and evaluation of protein-epitope interactions. Tumor antigen can be divided into two types: tumor associated antigen and tumor specific antigen. We will discuss the identification of tumor antigens using high-throughput technologies. Protein structure analysis comprises the physiochemical, hydrochemical, and antigenicity of the protein. T cell epitope prediction models are widely available with various prediction parameters as well as filtering tools for the prediction results. Epitope characterization such as allergenicity and toxicity can be done in silico as well using allergenicity and toxicity predictors. Evaluation of protein-epitope interactions can also be carried out in silico with molecular simulation. We will also discuss current and future developments of breast cancer vaccines using an immunoinformatics approach. Finally, although prediction models have high accuracy, the opposite can happen after being tested in vitro and in vivo. Therefore, further studies are needed to ensure the effectiveness of the vaccine to be developed. Although epitope-based peptide vaccines have the disadvantage of low immunogenicity, the addition of adjuvants can be a solution.
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The generation and application of antigen-specific T cell therapies for cancer and viral-associated disease. Mol Ther 2022; 30:2130-2152. [PMID: 35149193 PMCID: PMC9171249 DOI: 10.1016/j.ymthe.2022.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/27/2021] [Accepted: 02/03/2022] [Indexed: 11/23/2022] Open
Abstract
Immunotherapy with antigen-specific T cells is a promising, targeted therapeutic option for patients with cancer as well as for immunocompromised patients with virus infections. In this review, we characterize and compare current manufacturing protocols for the generation of T cells specific to viral and non-viral tumor-associated antigens. Specifically, we discuss: (1) the different methodologies to expand virus-specific T cell and non-viral tumor-associated antigen-specific T cell products, (2) an overview of the immunological principles involved when developing such manufacturing protocols, and (3) proposed standardized methodologies for the generation of polyclonal, polyfunctional antigen-specific T cells irrespective of donor source. Ex vivo expanded cells have been safely administered to treat numerous patients with virus-associated malignancies, hematologic malignancies, and solid tumors. Hence, we have performed a comprehensive review of the clinical trial results evaluating the safety, feasibility, and efficacy of these products in the clinic. In summary, this review seeks to provide new insights regarding antigen-specific T cell technology to benefit a rapidly expanding T cell therapy field.
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10
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Zaremba AA, Zaremba PY, Platonov MO. De novo designed EBAI as a potential inhibitor of the viral protein BHRF1. Research in silico. J Biomol Struct Dyn 2022; 41:3680-3685. [PMID: 35315740 DOI: 10.1080/07391102.2022.2053746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Epstein-Barr virus is a DNA-containing virus that, according to current data, is associated with approximately 1% of all cancers in the world. This viral effect on the human body is associated with its pronounced antiapoptotic activity. An important role in this process is played by the protein BHRF1, which is a structural and functional homologue of antiapoptotic proteins of the BCL-2 family. In this study, we investigate the selective low molecular weight inhibitor of the above viral protein - EBAI (Epstein-Barr virus Antiapoptotic Inhibitor), which we designed using in silico methods. We conducted two parallel simulation experiments where EBAI was intentionally destabilized to demonstrate its high-affinity recognition potential of the BHRF1 pocket, which binds BH3.Thus, although the potential inhibitor was in close proximity to the site of interaction, it contacted it only through orientation interactions (hydrogen and Coulomb interactions). Despite this complication of the standard ligand-receptor complex simulation procedure, we demonstrated in two parallel computational experiments the high affinity of EBAI for the BH3-binding pocket of BHRF1. In both cases, in the first nanoseconds of modeling, our inhibitor underwent the necessary conformational rearrangements and formed all the required interactions for effective complexation. Thus, further in vitro studies are logical and necessary step to fully evaluate the potential of EBAI as an inhibitor of the antiapoptotic protein BHRF1 of Epstein-Barr virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Andrii A. Zaremba
- Zabolotny Institute of Microbiology and Virology of NASU, Kyiv, Ukraine
| | - Polina Y. Zaremba
- Zabolotny Institute of Microbiology and Virology of NASU, Kyiv, Ukraine
| | - Maxim O. Platonov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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11
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Calado CRC. Antigenic and conserved peptides from diverse Helicobacter pylori antigens. Biotechnol Lett 2022; 44:535-545. [PMID: 35277779 PMCID: PMC8916697 DOI: 10.1007/s10529-022-03238-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Since the revolutionary finding of Helicobacter pylori as a common bacterial infection, that a high research effort for its eradication has been conducted. Epitope based-vaccine presents advantages over protein-based, as they can be designed to contain epitopes from diverse proteins, therefore, more easily representing the immune-variability of the bacterial population, while minimizing the toxicity associated to some whole proteins. In the present work, an iterative method, to design antigenic and conserved B-epitopes from diverse virulent factors of H. pylori, was established. The method considered the trade-off between epitopes antigenicity and conservation among the bacterial population. For the method validation, five virulent factors from H. pylori were selected. From each virulent factor, two epitopes were predicted, each with twelve residues of aminoacids. The corresponding ten peptides were synthesised and evaluated by enzyme-linked immunosorbent assay using polyclonal antibodies raised against a specific H. pylori strain. All ten peptides were recognised by the antibodies and were consequently antigenic and conserved. This result could strongly contribute to the design of a multivalent epitope-based vaccine, representing the immunogenetic variability within the bacterial population, leading to a sustained and effective immunogenic protection.
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Affiliation(s)
- Cecília R C Calado
- CIMOSM - Centro de Investigação em Modelação e Otimização de Sistemas Multifuncionais, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.
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12
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Antigenic sites in SARS-CoV-2 spike RBD show molecular similarity with pathogenic antigenic determinants and harbors peptides for vaccine development. Immunobiology 2021; 226:152091. [PMID: 34303920 PMCID: PMC8297981 DOI: 10.1016/j.imbio.2021.152091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 03/13/2021] [Accepted: 03/30/2021] [Indexed: 01/22/2023]
Abstract
The spike protein of coronavirus is key target for drug development and other pharmacological interventions. In current study, we performed an integrative approach to predict antigenic sites in SARS-CoV-2 spike receptor binding domain and found nine potential antigenic sites. The predicted antigenic sites were then assessed for possible molecular similarity with other known antigens in different organisms. Out of nine sites, seven sites showed molecular similarity with 54 antigenic determinants found in twelve pathogenic bacterial species (Mycobacterium tuberculosis, Mycobacterium leprae, Bacillus anthracis, Borrelia burgdorferi, Clostridium perfringens, Clostridium tetani, Helicobacter Pylori, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholera and Yersinia pestis), two malarial parasites (Plasmodium falciparum and Plasmodium knowlesi) and influenza virus A. Most of the bacterial antigens that displayed molecular similarity with antigenic sites in SARS-CoV-2 RBD (receptor binding domain) were toxins and virulent factors. Antigens from Mycobacterium that showed similarity were mainly involved in modulating host cell immune response and ensuring persistence and survival of pathogen in host cells. Presence of a large number of antigenic determinants, similar to those in highly pathogenic microorganisms, not merely accounts for complex etiology of the disease but also provides an explanation for observed pathophysiological complications, such as deregulated immune response, unleashed or dysregulated cytokine secretion (cytokine storm), multiple organ failure etc., that are more evident in aged and immune-compromised patients. Over-representation of antigenic determinants from Plasmodium and Mycobacterium in all antigenic sites suggests that anti-malarial and anti-TB drugs can prove to be clinical beneficial for COVID-19 treatment. Besides this, anti-leprosy, anti-lyme, anti-plague, anti-anthrax drugs/vaccine etc. are also expected to be beneficial in COVID-19 treatment. Moreover, individuals previously immunized/vaccinated or had previous history of malaria, tuberculosis or other disease caused by fifteen microorganisms are expected to display a considerable degree of resistance against SARS-CoV-2 infection. Out of the seven antigenic sites predicted in SARS-CoV-2, a part of two antigenic sites were also predicted as potent T-cell epitopes (KVGGNYNYL444-452 and SVLYNSASF366-374) against MHC class I and three (KRISNCVADYSVLYN356-370, DLCFTNVYADSFVI389-402, and YRVVVLSFELLHA508-520) against MHC class II. All epitopes possessed significantly lower predicted IC50 value which is a prerequisite for a preferred vaccine candidate for COVID-19.
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Danelli L, Cornish G, Merkenschlager J, Kassiotis G. Default polyfunctional T helper 1 response to ample signal 1 alone. Cell Mol Immunol 2021; 18:1809-1822. [PMID: 32313208 PMCID: PMC8245500 DOI: 10.1038/s41423-020-0415-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 03/14/2020] [Indexed: 12/27/2022] Open
Abstract
CD4+ T cells integrate well-defined signals from the T-cell receptor (TCR) (signal 1) and a host of costimulatory molecules (signal 2) to initiate clonal expansion and differentiation into diverse functional T helper (Th) subsets. However, our ability to guide the expansion of context-appropriate Th subsets by deploying these signals in vaccination remains limited. Using cell-based vaccines, we selectively amplified signal 1 by exclusive presentation of an optimized peptide:MHC II (pMHC II) complex in the absence of classic costimulation. Contrary to expectations, amplified signal 1 alone was strongly immunogenic and selectively expanded high-affinity TCR clonotypes, despite delivering intense TCR signals. In contrast to natural infection or standard vaccines, amplified signal 1, presented by a variety of professional and nonprofessional antigen-presenting cells (APCs), induced exclusively polyfunctional Th1 effector and memory cells, which protected against retroviral infection and tumor challenge, and expanded tumor-reactive CD4+ T cells otherwise rendered unresponsive in tumor-bearing hosts. Together, our findings uncover a default Th1 response to ample signal 1 and offer a means to selectively prime such protective responses by vaccination.
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Affiliation(s)
- Luca Danelli
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Georgina Cornish
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julia Merkenschlager
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London, W2 1PG, UK.
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Root-Bernstein R. Possible Cross-Reactivity between SARS-CoV-2 Proteins, CRM197 and Proteins in Pneumococcal Vaccines May Protect Against Symptomatic SARS-CoV-2 Disease and Death. Vaccines (Basel) 2020; 8:E559. [PMID: 32987794 PMCID: PMC7712751 DOI: 10.3390/vaccines8040559] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/08/2023] Open
Abstract
Various studies indicate that vaccination, especially with pneumococcal vaccines, protects against symptomatic cases of SARS-CoV-2 infection and death. This paper explores the possibility that pneumococcal vaccines in particular, but perhaps other vaccines as well, contain antigens that might be cross-reactive with SARS-CoV-2 antigens. Comparison of the glycosylation structures of SARS-CoV-2 with the polysaccharide structures of pneumococcal vaccines yielded no obvious similarities. However, while pneumococcal vaccines are primarily composed of capsular polysaccharides, some are conjugated to cross-reacting material CRM197, a modified diphtheria toxin, and all contain about three percent protein contaminants, including the pneumococcal surface proteins PsaA, PspA and probably PspC. All of these proteins have very high degrees of similarity, using very stringent criteria, with several SARS-CoV-2 proteins including the spike protein, membrane protein and replicase 1a. CRM197 is also present in Haemophilus influenzae type b (Hib) and meningitis vaccines. Equivalent similarities were found at lower rates, or were completely absent, among the proteins in diphtheria, tetanus, pertussis, measles, mumps, rubella, and poliovirus vaccines. Notably, PspA and PspC are highly antigenic and new pneumococcal vaccines based on them are currently in human clinical trials so that their effectiveness against SARS-CoV-2 disease is easily testable.
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Xu Z, Chokkalingam N, Tello-Ruiz E, Walker S, Kulp DW, Weiner DB. Incorporation of a Novel CD4+ Helper Epitope Identified from Aquifex aeolicus Enhances Humoral Responses Induced by DNA and Protein Vaccinations. iScience 2020; 23:101399. [PMID: 32763137 PMCID: PMC7409978 DOI: 10.1016/j.isci.2020.101399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 01/12/2023] Open
Abstract
CD4+ T cells play an important role in the maturation of the antibody responses. Conjugation of identified CD4+ T cell helper epitope to the target antigen has been developed as a strategy to enhance vaccine-induced humoral immunity. In this work, we reported the identification of a novel HLA-IAb helper epitope LS-3 from Aquifex aeolicus. In silico analysis predicted this epitope to have high binding affinity to common human HLA alleles and have complementary binding coverage to the established PADRE epitope. Introduction of HLA-IAb knockout mutations to the LS-3 epitope significantly attenuated humoral responses induced by a vaccine containing this epitope. Finally, engineered fusion of the epitope to a model antigen, influenza hemagglutinin, significantly improved both binding and hemagglutination inhibition antibody responses in mice receiving DNA or protein vaccines. In summary, LS-3 and additional identified CD4+ helper epitopes may be further explored to improve vaccine responses in translational studies. Identification of a novel CD4+ helper epitope, LS-3, from Aquifex aeolicus In silico analysis predicts high binding affinity of LS-3 to human HLA-DR alleles Fusing LS-3 to antigen enhances humoral response by vaccinations
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Affiliation(s)
- Ziyang Xu
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA; Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neethu Chokkalingam
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Edgar Tello-Ruiz
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Susanne Walker
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Daniel W Kulp
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA.
| | - David B Weiner
- The Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA.
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Masuda K, Sato A, Tanaka A, Kumagai A. Hydrolyzed diets may stimulate food-reactive lymphocytes in dogs. J Vet Med Sci 2019; 82:177-183. [PMID: 31875597 PMCID: PMC7041975 DOI: 10.1292/jvms.19-0222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hydrolyzed proteins are often prescribed for dogs with food hypersensitivity in food elimination programs. However, the potential of these diets to stimulate lymphocyte-mediated hypersensitivity is currently unknown. In this study, two commercially available hydrolyzed diets for dogs, D-1 (Aminopeptide Formula Dry, Royal Canin Japon, Tokyo, Japan), and D-2 (Canine z/d Ultra Dry, Hill's-Colgate (Japan) Ltd., Tokyo, Japan), were analyzed to identify residual proteins or peptides, as well as activated helper T-lymphocyte reactions in dogs with suspected food hypersensitivity. Proteins and peptides with molecular weights >1 kDa (majority 1.5-3.5 kDa) were detected in both diet extracts with sodium dodecyl sulfate polyacrylamide gel electrophoresis, and size exclusion chromatography. When peripheral blood mononuclear cells (PBMC's) from 316 dogs with suspected food allergies were cultured with hydrolyzed diet extracts, flow cytometry analysis revealed detectable levels of CD25low helper T-lymphocytes stimulated by D-1 and D-2 in 91 of 316, (28.8%), and 75 of 316 (23.7%) samples, respectively. These data indicated that the extracts contained proteins or peptides large enough to activate the lymphocytes. The percentages of CD25low helper T-lymphocytes stimulated by D-1 and D-2 extracts increased to 38.7% and 29.6%, respectively, in 186 of the original 316 samples (186/316, 58.9%), also reactive to poultry-related antigens. Thus, both poultry-related antigens, and D-1 and D-2 diet extracts may activate helper T-lymphocytes. These results demonstrate that hydrolyzed diets may contain proteins that stimulate helper T-lymphocytes, and may not be effective for treating all dogs with food hypersensitivity.
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Affiliation(s)
- Kenichi Masuda
- Animal Allergy Clinical Laboratories Inc., SIC-2 #301, 5-4-30, Nishihashimoto, Midori-ku, Sagamihara-shi, Kanagawa 252-0131, Japan
| | - Atsushi Sato
- Animal Allergy Clinical Laboratories Inc., SIC-2 #301, 5-4-30, Nishihashimoto, Midori-ku, Sagamihara-shi, Kanagawa 252-0131, Japan
| | - Atsushi Tanaka
- Animal Allergy Clinical Laboratories Inc., SIC-2 #301, 5-4-30, Nishihashimoto, Midori-ku, Sagamihara-shi, Kanagawa 252-0131, Japan
| | - Akiko Kumagai
- Animal Allergy Clinical Laboratories Inc., SIC-2 #301, 5-4-30, Nishihashimoto, Midori-ku, Sagamihara-shi, Kanagawa 252-0131, Japan
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Jazayeri SD, Poh CL. Development of Universal Influenza Vaccines Targeting Conserved Viral Proteins. Vaccines (Basel) 2019; 7:E169. [PMID: 31683888 PMCID: PMC6963725 DOI: 10.3390/vaccines7040169] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/31/2022] Open
Abstract
Vaccination is still the most efficient way to prevent an infection with influenza viruses. Nevertheless, existing commercial vaccines face serious limitations such as availability during epidemic outbreaks and their efficacy. Existing seasonal influenza vaccines mostly induce antibody responses to the surface proteins of influenza viruses, which frequently change due to antigenic shift and or drift, thus allowing influenza viruses to avoid neutralizing antibodies. Hence, influenza vaccines need a yearly formulation to protect against new seasonal viruses. A broadly protective or universal influenza vaccine must induce effective humoral as well as cellular immunity against conserved influenza antigens, offer good protection against influenza pandemics, be safe, and have a fast production platform. Nanotechnology has great potential to improve vaccine delivery, immunogenicity, and host immune responses. As new strains of human epidemic influenza virus strains could originate from poultry and swine viruses, development of a new universal influenza vaccine will require the immune responses to be directed against viruses from different hosts. This review discusses how the new vaccine platforms and nanoparticles can be beneficial in the development of a broadly protective, universal influenza vaccine.
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Affiliation(s)
- Seyed Davoud Jazayeri
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, Subang Jaya 47500, Malaysia.
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, Subang Jaya 47500, Malaysia.
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18
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Martínez L, Milanič M, Malaina I, Álvarez C, Pérez MB, M. de la Fuente I. Weighted lambda superstrings applied to vaccine design. PLoS One 2019; 14:e0211714. [PMID: 30735507 PMCID: PMC6368308 DOI: 10.1371/journal.pone.0211714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/19/2019] [Indexed: 11/23/2022] Open
Abstract
We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins.
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Affiliation(s)
- Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Basque Center for Applied Mathematics BCAM, Bilbao, Spain
- * E-mail:
| | - Martin Milanič
- University of Primorska, UP IAM and UP FAMNIT, Koper, Slovenia
| | - Iker Malaina
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Carmen Álvarez
- IDIVAL Valdecilla Biomedical Research Institute, Santander, Spain
| | - Martín-Blas Pérez
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Ildefonso M. de la Fuente
- Department of Mathematics, University of the Basque Country UPV/EHU, Bilbao, Spain
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
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Russell BL, Parbhoo N, Gildenhuys S. Analysis of Conserved, Computationally Predicted Epitope Regions for VP5 and VP7 Across three Orbiviruses. Bioinform Biol Insights 2018; 12:1177932218755348. [PMID: 29434468 PMCID: PMC5802602 DOI: 10.1177/1177932218755348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/04/2018] [Indexed: 12/15/2022] Open
Abstract
Orbiviruses are double-stranded RNA viruses that have profound economic and veterinary significance, 3 of the most important being African horse sickness virus (AHSV), bluetongue virus (BTV), and epizootic hemorrhagic disease virus (EHDV). Currently, vaccination and vector control are used as preventative measures; however, there are several problems with the current vaccines. Comparing viral amino acid sequences, we obtained an AHSV-BTV-EHDV consensus sequence for VP5 (viral protein 5) and for VP7 (viral protein 7) and generated homology models for these proteins. The structures and sequences were analyzed for amino acid sequence conservation, entropy, surface accessibility, and epitope propensity, to computationally determine whether consensus sequences still possess potential epitope regions. In total, 5 potential linear epitope regions on VP5 and 11 on VP7, as well as potential discontinuous B-cell epitopes, were identified and mapped onto the homology models created. Regions identified for VP5 and VP7 could be important in vaccine design against orbiviruses.
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Affiliation(s)
- Bonnie L Russell
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| | - Nishal Parbhoo
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| | - Samantha Gildenhuys
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
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Kanduc D, Shoenfeld Y. From HBV to HPV: Designing vaccines for extensive and intensive vaccination campaigns worldwide. Autoimmun Rev 2016; 15:1054-1061. [DOI: 10.1016/j.autrev.2016.07.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 07/12/2016] [Indexed: 12/12/2022]
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21
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Malm M, Tamminen K, Vesikari T, Blazevic V. Type-specific and cross-reactive antibodies and T cell responses in norovirus VLP immunized mice are targeted both to conserved and variable domains of capsid VP1 protein. Mol Immunol 2016; 78:27-37. [PMID: 27573255 DOI: 10.1016/j.molimm.2016.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/12/2016] [Accepted: 08/14/2016] [Indexed: 12/21/2022]
Abstract
Norovirus (NoV)-specific antibodies, which block binding of the virus-like particles (VLPs) to the cell receptors are conformation dependent and directed towards the most exposed domain of the NoV capsid VP1 protein, the P2 domain. Limited data are available on the antibodies directed to other domains of the VP1, and even less on the NoV VP1-specific T cell epitopes. In here, BALB/c mice were immunized with six VLPs derived from NoV GII.4-1999, GII.4-2009 (New Orleans), GII.4-2012 (Sydney), GII.12, GI.1, and G1.3. Serum immunoglobulin G binding antibodies, histo-blood group antigen blocking antibodies and T cell responses using type-specific and heterologous NoV VLPs, P-dimers and 76 overlapping synthetic peptides, spanning the entire 539 amino acid sequence of GII.4 VP1, were determined. The results showed that at least half of the total antibody content is directed towards conserved S domain of the VP1. Only a small fraction (<1%) of the VP1 binding antibodies were blocking/neutralizing. With the use of matrix peptide pools and individual peptides, seven CD4+ and CD8+ T cell restricted epitopes were mapped, two located in S domain, four in P2 domain and one in P1 domain of NoV VP1. The epitopes were GII.4 strain-specific but also common GII.4 genotype-specific T cell epitopes were identified. More importantly, the results suggest a 9-amino acids long sequence (318PAPLGTPDF326) in P2 domain of VP1 as a universal NoV genogroup II-specific CD8+ T cell epitope. Distribution of the T cell epitopes alongside the capsid VP1 indicates the need of the complete protein for high immunogenicity.
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Affiliation(s)
- Maria Malm
- Vaccine Research Center, University of Tampere Medical School, Biokatu 10, FI-33520 Tampere, Finland.
| | - Kirsi Tamminen
- Vaccine Research Center, University of Tampere Medical School, Biokatu 10, FI-33520 Tampere, Finland.
| | - Timo Vesikari
- Vaccine Research Center, University of Tampere Medical School, Biokatu 10, FI-33520 Tampere, Finland.
| | - Vesna Blazevic
- Vaccine Research Center, University of Tampere Medical School, Biokatu 10, FI-33520 Tampere, Finland.
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Bizikova P, Olivry T. A randomized, double-blinded crossover trial testing the benefit of two hydrolysed poultry-based commercial diets for dogs with spontaneous pruritic chicken allergy. Vet Dermatol 2016; 27:289-e70. [PMID: 27307314 DOI: 10.1111/vde.12302] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2016] [Indexed: 11/29/2022]
Abstract
BACKGROUND Hydrolysed protein diets are used to diagnose and treat dogs with cutaneous adverse food reactions (CAFR). Little is known about what proportion of dogs hypersensitive to the native protein would react to its hydrolysed form. OBJECTIVES To determine the clinical allergenicity of hydrolysed poultry feather (RCU) and chicken liver diets (HZD) in dogs with chicken induced CAFR. METHODS In this randomized, double-blinded, crossover trial, ten dogs with chicken induced CAFR were selected after a positive oral challenge to chicken meat and a negative one to corn. Test diets were fed for 14 days separated by a 14 day wash-out period. Owners rated pruritus daily with a Visual Analog Scale (PVAS). The challenge was ended if a flare in pruritus occurred (i.e. PVAS ≥5/10). RESULTS The median PVAS scores before feeding RCU and HZD were 0.9 and 1.7, respectively (Wilcoxon signed rank test, P = 0.46). Pruritus scores increased significantly after feeding HZD (Friedman's test, P < 0.001) but not after feeding RCU (P = 0.895). None of the dogs fed RCU, but four dogs fed HZD (40%), were withdrawn after a flare in pruritus developed (Fisher's test, P = 0.04). The maximal PVAS score was significantly higher after HZD (median: 4.7) compared to RCU (2.5) (Wilcoxon signed rank test, P = 0.01). One dog in each group was withdrawn due to diarrhoea. CONCLUSIONS The hydrolysed poultry feather diet did not induce pruritus flares in dogs allergic to chicken in contrast to the hydrolysed chicken liver diet that led to pruritus flares in 40% of these dogs.
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Affiliation(s)
- Petra Bizikova
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Institute for Comparative Medicine, North Carolina State University, Raleigh, NC, USA
| | - Thierry Olivry
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Institute for Comparative Medicine, North Carolina State University, Raleigh, NC, USA
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Ramadan A, Lucca LE, Carrié N, Desbois S, Axisa PP, Hayder M, Bauer J, Liblau RS, Mars LT. In situ expansion of T cells that recognize distinct self-antigens sustains autoimmunity in the CNS. Brain 2016; 139:1433-46. [PMID: 27000832 DOI: 10.1093/brain/aww032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/15/2016] [Indexed: 01/22/2023] Open
Abstract
Polyspecific T cells recognizing multiple distinct self-antigens have been identified in multiple sclerosis and other organ-specific autoimmune diseases, but their pathophysiological relevance remains undetermined. Using a mouse model of multiple sclerosis, we show that autoimmune encephalomyelitis induction is strictly dependent on reactivation of pathogenic T cells by a peptide (35-55) derived from myelin oligodendrocyte glycoprotein (MOG). This disease-inducing response wanes after onset. Strikingly, the progression of disease is driven by the in situ activation and expansion of a minority of MOG35-55-specific T cells that also recognize neurofilament-medium (NF-M)15-35, an intermediate filament protein expressed in neurons. This mobilization of bispecific T cells is critical for disease progression as adoptive transfer of NF-M15-35/MOG35-55 bispecific T cell lines caused full-blown disease in wild-type but not NF-M-deficient recipients. Moreover, specific tolerance through injection of NF-M15-35 peptide at the peak of disease halted experimental autoimmune encephalomyelitis progression. Our findings highlight the importance of polyspecific autoreactive T cells in the aggravation and perpetuation of central nervous system autoimmunity.
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Affiliation(s)
- Abdulraouf Ramadan
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Liliana E Lucca
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Nadège Carrié
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Sabine Desbois
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Pierre-Paul Axisa
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Myriam Hayder
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Jan Bauer
- Center for Brain Research, Department of Neuroimmunology, Medical University of Vienna, Vienna, Austria
| | - Roland S Liblau
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France
| | - Lennart T Mars
- INSERM UMR1043, Toulouse, F-31300, France CNRS, U5282, Toulouse, F-31300, France Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, F-31300, France INSERM UMR995, LIRIC, F-59000 Lille, France Université de Lille, centre d'excellence LICEND and FHU IMMINeNT, F-59000 Lille, France
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Aguirre ADAR, Lobo FP, Cunha RC, Garcia MV, Andreotti R. Design of the ATAQ peptide and its evaluation as an immunogen to develop a Rhipicephalus vaccine. Vet Parasitol 2016; 221:30-8. [PMID: 27084468 DOI: 10.1016/j.vetpar.2016.02.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 02/21/2016] [Accepted: 02/27/2016] [Indexed: 11/26/2022]
Abstract
Tick infestation may cause several problems including affecting domestic animal health and reducing the production of meat and milk, among others. Resistance to several classes of acaricides have been reported, forcing researchers to search for alternative measures, such as vaccines against ticks, to ensure tick control while having no or at least low negative impacts on the environment and public health. However, the current commercially available vaccines in different strains of Rhipicephalus microplus are reported to be of low efficacy. Fortunately, reverse vaccinology approaches have shown positive results in the new generation of vaccines. On this basis, a synthetic peptide from the ATAQ protein, which is present in the gut and Malpighi tubes of R. microplus, was synthesized. The ATAQ proteins were isolated, characterized and sequenced from several species of the genus Rhipicephalus. The alignment showed 93.3% identity among DNA sequences of ATAQs from these species. Because of this, immunization trials with this peptide were conducted on mice, rabbits and cattle to evaluate the humoral immune response and the efficacy against Rhipicephalus sanguineus in addition to R. microplus. Based on recent results, we conclude that reverse vaccinology is a promising approach because it is more accurate and faster than conventional methods in the detection of potential antigens to use in anti-tick vaccines. It is not only applicable against R. microplus but also against tick species that play important roles in spreading other diseases. ATAQ proteins should be considered as the antigen in new trials to develop a multi-antigenic vaccine. Although these peptides behave as hapten and are not able to be recognized by the immune system on its own, using carriers and adjuvants helps its presentation and induces strong immune responses. Furthermore, an efficiency of 35% reduction in overall life cycle parameters was reported for R. microplus (98% for ELISA responder animals) and 47% for R. sanguineus. Although not yet enough to prevent the environment to infestation of ticks, this still constitutes a promising strategy that could be applied to integrated measures on tick control and in new research that develops anti-tick vaccines.
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Affiliation(s)
- André de Abreu Rangel Aguirre
- Programa de Pós-graduação em Ciência Animal, FAMEZ, Universidade Federal de Mato Grosso do Sul, Av. Felinto Müller, No. 2443, Vila Ipiranga, CEP 79074-460 Campo Grande, MS, Brazil; Fundação Oswaldo Cruz, Fiocruz Rondônia, Rua da Beira, No. 7671, Bairro Lagoa, CEP 76812-245 Porto Velho, RO, Brazil.
| | - Francisco Pereira Lobo
- Embrapa Informática Agropecuária, Av. André Tosello, No. 209 Campus Unicamp, Barão Geraldo, CEP 13083-886 Campinas, SP, Brazil
| | - Rodrigo Casquero Cunha
- Programa de Pós-graduação em Ciência Animal, FAMEZ, Universidade Federal de Mato Grosso do Sul, Av. Felinto Müller, No. 2443, Vila Ipiranga, CEP 79074-460 Campo Grande, MS, Brazil; Embrapa Gado de Corte, Av. Rádio Maia, No. 830, Zona Rural, CEP 79106-550 Campo Grande, MS, Brazil
| | - Marcos Valério Garcia
- Embrapa Gado de Corte, Av. Rádio Maia, No. 830, Zona Rural, CEP 79106-550 Campo Grande, MS, Brazil; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brazil()
| | - Renato Andreotti
- Embrapa Gado de Corte, Av. Rádio Maia, No. 830, Zona Rural, CEP 79106-550 Campo Grande, MS, Brazil
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Lakshminarayanan V, Supekar NT, Wei J, McCurry DB, Dueck AC, Kosiorek HE, Trivedi PP, Bradley JM, Madsen CS, Pathangey LB, Hoelzinger DB, Wolfert MA, Boons GJ, Cohen PA, Gendler SJ. MUC1 Vaccines, Comprised of Glycosylated or Non-Glycosylated Peptides or Tumor-Derived MUC1, Can Circumvent Immunoediting to Control Tumor Growth in MUC1 Transgenic Mice. PLoS One 2016; 11:e0145920. [PMID: 26788922 PMCID: PMC4720451 DOI: 10.1371/journal.pone.0145920] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/05/2015] [Indexed: 01/21/2023] Open
Abstract
It remains challenging to produce decisive vaccines against MUC1, a tumor-associated antigen widely expressed by pancreas, breast and other tumors. Employing clinically relevant mouse models, we ruled out such causes as irreversible T-cell tolerance, inadequate avidity, and failure of T-cells to recognize aberrantly glycosylated tumor MUC1. Instead, every tested MUC1 preparation, even non-glycosylated synthetic 9mer peptides, induced interferon gamma-producing CD4+ and CD8+ T-cells that recognized glycosylated variants including tumor-associated MUC1. Vaccination with synthetic peptides conferred protection as long as vaccination was repeated post tumor challenge. Failure to revaccinate post challenge was associated with down-regulated tumor MUC1 and MHC molecules. Surprisingly, direct admixture of MUC1-expressing tumor with MUC1-hyperimmune T-cells could not prevent tumor outgrowth or MUC1 immunoediting, whereas ex vivo activation of the hyperimmune T-cells prior to tumor admixture rendered them curative. Therefore, surrogate T-cell preactivation outside the tumor bed, either in culture or by repetitive vaccination, can overcome tumor escape.
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Affiliation(s)
- Vani Lakshminarayanan
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Nitin T. Supekar
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States of America
| | - Jie Wei
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Dustin B. McCurry
- Hematology/Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Amylou C. Dueck
- Biostatistics, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Heidi E. Kosiorek
- Biostatistics, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Priyanka P. Trivedi
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Judy M. Bradley
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Cathy S. Madsen
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | - Latha B. Pathangey
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
| | | | - Margreet A. Wolfert
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States of America
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States of America
- * E-mail: (SJG); (PAC); (GJB)
| | - Peter A. Cohen
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
- Hematology/Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
- * E-mail: (SJG); (PAC); (GJB)
| | - Sandra J. Gendler
- Department of Immunology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
- Department of Biochemistry/Molecular Biology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
- Hematology/Oncology, Mayo Clinic in Arizona, Scottsdale, AZ, United States of America
- * E-mail: (SJG); (PAC); (GJB)
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26
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Fuchs YF, Jainta GW, Kühn D, Wilhelm C, Weigelt M, Karasinsky A, Upadhyaya B, Ziegler AG, Bonifacio E. Vagaries of the ELISpot assay: specific detection of antigen responsive cells requires purified CD8(+) T cells and MHC class I expressing antigen presenting cell lines. Clin Immunol 2015; 157:216-25. [PMID: 25728493 DOI: 10.1016/j.clim.2015.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 12/15/2014] [Accepted: 02/17/2015] [Indexed: 01/22/2023]
Abstract
Quantification of antigen-specific CD8(+) T cells is important for monitoring infection, vaccination, and response to therapy in cancer and immune-mediated diseases. Cytokine enzyme-linked-immunospot (ELISpot) assays are often used for this purpose. We found that substantial spot formation in IFNγ ELISpot assays occurred independently of CD8(+) T cells even when classical MHC class I restricted peptides are used for stimulation. Using fractionated cells and intracellular cytokine staining, the non-CD8(+) T cell IFNγ production was attributed to the CD4(+) T cell fraction. We therefore refined a cell line-based ELISpot assay combining HLA-A*0201 expressing K562 cells for antigen presentation with purified CD8(+) T cells and demonstrated that it specifically detected CD8(+) T cell responses with detection limits comparable to traditional ELISpot assays and dextramer-based quantification. The assay was further adapted to whole antigen responses with antigen (pre-proinsulin)-expressing HLA-A*0201K562 cells. Thus, we revealed and corrected a weak spot of the CD8(+) ELISpot assay.
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Affiliation(s)
- Yannick F Fuchs
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany; Paul Langerhans Institute Dresden, Germany; Forschergruppe Diabetes e.V., Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Gregor W Jainta
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Denise Kühn
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Carmen Wilhelm
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Marc Weigelt
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Anne Karasinsky
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Bhaskar Upadhyaya
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Anette-G Ziegler
- Forschergruppe Diabetes e.V., Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Diabetes Research, Helmholtz Zentrum München, and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Ezio Bonifacio
- Technische Universität Dresden, DFG-Center for Regenerative Therapies Dresden, Fetscherstr. 105, 01307 Dresden, Germany; Paul Langerhans Institute Dresden, Germany; Institute of Diabetes Research, Helmholtz Zentrum München, and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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27
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Capone G, Fasano C, Lucchese G, Calabrò M, Kanduc D. EBV-Associated Cancer and Autoimmunity: Searching for Therapies. Vaccines (Basel) 2015; 3:74-89. [PMID: 26344947 PMCID: PMC4494242 DOI: 10.3390/vaccines3010074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/12/2014] [Accepted: 01/27/2015] [Indexed: 12/26/2022] Open
Abstract
Epstein-Barr virus (EBV) infects B-, T-, and NK cells and has been associated not only with a wide range of lymphoid malignancies but also with autoimmune diseases such as lupus erythematosus, rheumatoid arthritis and, in particular, multiple sclerosis. Hence, effective immunotherapeutic approaches to eradicate EBV infection might overthrow cancer and autoimmunity incidence. However, currently no effective anti-EBV immunotherapy is available. Here we use the concept that protein immunogenicity is allocated in rare peptide sequences and search the Epstein-Barr nuclear antigen 1 (EBNA1) sequence for peptides unique to the viral protein and absent in the human host. We report on a set of unique EBV EBNA1 peptides that might be used in designing peptide-based therapies able to specifically hitting the virus or neutralizing pathogenic autoantibodies.
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Affiliation(s)
- Giovanni Capone
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Candida Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Guglielmo Lucchese
- Brain and Language Laboratory, Free University of Berlin, 14195 Berlin, Germany.
| | - Michele Calabrò
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
| | - Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari 70126, Italy.
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28
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Xu M, Zhang B, Liu Y, Zhang J, Sheng H, Shi R, Liao L, Liu N, Hu J, Wang J, Ning H, Liu T, Zhang Y, Chen H. The immunologic and hematopoietic profiles of mesenchymal stem cells derived from different sections of human umbilical cord. Acta Biochim Biophys Sin (Shanghai) 2014; 46:1056-65. [PMID: 25377438 DOI: 10.1093/abbs/gmu100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have been widely used in allogeneic stem cell transplantation. We compared immunologic and hematopoietic characteristics of MSCs derived from whole human umbilical cord (UC), as well as from different sections of UCs, including the amniotic membrane (AM), Wharton's jelly (WJ), and umbilical vessel (UV). Cell phenotypes were examined by flow cytometry. Lymphocyte transformation test and mixed lymphocyte reaction were performed to evaluate the immuno-modulatory activity of MSCs derived from UCs. The mRNA expression of cytokines was detected by real-time polymerase chain reaction. Hematopoietic function was studied by co-culturing MSCs with CD34(+) cells isolated from cord blood. Our results showed that MSCs separated from these four different sections including UC, WJ, UV, and AM had similar biological characteristics. All of the MSCs had multi-lineage differentiation ability and were able to differentiate into osteoblasts, adipocytes, and chondrocytes. The MSCs also inhibited the proliferation of allogeneic T cells in a dose-dependent manner. The relative mRNA expression of cytokines was examined, and the results showed that UCMSCs had higher interleukin-6 (IL6), IL11, stem cell factor, and FLT3 expression than MSCs derived from specific sections of UCs. CD34(+) cells had high propagation efficiencies when co-cultured with MSCs derived from different sections of UCs, among which UCMSCs are the most efficient feeding layer. Our study demonstrated that MSCs could be isolated from whole UC or specific sections of UC with similar immunomodulation and hematopoiesis supporting characteristics.
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Affiliation(s)
- Man Xu
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Bin Zhang
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Yuanlin Liu
- Institute of Basic Medical Science, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jin Zhang
- Department of cardiovascular medicine, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Hongxia Sheng
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Rui Shi
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Li Liao
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Na Liu
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Jiangwei Hu
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Wang
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Hongmei Ning
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Ting Liu
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
| | - Yi Zhang
- Institute of Basic Medical Science, Academy of Military Medical Sciences, Beijing 100850, China
| | - Hu Chen
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, China
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29
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Lucca LE, Desbois S, Ramadan A, Ben-Nun A, Eisenstein M, Carrié N, Guéry JC, Sette A, Nguyen P, Geiger TL, Mars LT, Liblau RS. Bispecificity for myelin and neuronal self-antigens is a common feature of CD4 T cells in C57BL/6 mice. THE JOURNAL OF IMMUNOLOGY 2014; 193:3267-77. [PMID: 25135834 DOI: 10.4049/jimmunol.1400523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The recognition of multiple ligands by a single TCR is an intrinsic feature of T cell biology, with important consequences for physiological and pathological processes. Polyspecific T cells targeting distinct self-antigens have been identified in healthy individuals as well as in the context of autoimmunity. We have previously shown that the 2D2 TCR recognizes the myelin oligodendrocyte glycoprotein epitope (MOG)35-55 as well as an epitope within the axonal protein neurofilament medium (NF-M15-35) in H-2(b) mice. In this study, we assess whether this cross-reactivity is a common feature of the MOG35-55-specific T cell response. To this end, we analyzed the CD4 T cell response of MOG35-55-immunized C57BL/6 mice for cross-reactivity with NF-M15-35. Using Ag recall responses, we established that an important proportion of MOG35-55-specific CD4 T cells also responded to NF-M15-35 in all mice tested. To study the clonality of this response, we analyzed 22 MOG35-55-specific T cell hybridomas expressing distinct TCR. Seven hybridomas were found to cross-react with NF-M15-35. Using an alanine scan of NF-M18-30 and an in silico predictive model, we dissected the molecular basis of cross-reactivity between MOG35-55 and NF-M15-35. We established that NF-M F24, R26, and V27 proved important TCR contacts. Strikingly, the identified TCR contacts are conserved within MOG38-50. Our data indicate that due to linear sequence homology, part of the MOG35-55-specific T cell repertoire of all C57BL/6 mice also recognizes NF-M15-35, with potential implications for CNS autoimmunity.
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Affiliation(s)
- Liliana E Lucca
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Sabine Desbois
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Abdulraouf Ramadan
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Avraham Ben-Nun
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miriam Eisenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nadège Carrié
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Jean-Charles Guéry
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, San Diego, CA 92109
| | - Phuong Nguyen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Lennart T Mars
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France
| | - Roland S Liblau
- INSERM, U1043, Toulouse F-31300, France; Centre National de la Recherche Scientifique, U5282, Toulouse F-31300, France; Centre de Physiopathologie Toulouse-Purpan, Université Toulouse 3, Toulouse F-31300, France; Département d'Immunologie, Centre Hospitalier Universitaire Toulouse, Hôpital Purpan, Toulouse F-31300, France
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30
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The Peptide Network between Tetanus Toxin and Human Proteins Associated with Epilepsy. EPILEPSY RESEARCH AND TREATMENT 2014; 2014:236309. [PMID: 24982805 PMCID: PMC4058587 DOI: 10.1155/2014/236309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/24/2014] [Accepted: 05/13/2014] [Indexed: 11/17/2022]
Abstract
Sequence matching analyses show that Clostridium tetani neurotoxin shares numerous pentapeptides (68, including multiple occurrences) with 42 human proteins that, when altered, have been associated with epilepsy. Such a peptide sharing is higher than expected, nonstochastic, and involves tetanus toxin-derived epitopes that have been validated as immunopositive in the human host. Of note, an unexpected high level of peptide matching is found in mitogen-activated protein kinase 10 (MK10), a protein selectively expressed in hippocampal areas. On the whole, the data indicate a potential for cross-reactivity between the neurotoxin and specific epilepsy-associated proteins and may help evaluate the potential risk for epilepsy following immune responses induced by tetanus infection. Moreover, this study may contribute to clarifying the etiopathogenesis of the different types of epilepsy.
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31
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Lucchese G, Capone G, Kanduc D. Peptide sharing between influenza A H1N1 hemagglutinin and human axon guidance proteins. Schizophr Bull 2014; 40:362-75. [PMID: 23378012 PMCID: PMC3932078 DOI: 10.1093/schbul/sbs197] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epidemiologic data suggest that maternal microbial infections may cause fetal neurodevelopmental disorders, potentially increasing susceptibility to heavy psychopathologies such as schizophrenia, schizophreniform disorder, autism, pervasive developmental disorders, bipolar disorders, psychosis, epilepsy, language and speech disorders, and cognitive impairment in adult offspring. However, the molecular pathomechanisms underlying such a relationship are not clear. Here we analyze the potential role of the maternal immune response to viral infection in determining fetal brain injuries that increase the risk of neurological disorders in the adult. We use influenza infection as a disease model and human axon guidance pathway, a key process in the formation of neural network during midgestation, as a potential fetal target of immune insults. Specifically, we examined influenza A H1N1 hemagglutinin (HA), an antigenic viral protein, for amino acid sequence similarity to a random library of 188 axon guidance proteins. We obtain the results that (1) contrary to any theoretical expectations, 45 viral pentapeptide matches are distributed throughout a subset of 36 guidance molecules; (2) in 24 guidance proteins, the peptide sharing with HA antigen involves already experimentally validated influenza HA epitopes; and (3) most of the axon guidance vs HA peptide overlap is conserved among influenza A viral strains and subsets. Taken together, our data indicate that immune cross-reactivity between influenza HA and axon guidance molecules is possible and may well represent a pathologic mechanism capable of determining neurodevelopmental disruption in the fetus.
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Affiliation(s)
- Guglielmo Lucchese
- To whom correspondence should be addressed; tel: +39.080.544.3321, fax: +39.080.544.3317, e-mail:
| | - Giovanni Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy
| | - Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences, University of Bari, Bari, Italy,To whom correspondence should be addressed; tel: +39.080.544.3321, fax: +39.080.544.3317, e-mail:
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32
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Vaughan K, Peters B, O'Connor KC, Martin R, Sette A. A molecular view of multiple sclerosis and experimental autoimmune encephalitis: what can we learn from the epitope data? J Neuroimmunol 2014; 267:73-85. [PMID: 24365494 PMCID: PMC4784960 DOI: 10.1016/j.jneuroim.2013.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/03/2013] [Accepted: 12/06/2013] [Indexed: 02/04/2023]
Abstract
An analysis to inventory all immune epitope data related to multiple sclerosis (MS) was performed using the Immune Epitope Database (IEDB). The analysis revealed that MS related data represent >20% of all autoimmune data, and that studies of EAE predominate; only 22% of the references describe human data. To date, >5800 unique peptides, analogs, mimotopes, and/or non-protein epitopes have been reported from 861 references, including data describing myelin-containing, as well as non-myelin antigens. This work provides a reference point for the scientific community of the universe of available data for MS-related adaptive immunity in the context of EAE and human disease.
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Affiliation(s)
- Kerrie Vaughan
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, USA.
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, USA
| | - Kevin C O'Connor
- Department of Neurology, Yale School of Medicine, 300 George Street, New Haven, CT 06511, USA; Human and Translational Immunology Program, Yale School of Medicine, 300 George Street, New Haven, CT 06511, USA
| | - Roland Martin
- Neuroimmunology and MS Research, Department of Neurology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, USA
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33
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Prickett SR, Voskamp AL, Phan T, Dacumos-Hill A, Mannering SI, Rolland JM, O'Hehir RE. Ara h 1 CD4+ T cell epitope-based peptides: candidates for a peanut allergy therapeutic. Clin Exp Allergy 2014; 43:684-97. [PMID: 23711131 PMCID: PMC3709139 DOI: 10.1111/cea.12113] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 12/01/2022]
Abstract
Background Peanut allergy is a life-threatening condition; there is currently no cure. While whole allergen extracts are used for specific immunotherapy for many allergies, they can cause severe reactions and even fatalities in peanut allergy. Objective To identify short, HLA-degenerate CD4+ T cell epitope-based peptides of the major peanut allergen Ara h 1 that target allergen-specific T cells without causing IgE-mediated inflammatory cell activation, as candidates for safe peanut-specific immunotherapy. Methods Ara h 1-specific CD4+ T cell lines (TCL) were generated from peripheral blood mononuclear cells (PBMC) of peanut-allergic subjects using CFSE-based methodology. T cell epitopes were identified using CFSE and thymidine-based proliferation assays. Epitope HLA-restriction was investigated using blocking antibodies, HLA-genotyping and epitope prediction algorithms. Functional peanut-specific IgE reactivity to peptides was assessed by basophil activation assay. Results A total of 145 Ara h 1-specific TCL were generated from 18 HLA-diverse peanut-allergic subjects. The TCL recognized 20-mer peptides throughout Ara h 1. Nine 20-mers containing the most frequently recognized epitopes were selected and their recognition confirmed in 18 additional peanut-allergic subjects. Ten core epitopes were mapped within these 20-mers. These were HLA-DQ and/or HLA–DR restricted, with each presented on at least two different HLA-molecules. Seven short (≤ 20 aa) non-basophil-reactive peptides encompassing all core epitopes were designed and validated in peanut-allergic donor PBMC T cell assays. Conclusions and Clinical Relevance Short CD4+ T cell epitope-based Ara h 1 peptides were identified as novel candidates for a safe, T cell targeted peanut-specific immunotherapy for HLA-diverse populations.
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Affiliation(s)
- S R Prickett
- Department of Immunology, Monash University, Melbourne, Vic., Australia
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Obregon DF, Zhu Y, Bailey AR, Portis SM, Hou H, Zeng J, Stock SL, Murphy TK, Bengtson MA, Tan J. Potential Autoepitope within the Extracellular Region of Contactin-Associated Protein-like 2 in Mice. BRITISH JOURNAL OF MEDICINE AND MEDICAL RESEARCH 2014; 4:416-432. [PMID: 24466509 PMCID: PMC3898533 DOI: 10.9734/bjmmr/2014/6135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Aims Implicated in autoimmune encephalitis, neuromyotonia and genetic forms of autism, here we report that contactin-associated protein-like 2 (CNTNAP2) contains a potential autoepitope within the extracellular region. Methodology CNTNAP2 sequence-similar regions (CSSRs) from human pathogens were identified. Sera from autistic and control children were obtained and analyzed for the presence of antibodies able to bind CSSRs. One such candidate CSSR was evaluated for evidence of autoimmune responses to CNTNAP2 in a mouse model of acute infection. Results Autistic and control children sera contained antibodies able to discrete regions of CNTNAP2. In a murine model of acute infection, a CSSR derived from the N-terminal extracellular region of CNTNAP2 resulted in anti-CNTNAP2 antibody production, proinflammatory cytokine elevation, cerebellar and cortical white matter T-cell infiltration as well as motor dysfunction. Conclusion Taken together, these data suggest that CNTNAP2 contains a potential autoepitope within the extracellular region.
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Affiliation(s)
- Demian F Obregon
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Yuyan Zhu
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Antoinette R Bailey
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Samantha M Portis
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Huayan Hou
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Jin Zeng
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Saundra L Stock
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Tanya K Murphy
- Psychiatry and Behavioral Neurosciences, Rothman Center for Neuropsychiatry, Morsani College of Medicine, University of South Florida, 800 6 Street South, Box 7523, Saint Petersburg, Florida, 33701, USA ; Department of Pediatrics, Rothman Center for Neuropsychiatry, Morsani College of Medicine, University of South Florida, 800 6 Street South, Box 7523, Saint Petersburg, Florida, 33701, USA
| | - Michael A Bengtson
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
| | - Jun Tan
- Rashid Laboratory for Developmental Neurobiology, Silver Child Development Center, Department of Psychiatry and Behavioral Neurosciences, Morsani College of Medicine, University of South Florida, MDT 14, 3515 East Fletcher Avenue, Tampa, Florida, 33613, USA
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Spinosa JP, Kanduc D. Ovarian cancer: designing effective vaccines and specific diagnostic tools. Immunotherapy 2014; 6:35-41. [DOI: 10.2217/imt.13.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: Notwithstanding a renewed interest in the application of immunotherapy as an alternative to chemotherapy and radiotherapy for the treatment of ovarian cancer (OC), and in spite of the available knowledge about ovarian tumor-associated-antigens, the search for a vaccine against OC remains a scientific and clinical challenge. Likewise, immunodiagnostics can detect only a late stage of the disease. Thus, the development of new therapeutic and diagnostic options is highly desirable. Methods: Based on the low-similarity hypothesis, which supports the concept that immunogenicity is preferentially associated to sequences with no/low-similarity to the host proteome, and using Protein Information Resource peptide match program, we searched the ovarian tumor antigen CA125 for amino acid sequences unique to CA125 and absent in the remaining human proteins. Results & conclusion: We identified a set of 159 pentapeptides unique to CA125 that might be used to design specific and effective immunological tools for diagnosis and treatment of OC.
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Affiliation(s)
- Jean Pierre Spinosa
- Department Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
- Faculty of Biology & Medicine, University of Lausanne, Lausanne, Switzerland
| | - Darja Kanduc
- Department Biosciences, Biotechnologies & Biopharmaceutics, University of Bari, Bari, Italy
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Capone G, Lucchese G, Calabrò M, Kanduc D. West Nile virus diagnosis and vaccination: using unique viral peptide sequences to evoke specific immune responses. Immunopharmacol Immunotoxicol 2012; 35:64-70. [DOI: 10.3109/08923973.2012.736521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Lucchese G. A peptide talk between JC virus and the human host: from silent infection to autoimmunity. Immunopharmacol Immunotoxicol 2012; 34:1067-74. [PMID: 22594935 DOI: 10.3109/08923973.2012.686510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Analysis of JC virus (JCV) polyprotein for peptide sharing with the human proteome reveals that the virus has hundreds of pentapeptide sequences in common with the human proteins. The datum is interesting in light of the fundamental role exerted by short amino acid sequences in protein-protein interactions and, consequently, in biochemical reactions and immune recognition. Searching for new approaches to understand the JCV infection scenarios, from the immunoevasion phenomenon underlying the viral asymptomatic stay in the human host to the (re)activation phase and associated pathogenic sequelae, the present study describes the diffuse pentapeptide communication network between JCV and the human host.
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Affiliation(s)
- Guglielmo Lucchese
- Department of Biochemistry and Molecular Biology, University of Bari, Italy.
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Lobanov MY, Galzitskaya OV. Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes. ACTA ACUST UNITED AC 2012; 8:327-37. [DOI: 10.1039/c1mb05318c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Lobanov MY, Galzitskaya OV. Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes. PLoS One 2011; 6:e27142. [PMID: 22073276 PMCID: PMC3208572 DOI: 10.1371/journal.pone.0027142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/11/2011] [Indexed: 11/18/2022] Open
Abstract
We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. We have compiled the largest database of disordered patterns (141) from the clustered PDB where identity between chains inside of a cluster is larger or equal to 75% (version of 28 June 2010) by using simple rules of selection. The results of these analyses would help to further our understanding of the physicochemical and structural determinants of intrinsically disordered regions that serve as molecular recognition elements. We have analyzed the occurrence of the selected patterns in 97 eukaryotic and in 26 bacterial proteomes. The disordered patterns appear more often in eukaryotic than in bacterial proteomes. The matrix of correlation coefficients between numbers of proteins where a disordered pattern from the library of 141 disordered patterns appears at least once in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside of the considered kingdom than between them. The patterns with the frequent occurrence in proteomes have low complexity (PPPPP, GGGGG, EEEED, HHHH, KKKKK, SSTSS, QQQQQP), and the type of patterns vary across different proteomes, http://bioinfo.protres.ru/fp/search_new_pattern.html.
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Affiliation(s)
- Michail Yu. Lobanov
- Group of Bioinformatics, Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V. Galzitskaya
- Group of Bioinformatics, Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- * E-mail:
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Bavaro SL, Kanduc D. Pentapeptide commonality between Corynebacterium diphtheriae toxin and the Homo sapiens proteome. Immunotherapy 2010; 3:49-58. [PMID: 21174557 DOI: 10.2217/imt.10.83] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cross-reactivity may affect diagnostic tests and cause harmful autoimmune reactions following immunotherapy. To predict potential cross-reactivity and search for safe immunotherapeutic approaches, we analyzed sequence identity between microbial antigens and the human proteome. Using diphtheria toxin (DT) as a model, we examined its patterns of identity with human proteins at the pentapeptide level. DT shares 503 pentapeptides with the human proteome, while only 31 pentapeptides are unique to the toxin. DT pentapeptide identity involves multiple/repeated matches in human proteins (a total of 4966 occurrences). Human proteins containing bacterial peptide matches include antigens linked to fundamental cellular functions, such as cell cycle control, proliferation, development and differentiation. The data presented in this article offer a rational basis for designing peptide-based vaccines that specifically target DT and thus eliminate the potential risk of cross-reactivity with human proteins. More generally, this study proposes a methodological approach for avoiding cross-reactivity in immune reactions.
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Affiliation(s)
- Simona Lucia Bavaro
- Department of Biochemistry & Molecular Biology, University of Bari, Bari 70126, Italy
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Kanduc D. Describing the hexapeptide identity platform between the influenza A H5N1 and Homo sapiens proteomes. Biologics 2010; 4:245-61. [PMID: 20859452 PMCID: PMC2943197 DOI: 10.2147/btt.s12097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Indexed: 11/23/2022]
Abstract
We searched the primary sequence of influenza A H5N1 polyprotein for hexamer amino acid sequences shared with human proteins using the Protein International Resource database and the exact peptide matching analysis program. We find that the viral polyprotein shares numerous hexapeptides with the human proteome. The human proteins involved in the viral overlap are represented by antigens associated with basic cell functions such as proliferation, development, and differentiation. Of special importance, many human proteins that share peptide sequences with influenza A polyprotein are antigens such as reelin, neurexin I-α, myosin-IXa, Bardet–Biedl syndrome 10 protein, Williams syndrome transcription factor, disrupted in schizophrenia 1 protein, amyotrophic lateral sclerosis 2 chromosomal region candidate gene 17 protein, fragile X mental retardation 2 protein, and jouberin. That is, the viral-vs-human overlap involves human proteins that, when altered, have been reported to be potentially associated with multiple neurological disorders that can include autism, epilepsy, obesity, dystonia, ataxia–telangiectasia, amyotrophic lateral sclerosis, sensorineural deafness, sudden infant death syndrome, Charcot-Marie-Tooth disease, and myelination. The present data are discussed as a possible molecular basis for understanding influenza A viral escape from immunosurveillance and for defining anti-influenza immune-therapeutic approaches devoid of collateral adverse events.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Italy
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Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis. J Biomed Biotechnol 2010; 2010:832341. [PMID: 20625421 PMCID: PMC2896900 DOI: 10.1155/2010/832341] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/02/2009] [Accepted: 03/24/2010] [Indexed: 12/03/2022] Open
Abstract
Using the currently available proteome databases and based on the concept that a rare sequence is a potential epitope, epitopic sequences derived from Mycobacterium tuberculosis were examined for similarity score to the proteins of the host in which the epitopes were defined. We found that: (i) most of the bacterial linear determinants had peptide fragment(s) that were rarely found in the host proteins and (ii) the relationship between low similarity and epitope definition appears potentially applicable to T-cell determinants. The data confirmed the hypothesis that low-sequence similarity shapes or determines the epitope definition at the molecular level and provides a potential tool for designing new approaches to prevent, diagnose, and treat tuberculosis and other infectious diseases.
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Immunogenicity in peptide-immunotherapy: from self/nonself to similar/dissimilar sequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 640:198-207. [PMID: 19065793 DOI: 10.1007/978-0-387-09789-3_15] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nature of the relationship between an antigenic amino acid sequence and its capability to evoke an immune response is still an unsolved problem. Although experiments indicate that specific (dis)continuous amino acid sequences may determine specific immune responses, how immunogenic properties and recognition informations are mapped onto a non-linear sequence is not understood. Immunology has invoked the concept of self/nonself discrimination in order to explain the capability of the organism to selectively immunoreact. However, no clear, logical and rational pathway has emerged to relate a structure and its immuno-nonreactivity. It cannot yet be dismissed what Koshland wrote in 1990: "Of all the mysteries of modern science, the mechanism of self versus nonself recognition in the immune system ranks at or near the top". This chapter reviews the concept of self/nonself discrimination in the immune system starting from the historical perspective and the conceptual framework that underlie immune reaction pattern. It also introduces future research directions based on a proteomic dissection of the immune unit, qualitatively defined as a low-similarity sequence and quantitatively delimitated by the minimum amino acid requisite able to evoke an immune response, independently ofany, microbial or viral, "foreignness".
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Kanduc D, Stufano A, Lucchese G, Kusalik A. Massive peptide sharing between viral and human proteomes. Peptides 2008; 29:1755-66. [PMID: 18582510 PMCID: PMC7115663 DOI: 10.1016/j.peptides.2008.05.022] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/28/2008] [Accepted: 05/30/2008] [Indexed: 11/10/2022]
Abstract
Thirty viral proteomes were examined for amino acid sequence similarity to the human proteome, and, in parallel, a control of 30 sets of human proteins was analyzed for internal human overlapping. We find that all of the analyzed 30 viral proteomes, independently of their structural or pathogenic characteristics, present a high number of pentapeptide overlaps to the human proteome. Among the examined viruses, human T-lymphotropic virus 1, Rubella virus, and hepatitis C virus present the highest number of viral overlaps to the human proteome. The widespread and ample distribution of viral amino acid sequences through the human proteome indicates that viral and human proteins are formed of common peptide backbone units and suggests a fluid compositional chimerism in phylogenetic entities canonically classified distantly as viruses and Homo sapiens. Importantly, the massive viral to human peptide overlapping calls into question the possibility of a direct causal association between virus-host sharing of amino acid sequences and incitement to autoimmune reactions through molecular recognition of common motifs.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Bari 70126, Italy.
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Kanduc D, Tessitore L, Lucchese G, Kusalik A, Farber E, Marincola FM. Sequence uniqueness and sequence variability as modulating factors of human anti-HCV humoral immune response. Cancer Immunol Immunother 2008; 57:1215-23. [PMID: 18256830 PMCID: PMC11031074 DOI: 10.1007/s00262-008-0456-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Accepted: 01/14/2008] [Indexed: 01/06/2023]
Abstract
We recently compared the HCV polyprotein to the human proteome in order to test whether amino acid sequences unique to the virus could represent immunodominant epitopic determinants of the human humoral immune response against HCV. We identified a relatively limited number of HCV fragments with no/low similarity to the human host that represented exclusive HCV motifs. In this study, the peptides corresponding to low/zero similarity sequences were synthesized and assayed with HCV-infected sera. With different patterns, the synthetic HCV peptides corresponding to low/zero similarity sequences were found to be immunoreactive. In particular, the HCV E1 (315-323) HRMAWDMMM, HCV E2/NS1 (547-555) NWFGCTWMN, and HCV NS5 (2638-2646) YDTRCFDST sequences were immunodominant in the HCV-infected cohort under study. These three peptides correspond to sequences that are endowed with low-similarity to the human proteome, are highly conserved among various HCV strains, and have, potentially, a scarce susceptibility to proteolytic attacks. These data may be of help in defining the multiple factors which concur in the modulation of the human immune response against HCV, eventually providing information for the design of effective anti-HCV vaccines.
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Affiliation(s)
- Darja Kanduc
- Infectious Diseases and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.
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Biddison WE, Martin R. Peptide binding motifs for MHC class I and II molecules. ACTA ACUST UNITED AC 2008; Appendix 1:Appendix 1I. [PMID: 18432645 DOI: 10.1002/0471142735.ima01is36] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This overview discusses the use of peptide-binding motifs to predict interaction with a specific MHC class I or II allele, and gives examples for the use of MHC binding motifs to predict T-cell recognition.
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Affiliation(s)
- W E Biddison
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
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Capone G, De Marinis A, Simone S, Kusalik A, Kanduc D. Mapping the human proteome for non-redundant peptide islands. Amino Acids 2007; 35:209-16. [PMID: 17701099 DOI: 10.1007/s00726-007-0563-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 05/08/2007] [Indexed: 12/11/2022]
Abstract
We describe immune-proteome structures using libraries of protein fragments that define a structural immunological alphabet. We propose and validate such an alphabet as i) composed of letters of five consecutive amino acids, pentapeptide units being sufficient minimal antigenic determinants in a protein, and ii) characterized by low-similarity to human proteins, so representing structures unknown to the host and potentially able to evoke an immune response. In this context, we have thoroughly sifted through the entire human proteome searching for non-redundant protein motifs. Here, for the first time, a complete sequence redundancy dissection of the human proteome has been conducted. The non-redundant peptide islands in the human proteome have been quantified and catalogued according to the amino acid length. The library of uniquely occurring n-peptide sequences that was obtained is characterized by a logarithmic decrease of the number of non-redundant peptides as a function of the peptide length. This library represents a highly specific catalogue of molecular protein signatures, the possible use of which in cancer/autoimmunity research is discussed, with a major focus on non-redundant dodecamer sequences.
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Affiliation(s)
- G Capone
- Department of Biochemistry and Molecular Biology Ernesto Quagliariello, University of Bari, Bari, Italy
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Kusalik A, Bickis M, Lewis C, Li Y, Lucchese G, Marincola FM, Kanduc D. Widespread and ample peptide overlapping between HCV and Homo sapiens proteomes. Peptides 2007; 28:1260-7. [PMID: 17485143 DOI: 10.1016/j.peptides.2007.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2007] [Revised: 03/29/2007] [Accepted: 04/03/2007] [Indexed: 11/24/2022]
Abstract
Alignment of protein sequences is fundamental in analyzing homology, evolutionary events and functional relationships. Searching for the epitopic peptide platform underlying hepatitis C virus (HCV) infection and autoimmune phenomena, we have used sequence-sequence peptide matching to compare the HCV polyprotein sequence to the human proteome. The following results were obtained: (1) pentamers from HCV polyprotein have a widespread and high level of similarity to a large number of human proteins (19,605 human proteins, that is 57.6% of the human proteome); (2) remarkable similarity between the two proteomes persists even using longer peptide motifs as probes for identity scanning; (3) only a limited number of HCV pentameric fragments have no similarity to the human host, so representing molecular sequence signatures of the virus. We conclude that the widespread sharing of numerous perfect exact matches between HCV and human proteomes might explain HCV persistence in humans.
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Affiliation(s)
- Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
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Sukati H, Watson HG, Urbaniak SJ, Barker RN. Mapping helper T-cell epitopes on platelet membrane glycoprotein IIIa in chronic autoimmune thrombocytopenic purpura. Blood 2007; 109:4528-38. [PMID: 17272505 DOI: 10.1182/blood-2006-09-044388] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Chronic autoimmune thrombocytopenic purpura (AITP) is associated with autoantibodies specific for platelet membrane components, often including glycoprotein GPIIIa. T helper (Th) cells reactive with GPIIIa, which are capable of driving the autoantibody response, are activated in AITP, and the aim here was to map the epitopes that they recognize. Peripheral blood mononuclear cells (PBMCs) were obtained from 31 patients with AITP and 30 control donors and stimulated with a panel of 86 overlapping synthetic 15-mer peptides spanning the complete sequence of GPIIIa. One or more peptides elicited recall proliferation by PBMCs from 28 of the patients, and, typically, multiple sequences were stimulatory. In contrast, responses in healthy control donors were rare (chi-square test = 115.967; P ≤ .001). It was confirmed that the proliferating PBMCs from patients were cells of the CD3+CD4+ helper phenotype that were MHC class II restricted. Despite variation between different cases of AITP, particular sequences were commonly recognized with PBMCs from 24 patients (77%) responding to 1 or more of the 4 most dominant peptides. Mapping such dominant autoreactive helper epitopes is the first step in the development of new approaches to the treatment of AITP, based on the use of peptides to tolerize Th cells specific for platelet glycoproteins.
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Affiliation(s)
- Hosea Sukati
- Department of Medicine and Therapeutics, University of Aberdeen, Aberdeen, United Kingdom
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Lucchese A, Mittelman A, Tessitore L, Serpico R, Sinha AA, Kanduc D. Proteomic definition of a desmoglein linear determinant common to Pemphigus vulgaris and Pemphigus foliaceous. J Transl Med 2006; 4:37. [PMID: 16925820 PMCID: PMC1590053 DOI: 10.1186/1479-5876-4-37] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 08/22/2006] [Indexed: 11/25/2022] Open
Abstract
Background A number of autoimmune diseases have been clinically and pathologically characterized. In contrast, target antigens have been identified only in a few cases and, in these few cases, the knowledge of the exact epitopic antigenic sequence is still lacking. Thus the major objective of current work in the autoimmunity field is the identification of the epitopic sequences that are related to autoimmune reactions. Our labs propose that autoantigen peptide epitopes able to evoke humoral (auto)immune response are defined by the sequence similarity to the host proteome. The underlying scientific rationale is that antigen peptides acquire immunoreactivity in the context of their proteomic similarity level. Sequences uniquely owned by a protein will have high potential to evoke an immune reaction, whereas motifs with high proteomic redundancy should be immunogenically silenced by the tolerance phenomenon. The relationship between sequence redundancy and peptide immunoreactivity has been successfully validated in a number of experimental models. Here the hypothesis has been applied to pemphigus diseases and the corresponding desmoglein autoantigens. Methods Desmoglein 3 sequence similarity analysis to the human proteome followed by dot-blot/NMR immunoassays were carried out to identify and validate possible epitopic sequences. Results Computational analysis led to identifying a linear immunodominant desmoglein-3 epitope highly reactive with the sera from Pemphigus vulgaris as well as Pemphigus foliaceous. The epitopic peptide corresponded to the amino acid REWVKFAKPCRE sequence, was located in the extreme N-terminal region (residues 49 to 60), and had low redundancy to the human proteome. Sequence alignment showed that human desmoglein 1 and 3 share the REW-KFAK–RE sequence as a common motif with 75% residue identity. Conclusion This study 1) validates sequence redundancy to autoproteome as a main factor in shaping desmoglein peptide immunogenicity; 2) offers a molecular mechanicistic basis in analyzing the commonality of autoimmune responses exhibited by the two forms of pemphigus; 3) indicates possible peptide-immunotherapeutical approaches for pemphigus diseases.
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Affiliation(s)
| | | | | | - Rosario Serpico
- Institute of Clinical Odontostomatology, 2University of Naples, Italy
| | - Animesh A Sinha
- Division of Dermatology and Cutaneous Sciences, Center for Investigative Dermatology, Michigan State University, East Lansing, MI, USA
| | - Darja Kanduc
- Dept. of Biochemistry and Molecular Biology, University of Bari, Italy
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