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Odales J, Servín-Blanco R, Martínez-Cortés F, Guzman Valle J, Domínguez-Romero AN, Gevorkian G, Manoutcharian K. Antitumor efficacy of MUC1-derived variable epitope library treatments in a mouse model of breast cancer. Vaccine 2022; 40:4796-4805. [PMID: 35788294 DOI: 10.1016/j.vaccine.2022.06.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/13/2022] [Accepted: 06/21/2022] [Indexed: 11/15/2022]
Abstract
The identification of novel targets for cancer immunotherapy and the development of new vaccine immunogens are subjects of permanent interest. MUC1 is an overexpressed antigen found in most tumors, and its overexpression correlates with poor prognosis. Many attempts to direct the immune response against MUC1 in tumor cells have failed, including several clinical trials. We have previously developed an innovative Variable Epitope Library (VEL) vaccine platform that carries massively substituted mutant variants of defined epitopes or epitope regions as an alternative to using wild-type peptide sequences-based immunogens. Here, two murine MUC1-derived epitopes equivalent to the previously tested in cancer immunotherapy human MUC1 regions were used to generate VELs. We observed that vaccination with the 23L VEL immunogens, encompassing the entire signal peptide region of MUC1, reduces the tumor area compared to the wild-type sequence treatment. Contrastingly, vaccination with the MUC1 signal peptide-derived predicted CD8++ T cell epitope-based VEL, 9MUC1spL, showed similar tumor area reduction as the wild-type treatment; however, a decrease in lung metastasis after 9MUC1spL treatment was observed. In addition, vaccination induced a large pool of CD8+ T cells which recognized most variant epitopes from 9MUC1spL. Also, we generated MUC1 variable number tandem repeat (VNTR)-based VELs that reduced the metastatic burden when dendritic cells and M13 recombinant bacteriophages were used as vaccine carriers. Collectively, our data demonstrate the immunogenic and antitumor properties of MUC1 signal peptide- and VNTR-derived VEL immunogens.
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Affiliation(s)
- Josué Odales
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO
| | - Rodolfo Servín-Blanco
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO
| | - Fernando Martínez-Cortés
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO
| | - Jesus Guzman Valle
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO
| | - Allan Noé Domínguez-Romero
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO
| | - Goar Gevorkian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO
| | - Karen Manoutcharian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), AP 70228, Ciudad Universitaria, México DF 04510, MÉXICO.
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Kangabam R, Sahoo S, Ghosh A, Roy R, Silla Y, Misra N, Suar M. Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery. Comput Biol Med 2021; 128:104158. [PMID: 33301953 PMCID: PMC7705366 DOI: 10.1016/j.compbiomed.2020.104158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has affected 215 countries and territories around the world with 60,187,347 coronavirus cases and 17,125,719 currently infected patients confirmed as of the November 25, 2020. Currently, many countries are working on developing new vaccines and therapeutic drugs for this novel virus strain, and a few of them are in different phases of clinical trials. The advancement in high-throughput sequence technologies, along with the application of bioinformatics, offers invaluable knowledge on genomic characterization and molecular pathogenesis of coronaviruses. Recent multi-disciplinary studies using bioinformatics methods like sequence-similarity, phylogenomic, and computational structural biology have provided an in-depth understanding of the molecular and biochemical basis of infection, atomic-level recognition of the viral-host receptor interaction, functional annotation of important viral proteins, and evolutionary divergence across different strains. Additionally, various modern immunoinformatic approaches are also being used to target the most promiscuous antigenic epitopes from the SARS-CoV-2 proteome for accelerating the vaccine development process. In this review, we summarize various important computational tools and databases available for systematic sequence-structural study on coronaviruses. The features of these public resources have been comprehensively discussed, which may help experimental biologists with predictive insights useful for ongoing research efforts to find therapeutics against the infectious COVID-19 disease.
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Affiliation(s)
- Rajiv Kangabam
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Susrita Sahoo
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Arpan Ghosh
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Riya Roy
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Yumnam Silla
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, 785006, India
| | - Namrata Misra
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India
| | - Mrutyunjay Suar
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India.
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3
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Rakib A, Sami SA, Islam MA, Ahmed S, Faiz FB, Khanam BH, Marma KKS, Rahman M, Uddin MMN, Nainu F, Emran TB, Simal-Gandara J. Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2. Molecules 2020; 25:E5088. [PMID: 33147821 PMCID: PMC7663370 DOI: 10.3390/molecules25215088] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.
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Affiliation(s)
- Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Md. Ashiqul Islam
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
- Department of Pharmacy, Mawlana Bhashani Science & Technology University, Santosh, Tangail 1902, Bangladesh
| | - Shahriar Ahmed
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Farhana Binta Faiz
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Bibi Humayra Khanam
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Kay Kay Shain Marma
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Maksuda Rahman
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Mir Muhammad Nasir Uddin
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh; (A.R.); (S.A.S.); (M.A.I.); (S.A.); (F.B.F.); (B.H.K.); (K.K.S.M.); (M.R.); (M.M.N.U.)
| | - Firzan Nainu
- Faculty of Pharmacy, Hasanuddin University, Tamalanrea, Kota Makassar, Sulawesi Selatan 90245, Indonesia;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain
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Mahapatra SR, Sahoo S, Dehury B, Raina V, Patro S, Misra N, Suar M. Designing an efficient multi-epitope vaccine displaying interactions with diverse HLA molecules for an efficient humoral and cellular immune response to prevent COVID-19 infection. Expert Rev Vaccines 2020; 19:871-885. [PMID: 32869699 PMCID: PMC7544970 DOI: 10.1080/14760584.2020.1811091] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background The novel SARS-CoV-2 coronavirus, the causative agent of the ongoing pandemic COVID-19 disease continues to infect people globally and has infected millions of humans worldwide. However, no effective vaccine against this virus exists. Method Using Immunoinformatics, epitopic sequences from multiple glycoproteins that play crucial role in pathogenesis were identified. Particularly, epitopes were mapped from conserved receptor-binding domain of spike protein which have been experimentally validated in SARS-CoV-1 as a promising target for vaccine development. Results A multi-epitopic vaccine construct comprising of B-cell, CTL, HTL epitopes was developed along with fusion of adjuvant and linkers. The epitopes identified herein are reported for the first time and were predicted to be highly antigenic, stable, nonallergen, nontoxic and displayed conservation across several SARS-CoV-2 isolates from different countries. Additionally, the epitopes associated with maximum HLA alleles and population coverage analysis shows the proposed epitopes would be a relevant representative of large proportion of the world population. A reliable three-dimensional structure of the vaccine construct was developed. Consequently, docking and molecular-dynamics simulation ensured the stable interaction between vaccine and innate-immune receptor.
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Affiliation(s)
- Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
| | - Susrita Sahoo
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
| | - Budheswar Dehury
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
| | - Vishakha Raina
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
| | - Shubhransu Patro
- Kalinga Institute of Medical Sciences (KIMS) Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India
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5
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Uray K, Pimm MV, Hudecz F. The effect of the branched chain polypeptide carrier on biodistribution of covalently attached B-cell epitope peptide (APDTRPAPG) derived from mucin 1 glycoprotein. Arch Biochem Biophys 2019; 664:127-133. [DOI: 10.1016/j.abb.2019.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 12/16/2022]
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Functionalisation of Virus-Like Particles Enhances Antitumour Immune Responses. J Immunol Res 2019; 2019:5364632. [PMID: 30729137 PMCID: PMC6341245 DOI: 10.1155/2019/5364632] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/30/2018] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles (VLP) from the rabbit haemorrhagic disease virus (RHDV) can deliver tumour antigens to induce anticancer immune responses. In this study, we explored how RHDV VLP can be functionalised to enhance the immune response by increasing antigen loading, incorporating linkers to enhance epitope processing, and targeting receptor-mediated internalisation of VLP. RHDV VLP were developed to deliver up to three copies of gp10025–33 which contained proteasome cleavable linkers to target the correct processing of the epitope. Addition of mono- and dimannosides, conjugated to the surface of the gp100 VLP, would utilise a second pathway of internalisation, mannose receptor mediated, to further augment antigen internalised by phagocytosis/macropinocytosis. In vitro cell culture studies showed that a processing linker at the C-terminus of the epitope (gp100.1LC) induced enhanced T-cell activation (7.3 ng/ml interferon- (IFN-) γ release) compared to no linker (3.0 ng/ml IFN-γ) or the linker at the N-terminus (0.8 ng/ml IFN-γ). VLP delivering two (gp100.2L) or three (gp100.3L) gp100 epitopes induced similar high T-cell activation (7.6 ng/ml IFN-γ) compared to gp100.1LC. An in vivo cytotoxicity assay and a therapeutic tumour trial confirmed that mice vaccinated with either gp100.2L or gp100.3L induced a specific antitumour immune response. Mannosylation of the gp100.2L VLP further enhanced the generated immune response, demonstrated by prolonged survival of mice vaccinated with dimannosylated gp100.2L VLP (D-gp100.2L) by 22 days compared to gp100.2L-vaccinated mice. This study showed that functionalisation of RHDV VLP by addition of an epitope-processing linker and mannosylation of the surface facilitates the efficacy of VLP as vaccination vectors for tumour immunotherapy.
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7
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Deraos G, Kritsi E, Matsoukas MT, Christopoulou K, Kalbacher H, Zoumpoulakis P, Apostolopoulos V, Matsoukas J. Design of Linear and Cyclic Mutant Analogues of Dirucotide Peptide (MBP 82⁻98) against Multiple Sclerosis: Conformational and Binding Studies to MHC Class II. Brain Sci 2018; 8:brainsci8120213. [PMID: 30518150 PMCID: PMC6316436 DOI: 10.3390/brainsci8120213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Abstract
Background: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system. MS is a T cell-mediated disease characterized by the proliferation, infiltration, and attack of the myelin sheath by immune cells. Previous studies have shown that cyclization provides molecules with strict conformation that could modulate the immune system. Methods: In this study, we synthesized peptide analogues derived from the myelin basic protein (MBP)82–98 encephalitogenic sequence (dirucotide), the linear altered peptide ligand MBP82–98 (Ala91), and their cyclic counterparts. Results: The synthesized peptides were evaluated for their binding to human leukocyte antigen (HLA)-DR2 and HLA-DR4 alleles, with cyclic MBP82–98 being a strong binder with the HLA-DR2 allele and having lower affinity binding to the HLA-DR4 allele. In a further step, conformational analyses were performed using NMR spectroscopy in solution to describe the conformational space occupied by the functional amino acids of both linear and cyclic peptide analogues. This structural data, in combination with crystallographic data, were used to study the molecular basis of their interaction with HLA-DR2 and HLA-DR4 alleles. Conclusion: The cyclic and APL analogues of dirucotide are promising leads that should be further evaluated for their ability to alter T cell responses for therapeutic benefit against MS.
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Affiliation(s)
- George Deraos
- Department of Chemistry, University of Patras, 26500 Patras, Greece.
- ELDrug S.A., Patras Science Park, Platani, 26504 Patras, Greece.
| | - Eftichia Kritsi
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | | | - Konstantina Christopoulou
- Department of Chemistry, University of Patras, 26500 Patras, Greece.
- ELDrug S.A., Patras Science Park, Platani, 26504 Patras, Greece.
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tubingen, 72076 Tubingen, Germany.
| | - Panagiotis Zoumpoulakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne VIC 3030, Australia.
| | - John Matsoukas
- Department of Chemistry, University of Patras, 26500 Patras, Greece.
- ELDrug S.A., Patras Science Park, Platani, 26504 Patras, Greece.
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Abstract
DNA vaccines offer many advantages over other anti-tumor vaccine approaches due to their simplicity, ease of manufacturing, and safety. Results from several clinical trials in patients with cancer have demonstrated that DNA vaccines are safe and can elicit immune responses. However, to date few DNA vaccines have progressed beyond phase I clinical trial evaluation. Studies into the mechanism of action of DNA vaccines in terms of antigen-presenting cell types able to directly present or cross-present DNA-encoded antigens, and the activation of innate immune responses due to DNA itself, have suggested opportunities to increase the immunogenicity of these vaccines. In addition, studies into the mechanisms of tumor resistance to anti-tumor vaccination have suggested combination approaches that can increase the anti-tumor effect of DNA vaccines. This review focuses on these mechanisms of action and mechanisms of resistance using DNA vaccines, and how this information is being used to improve the anti-tumor effect of DNA vaccines. These approaches are then specifically discussed in the context of human prostate cancer, a disease for which DNA vaccines have been and continue to be explored as treatments.
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Affiliation(s)
- Christopher D Zahm
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Viswa Teja Colluru
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Douglas G McNeel
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, United States.
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Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction. Adv Bioinformatics 2016; 2016:1276594. [PMID: 27274725 PMCID: PMC4870339 DOI: 10.1155/2016/1276594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 03/29/2016] [Accepted: 04/10/2016] [Indexed: 01/15/2023] Open
Abstract
Epitope-based design of vaccines, immunotherapeutics, and immunodiagnostics is complicated by structural changes that radically alter immunological outcomes. This is obscured by expressing redundancy among linear-epitope data as fractional sequence-alignment identity, which fails to account for potentially drastic loss of binding affinity due to single-residue substitutions even where these might be considered conservative in the context of classical sequence analysis. From the perspective of immune function based on molecular recognition of epitopes, functional redundancy of epitope data (FRED) thus may be defined in a biologically more meaningful way based on residue-level physicochemical similarity in the context of antigenic cross-reaction, with functional similarity between epitopes expressed as the Shannon information entropy for differential epitope binding. Such similarity may be estimated in terms of structural differences between an immunogen epitope and an antigen epitope with reference to an idealized binding site of high complementarity to the immunogen epitope, by analogy between protein folding and ligand-receptor binding; but this underestimates potential for cross-reactivity, suggesting that epitope-binding site complementarity is typically suboptimal as regards immunologic specificity. The apparently suboptimal complementarity may reflect a tradeoff to attain optimal immune function that favors generation of immune-system components each having potential for cross-reactivity with a variety of epitopes.
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10
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Rekoske BT, Smith HA, Olson BM, Maricque BB, McNeel DG. PD-1 or PD-L1 Blockade Restores Antitumor Efficacy Following SSX2 Epitope-Modified DNA Vaccine Immunization. Cancer Immunol Res 2015; 3:946-55. [PMID: 26041735 DOI: 10.1158/2326-6066.cir-14-0206] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 05/17/2015] [Indexed: 01/22/2023]
Abstract
DNA vaccines have demonstrated antitumor efficacy in multiple preclinical models, but low immunogenicity has been observed in several human clinical trials. This has led to many approaches seeking to improve the immunogenicity of DNA vaccines. We previously reported that a DNA vaccine encoding the cancer-testis antigen SSX2, modified to encode altered epitopes with increased MHC class I affinity, elicited a greater frequency of cytolytic, multifunctional CD8(+) T cells in non-tumor-bearing mice. We sought to test whether this optimized vaccine resulted in increased antitumor activity in mice bearing an HLA-A2-expressing tumor engineered to express SSX2. We found that immunization of tumor-bearing mice with the optimized vaccine elicited a surprisingly inferior antitumor effect relative to the native vaccine. Both native and optimized vaccines led to increased expression of PD-L1 on tumor cells, but antigen-specific CD8(+) T cells from mice immunized with the optimized construct expressed higher PD-1. Splenocytes from immunized animals induced PD-L1 expression on tumor cells in vitro. Antitumor activity of the optimized vaccine could be increased when combined with antibodies blocking PD-1 or PD-L1, or by targeting a tumor line not expressing PD-L1. These findings suggest that vaccines aimed at eliciting effector CD8(+) T cells, and DNA vaccines in particular, might best be combined with PD-1 pathway inhibitors in clinical trials. This strategy may be particularly advantageous for vaccines targeting prostate cancer, a disease for which antitumor vaccines have demonstrated clinical benefit and yet PD-1 pathway inhibitors alone have shown little efficacy to date.
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Affiliation(s)
- Brian T Rekoske
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Heath A Smith
- Department of Oncology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Brian M Olson
- The Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Brett B Maricque
- The Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Douglas G McNeel
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin. The Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
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11
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Marcelo F, Garcia-Martin F, Matsushita T, Sardinha J, Coelho H, Oude-Vrielink A, Koller C, André S, Cabrita EJ, Gabius HJ, Nishimura SI, Jiménez-Barbero J, Cañada FJ. Delineating Binding Modes of Gal/GalNAc and Structural Elements of the Molecular Recognition of Tumor-Associated Mucin Glycopeptides by the Human Macrophage Galactose-Type Lectin. Chemistry 2014; 20:16147-55. [DOI: 10.1002/chem.201404566] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 01/05/2023]
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12
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Afzal S, Idrees M, Hussain M. De Novo modeling of Envelope 2 protein of HCV isolated from Pakistani patient and epitopes prediction for vaccine development. J Transl Med 2014; 12:115. [PMID: 24885362 PMCID: PMC4024208 DOI: 10.1186/1479-5876-12-115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/26/2014] [Indexed: 01/27/2023] Open
Abstract
Hepatitis C virus (HCV) is a universal health issue and a significant risk factor leading to hepatocellular carcinoma. HCV has infected approximately 170 million individuals worldwide. It is a member of Flaviviridae with positive sense RNA genome. In the absence of any effective vaccine against HCV, pegylated interferon with ribavirin is the standard of treatment against HCV infection. In this study, sequence and structural analysis of envelope 2 (E2) protein was performed which was isolated from patients of HCV genotype 3a in Pakistan. Then, epitopes were predicted which were specific for both B-cells and T-cells. Later, conservancy of epitopes was checked with the HCV 3a and 1a sequences from different countries. A total of 6 conserved epitopes were found from extra-membranous regions of E2 protein. Presence of conserved epitopes in E2 protein generates the possibility that these epitopes can be used to elicit the immune response against HCV.
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Affiliation(s)
| | - Muhammad Idrees
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore 53700, Pakistan.
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Smith HA, Rekoske BT, McNeel DG. DNA vaccines encoding altered peptide ligands for SSX2 enhance epitope-specific CD8+ T-cell immune responses. Vaccine 2014; 32:1707-15. [PMID: 24492013 DOI: 10.1016/j.vaccine.2014.01.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/19/2013] [Accepted: 01/18/2014] [Indexed: 12/22/2022]
Abstract
Plasmid DNA serves as a simple and easily modifiable form of antigen delivery for vaccines. The USDA approval of DNA vaccines for several non-human diseases underscores the potential of this type of antigen delivery method as a cost-effective approach for the treatment or prevention of human diseases, including cancer. However, while DNA vaccines have demonstrated safety and immunological effect in early phase clinical trials, they have not consistently elicited robust anti-tumor responses. Hence many recent efforts have sought to increase the immunological efficacy of DNA vaccines, and we have specifically evaluated several target antigens encoded by DNA vaccine as treatments for human prostate cancer. In particular, we have focused on SSX2 as one potential target antigen, given its frequent expression in metastatic prostate cancer. We have previously identified two peptides, p41-49 and p103-111, as HLA-A2-restricted SSX2-specific epitopes. In the present study we sought to determine whether the efficacy of a DNA vaccine could be enhanced by an altered peptide ligand (APL) strategy wherein modifications were made to anchor residues of these epitopes to enhance or ablate their binding to HLA-A2. A DNA vaccine encoding APL modified to increase epitope binding elicited robust peptide-specific CD8+ T cells producing Th1 cytokines specific for each epitope. Ablation of one epitope in a DNA vaccine did not enhance immune responses to the other epitope. These results demonstrate that APL encoded by a DNA vaccine can be used to elicit increased numbers of antigen-specific T cells specific for multiple epitopes simultaneously, and suggest this could be a general approach to improve the immunogenicity of DNA vaccines encoding tumor antigens.
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Affiliation(s)
- Heath A Smith
- Department of Oncology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Brian T Rekoske
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Douglas G McNeel
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA.
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Apostolopoulos V. Peptide-based vaccines for cancer: are we choosing the right peptides? Expert Rev Vaccines 2014; 8:259-60. [DOI: 10.1586/14760584.8.3.259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Chen X, Chang CH, Goldenberg DM. Novel strategies for improved cancer vaccines. Expert Rev Vaccines 2014; 8:567-76. [DOI: 10.1586/erv.09.11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Katsara M, Minigo G, Plebanski M, Apostolopoulos V. The good, the bad and the ugly: how altered peptide ligands modulate immunity. Expert Opin Biol Ther 2009; 8:1873-84. [PMID: 18990075 DOI: 10.1517/14712590802494501] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The basis of T cell immune responses is the specific recognition of an immunogenic peptide epitope by a T cell receptor. Peptide alterations of such T cell epitopes with single or few amino acid variations can have drastic effects on the outcome of this recognition. These altered peptide ligands can act as modulators of immune responses as they are capable of downregulating or upregulating responses. OBJECTIVE/METHODS We review how altered peptide ligands can have 'good' 'bad' and 'ugly' outcomes in treating diseases. RESULTS/CONCLUSION Altered peptide ligands have been used as immunotherapeutics in autoimmune (and allergic) diseases, infectious diseases and cancer. In the next five years we anticipate seeing a number of altered peptide ligands in clinical trials, progressing from contradictory classifications of good, bad or ugly, to the exciting outcome of 'useful'.
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Affiliation(s)
- Maria Katsara
- Immunology and Vaccine Laboratory, The Macfarlane Burnet Institute incorporating The Austin Research Institute, Studley Road, Heidelberg, VIC 3084, Australia
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Lazoura E, Lodding J, Farrugia W, Day S, Ramsland PA, Apostolopoulos V. Non-canonical anchor motif peptides bound to MHC class I induce cellular responses. Mol Immunol 2008; 46:1171-8. [PMID: 19118903 DOI: 10.1016/j.molimm.2008.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 11/05/2008] [Accepted: 11/11/2008] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC) on the surface of antigen presenting cells functions to display peptides to the T cell receptor (TCR). Recognition of peptide-MHC by T cells initiates a cascade of signals, which results in the initiation of a T cell dependent immune response. An understanding of how peptides bind to MHC molecules is important for determining the structural basis for T cell dependent immune responses and facilitates the structure-based design of peptides as candidate vaccines to elicit a specific immune response. To date, crystal structures, immunogenicity and in vivo biological relevance have mainly been characterized for high affinity peptide-MHC interactions. From the crystal structures of numerous peptide-MHC complexes it became apparent what canonical sequence features were required for high affinity binding, which led to the ability to predict in most instances peptides with high affinity for MHC. We previously identified the crystal structures of non-canonical peptides in complex with MHC class I (one bound with low affinity and the other with high affinity, but utilizing novel peptide anchors and MHC pockets). It is becoming increasingly evident that other non-canonical peptides can also bind, such as long-, short- and glyco-peptides. However, the in vivo role of non-canonical peptides is not clear and we present here the immunogenicity of two non-canonical peptides and their affinity when bound to MHC class I, H2K(b). Comparison of the three-dimensional structures in complex with MHC suggests major differences in hydrogen bonding patterns with H2K(b), despite sharing similar binding modes, which may account for the differences in affinity and immunogenicity. These studies provide further evidence for the diverse range of peptide ligands that can bind to MHC and be recognized by the TCR, which will facilitate approaches to peptide-based vaccine design.
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Affiliation(s)
- Eliada Lazoura
- Immunology and Vaccine Laboratory, Centre for Immunology, The Macfarlane Burnet Institute for Medical Research and Public Health, Austin Campus, VIC, Australia
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Vivona S, Gardy JL, Ramachandran S, Brinkman FSL, Raghava GPS, Flower DR, Filippini F. Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol 2008; 26:190-200. [PMID: 18291542 DOI: 10.1016/j.tibtech.2007.12.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 12/06/2007] [Accepted: 12/19/2007] [Indexed: 11/18/2022]
Abstract
Genome sequences from many organisms, including humans, have been completed, and high-throughput analyses have produced burgeoning volumes of 'omics' data. Bioinformatics is crucial for the management and analysis of such data and is increasingly used to accelerate progress in a wide variety of large-scale and object-specific functional analyses. Refined algorithms enable biotechnologists to follow 'computer-aided strategies' based on experiments driven by high-confidence predictions. In order to address compound problems, current efforts in immuno-informatics and reverse vaccinology are aimed at developing and tuning integrative approaches and user-friendly, automated bioinformatics environments. This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations.
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Affiliation(s)
- Sandro Vivona
- Molecular Biology and Bioinformatics Unit, Department of Biology, University of Padua, Padua, Italy
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