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Zolfaghari Emameh R, Barker HR, Turpeinen H, Parkkila S, Hytönen VP. A reverse vaccinology approach on transmembrane carbonic anhydrases from Plasmodium species as vaccine candidates for malaria prevention. Malar J 2022; 21:189. [PMID: 35706028 PMCID: PMC9199335 DOI: 10.1186/s12936-022-04186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria is a significant parasitic infection, and human infection is mediated by mosquito (Anopheles) biting and subsequent transmission of protozoa (Plasmodium) to the blood. Carbonic anhydrases (CAs) are known to be highly expressed in the midgut and ectoperitrophic space of Anopheles gambiae. Transmembrane CAs (tmCAs) in Plasmodium may be potential vaccine candidates for the control and prevention of malaria. METHODS In this study, two groups of transmembrane CAs, including α-CAs and one group of η-CAs were analysed by immunoinformatics and computational biology methods, such as predictions on transmembrane localization of CAs from Plasmodium spp., affinity and stability of different HLA classes, antigenicity of tmCA peptides, epitope and proteasomal cleavage of Plasmodium tmCAs, accessibility of Plasmodium tmCAs MHC-ligands, allergenicity of Plasmodium tmCAs, disulfide-bond of Plasmodium tmCAs, B cell epitopes of Plasmodium tmCAs, and Cell type-specific expression of Plasmodium CAs. RESULTS Two groups of α-CAs and one group of η-CAs in Plasmodium spp. were identified to contain tmCA sequences, having high affinity towards MHCs, high stability, and strong antigenicity. All putative tmCAs were predicted to contain sequences for proteasomal cleavage in antigen presenting cells (APCs). CONCLUSIONS The predicted results revealed that tmCAs from Plasmodium spp. can be potential targets for vaccination against malaria.
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Affiliation(s)
- Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran.
| | - Harlan R Barker
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories Ltd and Tampere University Hospital, Tampere, Finland
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories Ltd and Tampere University Hospital, Tampere, Finland
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Mossallam GI, Fattah RA, Bokhary M, Moneer M, Mahmoud HK. LMP7 polymorphism may modify the presentation and clinical impact of minor histocompatibility antigens in matched related hematopoietic stem cell transplantation. Cell Immunol 2021; 364:104329. [PMID: 33798908 DOI: 10.1016/j.cellimm.2021.104329] [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: 12/04/2020] [Revised: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 10/22/2022]
Abstract
Differential expression of minor histocompatibility antigens between the recipient and donor determines their disparity and can be modified by immunoproteasomes that regulate their processing and presentation. We examined the impact of HA-1 and HA-8 disparity, and immunoproteasome LMP7 polymorphism in 130 pairs. In multivariate analysis, HA-1 disparity showed a statistically significant association with an increased incidence of acute graft-versus-host disease (aGVHD) II-IV (p = 0.043, HR: 3.71, 95%CI = 1.04-13.26), while LMP7-Q/Q showed a trend toward increased incidence of aGVHD compared to LMP7-Q/K and K/K genotypes (p = 0.087, HR: 2.36, 95%CI = 0.88-6.31). All HA-1 and HA-8 disparate patients who developed aGVHD had the LMP7-Q/Q genotype. No significant association could be detected between HA-1, HA-8, or LMP7 and chronic GVHD, relapse-free survival (RFS), overall survival (OS), or transplant-related mortality (TRM). In conclusion, we suggested an association between the HA-1 disparity and the risk of developing aGVHD with a possible modifying effect of LMP7.
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Affiliation(s)
- Ghada I Mossallam
- Bone Marrow Transplantation Laboratory Unit, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Raafat Abdel Fattah
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt; Bone Marrow Transplantation Unit, Nasser Institute Hospital for Research and Treatment, Cairo, Egypt
| | - Mahmoud Bokhary
- Bone Marrow Transplantation Unit, Nasser Institute Hospital for Research and Treatment, Cairo, Egypt
| | - Manar Moneer
- Department of Epidemiology and Biostatistics, National Cancer Institute, Cairo University, Egypt
| | - Hossam K Mahmoud
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt; Bone Marrow Transplantation Unit, Nasser Institute Hospital for Research and Treatment, Cairo, Egypt
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Romaniuk DS, Postovskaya AM, Khmelevskaya AA, Malko DB, Efimov GA. Rapid Multiplex Genotyping of 20 HLA-A *02:01 Restricted Minor Histocompatibility Antigens. Front Immunol 2019; 10:1226. [PMID: 31275297 PMCID: PMC6593292 DOI: 10.3389/fimmu.2019.01226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
A subset of MHC-associated self-peptides presented by the recipient's cells and immunologically foreign to the donor can induce an allogeneic immune response after hematopoietic stem cell transplantation (HSCT). These immunogenic peptides originate from the genomic polymorphisms and are known as minor histocompatibility antigens (MiHA). MiHA mismatches trigger the post-transplant immune response, which could manifest in both the deleterious “graft-vs.-host” disease and the beneficial “graft-vs.-leukemia” effect. Importantly, some MiHAs are considered to be promising targets for posttransplant T-cell immunotherapy of hematopoietic malignancies. This creates a demand for a robust and fast approach to genotyping MiHA-encoding polymorphisms. We report a multiplex real-time PCR method for the genotyping of 20 polymorphisms that are encoding HLA-A*02:01-restricted MiHAs. This method uses allele-specific primers and gene-specific hydrolysis probes. In 1 h it allows for the detection of MiHA mismatches in a donor-recipient pair without the need for electrophoresis, sequencing, or other time-consuming techniques. We validated the method with Sanger and NGS sequencing and demonstrated good performance over a wide range of DNA concentrations. We propose our protocol as a fast and accurate method of identifying mismatched MiHAs. The information on the MiHA mismatches is useful for studying the allogeneic immune response following HSCT and for selecting the targets for post-transplant T-cell therapy.
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Affiliation(s)
- Dmitrii S Romaniuk
- Laboratory for Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Anna M Postovskaya
- Laboratory for Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Alexandra A Khmelevskaya
- Laboratory for Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Dmitry B Malko
- Laboratory for Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Grigory A Efimov
- Laboratory for Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
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Abstract
Somatic variations are frequent and important drivers in cancers. Amino acid substitutions can yield neoantigens that are detected by the immune system. Neoantigens can lead to immune response and tumor rejection. Although neoantigen load and occurrence have been widely studied, a detailed pan-cancer analysis of the occurrence and characterization of neoepitopes is missing. We investigated the proteome-wide amino acid substitutions in 8-, 9-, 10-, and 11-mer peptides in 30 cancer types with the NetMHC 4.0 software. 11,316,078 (0.24%) of the predicted 8-, 9-, 10-, and 11-mer peptides were highly likely neoepitope candidates and were derived from 95.44% of human proteins. Binding affinity to MHC molecules is just one of the many epitope features. The most likely epitopes are those which are detected by several MHCs and of several peptide lengths. 9-mer peptides are the most common among the high binding neoantigens. 0.17% of all variants yield more than 100 neoepitopes and are considered as the best candidates for any application. Amino acid distributions indicate that variants at all positions in neoepitopes of any length are, on average, more hydrophobic than the wild-type residues. We characterized properties of neoepitopes in 30 cancer types and estimated the likely numbers of tumor-derived epitopes that could induce an immune response. We found that amino acid distributions, at all positions in neoepitopes of all lengths, contain more hydrophobic residues than the wild-type sequences implying that the hydropathy nature of neoepitopes is an important property. The neoepitope characteristics can be employed for various applications including targeted cancer vaccine development for precision medicine.
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Bijen HM, Hassan C, Kester MGD, Janssen GMC, Hombrink P, de Ru AH, Drijfhout JW, Meiring HD, de Jong AP, Falkenburg JHF, Jimenez CR, Heemskerk MHM, van Veelen PA. Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface. Proteomics 2018; 18:e1700250. [PMID: 29251415 DOI: 10.1002/pmic.201700250] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/22/2017] [Indexed: 12/20/2022]
Abstract
Allogeneic stem cell transplantation has emerged as immunotherapy in the treatment of a variety of hematological malignancies. Its efficacy depends on induction of graft versus leukemia by donor lymphocytes. Both graft versus leukemia and graft versus host disease are induced by T cells reactive against polymorphic peptides, called minor histocompatibility antigens (MiHA), which differ between patient and donor and are presented in the context of self-HLA (where HLA is human leukocyte antigen). The allelic counterpart (AC) of the MiHA is generally considered to be absent at the cell surface, based on the absence of immune responses directed against the AC. To study this in detail, we evaluate the recognition, HLA-binding affinity, and cell surface expression of three selected MiHA. By quantitative MS, we demonstrate the similarly abundant expression of both MiHA and AC at the cell surface. We conclude that the absent recognition of the AC cannot generally be explained by insufficient processing and presentation at the cell surface of the AC.
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Affiliation(s)
- Helena M Bijen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chopie Hassan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pleun Hombrink
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hugo D Meiring
- Laboratory for Vaccine Research, Unit Research and Development, Netherlands Vaccine Institute, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ad P de Jong
- Laboratory for Vaccine Research, Unit Research and Development, Netherlands Vaccine Institute, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Connie R Jimenez
- OncoProteomics Laboratory, Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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