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Pluta A, Taxis TM, van der Meer F, Shrestha S, Qualley D, Coussens P, Rola-Łuszczak M, Ryło A, Sakhawat A, Mamanova S, Kuźmak J. An immunoinformatics study reveals a new BoLA-DR-restricted CD4+ T cell epitopes on the Gag protein of bovine leukemia virus. Sci Rep 2023; 13:22356. [PMID: 38102157 PMCID: PMC10724172 DOI: 10.1038/s41598-023-48899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leucosis (EBL), which has been reported worldwide. The expression of viral structural proteins: surface glycoprotein (gp51) and three core proteins - p15 (matrix), p24 (capsid), and p12 (nucleocapsid) induce a strong humoral and cellular immune response at first step of infection. CD4+ T-cell activation is generally induced by bovine leukocyte antigen (BoLA) region- positive antigen-presenting cells (APC) after processing of an exogenous viral antigen. Limited data are available on the BLV epitopes from the core proteins recognized by CD4+ T-cells. Thus, immunoinformatic analysis of Gag sequences obtained from 125 BLV isolates from Poland, Canada, Pakistan, Kazakhstan, Moldova and United States was performed to identify the presence of BoLA-DRB3 restricted CD4+ T-cell epitopes. The 379 15-mer overlapping peptides spanning the entire Gag sequence were run in BoLA-DRB3 allele-binding regions using a BoLA-DRB- peptide binding affinity prediction algorithm. The analysis identified 22 CD4+ T-cell peptide epitopes of variable length ranging from 17 to 22 amino acids. The predicted epitopes interacted with 73 different BoLA-DRB3 alleles found in BLV-infected cattle. Importantly, two epitopes were found to be linked with high proviral load in PBMC. A majority of dominant and subdominant epitopes showed high conservation across different viral strains, and therefore could be attractive targets for vaccine development.
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Affiliation(s)
- Aneta Pluta
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland.
| | - Tasia Marie Taxis
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
| | - Frank van der Meer
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sulav Shrestha
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Dominic Qualley
- Department of Chemistry and Biochemistry, and Center for One Health Studies, Berry College, Mt. Berry, GA, 30149, USA
| | - Paul Coussens
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
| | - Marzena Rola-Łuszczak
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland
| | - Anna Ryło
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland
| | - Ali Sakhawat
- Animal Quarantine Department, Ministry of National Food Security and Research, Peshawar, 25000, Pakistan
| | - Saltanat Mamanova
- Laboratory of Virology, Kazakh Scientific Research Veterinary Institute, LLP, 223 Raiymbek Avenue, 050000, Almaty, Republic of Kazakhstan
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, 24-100, Puławy, Poland
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Kaplan BS, Hofstetter AR, McGill JL, Lippolis JD, Norimine J, Dassanayake RP, Sacco RE. Identification of a DRB3*011:01-restricted CD4 + T cell response against bovine respiratory syncytial virus fusion protein. Front Immunol 2023; 14:1040075. [PMID: 36891302 PMCID: PMC9986546 DOI: 10.3389/fimmu.2023.1040075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Although Human Respiratory Syncytial Virus (HRSV) is a significant cause of severe respiratory disease with high morbidity and mortality in pediatric and elderly populations worldwide there is no licensed vaccine. Bovine Respiratory Syncytial Virus (BRSV) is a closely related orthopneumovirus with similar genome structure and high homology between structural and nonstructural proteins. Like HRSV in children, BRSV is highly prevalent in dairy and beef calves and known to be involved in the etiology of bovine respiratory disease, in addition to being considered an excellent model for HRSV. Commercial vaccines are currently available for BRSV, though improvements in efficacy are needed. The aims of this study were to identify CD4+ T cell epitopes present in the fusion glycoprotein of BRSV, an immunogenic surface glycoprotein that mediates membrane fusion and a major target of neutralizing antibodies. Overlapping peptides representing three regions of the BRSV F protein were used to stimulate autologous CD4+ T cells in ELISpot assays. T cell activation was observed only in cells from cattle with the DRB3*011:01 allele by peptides from AA249-296 of the BRSV F protein. Antigen presentation studies with C-terminal truncated peptides further defined the minimum peptide recognized by the DRB3*011:01 allele. Computationally predicted peptides presented by artificial antigen presenting cells further confirmed the amino acid sequence of a DRB3*011:01 restricted class II epitope on the BRSV F protein. These studies are the first to identify the minimum peptide length of a BoLA-DRB3 class II-restricted epitope in BRSV F protein.
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Affiliation(s)
- Bryan S. Kaplan
- Ruminant Diseases & Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Amelia R. Hofstetter
- Ruminant Diseases & Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Jodi L. McGill
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
| | - John D. Lippolis
- Ruminant Diseases & Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Junzo Norimine
- Department of Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Rohana P. Dassanayake
- Ruminant Diseases & Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Randy E. Sacco
- Ruminant Diseases & Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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Ribeiro G, Baldi F, Cesar ASM, Alexandre PA, Peripolli E, Ferraz JBS, Fukumasu H. Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle. BMC Genomics 2022; 23:774. [PMID: 36434498 PMCID: PMC9700932 DOI: 10.1186/s12864-022-08958-y] [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: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. RESULTS The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). CONCLUSION Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
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Affiliation(s)
- Gabriela Ribeiro
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Fernando Baldi
- grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Aline S. M. Cesar
- grid.11899.380000 0004 1937 0722Escola Superior de Agricultura “Luiz de Queiroz”, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Pâmela A. Alexandre
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067 Australia
| | - Elisa Peripolli
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - José B. S. Ferraz
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
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