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Youk S, Kang M, Ahn B, Koo Y, Park C. Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes (Basel) 2023; 15:7. [PMID: 38275589 PMCID: PMC10815642 DOI: 10.3390/genes15010007] [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: 11/30/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.
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Affiliation(s)
- Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Yangmo Koo
- Genetic & Breeding Department, Korea Animal Improvement Association, Seocho, Seoul 06668, Republic of Korea;
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
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2
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Kang M, Ahn B, Youk S, Jeon H, Soundarajan N, Cho ES, Park W, Park C. Individual and population diversity of 20 representative olfactory receptor genes in pigs. Sci Rep 2023; 13:18668. [PMID: 37907519 PMCID: PMC10618239 DOI: 10.1038/s41598-023-45784-y] [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: 01/26/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023] Open
Abstract
Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.
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Affiliation(s)
- Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | | | - Eun-Seok Cho
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Woncheoul Park
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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3
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Le QVC, Youk S, Choi M, Jeon H, Kim WI, Ho CS, Park C. Development of an Immortalized Porcine Fibroblast Cell Panel With Different Swine Leukocyte Antigen Genotypes. Front Genet 2022; 13:815328. [PMID: 35198008 PMCID: PMC8859410 DOI: 10.3389/fgene.2022.815328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Immortalized cell lines are valuable resources to expand the molecular characterization of major histocompatibility complex genes and their presented antigens. We generated a panel of immortalized cell lines by transfecting human telomerase reverse transcriptase (hTERT) into primary fibroblast cells prepared from ear, fetal, and lung tissues of 10 pigs from five breeds and successfully cultured them for 30-45 passages. The cell growth characteristic of the immortalized fibroblasts was similar to that of primary fibroblast, which was unable to form colonies on soft agar. The genotypes of major swine leukocyte antigen (SLA) genes, including three classical class I (SLA-1, -2, and -3) and three class II genes (DQB1, DRB1, and DQA), were determined using high-resolution typing. A total of 58 alleles, including a novel allele for SLA-2, were identified. Each cell line was unique. A cell line derived from a National Institutes of Health miniature pig was homozygous across the six major SLA genes. The expression levels of SLA classical class I genes varied among the cell lines and were slightly upregulated in the immortalized compared to the primary cells based on semiquantitative reverse transcription polymerase chain reaction. The immortalized porcine fibroblast cell lines with diverse SLA haplotypes that were developed in this study have potential to be applied in studies regarding the molecular characteristics and genetic structure of SLA genes and epitope-major histocompatibility complex interactions in pigs.
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Affiliation(s)
- Quy Van Chanh Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - SeungYeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Munjeong Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Chonbuk National University, Iksan, South Korea
| | - Chak-Sum Ho
- Gift of Hope Organ & Tissue Donor Network, Itasca, IL, United States
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, South Korea
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Youk S, Le MT, Kang M, Ahn B, Choi M, Kim K, Kim TH, Kim JH, Ho CS, Park C. Development of a high-resolution typing method for SLA-3, swine MHC class I antigen 3. Anim Genet 2021; 53:166-170. [PMID: 34910829 DOI: 10.1111/age.13161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
We developed a high-resolution and comprehensive typing method for swine leukocyte antigen 3 (SLA-3), an MHC class I gene, employing locus-specific genomic PCR followed by subsequent direct sequencing. A total of 292 individuals from nine pure, one cross-breed and six cell lines were successfully typed. A total of 21 SLA-3 alleles were identified, of which four were found to be novel alleles. However, the allelic diversity of SLA-3 was lower than that of previously reported class I genes, SLA-1 and -2. More SLA-3 alleles were observed in the Landrace and Yorkshire breeds than the other breeds. SLA-3*04:01 was identified in seven out of nine breeds and was the most widely distributed allele across all breeds. Therefore, the typing method reported in this study completes our efforts to develop high-resolution typing methods for major SLA molecules, facilitating the combined analysis of major SLA genes from field samples, which is important to understand the relationship between the adaptive immune responses against pathogens and the immunogenetic makeup of an individual.
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Affiliation(s)
- S Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
| | - M T Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
| | - M Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
| | - B Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
| | - M Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
| | - K Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea.,Livestock Support Department, National Agricultural Cooperative Federation Agribusiness Group, Seoul, 04516, Korea
| | - T H Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Korea
| | - J H Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
| | - C S Ho
- Gift of Hope Organ and Tissue Donor Network, 425 Spring Lake Drive, Itasca, IL, 60143, USA
| | - C Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, 05029, Korea
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Mooring stone-like Arg 114 pulls diverse bulged peptides: first insight into African swine fever virus-derived T cell epitopes presented by swine MHC class I. J Virol 2021; 96:e0137821. [PMID: 34851145 DOI: 10.1128/jvi.01378-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
African swine fever virus (ASFV) is the causative agent of African swine fever (ASF), which is a devastating pig disease threatening the global pork industry. However, currently no commercial vaccines are available. During the immune response, major histocompatibility complex (MHC) class I molecules select viral peptide epitopes and present them to host cytotoxic T lymphocytes, thereby playing critical roles in eliminating viral infections. Here we screened peptides derived from ASFV and determined the molecular basis of ASFV-derived peptides presented by the swine leukocyte antigen (SLA)-1*0101. We found that peptide binding in SLA-1*0101 differs from the traditional mammalian binding patterns. Unlike the typical B and F pockets used by the common MHC-I molecule, SLA-1*0101 uses the D and F pockets as major peptide anchor pockets. Furthermore, the conformationally stable Arg114 residue located in the peptide-binding groove (PBG) was highly selective for the peptides. Arg114 draws negatively charged residues at positions P5 to P7 of the peptides, which led to multiple bulged conformations of different peptides binding to SLA-1*0101 and creating diversity for T cells receptor docking. Thus, the solid Arg114 residue acts as a "mooring stone" and pulls the peptides into the PBG of SLA-1*0101. Notably, the T cells recognition and activation of p72-derived peptides were verified by SLA-1*0101 tetramer-based flow cytometry in peripheral blood mononuclear cells (PBMCs) of the donor pigs. These results refresh our understanding of MHC I molecular anchor peptides, and provide new insights into vaccine development for the prevention and control of ASF. IMPORTANCE The spread of African swine fever virus (ASFV) has caused enormous losses to the pork industry worldwide. Here, a series of ASFV-derived peptides were identified, which could bind to swine leukocyte antigen SLA-1*0101, a prevalent SLA allele among Yorkshire pigs. The crystal structure of four ASFV-derived peptides and one foot-and-mouth disease virus (FMDV)-derived peptide complexed with SLA-1*0101 revealed an unusual peptide anchoring mode of SLA-1*0101 with D and F pockets as anchoring pockets. Negatively-charged residues are preferred within the middle portion of SLA-1*0101-binding peptides. Notably, we determined an unexpected role of Arg114 of SLA-1*0101 as a "mooring stone" which pulls the peptide anchoring into the PBG in diverse "M" or "n" shaped conformation. Furthermore, T cells from donor pigs could activate through the recognition of ASFV-derived peptides. Our study sheds light on the uncommon presentation of ASFV peptides by swine MHC I and benefits the development of ASF vaccines.
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Machuka EM, Muigai AWT, Amimo JO, Domelevo Entfellner JB, Lekolool I, Abworo EO, Pelle R. Comparative Analysis of SLA-1, SLA-2, and DQB1 Genetic Diversity in Locally-Adapted Kenyan Pigs and Their Wild Relatives, Warthogs. Vet Sci 2021; 8:180. [PMID: 34564574 PMCID: PMC8473215 DOI: 10.3390/vetsci8090180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.
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Affiliation(s)
- Eunice Magoma Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
- Institute for Basic Sciences Technology and Innovation (PAUSTI), Pan African University, Nairobi P.O. Box 62000-00200, Kenya
| | - Anne W. Thairu Muigai
- Botany Department, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya;
| | - Joshua Oluoch Amimo
- Center for Food Animal Health, Department of Animal Sciences, 1680 Madison Avenue, The Ohio State University, Wooster, OH 44691, USA;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
| | - Isaac Lekolool
- Kenya Wildlife Services, Nairobi P.O. Box 40241-00100, Kenya;
| | - Edward Okoth Abworo
- Animal and Human Health Program, International Livestock Research Institute, Nairobi P.O. Box 30709-00100, Kenya;
| | - Roger Pelle
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya;
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Kang M, Ahn B, Youk S, Cho HS, Choi M, Hong K, Do JT, Song H, Jiang H, Kennedy LJ, Park C. High Allelic Diversity of Dog Leukocyte Antigen Class II in East Asian Dogs: Identification of New Alleles and Haplotypes. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09560-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Techakriengkrai N, Nedumpun T, Golde WT, Suradhat S. Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations. Front Vet Sci 2021; 8:637682. [PMID: 33996967 PMCID: PMC8121083 DOI: 10.3389/fvets.2021.637682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Among swine genetic markers, the highly polymorphic swine leukocyte antigen (SLA) is one of the key determinants, associated with not only immune responses but also reproductive performance and meat quality. The objective of this study was to characterize the SLA class I and II diversities in the commercial pig populations. In this study, a total number of 158 pigs (126 gilts and 32 boars) were randomly selected from different breeding herds of five major pig-producing companies, which covered ~70% of Thai swine production. The results indicate that a moderate level of SLA diversity was maintained in the Thai swine population, despite the performance-oriented breeding scheme. The highly common SLA class I alleles were SLA-1*08:XX, SLA-2*02:XX, and SLA-3*04:XX at a combined frequency of 30.1, 18.4, and 34.5%, respectively, whereas DRB1*04:XX, DQB1*02:XX and DQA*02:XX were the common class II alleles at 22.8, 33.3, and 38.6%, respectively. The haplotype Lr-32.0 (SLA-1*07:XX, SLA-2*02:XX, and SLA-3*04:XX) and Lr-0.23 (DRB1*10:XX, DQB1*06:XX, DQA* 01:XX) was the most common SLA class I and II haplotype, at 15.5 and 14.6%, respectively. Common class I and II haplotypes were also observed, which Lr-22.15 was the most predominant at 11.1%, followed by Lr-32.12 and Lr-4.2 at 10.8 and 7.9%, respectively. To our knowledge, this is the first report of SLA class I and II diversities in the commercial pigs in Southeast Asia. The information of the common SLA allele(s) in the population could facilitate swine genetic improvement and future vaccine design.
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Affiliation(s)
- Navapon Techakriengkrai
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogens Research Unit, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
| | - Teerawut Nedumpun
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
| | - William T Golde
- Department of Vaccines and Diagnostics, Moredun Research Institute, Penicuik, United Kingdom
| | - Sanipa Suradhat
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
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Bosch-Camós L, López E, Navas MJ, Pina-Pedrero S, Accensi F, Correa-Fiz F, Park C, Carrascal M, Domínguez J, Salas ML, Nikolin V, Collado J, Rodríguez F. Identification of Promiscuous African Swine Fever Virus T-Cell Determinants Using a Multiple Technical Approach. Vaccines (Basel) 2021; 9:29. [PMID: 33430316 PMCID: PMC7825812 DOI: 10.3390/vaccines9010029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 11/23/2022] Open
Abstract
The development of subunit vaccines against African swine fever (ASF) is mainly hindered by the lack of knowledge regarding the specific ASF virus (ASFV) antigens involved in protection. As a good example, the identity of ASFV-specific CD8+ T-cell determinants remains largely unknown, despite their protective role being established a long time ago. Aiming to identify them, we implemented the IFNγ ELISpot as readout assay, using as effector cells peripheral blood mononuclear cells (PBMCs) from pigs surviving experimental challenge with Georgia2007/1. As stimuli for the ELISpot, ASFV-specific peptides or full-length proteins identified by three complementary strategies were used. In silico prediction of specific CD8+ T-cell epitopes allowed identifying a 19-mer peptide from MGF100-1L, as frequently recognized by surviving pigs. Complementarily, the repertoire of SLA I-bound peptides identified in ASFV-infected porcine alveolar macrophages (PAMs), allowed the characterization of five additional SLA I-restricted ASFV-specific epitopes. Finally, in vitro stimulation studies using fibroblasts transfected with plasmids encoding full-length ASFV proteins, led to the identification of MGF505-7R, A238L and MGF100-1L as promiscuously recognized antigens. Interestingly, each one of these proteins contain individual peptides recognized by surviving pigs. Identification of the same ASFV determinants by means of such different approaches reinforce the results presented here.
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Affiliation(s)
- Laia Bosch-Camós
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Elisabet López
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - María Jesús Navas
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Sonia Pina-Pedrero
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Francesc Accensi
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193 Bellaterra, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
| | - Chankyu Park
- Department of Stem Cells and Regenerative Biology, Konkuk University, Seoul 05029, Korea;
| | - Montserrat Carrascal
- Instituto de Investigaciones Biomédicas de Barcelona-Unidad de Espectrometría de Masas Biológica y Proteómica, Consejo Superior de Investigaciones Científicas (CSIC), 08193 Bellaterra, Spain;
| | - Javier Domínguez
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28049 Madrid, Spain;
| | - Maria Luisa Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autònoma de Madrid, 28049 Madrid, Spain;
| | - Veljko Nikolin
- Boehringer Ingelheim Veterinary Research Center (BIVRC) GmbH & Co. KG, 30559 Hannover, Germany;
| | - Javier Collado
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
| | - Fernando Rodríguez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA), Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (L.B.-C.); (E.L.); (M.J.N.); (S.P.-P.); (F.C.-F.)
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain;
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10
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Siañez-Estrada LI, Rivera-Benítez JF, Rosas-Murrieta NH, Reyes-Leyva J, Santos-López G, Herrera-Camacho I. Immunoinformatics approach for predicting epitopes in HN and F proteins of Porcine rubulavirus. PLoS One 2020; 15:e0239785. [PMID: 32976525 PMCID: PMC7518572 DOI: 10.1371/journal.pone.0239785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/14/2020] [Indexed: 12/19/2022] Open
Abstract
Porcine rubulavirus (PRV), which belongs to the family Paramyxoviridae, causes blue eye disease in pigs, characterized by encephalitis and reproductive failure in newborn and adult pigs, respectively. There is no effective treatment against PRV and no information on the effectiveness of the available vaccines. Continuous outbreaks have occurred in Mexico since the early 1980s, which have caused serious economic losses to pig producers. Vaccination can be used to control this disease. Searching for effective antigen candidates against PRV, we first sequenced the PAC1 F protein, then we used various immunoinformatics tools to predict antigenic determinants of B-cells and T-cells against the two glycoproteins of the virus (HN and F proteins). Finally, we used AutoDock Vina to determine the binding energies. We obtained the F gene sequence of a PRV strain collected in the early 1990s in Mexico and compared its amino acid profile with previous and more recent strains, obtaining an identity similarity of 97.78 to 99.26%. For the F proteins, seven linear B-cell epitopes, six conformational B-cell epitopes and twenty-nine T-cell MHC class I epitopes were predicted. For the HN proteins, sixteen linear B-cell epitopes, seven conformational B-cell epitopes and thirty-four T-cell MHC class I epitopes were predicted. The ATRSETDYY and AAYTTTTCF epitopes of the HN protein might be important for neutralizing the viral infection. We determined the in silico binding energy between the predicted epitopes on the F and HN proteins and swine MHC-I molecules. The binding energy of these epitopes ranged from -5.8 to -7.8 kcal/mol. The present study aimed to assess the use of HN and F proteins as antigens, either as recombinant proteins or as a series of peptides that could activate different responses of the immune system. This may help identify relevant immunogens, saving time and costs in the development of new vaccines or diagnostic tools.
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Affiliation(s)
- Luis I. Siañez-Estrada
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Posgrado en Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, México
| | - José F. Rivera-Benítez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Ciudad de México, México
| | - Nora H. Rosas-Murrieta
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Julio Reyes-Leyva
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, México
| | - Gerardo Santos-López
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social (IMSS), Metepec, México
| | - Irma Herrera-Camacho
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
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Sehl J, Pikalo J, Schäfer A, Franzke K, Pannhorst K, Elnagar A, Blohm U, Blome S, Breithaupt A. Comparative Pathology of Domestic Pigs and Wild Boar Infected with the Moderately Virulent African Swine Fever Virus Strain "Estonia 2014". Pathogens 2020; 9:E662. [PMID: 32824331 PMCID: PMC7459997 DOI: 10.3390/pathogens9080662] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/20/2022] Open
Abstract
Endemically infected European wild boar are considered a major reservoir of African swine fever virus in Europe. While high lethality was observed in the majority of field cases, strains of moderate virulence occurred in the Baltic States. One of these, "Estonia 2014", led to a higher number of clinically healthy, antibody-positive animals in the hunting bag of North-Eastern Estonia. Experimental characterization showed high virulence in wild boar but moderate virulence in domestic pigs. Putative pathogenic differences between wild boar and domestic pigs are unresolved and comparative pathological studies are limited. We here report on a kinetic experiment in both subspecies. Three animals each were euthanized at 4, 7, and 10 days post infection (dpi). Clinical data confirmed higher virulence in wild boar although macroscopy and viral genome load in blood and tissues were comparable in both subspecies. The percentage of viral antigen positive myeloid cells tested by flow cytometry did not differ significantly in most tissues. Only immunohistochemistry revealed consistently higher viral antigen loads in wild boar tissues in particular 7 dpi, whereas domestic pigs already eliminated the virus. The moderate virulence in domestic pigs could be explained by a more effective viral clearance.
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Affiliation(s)
| | | | | | | | | | | | | | - Sandra Blome
- Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (J.S.); (J.P.); (A.S.); (K.F.); (K.P.); (A.E.); (U.B.); (A.B.)
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