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Liu Y, Su Y, Zhou Z, Zhu J, Zhu Q, Xie P, Qian S, Wang L, Qin T, Zhou G. Conjoint analysis of transcriptome and metabolome profiles of normal captivity and arch soil free-range in Meishan pigs. Front Vet Sci 2023; 10:1187877. [PMID: 37576833 PMCID: PMC10421962 DOI: 10.3389/fvets.2023.1187877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
The hygiene hypothesis has been advanced as a potential explanation for the increasingly high levels of atopy and allergic disease in the general human population. In an effort to conduct a more detailed study of the link between immune activity and the hygiene hypothesis, Meishan pigs raised under normal captivity (NC) or arch soil free-range (ASF) conditions were selected as an experimental model system. Cytokine levels were found to differ significantly between these two groups consistent with a difference in cellular immune status. Integrated transcriptomic and metabolomic profiling of duodenal tissue samples from Meishan pigs were then performed, leading to the identification of differentially expressed genes (DEGs), differentially abundant metabolites (DAMs), and key pathways that were able to distinguish the NC and ASF groups. This approach led to the identification of 1,113 DEGs, as well as 577 and 372 DAMs in positive and negative ion modes, respectively. When an interaction network incorporating DEGs and metabolites associated with immune responsivity was constructed, it included factors such as 9-cis-Retinoic acid, (9Z,11E)-(13S)-13-Hydroxyoctadeca-9,11-dienoic acid and (10E,12Z)-(9S)-9-Hydroxyoctadeca-10,12-dienoic acid. Functional enrichment analyses confirmed that identified DEGs and DAMs were associated with immune-related pathways including the intestinal IgA production and PPAR signaling pathways. Together, these results offer new insight into the roles that particular genes and metabolites enriched in response to environmental stressors in free-range Meishan pigs may play in the regulation of cellular immunity, thus offering a foundation for future efforts to better understand the immunological mechanisms underlying the hygiene hypothesis.
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Affiliation(s)
- Ying Liu
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Yanlong Su
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Zhijie Zhou
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Jie Zhu
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Qianqian Zhu
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Peng Xie
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Shiquan Qian
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Liwei Wang
- Huaiyin Institute of Agricultural Sciences in Xuhuai Region, Huaian, China
| | - Tong Qin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gang Zhou
- Huaiyin Institute of Agricultural Sciences in Xuhuai Region, Huaian, China
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Schäfer A, Franzoni G, Netherton CL, Hartmann L, Blome S, Blohm U. Adaptive Cellular Immunity against African Swine Fever Virus Infections. Pathogens 2022; 11:pathogens11020274. [PMID: 35215216 PMCID: PMC8878497 DOI: 10.3390/pathogens11020274] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) remains a threat to global pig populations. Infections with ASFV lead to a hemorrhagic disease with up to 100% lethality in Eurasian domestic and wild pigs. Although myeloid cells are the main target cells for ASFV, T cell responses are impacted by the infection as well. The complex responses remain not well understood, and, consequently, there is no commercially available vaccine. Here, we review the current knowledge about the induction of antiviral T cell responses by cells of the myeloid lineage, as well as T cell responses in infected animals, recent efforts in vaccine research, and T cell epitopes present in ASFV.
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Affiliation(s)
- Alexander Schäfer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (A.S.); (L.H.); (S.B.)
| | - Giulia Franzoni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy;
| | | | - Luise Hartmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (A.S.); (L.H.); (S.B.)
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (A.S.); (L.H.); (S.B.)
| | - Ulrike Blohm
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany; (A.S.); (L.H.); (S.B.)
- Correspondence: ; Tel.: +49-38351-7-1543; +49-38351-7-1236
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Chen AYA, Huang CW, Liu SH, Liu AC, Chaung HC. Single Nucleotide Polymorphisms of Immunity-Related Genes and Their Effects on Immunophenotypes in Different Pig Breeds. Genes (Basel) 2021; 12:genes12091377. [PMID: 34573362 PMCID: PMC8471458 DOI: 10.3390/genes12091377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Enhancing resistance and tolerance to pathogens remains an important selection objective in the production of livestock animals. Single nucleotide polymorphisms (SNPs) vary gene expression at the transcriptional level, influencing an individual's immune regulation and susceptibility to diseases. In this study, we investigated the distribution of SNP sites in immune-related genes and their correlations with cell surface markers of immune cells within purebred (Taiwan black, Duroc, Landrace and Yorkshire) and crossbred (Landrace-Yorkshire) pigs. Thirty-nine SNPs of immune-related genes, including 11 cytokines, 5 chemokines and 23 Toll-like receptors (TLRs) (interferon-α and γ (IFN-α, γ), tumor necrosis factor-α (TNF-α), granulocyte-macrophage colony-stimulating factor (GM-CSF), Monocyte chemoattractant protein-1 (MCP-1) and TLR3, TLR4, TLR7, TLR8, and TLR9) were selected, and the percentages of positive cells with five cell surface markers of CD4, CD8, CD80/86, MHCI, and MHCII were analyzed. There were 28 SNPs that were significantly different among breeds, particularly between Landrace and Taiwan black. For instance, the frequency of SNP1 IFN-α -235A/G in Taiwan black and Landrace was 11.11% and 96.15%, respectively. In addition, 18 SNPs significantly correlated with the expression of cell surface markers, including CD4, CD8, CD80/86, and MHCII. The percentage of CD4+ (39.27%) in SNP33 TLR-8 543C/C was significantly higher than those in A/C (24.34%), at p < 0.05. Together, our findings show that Taiwan black pigs had a unique genotype distribution, whereas Landrace and Yorkshire had a more similar genotype distribution. Thus, an understanding of the genetic uniqueness of each breed could help to identify functionally important SNPs in immunoregulation.
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Affiliation(s)
- Ann Ying-An Chen
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan; (A.Y.-A.C.); (A.-C.L.)
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan
| | - Chao-Wei Huang
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan;
| | - Shyh-Hwa Liu
- Department of Animal Science, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan;
| | - An-Chi Liu
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan; (A.Y.-A.C.); (A.-C.L.)
| | - Hso-Chi Chaung
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan; (A.Y.-A.C.); (A.-C.L.)
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan
- Correspondence:
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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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Bâlteanu VA, Cardoso TF, Amills M, Egerszegi I, Anton I, Beja-Pereira A, Zsolnai A. The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs. Animal 2019; 13:2440-2446. [PMID: 30947762 DOI: 10.1017/s1751731119000582] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size.
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Affiliation(s)
- V A Bâlteanu
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania
| | - T F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- CAPES Foundation, Ministry of Education of Brazil, 7004020 Brasilia D. F., Brazil
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - I Egerszegi
- Szent István University, Páter Károly u. 1., 2100 Gödöllő, Hungary
| | - I Anton
- NAIK-Research Institute for Animal Breeding, Nutrition and Food Science, Gesztenyes u. 1., 2053 Herceghalom, Hungary
| | - A Beja-Pereira
- Centro de Investigacao em Biodiversidade e Recursos Geneticos, Universidade do Porto (CIBIO-UP), Rua Padre Armando Quintas 7, 4485-661 Vairao, Portugal
| | - A Zsolnai
- NAIK-Research Institute for Animal Breeding, Nutrition and Food Science, Gesztenyes u. 1., 2053 Herceghalom, Hungary
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Abstract
Naturally endemic infectious diseases provide selective pressures for pig populations. Toll-like receptors (TLRs) represent the first line of immune defense against pathogens and are likely to play a crucial adaptive role for pig populations. This study was done to determine whether wild and domestic pig populations representing diverse global environments demonstrate local TLR adaptation. The genomic sequence encoding the ectodomain, responsible for interacting with pathogen ligands of bacterial (TLR1, TLR2 and TLR6) and viral (TLR3, TLR7 and TLR8) receptors, was obtained. Mitochondrial D-loop region sequences were obtained and a phylogenetic analysis using these sequences revealed a clear separation of animals into Asian (n = 27) and European (n = 40) clades. The TLR sequences were then analyzed for population-specific positive selection signatures within wild boars and domesticated pig populations derived from Asian and European clades. Using within-population and between-population tests for positive selection, a TLR2-derived variant 376A (126Thr), estimated to have arisen in 163,000 years ago with a frequency of 83.33 % within European wild boars, 98.00 % within domestic pig breeds of European origin, 40.00 % within Asian wild boars, and 11.36 % within Asian domestic pigs, was identified to be under positive selection in pigs of European origin. The variant is located within the N terminal domain of the TLR2 protein 3D crystal structure and could affect ligand binding. This study suggests the TLR2 gene contributing to responses to bacterial pathogens has been crucial in adaptation of pigs to pathogens.
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Bergman IM, Okumura N, Uenishi H, Hammer SE, Knoll A, Edfors I, Juul-Madsen HR. Wild boars from Sweden, Austria, the Czech Republic and Japan possess intact mannose-binding lectin 2 (MBL2) genes. Int J Immunogenet 2015; 42:204-7. [PMID: 25809846 DOI: 10.1111/iji.12195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 02/01/2015] [Accepted: 03/04/2015] [Indexed: 11/29/2022]
Abstract
The two-nucleotide deletion recently detected in the mannose-binding lectin 2 gene in purebred and crossbred domestic pigs was not found among 68 wild boars representing 4 populations from Europe and Asia. This suggests that the deletion is a result of breeding and/or genetic drift/bottle necks.
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Affiliation(s)
- I M Bergman
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Tjele, Denmark
| | - N Okumura
- Animal Research Division, Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Japan
| | - H Uenishi
- Animal Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Japan.,Animal Immune and Cell Biology Research Unit, Division of Animal Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - S E Hammer
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Knoll
- Ceitec Mendelu, Mendel University, Brno, Czech Republic
| | - I Edfors
- School of Natural Sciences, Faculty of Science and Engineering, Linnaeus University, Kalmar, Sweden
| | - H R Juul-Madsen
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Tjele, Denmark
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