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Herrera-Uribe J, Lim KS, Byrne KA, Daharsh L, Liu H, Corbett RJ, Marco G, Schroyen M, Koltes JE, Loving CL, Tuggle CK. Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. Front Genet 2023; 14:1107462. [PMID: 37287538 PMCID: PMC10242145 DOI: 10.3389/fgene.2023.1107462] [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: 11/24/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Department of Animal Resource Science, Kongju National University, Yesan, Republic of Korea
| | - Kristen A. Byrne
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Ryan J. Corbett
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gianna Marco
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Martine Schroyen
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Crystal L. Loving
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
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2
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Prenzler S, Rudrawar S, Waespy M, Kelm S, Anoopkumar-Dukie S, Haselhorst T. The role of sialic acid-binding immunoglobulin-like-lectin-1 (siglec-1) in immunology and infectious disease. Int Rev Immunol 2023; 42:113-138. [PMID: 34494938 DOI: 10.1080/08830185.2021.1931171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Siglec-1, also known as Sialoadhesin (Sn) and CD169 is highly conserved among vertebrates and with 17 immunoglobulin-like domains is Siglec-1 the largest member of the Siglec family. Expression of Siglec-1 is found primarily on dendritic cells (DCs), macrophages and interferon induced monocyte. The structure of Siglec-1 is unique among siglecs and its function as a receptor is also different compared to other receptors in this class as it contains the most extracellular domains out of all the siglecs. However, the ability of Siglec-1 to internalize antigens and to pass them on to lymphocytes by allowing dendritic cells and macrophages to act as antigen presenting cells, is the main reason that has granted Siglec-1's key role in multiple human disease states including atherosclerosis, coronary artery disease, autoimmune diseases, cell-cell signaling, immunology, and more importantly bacterial and viral infections. Enveloped viruses for example have been shown to manipulate Siglec-1 to increase their virulence by binding to sialic acids present on the virus glycoproteins allowing them to spread or evade immune response. Siglec-1 mediates dissemination of HIV-1 in activated tissues enhancing viral spread via infection of DC/T-cell synapses. Overall, the ability of Siglec-1 to bind a variety of target cells within the immune system such as erythrocytes, B-cells, CD8+ granulocytes and NK cells, highlights that Siglec-1 is a unique player in these essential processes.
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Affiliation(s)
- Shane Prenzler
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Santosh Rudrawar
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Mario Waespy
- Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Sørge Kelm
- Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Shailendra Anoopkumar-Dukie
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
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3
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Milk yield variation partially attributed to blood oxygen-mediated neutrophil activation in lactating dairy goats. Br J Nutr 2023; 129:369-380. [PMID: 35604023 DOI: 10.1017/s0007114522001015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Blood oxygen is an essential component for numerous biological processes of mammalian animals. Milk production of ruminants largely relies on the supply of nutrients, such as glucose, amino acids and fatty acids. To define the regulatory role of blood oxygen availability in regard to milk production, seventy-five healthy Guanzhong dairy goats with similar body weight, days in milk and parities were selected. For each animal, milk yield was recorded and milk sample was collected to determine compositions. Milk vein blood was collected to determine parameters including blood gas, physio-biochemistry and haematology. Another blood sample was prepared for transcriptome and RT-qPCR. Results showed that both pressure of oxygen (pO2) in the milk vein (positively) and numbers of neutrophils in mammary vein (negatively) were associated with milk yield of the animals. To learn the role of pO2 in blood cell functionality, twelve animals (six with higher yield (H-group) and six with lower yield (L-group)) from seventy-five goats were selected. Compared with animals in L-group, goats in H-group were higher in pO2 but lower in pCO2, lactate, lactate dehydrogenase activity and neutrophil abundance in milk vein, compared with L-group. The blood transcriptome analysis suggested that compared with L-group, animals in H-group were depressed in functionality including neutrophil activation and metabolic pathways including glycolysis, NF-κB and HIF-1. Our result revealed that lower milk production could be associated with neutrophil activation responding to low pO2 in the mammary vein. In the meantime, we highlighted the potential importance of blood oxygen as a milk yield regulator.
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4
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Occurrence of Mycoplasma parvum in German Pigs of Different Age Groups Using a Novel Quantitative Real-Time PCR Assay. Pathogens 2022; 11:pathogens11111374. [PMID: 36422625 PMCID: PMC9692515 DOI: 10.3390/pathogens11111374] [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: 10/24/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma (M.) parvum is a hemotrophic bacterium circulating in the blood of pigs but is not considered a primary pathogen. Only a handful of studies dealing with this agent have been published since its first description in 1951, and many issues, including epidemiology and the impact of subclinical infections, are yet to be elucidated. This study aimed to establish a M. parvum specific real-time PCR for its detection and quantification in porcine blood and the application of this assay to obtain insights into the occurrence of M. parvum in German pigs. Furthermore, 16S rDNA amplicons of M. parvum positive blood samples were phylogenetically analyzed using MEGA 11 software. The established qPCR targeting the M. parvum glyceraldehyde-3-phosphate dehydrogenase encoding gene (gap) showed a lower detection limit of 10 gene copies per reaction and no cross-reactivity within the specificity test. A total of 36.0% (n = 72) of the sampled fattening pigs, 25.0% (n = 15) of the sows, and 4.37% (n = 8) of the boars tested M. parvum positive. The dendrogram showed the typical allocation of the M. parvum isolates into the "haemominutum group" subgroup within the hemotrophic Mycoplasma species. Both the novel established qPCR and the obtained epidemiological data can serve as an important basis for future studies dealing with M. parvum.
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5
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Chen Q, Tong M, Sun N, Yang Y, Cheng Y, Yi L, Wang G, Cao Z, Zhao Q, Cheng S. Integrated Analysis of miRNA-mRNA Expression in Mink Lung Epithelial Cells Infected With Canine Distemper Virus. Front Vet Sci 2022; 9:897740. [PMID: 35711811 PMCID: PMC9194998 DOI: 10.3389/fvets.2022.897740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023] Open
Abstract
Canine distemper (CD) caused by canine distemper virus (CDV) is one of the major infectious diseases in minks, bringing serious economic losses to the mink breeding industry. By an integrated analysis of microRNA (miRNA)-messenger RNA (mRNA), the present study analyzed the changes in the mink transcriptome upon CDV infection in mink lung epithelial cells (Mv. l. Lu cells) for the first time. A total of 4,734 differentially expressed mRNAs (2,691 upregulated and 2,043 downregulated) with |log2(FoldChange) |>1 and P-adj<0.05 and 181 differentially expressed miRNAs (152 upregulated and 29 downregulated) with |log2(FoldChange) |>2 and P-adj<0.05 were identified. Gene Ontology (GO) enrichment indicated that differentially expressed genes (DEGs) were associated with various biological processes and molecular function, such as response to stimulus, cell communication, signaling, cytokine activity, transmembrane signaling receptor activity and signaling receptor activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the combination of miRNA and mRNA was done for immune and inflammatory responses, such as Janus kinase (JAK)-signal transducer and activator (STAT) signaling pathway and nuclear factor (NF)-kappa B signaling pathway. The enrichment analysis of target mRNA of differentially expressed miRNA revealed that mir-140-5p and mir-378-12 targeted corresponding genes to regulate NF-kappa B signaling pathway. JAK-STAT signaling pathway could be modulated by mir-425-2, mir-139-4, mir-140-6, mir-145-3, mir-140-5p and mir-204-2. This study compared the influence of miRNA-mRNA expression in Mv. l. Lu cells before and after CDV infection by integrated analysis of miRNA-mRNA and analyzed the complex network interaction between virus and host cells. The results can help understand the molecular mechanism of the natural immune response induced by CDV infection in host cells.
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Affiliation(s)
- Qiang Chen
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
- College of Landscape Architecture, Changchun University, Changchun, China
| | - Mingwei Tong
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Na Sun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin City, China
| | - Yong Yang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Yuening Cheng
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Li Yi
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Gaili Wang
- Jilin Academy of Animal Husbandry and Veterinary Medicine, Changchun, China
| | - Zhigang Cao
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Quan Zhao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- *Correspondence: Quan Zhao
| | - Shipeng Cheng
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun, China
- Shipeng Cheng
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6
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Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9991726. [PMID: 34580642 PMCID: PMC8464434 DOI: 10.1155/2021/9991726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/27/2021] [Indexed: 01/11/2023]
Abstract
Dermatomyositis is an autoimmune disease characterized by severe symmetrical muscle dysfunction and pain. This study was aimed at discovering vital hub genes and potential molecular pathways of DM through bioinformatics analysis, which contributes to identifying potential diagnostic or therapeutic biomarkers and targets. In this study, a total of 915 DEGs in DM samples including 167 upregulated genes and 748 downregulated genes were screened out by the limma package based on the GSE142807 dataset from the Gene Expression Omnibus (GEO) database. Furthermore, the results of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that these downregulated genes were highly associated with the immune-related biological processes and pathways. Therefore, 41 genes closely related to DM were extracted for further study based on the subcluster analysis through the Molecular Complex Detection (MCODE) software plugin in Cytoscape. Ultimately, 10 hub genes (including ISG15, DDX58, IFIT3, CXCL10, and STAT1) were identified as the potential candidate biomarkers and targets. Besides, we found that the identified hub genes directly or indirectly communicated with each other via molecular signaling pathways on the protein and transcription level. In general, under the guidance of bioinformatics analysis, 10 vital hub genes and molecular mechanisms in DM were identified and the expression of proinflammatory factors and interferon family proteins and genes showed high association with DM, which might help provide a theoretical foundation for the development of point-to-point targeted therapy in the future treatment of DM.
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7
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Lim KS, Cheng J, Putz A, Dong Q, Bai X, Beiki H, Tuggle CK, Dyck MK, Canada PG, Fortin F, Harding JCS, Plastow GS, Dekkers JCM. Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience. BMC Genomics 2021; 22:614. [PMID: 34384354 PMCID: PMC8361860 DOI: 10.1186/s12864-021-07912-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
Background Disease resilience, which is the ability of an animal to maintain performance under disease, is important for pigs in commercial herds, where they are exposed to various pathogens. Our objective was to investigate population-level gene expression profiles in the blood of 912 healthy F1 barrows at ~ 27 days of age for associations with performance and health before and after their exposure to a natural polymicrobial disease challenge at ~ 43 days of age. Results Most significant (q < 0.20) associations of the level of expression of individual genes in blood of young healthy pigs were identified for concurrent growth rate and subjective health scores prior to the challenge, and for mortality, a combined mortality-treatment trait, and feed conversion rate after the challenge. Gene set enrichment analyses revealed three groups of gene ontology biological process terms that were related to disease resilience: 1) immune and stress response-related terms were enriched among genes whose increased expression was unfavorably associated with both pre- and post-challenge traits, 2) heme-related terms were enriched among genes that had favorable associations with both pre- and post-challenge traits, and 3) terms related to protein localization and viral gene expression were enriched among genes that were associated with reduced performance and health traits after but not before the challenge. Conclusions Gene expression profiles in blood from young healthy piglets provide insight into their performance when exposed to disease and other stressors. The expression of genes involved in stress response, heme metabolism, and baseline expression of host genes related to virus propagation were found to be associated with host response to disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07912-8.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, Iowa, 50011, USA
| | - Jian Cheng
- Department of Animal Science, Iowa State University, Ames, Iowa, 50011, USA
| | - Austin Putz
- Department of Animal Science, Iowa State University, Ames, Iowa, 50011, USA.,Swine Business Unit, Hendrix Genetics, Boxmeer, 5831, CK, The Netherlands
| | - Qian Dong
- Department of Animal Science, Iowa State University, Ames, Iowa, 50011, USA.,Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xuechun Bai
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Hamid Beiki
- Department of Animal Science, Iowa State University, Ames, Iowa, 50011, USA
| | | | - Michael K Dyck
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Pig Gen Canada
- PigGen Canada Research Consortium, Guelph, Ontario, N1H4G8, Canada
| | - Frederic Fortin
- Centre de Développement du Porc du Québec Inc. (CDPQ), Québec City, QC, G1V 4M6, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A2, Canada
| | - Graham S Plastow
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, Iowa, 50011, USA.
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Wang S, Wu P, Wang K, Ji X, Chen D, Jiang A, Liu Y, Xiao W, Jiang Y, Zhu L, Xu X, Li M, Li X, Tang G. Transcriptome Analysis Reveals Key Genes and Pathways Associated with Mummify Piglets. Genome 2021; 64:1029-1040. [PMID: 34139142 DOI: 10.1139/gen-2021-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
China is the country with the largest pork consumption in the world. However, the incidence of high mummify piglets (3-5%) is one of the important factors that cause the slow improvement of pig reproductive capacity, and the genetic mechanism is still unclear. This study aimed to identify candidate genes related to high mummify piglets. RNA-seq technology was used to comparative transcriptome profiling of blood from high piglets mummified and healthy sow at different stages of pregnancy (35d, 56d, 77d and 98d). A total of 137 to 420 DEGs were detected in each stage. Seven differentially expressed genes were significantly differentially expressed at various stages. IL-9R, TLR8, ABLIM3, FSH-α, ASCC1, PRKCZ, and GCK may play an important role in course of mummify piglets. The differential genes we identified between the groups were mainly enriched in immune and inflammation regulation, and others were mainly enriched in reproduction. Considering the function of candidate genes, IL-9R and TLR8 were suggested as the most promising candidate genes involved in mummify piglet traits. We speculate that during pregnancy, it may be the combined effects of the above-mentioned inflammation, immune response, and reproduction-related signal pathways that affect the occurrence of mummifying piglets, and further affect pig reproduction.
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Affiliation(s)
- Shujie Wang
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Pingxian Wu
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Kai Wang
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Xiang Ji
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Dong Chen
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Anan Jiang
- Sichuan Agricultural University - Chengdu Campus, 506176, Chengdu, Sichuan, China;
| | - Yihui Liu
- Sichuan Animal Husbandry Station, Chengdu, Sichuan, China;
| | - Weihang Xiao
- Sichuan Agricultural University - Chengdu Campus, 506176, Chengdu, Sichuan, China;
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an, China;
| | - Li Zhu
- Sichuan Agricultural University - Chengdu Campus, 506176, Chengdu, Sichuan, China;
| | - Xu Xu
- Sichuan Provincial Animal Husbandry and Food Bureau, 177358, Chengdu, Sichuan, China;
| | - Mingzhou Li
- Sichuan Agricultural University, 12529, Chengdu, Sichuan, China;
| | - Xuewei Li
- Sichuan Agricultural University - Chengdu Campus, 506176, Chengdu, Sichuan, China;
| | - Guoqing Tang
- Sichuan Agricultural University - Chengdu Campus, 506176, Chengdu, Sichuan, China;
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9
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Stadler J, Ade J, Hermanns W, Ritzmann M, Wentzel S, Hoelzle K, Hoelzle LE. Clinical, haematological and pathomorphological findings in Mycoplasma suis infected pigs. BMC Vet Res 2021; 17:214. [PMID: 34112157 PMCID: PMC8193878 DOI: 10.1186/s12917-021-02919-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycoplasma suis (M. suis) belongs to the group of haemotrophic mycoplasmas and is known as the causative agent of infectious anaemia in pigs. In the last few years valuable insights into the mechanism of adhesion and invasion, shedding patterns and cell tropism of M. suis were gained by the use of new molecular techniques. However, details on M. suis induced lesions as well as the distribution of M. suis in different organs are still lacking. Therefore, seven splenectomised pigs were experimentally infected and clinical and laboratory investigations as well as a detailed histopathological examination were performed. Detection and quantification of M. suis DNA in blood and various tissue samples was done using a quantitative real-time PCR. RESULTS During the course of experimental infection, periodically occurring signs of infectious anaemia of pigs including severe icteroanaemia, fever, apathy and anorexia were observed. In addition, dermatological manifestations such as haemorrhagic diathesis presenting as petechiae occurred. The most important haematological alterations were normochromic, normocytic anaemia, hypoglycaemia as well as increased bilirubin and urea concentrations. Necropsy revealed predominant evidence of haemolysis with consecutive anaemia, as well as disseminated intravascular coagulation. M. suis was found in all investigated tissues with the highest copy numbers found in the kidneys. In Giemsa stained sections M. suis was only detected red blood cell (RBC)-associated. CONCLUSION In the present study, no RBC independent sequestration of M. suis was detected in organs of experimentally infected pigs. Pathological findings are most likely resulting from haemolysis, consecutive anaemia as well as from disseminated intravascular coagulation and subsequent organ impairments.
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Affiliation(s)
- Julia Stadler
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleissheim, Germany.
| | - Julia Ade
- Institute of Animal Science, University of Hohenheim, Garbenstrasse 30, 70593, Stuttgart, Germany
| | - Walter Hermanns
- Institute of Veterinary Pathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Mathias Ritzmann
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleissheim, Germany
| | - Sarah Wentzel
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleissheim, Germany
| | - Katharina Hoelzle
- Institute of Animal Science, University of Hohenheim, Garbenstrasse 30, 70593, Stuttgart, Germany
| | - Ludwig E Hoelzle
- Institute of Animal Science, University of Hohenheim, Garbenstrasse 30, 70593, Stuttgart, Germany
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10
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Borchert C, Herman A, Roth M, Brooks AC, Friedenberg SG. RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis. PLoS One 2020; 15:e0240975. [PMID: 33091028 PMCID: PMC7580939 DOI: 10.1371/journal.pone.0240975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/06/2020] [Indexed: 11/29/2022] Open
Abstract
Immune-mediated hemolytic anemia (IMHA) is a life-threatening autoimmune disorder characterized by a self-mediated attack on circulating red blood cells. The disease occurs naturally in both dogs and humans, but is significantly more prevalent in dogs. Because of its shared features across species, dogs offer a naturally occurring model for studying IMHA in people. In this study, we used RNA sequencing of whole blood from treatment-naïve dogs to study transcriptome-wide changes in gene expression in newly diagnosed animals compared to healthy controls. We found many overexpressed genes in pathways related to neutrophil function, coagulation, and hematopoiesis. In particular, the most highly overexpressed gene in cases was a phospholipase scramblase, which mediates the externalization of phosphatidylserine from the inner to the outer leaflet of cell membranes. This family of genes has been shown to be critically important for programmed cell death of erythrocytes as well as the initiation of the clotting cascade. Unexpectedly, we found marked underexpression of many genes related to lymphocyte function. We also identified groups of genes that are highly associated with the inflammatory response and red blood cell regeneration in affected dogs. We did not find any genes that distinguished dogs that lived vs. those that died at 30 days following diagnosis, nor did we find any relevant genomic signatures of microbial organisms in the blood of affected animals. Future studies are warranted to validate these findings and assess their implication in developing novel therapeutic approaches for dogs and humans with IMHA.
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Affiliation(s)
- Corie Borchert
- Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, Minnesota, United States of America
| | - Adam Herman
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Megan Roth
- Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, Minnesota, United States of America
| | - Aimee C. Brooks
- Department of Veterinary Clinical Sciences, Purdue University College of Veterinary Medicine, West Lafayette, Indiana, United States of America
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, Minnesota, United States of America
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11
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Liu W, Zhao WJ, Wu YH. Study on the differentially expressed genes and signaling pathways in dermatomyositis using integrated bioinformatics method. Medicine (Baltimore) 2020; 99:e21863. [PMID: 32846838 PMCID: PMC7447406 DOI: 10.1097/md.0000000000021863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dermatomyositis is a common connective tissue disease. The occurrence and development of dermatomyositis is a result of multiple factors, but its exact pathogenesis has not been fully elucidated. Here, we used biological information method to explore and predict the major disease related genes of dermatomyositis and to find the underlying pathogenic molecular mechanism.The gene expression data of GDS1956, GDS2153, GDS2855, and GDS3417 including 94 specimens, 66 cases of dermatomyositis specimens and 28 cases of normal specimens, were obtained from the Gene Expression Omnibus database. The 4 microarray gene data groups were combined to get differentially expressed genes (DEGs). The gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of DEGs were operated by the database for annotation, visualization and integrated discovery and KEGG orthology based annotation system databases, separately. The protein-protein interaction networks of the DEGs were built from the STRING website. A total of 4097 DEGs were extracted from the 4 Gene Expression Omnibus datasets, of which 2213 genes were upregulated, and 1884 genes were downregulated. Gene ontology analysis indicated that the biological functions of DEGs focused primarily on response to virus, type I interferon signaling pathway and negative regulation of viral genome replication. The main cellular components include extracellular space, cytoplasm, and blood microparticle. The molecular functions include protein binding, double-stranded RNA binding and MHC class I protein binding. KEGG pathway analysis showed that these DEGs were mainly involved in the toll-like receptor signaling pathway, cytosolic DNA-sensing pathway, RIG-I-like receptor signaling pathway, complement and coagulation cascades, arginine and proline metabolism, phagosome signaling pathway. The following 13 closely related genes, XAF1, NT5E, UGCG, GBP2, TLR3, DDX58, STAT1, GBP1, PLSCR1, OAS3, SP100, IGK, and RSAD2, were key nodes from the protein-protein interaction network.This research suggests that exploring for DEGs and pathways in dermatomyositis using integrated bioinformatics methods could help us realize the molecular mechanism underlying the development of dermatomyositis, be of actual implication for the early detection and prophylaxis of dermatomyositis and afford reliable goals for the curing of dermatomyositis.
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Affiliation(s)
- Wei Liu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine
- Tianjin Key Laboratory of Translational Research of TCM Prescription and Syndrome, Tianjin, China
| | - Wen-Jia Zhao
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine
| | - Yuan-Hao Wu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine
- Tianjin Key Laboratory of Translational Research of TCM Prescription and Syndrome, Tianjin, China
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Persistence in Livestock Mycoplasmas—a Key Role in Infection and Pathogenesis. CURRENT CLINICAL MICROBIOLOGY REPORTS 2020. [DOI: 10.1007/s40588-020-00149-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Purpose of Review
Mycoplasma, economically important pathogens in livestock, often establishes immunologically complex persistent infections that drive their pathogenesis and complicate prophylaxis and therapy of the caused diseases. In this review, we summarize some of the recent findings concerning cellular and molecular persistence mechanisms related to the pathogenesis of mycoplasma infections in livestock.
Recent Findings
Data from recent studies prove several mechanisms including intracellular lifestyle, immune dysregulation, and autoimmunity as well as microcolony and biofilm formation and apoptosis of different host cell types as important persistence mechanisms in several clinically significant Mycoplasma species, i.e., M. bovis, M. gallisepticum, M. hyopneumoniae, and M. suis.
Summary
Evasion of the immune system and the establishment of persistent infections are key features in the pathogenesis of livestock mycoplasmas. In-depth knowledge of the underlying mechanisms will provide the basis for the development of therapy and prophylaxis strategies against mycoplasma infections.
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Augustino SMA, Xu Q, Liu X, Liu L, Zhang Q, Yu Y. Transcriptomic Study of Porcine Small Intestine Epithelial Cells Reveals Important Genes and Pathways Associated With Susceptibility to Escherichia coli F4ac Diarrhea. Front Genet 2020; 11:68. [PMID: 32174961 PMCID: PMC7056726 DOI: 10.3389/fgene.2020.00068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/20/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Diarrhea represents one of the most frequent major problems during piglets' neonatal and post-weaning periods leading to tremendous economic losses in the swine industry. Enterotoxigenic Escherichia coli (ETEC) F4 is regarded as the most important cause of diarrhea in piglets. However, some pigs are naturally resistant to those diarrheas caused by ETEC-F4, because they have no F4 receptors (F4R) on their small intestine epithelial cells that allow F4 fimbriae attachment. Thus, our study characterized a complete transcriptome of small intestine epithelial cells of Large White piglets using RNA-Seq. The aim of the study was to identify DEGs with regard to differences in the F4R phenotypes and SNP (C/T) genotypes at ITGB5 and important pathways associated with ETEC-F4ac susceptibility in small intestine epithelial cells of Large White piglets and derive molecular markers as a result of loss of F4acR in swine. METHODS A total of eight samples of small intestine epithelial cells obtained from Large White piglets (35 days old) used in this study were selected on the basis of two criteria. One was the adhesion phenotype to ETEC-F4ac fimbriae, and the other was the comparison of ITGB5 SNP (C > T) genotype sequences across all the samples. The samples were then divided into two groups, non-adhesive with CC genotype (n = 4), and adhesive with TT genotype (n = 4). RESULTS More down-regulated DEGs (p < 0.05, |log2FC| > 2) were detected in the comparison of non-adhesive vs. adhesive small intestine epithelial cells in the present study. Six genes, of which two (CNGA4, SLC25A31) exclusively expressed and four (HCN4, MYLK, KCNMA1, and KCNMB1) DEGs with up-regulation pattern in adhesive (F4R positive) pigs were involved in two pathways associated with diarrhea. The DEGs with up-regulation pattern in non-adhesive (F4R negative) pigs were mostly engaged in multiple immune response-related pathways. CONCLUSION The results provide insights on the biology of the phenotypes of F4R positive and negative pigs. One gene (MYLK) located on SSC13 locus for F4acR strongly support that it might have played a role in the adhesion phenotype which was obviously detected by adhesion assay in adhesive (F4R positive) group.
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Affiliation(s)
- Serafino M. A. Augustino
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qinglei Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueqin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Research Centre for Animal Genomic, Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Bick JT, Zeng S, Robinson MD, Ulbrich SE, Bauersachs S. Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5539597. [PMID: 31353404 PMCID: PMC6661403 DOI: 10.1093/database/baz086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 03/08/2019] [Accepted: 06/05/2019] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing technologies and the availability of an increasing number of mammalian and other genomes allow gene expression studies, particularly RNA sequencing, in many non-model organisms. However, incomplete genome annotation and assignments of genes to functional annotation databases can lead to a substantial loss of information in downstream data analysis. To overcome this, we developed Mammalian Annotation Database tool (MAdb, https://madb.ethz.ch) to conveniently provide homologous gene information for selected mammalian species. The assignment between species is performed in three steps: (i) matching official gene symbols, (ii) using ortholog information contained in Ensembl Compara and (iii) pairwise BLAST comparisons of all transcripts. In addition, we developed a new tool (AnnOverlappeR) for the reliable assignment of the National Center for Biotechnology Information (NCBI) and Ensembl gene IDs. The gene lists translated to gene IDs of well-annotated species such as a human can be used for improved functional annotation with relevant tools based on Gene Ontology and molecular pathway information. We tested the MAdb on a published RNA-seq data set for the pig and showed clearly improved overrepresentation analysis results based on the assigned human homologous gene identifiers. Using the MAdb revealed a similar list of human homologous genes and functional annotation results regardless of whether starting with gene IDs from NCBI or Ensembl. The MAdb database is accessible via a web interface and a Galaxy application.
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Affiliation(s)
- Jochen T Bick
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Shuqin Zeng
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.,Genetics and Functional Genomics, Vetsuisse Faculty Zurich, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Susanne E Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Stefan Bauersachs
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.,Genetics and Functional Genomics, Vetsuisse Faculty Zurich, University of Zurich, Zurich, Switzerland
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Gatto IRH, Sonálio K, Amaral RBD, Morés N, Dalla Costa OA, André MR, de Oliveira LG. High frequency and molecular characterization of porcine hemotrophic mycoplasmas in Brazil. Vet Microbiol 2019; 231:33-39. [PMID: 30955820 DOI: 10.1016/j.vetmic.2019.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/06/2019] [Accepted: 02/19/2019] [Indexed: 02/07/2023]
Abstract
Mycoplasma suis and Mycoplasma parvum are the two hemotrophic mycoplasmas species described in pigs. M. suis is involved in infectious anemia, while M parvum infection is commonly subclinical. The objectives of this study were twofold: (i) to investigate the prevalence of porcine hemotrophic mycoplasmas in sows from the southern region of Brazil by quantitative real-time PCR (qPCR) and (ii) to genetically characterize a subset of the samples based on the 16S rRNA gene. A total of 429 blood samples were evaluated from 53 different farm sites. Porcine hemoplasmas was detected at all the 53 tested sites and in 79.72% of the samples (342/429). Two sequences were obtained for Mycoplasma spp. The phylogenetic analysis based on the 16S rRNA gene (900 bp) showed that the Mycoplasma sequences were closely related to the M. suis cluster and that one sequence was positioned in the M. parvum cluster. In conclusion, porcine hemoplasmas have a high rate of prevalence in sows from commercial farms in the southern region of Brazil. This study demonstrated the first molecular detection and characterization of partial 16S rRNA gene of M. parvum in Brazil.
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Affiliation(s)
- Igor Renan Honorato Gatto
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP 14884-900, Brazil
| | - Karina Sonálio
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP 14884-900, Brazil
| | - Renan Bressianini do Amaral
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP 14884-900, Brazil
| | - Nelson Morés
- Embrapa Swine and Poultry, Animal Health Laboratory, BR 153, Km 110, P.O. Box 21, Distrito de Tamanduá, Concórdia, CEP 89.700-000, Santa Catarina, Brazil
| | - Osmar Antonio Dalla Costa
- Embrapa Swine and Poultry, Animal Health Laboratory, BR 153, Km 110, P.O. Box 21, Distrito de Tamanduá, Concórdia, CEP 89.700-000, Santa Catarina, Brazil
| | - Marcos Rogério André
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP 14884-900, Brazil
| | - Luís Guilherme de Oliveira
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP 14884-900, Brazil.
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