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Kelly PA, McHugo GP, Scaife C, Peters S, Stevenson ML, McKay JS, MacHugh DE, Saez IL, Breathnach R. Unveiling the Role of Endoplasmic Reticulum Stress Pathways in Canine Demodicosis. Parasite Immunol 2024; 46:e13033. [PMID: 38607285 DOI: 10.1111/pim.13033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 04/13/2024]
Abstract
Canine demodicosis is a prevalent skin disease caused by overpopulation of a commensal species of Demodex mite, yet its precise cause remains unknown. Research suggests that T-cell exhaustion, increased immunosuppressive cytokines, induction of regulatory T cells and increased expression of immune checkpoint inhibitors may contribute to its pathogenesis. This study aimed to gain a deeper understanding of the molecular changes occurring in canine demodicosis using mass spectrometry and pathway enrichment analysis. The results indicate that endoplasmic reticulum stress promotes canine demodicosis through regulation of three linked signalling pathways: eIF2, mTOR, and eIF4 and p70S6K. These pathways are involved in the modulation of Toll-like receptors, most notably TLR2, and have been shown to play a role in the pathogenesis of skin diseases in both dogs and humans. Moreover, these pathways are also implicated in the promotion of immunosuppressive M2 phenotype macrophages. Immunohistochemical analysis, utilising common markers of dendritic cells and macrophages, verified the presence of M2 macrophages in canine demodicosis. The proteomic analysis also identified immunological disease, organismal injury and abnormalities and inflammatory response as the most significant underlying diseases and disorders associated with canine demodicosis. This study demonstrates that Demodex mites, through ER stress, unfolded protein response and M2 macrophages contribute to an immunosuppressive microenvironment, thereby assisting in their proliferation.
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Affiliation(s)
- Pamela A Kelly
- UCD School of Veterinary Medicine, University College Dublin, Dublin, 4, Ireland
| | - Gillian P McHugo
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, 4, Ireland
| | - Caitriona Scaife
- Proteomics Core, Mass Spectrometry Resource, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, 4, Ireland
| | - Susan Peters
- UCD School of Veterinary Medicine, University College Dublin, Dublin, 4, Ireland
| | - M Lynn Stevenson
- School of Biodiversity, One Health and Veterinary Medicine, Bearsden, University of Glasgow, Glasgow, UK
| | | | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, 4, Ireland
| | - Irene Lara Saez
- UCD Charles Institute of Dermatology, University College Dublin, Dublin, 4, Ireland
| | - Rory Breathnach
- UCD School of Veterinary Medicine, University College Dublin, Dublin, 4, Ireland
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Ward JA, Ng'ang'a SI, Randhawa IAS, McHugo GP, O'Grady JF, Flórez JM, Browne JA, Pérez O’Brien AM, Landaeta-Hernández AJ, Garcia JF, Sonstegard TS, Frantz LAF, Salter-Townshend M, MacHugh DE. Genomic insights into the population history and adaptive traits of Latin American Criollo cattle. R Soc Open Sci 2024; 11:231388. [PMID: 38571912 PMCID: PMC10990470 DOI: 10.1098/rsos.231388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/04/2024] [Accepted: 01/31/2024] [Indexed: 04/05/2024]
Abstract
Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.
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Affiliation(s)
- James A. Ward
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Said I. Ng'ang'a
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, MunichD-80539, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | | | - Gillian P. McHugo
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - John F. O'Grady
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Julio M. Flórez
- Acceligen, Eagan, MN55121, USA
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - John A. Browne
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
| | | | - Antonio J. Landaeta-Hernández
- Unidad de Investigaciones Zootécnicas, Facultad de Ciencias Veterinarias, Universidad del Zulia, Maracaibo, Venezuela
| | - Jóse F. Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | - Laurent A. F. Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, MunichD-80539, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonE1 4NS, UK
| | | | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture and Food Science, University College Dublin, DublinD04 V1W8, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, DublinD04 V1W8, Ireland
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Bhat SA, Elnaggar M, Hall TJ, McHugo GP, Reid C, MacHugh DE, Meade KG. Preferential differential gene expression within the WC1.1 + γδ T cell compartment in cattle naturally infected with Mycobacterium bovis. Front Immunol 2023; 14:1265038. [PMID: 37942326 PMCID: PMC10628470 DOI: 10.3389/fimmu.2023.1265038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/02/2023] [Indexed: 11/10/2023] Open
Abstract
Bovine tuberculosis (bTB), caused by infection with Mycobacterium bovis, continues to cause significant issues for the global agriculture industry as well as for human health. An incomplete understanding of the host immune response contributes to the challenges of control and eradication of this zoonotic disease. In this study, high-throughput bulk RNA sequencing (RNA-seq) was used to characterise differential gene expression in γδ T cells - a subgroup of T cells that bridge innate and adaptive immunity and have known anti-mycobacterial response mechanisms. γδ T cell subsets are classified based on expression of a pathogen-recognition receptor known as Workshop Cluster 1 (WC1) and we hypothesised that bTB disease may alter the phenotype and function of specific γδ T cell subsets. Peripheral blood was collected from naturally M. bovis-infected (positive for single intradermal comparative tuberculin test (SICTT) and IFN-γ ELISA) and age- and sex-matched, non-infected control Holstein-Friesian cattle. γδ T subsets were isolated using fluorescence activated cell sorting (n = 10-12 per group) and high-quality RNA extracted from each purified lymphocyte subset (WC1.1+, WC1.2+, WC1- and γδ-) was used to generate transcriptomes using bulk RNA-seq (n = 6 per group, representing a total of 48 RNA-seq libraries). Relatively low numbers of differentially expressed genes (DEGs) were observed between most cell subsets; however, 189 genes were significantly differentially expressed in the M. bovis-infected compared to the control groups for the WC1.1+ γδ T cell compartment (absolute log2 FC ≥ 1.5 and FDR P adj. ≤ 0.1). The majority of these DEGs (168) were significantly increased in expression in cells from the bTB+ cattle and included genes encoding transcription factors (TBX21 and EOMES), chemokine receptors (CCR5 and CCR7), granzymes (GZMA, GZMM, and GZMH) and multiple killer cell immunoglobulin-like receptor (KIR) proteins indicating cytotoxic functions. Biological pathway overrepresentation analysis revealed enrichment of genes with multiple immune functions including cell activation, proliferation, chemotaxis, and cytotoxicity of lymphocytes. In conclusion, γδ T cells have important inflammatory and regulatory functions in cattle, and we provide evidence for preferential differential activation of the WC1.1+ specific subset in cattle naturally infected with M. bovis.
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Affiliation(s)
- Sajad A. Bhat
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - Mahmoud Elnaggar
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - Thomas J. Hall
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Gillian P. McHugo
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Cian Reid
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - David E. MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Kieran G. Meade
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- UCD Institute of Food and Health, University College Dublin, Dublin, Ireland
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Correia CN, McHugo GP, Browne JA, McLoughlin KE, Nalpas NC, Magee DA, Whelan AO, Villarreal-Ramos B, Vordermeier HM, Gormley E, Gordon SV, MacHugh DE. High-resolution transcriptomics of bovine purified protein derivative-stimulated peripheral blood from cattle infected with Mycobacterium bovis across an experimental time course. Tuberculosis (Edinb) 2022; 136:102235. [DOI: 10.1016/j.tube.2022.102235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
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Hall TJ, Mullen MP, McHugo GP, Killick KE, Ring SC, Berry DP, Correia CN, Browne JA, Gordon SV, MacHugh DE. Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria. BMC Genomics 2021; 22:343. [PMID: 33980141 PMCID: PMC8117616 DOI: 10.1186/s12864-021-07643-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macrophage, previously shown to be substantially reprogrammed during intracellular infection by the pathogen. Here we use differential expression, and correlation- and interaction-based network approaches to analyse the host response to infection with M. bovis at the transcriptome level to identify core infection response pathways and gene modules. These outputs were then integrated with genome-wide association study (GWAS) data sets to enhance detection of genomic variants for susceptibility/resistance to M. bovis infection. Results The host gene expression data consisted of RNA-seq data from bovine alveolar macrophages (bAM) infected with M. bovis at 24 and 48 h post-infection (hpi) compared to non-infected control bAM. These RNA-seq data were analysed using three distinct computational pipelines to produce six separate gene sets: 1) DE genes filtered using stringent fold-change and P-value thresholds (DEG-24: 378 genes, DEG-48: 390 genes); 2) genes obtained from expression correlation networks (CON-24: 460 genes, CON-48: 416 genes); and 3) genes obtained from differential expression networks (DEN-24: 339 genes, DEN-48: 495 genes). These six gene sets were integrated with three bTB breed GWAS data sets by employing a new genomics data integration tool—gwinteR. Using GWAS summary statistics, this methodology enabled detection of 36, 102 and 921 prioritised SNPs for Charolais, Limousin and Holstein-Friesian, respectively. Conclusions The results from the three parallel analyses showed that the three computational approaches could identify genes significantly enriched for SNPs associated with susceptibility/resistance to M. bovis infection. Results indicate distinct and significant overlap in SNP discovery, demonstrating that network-based integration of biologically relevant transcriptomics data can leverage substantial additional information from GWAS data sets. These analyses also demonstrated significant differences among breeds, with the Holstein-Friesian breed GWAS proving most useful for prioritising SNPS through data integration. Because the functional genomics data were generated using bAM from this population, this suggests that the genomic architecture of bTB resilience traits may be more breed-specific than previously assumed. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07643-w.
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Affiliation(s)
- Thomas J Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Michael P Mullen
- Bioscience Research Institute, Athlone Institute of Technology, Dublin Road, Athlone, Westmeath, N37 HD68, Ireland
| | - Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Kate E Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,Present address: Genuity Science, Cherrywood Business Park. Loughlinstown, Dublin, D18 K7W4, Ireland
| | - Siobhán C Ring
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Cork, P72 X050, Ireland
| | - Donagh P Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
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6
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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McHugo GP, Browett S, Randhawa IAS, Howard DJ, Mullen MP, Richardson IW, Park SDE, Magee DA, Scraggs E, Dover MJ, Correia CN, Hanrahan JP, MacHugh DE. A Population Genomics Analysis of the Native Irish Galway Sheep Breed. Front Genet 2019; 10:927. [PMID: 31649720 PMCID: PMC6792165 DOI: 10.3389/fgene.2019.00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022] Open
Abstract
The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in production and health traits.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sam Browett
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Imtiaz A S Randhawa
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Dawn J Howard
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - Michael P Mullen
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | | | | | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Erik Scraggs
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - James P Hanrahan
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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