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Nisa FU, Naqvi RZ, Arshad F, Ilyas I, Asif M, Amin I, Mrode R, Mansoor S, Mukhtar Z. Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan. Biochem Genet 2024; 62:4137-4156. [PMID: 38664326 DOI: 10.1007/s10528-024-10809-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/08/2024] [Indexed: 09/28/2024]
Abstract
Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others.
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Affiliation(s)
- Fakhar Un Nisa
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Fazeela Arshad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Iram Ilyas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, UK
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan
- International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan.
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan.
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Ghafouri F, Dehghanian Reyhan V, Sadeghi M, Miraei-Ashtiani SR, Kastelic JP, Barkema HW, Shirali M. Integrated Analysis of Transcriptome Profiles and lncRNA-miRNA-mRNA Competing Endogenous RNA Regulatory Network to Identify Biological Functional Effects of Genes and Pathways Associated with Johne's Disease in Dairy Cattle. Noncoding RNA 2024; 10:38. [PMID: 39051372 PMCID: PMC11270299 DOI: 10.3390/ncrna10040038] [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: 04/12/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Paratuberculosis or Johne's disease (JD), a chronic granulomatous gastroenteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP), causes huge economic losses and reduces animal welfare in dairy cattle herds worldwide. At present, molecular mechanisms and biological functions involved in immune responses to MAP infection of dairy cattle are not clearly understood. Our purpose was to integrate transcriptomic profiles and competing endogenous RNA (ceRNA) network analyses to identify key messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of peripheral blood mononuclear cells (PBMCs) for MAP infection in dairy cattle. In total, 28 lncRNAs, 42 miRNAs, and 370 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In this regard, we identified 21 hub genes (CCL20, CCL5, CD40, CSF2, CXCL8, EIF2AK2, FOS, IL10, IL17A, IL1A, IL1B, IRF1, MX2, NFKB1, NFKBIA, PTGS2, SOCS3, TLR4, TNF, TNFAIP3, and VCAM1) involved in MAP infection. Furthermore, eight candidate subnets with eight lncRNAs, 29 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 510, 22, and 11 significantly enriched GO terms related to MAP infection in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways related to MAP infection that were enriched included the immune system process, defense response, response to cytokine, leukocyte migration, regulation of T cell activation, defense response to bacterium, NOD-like receptor, B cell receptor, TNF, NF-kappa B, IL-17, and T cell receptor signaling pathways. Contributions of transcriptome profiles from MAP-positive and MAP-negative sample groups plus a ceRNA regulatory network underlying phenotypic differences in the intensity of pathogenicity of JD provided novel insights into molecular mechanisms associated with immune system responses to MAP infection in dairy cattle.
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Affiliation(s)
- Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (F.G.); (V.D.R.); (S.R.M.-A.)
| | - Vahid Dehghanian Reyhan
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (F.G.); (V.D.R.); (S.R.M.-A.)
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (F.G.); (V.D.R.); (S.R.M.-A.)
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (F.G.); (V.D.R.); (S.R.M.-A.)
| | - John P. Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (J.P.K.); (H.W.B.)
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (J.P.K.); (H.W.B.)
| | - Masoud Shirali
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5AJ, UK
- Agri-Food and Biosciences Institute, Hillsborough BT26 6DR, UK
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Fong A, Rochus CM, Shandilya UK, Muniz MMM, Sharma A, Schenkel FS, Karrow NA, Baes CF. The role of interleukin-10 receptor alpha (IL10Rα) in Mycobacterium avium subsp. paratuberculosis infection of a mammary epithelial cell line. BMC Genom Data 2024; 25:58. [PMID: 38867147 PMCID: PMC11167801 DOI: 10.1186/s12863-024-01234-w] [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: 01/29/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Johne's disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne's disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne's disease in dairy cattle. Our objective was to determine how IL10Rα affects the pathogenesis of MAP by examining the effect of a live MAP challenge on a mammary epithelial cell line (MAC-T) that had IL10Rα knocked out using CRISPR/cas9. The wild type and the IL10Rα knockout MAC-T cell lines were exposed to live MAP bacteria for 72 h. Thereafter, mRNA was extracted from infected and uninfected cells. Differentially expressed genes were compared between the wild type and the IL10Rα knockout cell lines. Gene ontology was performed based on the differentially expressed genes to determine which biological pathways were involved. RESULTS Immune system processes pathways were targeted to determine the effect of IL10Rα on the response to MAP infection. There was a difference in immune response between the wild type and IL10Rα knockout MAC-T cell lines, and less difference in immune response between infected and not infected IL10Rα knockout MAC-T cells, indicating IL10Rα plays an important role in the progression of MAP infection. Additionally, these comparisons allowed us to identify other genes involved in inflammation-mediated chemokine and cytokine signalling, interleukin signalling and toll-like receptor pathways. CONCLUSIONS Identifying differentially expressed genes in wild type and ILR10α knockout MAC-T cells infected with live MAP bacteria provided further evidence that IL10Rα contributes to mounting an immune response to MAP infection and allowed us to identify additional potential candidate genes involved in this process. We found there was a complex immune response during MAP infection that is controlled by many genes.
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Affiliation(s)
- Aisha Fong
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christina M Rochus
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Umesh K Shandilya
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Maria M M Muniz
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ankita Sharma
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christine F Baes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3002, Switzerland.
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Criado M, Silva M, Mendívil P, Molina E, Pérez V, Benavides J, Elguezabal N, Gutiérrez-Expósito D. No Evidence of Neutrophil Response Modulation in Goats after Immunization against Paratuberculosis with a Heat-Inactivated Vaccine. Animals (Basel) 2024; 14:1694. [PMID: 38891741 PMCID: PMC11171245 DOI: 10.3390/ani14111694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Neutrophils are believed to play a role in the initial stages of paratuberculosis, and it has recently been demonstrated that vaccination can modulate their function via priming or through epigenetic and metabolic reprogramming (training). Modulation of the neutrophil response against Mycobacterium avium subspecies paratuberculosis (Map) through vaccination has been demonstrated in a rabbit model but not in ruminants. Therefore, in the present work, the effect of vaccination on the response of caprine neutrophils against Map was studied. Neutrophils were isolated from non-vaccinated (n = 7) and Gudair®-vaccinated goat kids (n = 7), before vaccination and 30 days post-vaccination. Then, several neutrophil functions were quantified ex vivo: cell-free and anchored neutrophil extracellular trap (NET) release, phagocytosis, and the differential expression of several cytokines and TLR2. The induction of cell-free NETosis and TLR2 expression by Map is reported for the first time. However, vaccination showed no significant effect on any of the functions studied. This suggests that the protection conferred by Gudair® vaccination is based on mechanisms that are independent of the neutrophil function modulation. Further research into the impact of alternative vaccination strategies or the paratuberculosis infection stage on ruminant neutrophil function could provide valuable insights into its role in paratuberculosis.
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Affiliation(s)
- Miguel Criado
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Marta Silva
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Pedro Mendívil
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Elena Molina
- Departamento de Sanidad Animal, NEIKER-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 48160 Derio, Spain; (E.M.); (N.E.)
| | - Valentín Pérez
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Julio Benavides
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
| | - Natalia Elguezabal
- Departamento de Sanidad Animal, NEIKER-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 48160 Derio, Spain; (E.M.); (N.E.)
| | - Daniel Gutiérrez-Expósito
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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Kaur R, Ahlawat S, Choudhary V, Kumari A, Kumar A, Kaur M, Arora R, Sharma R, Vijh RK. Expression profiling of cytokine genes in peripheral blood mononuclear cells from Anaplasma marginale infected and healthy cattle. Anim Biotechnol 2023; 34:4281-4290. [PMID: 36409691 DOI: 10.1080/10495398.2022.2146589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this study, changes in expression profiles of genes encoding 14 cytokines (IL1A, IL1B, IL2, IL4, IL6, IL8, IL10, IL12A, IL12B, IL16, IFNA, IFNB, TGFB1, and TNFA) were investigated amongst six Anaplasma marginale infected and six healthy crossbred cattle. Health status of the animals was determined based on clinical signs, blood smear examination and molecular detection using A. marginale-specific primers. Total RNA was isolated from the peripheral blood mononuclear cells of the infected animals as well as the healthy controls, which was further reverse transcribed to cDNA. Primers for real time PCR were designed using Primer3 software and the results were analyzed by the 2-ΔΔCt method with RPS15 and GAPDH as the reference genes. The expression levels of IL1A, IL1B, IL6, IL10, IL12A, IL12B, and TNFA varied significantly between the two groups, with higher expression in the infected cattle. The transcript abundance of IL4, IL16, and TGFB1 did not vary between the diseased and healthy animals. The expression of IL2 and IL8 was higher in the healthy animals, but the results were non-significant. Taken together, this study provides evidence for difference in expression of cytokine genes in response to anaplasmosis in crossbred cattle.
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Affiliation(s)
- Rashmeet Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Vikas Choudhary
- Department of Animal Husbandry and Dairying, District Disease Diagnostic Laboratory, Karnal, India
| | - Anisha Kumari
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Triantaphyllopoulos KA. Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review. Int J Mol Sci 2023; 24:13566. [PMID: 37686376 PMCID: PMC10487966 DOI: 10.3390/ijms241713566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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Magro S, Costa A, Santinello M, Penasa M, De Marchi M. Udder health-related traits in cow milk: phenotypic variability and effect on milk yield and composition. Animal 2023; 17:100823. [PMID: 37196579 DOI: 10.1016/j.animal.2023.100823] [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: 10/25/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/19/2023] Open
Abstract
The milk differential somatic cell count (DSCC) has been proposed in recent years as a mean by which to better monitor the udder health status (UHS) in dairy cows. Milk DSCC is the amount of polymorphonuclear neutrophils and lymphocytes contributing to the total somatic cell count (SCC) and can be determined on a routine basis in individual milk samples subjected to official analysis. In the present study, 522 865 milk test-day records of 77 143 cows were scrutinised to identify factors affecting the variability of both DSCC and SCC in Holstein Friesian, Jersey, Simmental and Rendena cows through linear mixed models. The fixed effects were breed, parity, lactation stage, sampling season, and all the first-order interactions of breed. Cow and herd-test-date were considered as random. Subsequently, four UHS groups were created (1: SCC ≤ 200 000 cells/mL and DSCC ≤ 65%; 2: SCC ≤ 200 000 cells/mL and DSCC > 65%; 3: SCC > 200 000 cells/mL and DSCC > 65%; 4: SCC > 200 000 cells/mL and DSCC ≤ 65%) to compare milk yield and quality. Milk SCS and DSCC differed across lactation, parity, sampling season and breed. In particular, Simmental cows had the lowest SCC and Jersey the lowest DSCC. Depending on the breed, UHS affected daily milk yield and composition to a different extent. The UHS group 4, i.e. the one grouping test-day records with high SCC and low DSCC, presented the lowest estimate of milk yield and lactose content no matter the breeds. Our findings support that udder health-related traits (SCS and DSCC) are useful information to improve udder health at individual cow and herd levels. Moreover, the combination of SCS and DSCC is useful to monitor milk yield and composition.
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Affiliation(s)
- S Magro
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35030 Legnaro, Italy
| | - A Costa
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Ozzano dell'Emilia, Italy.
| | - M Santinello
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35030 Legnaro, Italy
| | - M Penasa
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35030 Legnaro, Italy
| | - M De Marchi
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, 35030 Legnaro, Italy
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Magro S, Costa A, De Marchi M. Total and Differential Somatic Cell Count in Italian Local Cattle Breeds: Phenotypic Variability and Effect on Milk Yield and Composition. Animals (Basel) 2023; 13:ani13071249. [PMID: 37048505 PMCID: PMC10093597 DOI: 10.3390/ani13071249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/24/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Milk differential somatic cell count (DSCC) represents the percentage of polymorphonuclear neutrophils and lymphocytes out of the total somatic cell count (SCC) and has been proposed in recent years as a proxy for udder health in dairy cows. We investigated phenotypic factors affecting SCC and DSCC using 3978 records of 212 Alpine Grey and 426 Burlina cows farmed in Northern Italy. The linear mixed model accounted for the fixed effects of breed, parity, lactation stage, sampling season, and first-order interactions of breed with the other effects. Cow, herd-test-date nested within breed were random. Subsequently, four udder health status groups (UHS) were created by combining SCC and DSCC to assess the UHS impact on milk yield and quality. DSCC was greater in Alpine Grey (66.2 ± 0.8%) than Burlina cows (63.2 ± 0.6%) and, similarly to SCC, it increased with days in milk and parity regardless of breed. Milk yield and composition were affected by UHS in both breeds. These results suggest that also udder health of local breeds can be monitored on a large scale through SCC and DSCC for reduction in biodiversity loss and increased farm profitability. However, in addition to milk data, the introduction of mastitis recording and monitoring plans is advisable.
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Affiliation(s)
- Silvia Magro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Padova, Italy
| | - Angela Costa
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, 40064 Bologna, Italy
| | - Massimo De Marchi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Padova, Italy
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9
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Byrne A, Ollier S, Tahlan K, Biet F, Bissonnette N. Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events. Front Genet 2023; 14:1043598. [PMID: 36816022 PMCID: PMC9934062 DOI: 10.3389/fgene.2023.1043598] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen responsible for paratuberculosis or Johne's Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an important transmission route. In the current study, we characterized MAP isolates from 67 cows identified in 20 herds from the provinces of Quebec and Ontario, Canada. Whole genome sequencing (WGS) was performed and an average genome coverage (relative to K-10) of ∼14.9 fold was achieved. The total number of SNPs present in each isolate varied from 51 to 132 and differed significantly between herds. Isolates with the highest genetic variability were generally present in herds from Quebec. The isolates were broadly separated into two main clades and this distinction was not influenced by the province from which they originated. Analysis of 8 MIRU-VNTR loci and 11 SSR loci was performed on the 67 isolates from the 20 dairy herds and publicly available references, notably major genetic lineages and six isolates from the province of Newfoundland and Labrador. All 67 field isolates were phylogenetically classified as Type II (C-type) and according to MIRU-VNTR, the predominant type was INMV 2 (76.1%) among four distinct patterns. Multilocus SSR typing identified 49 distinct INMV SSR patterns. The discriminatory index of the multilocus SSR typing was 0.9846, which was much higher than MIRU-VNTR typing (0.3740). Although multilocus SSR analysis provides good discriminatory power, the resolution was not informative enough to determine inter-herd transmission. In select cases, SNP-based analysis was the only approach able to document disease transmission between herds, further validated by animal movement data. The presence of SNPs in several virulence genes, notably for PE, PPE, mce and mmpL, is expected to explain differential antigenic or pathogenetic host responses. SNP-based studies will provide insight into how MAP genetic variation may impact host-pathogen interactions. Our study highlights the informative power of WGS which is now recommended for epidemiological studies and to document mixed genotypes infections.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada,*Correspondence: Nathalie Bissonnette,
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10
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Hu W, Koch BEV, Lamers GEM, Forn-Cuní G, Spaink HP. Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria. Front Immunol 2023; 13:1075473. [PMID: 36741407 PMCID: PMC9890051 DOI: 10.3389/fimmu.2022.1075473] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/22/2022] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases.
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11
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Gupta SK, Wilson T, Maclean PH, Rehm BHA, Heiser A, Buddle BM, Wedlock DN. Mycobacterium avium subsp. paratuberculosis antigens induce cellular immune responses in cattle without causing reactivity to tuberculin in the tuberculosis skin test. Front Immunol 2023; 13:1087015. [PMID: 36741398 PMCID: PMC9889921 DOI: 10.3389/fimmu.2022.1087015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) causes chronic progressive granulomatous enteritis leading to diarrhea, weight-loss, and eventual death in ruminants. Commercially available vaccine provides only partial protection against MAP infection and can interfere with the use of current diagnostic tests for bovine tuberculosis in cattle. Here, we characterized immune responses in calves to vaccines containing four truncated MAP antigens as a fusion (Ag85A202-347-SOD1-72-Ag85B173-330-74F1-148+669-786), either displayed on protein particles, or expressed as a soluble recombinant MAP (rMAP) fusion protein as well as to commercially available Silirum® vaccine. The rMAP fusion protein elicited the strongest antigen-specific antibody responses to both PPDA and recombinant antigen and strong and long-lasting T-cell immune responses to these antigens, as indicated by increased production of IFN-γ and IL-17A in antigen-stimulated whole blood cultures. The MAP fusion protein particle vaccine induced minimal antibody responses and weak IFN-γ responses but stimulated IL-17A responses to recombinant antigen. The immune response profile of Silirum® vaccine was characterized by weak antibodies and strong IFN-γ and IL-17A responses to PPDA. Transcription analysis on antigen-stimulated leukocytes from cattle vaccinated with rMAP fusion protein showed differential expression of several immune response genes and genes involved in costimulatory signaling, TLR4, TLR2, PTX3, PTGS2, PD-L1, IL1B, IL2, IL6, IL12B, IL17A, IL22, IFNG, CD40, and CD86. Moreover, the expression of several genes of immune pathways correlated with cellular immune responses in the rMAP fusion protein vaccinated group. These genes have key roles in pathways of mycobacterial immunity, including autophagy, manipulation of macrophage-mediated killing, Th17- and regulatory T cells- (Treg) mediated responses. Calves vaccinated with either the rMAP fusion protein or MAP fusion protein particle vaccine did not induce reactivity to PPDA and PPDB in a comparative cervical skin test, whereas Silirum® induced reactivity to these tuberculins in most of the vaccinated animals. Overall, our results suggest that a combination of recombinant MAP antigens in the form of a soluble fusion protein vaccine are capable of inducing strong antigen-specific humoral and a balanced Th1/Th17-cell immune response. These findings, together with the absence of reactivity to tuberculin, suggest this subunit vaccine could provide protective immunity against intracellular MAP infection in cattle without compromising the use of current bovine tuberculosis surveillance test.
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Affiliation(s)
- Sandeep K. Gupta
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand,*Correspondence: Sandeep K. Gupta,
| | - Tania Wilson
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | | | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia,Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast, QLD, Australia
| | - Axel Heiser
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Bryce M. Buddle
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - D. Neil Wedlock
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
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12
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Badia-Bringué G, Canive M, Alonso-Hearn M. Control of Mycobacterium avium subsp. paratuberculosis load within infected bovine monocyte-derived macrophages is associated with host genetics. Front Immunol 2023; 14:1042638. [PMID: 36911672 PMCID: PMC9992791 DOI: 10.3389/fimmu.2023.1042638] [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: 09/12/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The genetic loci influencing individual resistance to Mycobacterium avium subsp. paratuberculosis (MAP) infection are still largely unknown. In the current study, we searched for genetic loci associated with resistance to MAP infection by evaluating the performance of monocyte-derived macrophages (MDMs) isolated from the peripheral blood of 75 healthy Holsteins cows and infected ex vivo with MAP. Bacterial load (log colony-forming units, log CFUs) within MDMs was quantified at 2 h and 7 days p. i. using a BACTEC MGIT 960 instrument. In addition, the expression levels of some genes with important roles in the innate immune response including epiregulin (EREG), complement component C3 (C3), galectin-9 (Gal9), and nitric oxide (NO-) were measured in the supernatant of the infected cells. DNA from peripheral blood samples of the animals included in the study was isolated and genotyped with the EuroG MD bead Chip (44,779 single nucleotide-polymorphisms, SNPs). Linear mixed models were used to calculate the heritability (h2 ) estimates for each indicator of MDM performance, MAP load within MDMs and EREG, C3, Gal9, and NO-expression. After performing a genome-wide association study, the only phenotypes that showed SNPs with a significant association were the bacterial load within MDMs at 2 h (h2 = 0. 87) and 7 days (h2 = 0.83) p.i. A total of 6 SNPs, 5 candidate genes, and one microRNA on the Bos taurus chromosomes BTA2, BTA17, BTA18, and BTA21 were associated with MAP load at 2 h p.i. Overlap was seen in two SNPs associated with the log CFUs at 2 h and 7 d p.i. The identified SNPs had negative regression coefficients, and were, therefore, associated with a low bacterial load within MDMs. Some of the identified SNPs were located within QTLs previously associated with longevity, reproductive, and udder health traits. Some of the identified candidate genes; Oxysterol Binding Protein Like 6, Cysteine and Serine Rich Nuclear Protein 3, and the Coiled-Coil Domain Containing 92 regulate cellular cholesterol trafficking and efflux, apoptosis, and interferon production, respectively. Taken together, our results define a heritable and distinct immunogenetic profile in MAP-infected macrophages designed to limit bacterial load early after infection.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - María Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
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13
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Wherry TLT, Dassanayake RP, Bannantine JP, Mooyottu S, Stabel JR. Vitamin D3 alters macrophage phenotype and endosomal trafficking markers in dairy cattle naturally infected with Mycobacterium avium subsp. paratuberculosis. Front Cell Infect Microbiol 2022; 12:1021657. [PMID: 36275033 PMCID: PMC9579537 DOI: 10.3389/fcimb.2022.1021657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Macrophages are important host defense cells in ruminant paratuberculosis (Johne’s Disease; JD), a chronic enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP). Classical macrophage functions of pathogen trafficking, degradation, and antigen presentation are interrupted in mycobacterial infection. Immunologic stimulation by 25-hydroxyvitamin D3 (25(OH)D3) and 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) enhances bovine macrophage function. The present study aimed to investigate the role of vitamin D3 on macrophage phenotype and endosomal trafficking of MAP in monocyte-derived macrophages (MDMs) cultured from JD-, JD+ subclinical, and JD+ clinically infected cattle. MDMs were pre-treated 100 ng/ml 25(OH)D3 or 4 ng/ml 1,25(OH)2D3 and incubated 24 hrs with MAP at 10:1 multiplicity of infection (MOI). In vitro MAP infection upregulated pro-inflammatory (M1) CD80 and downregulated resolution/repair (M2) CD163. Vitamin D3 generally decreased CD80 and increased CD163 expression. Furthermore, early endosomal marker Rab5 was upregulated 140× across all stages of paratuberculosis infection following in vitro MAP infection; however, Rab5 was reduced in MAP-activated MDMs from JD+ subclinical and JD+ clinical cows compared to healthy controls. Rab7 expression decreased in control and clinical cows following MDM infection with MAP. Both forms of vitamin D3 reduced Rab5 expression in infected MDMs from JD- control cows, while 1,25(OH)2D3 decreased Rab7 expression in JD- and JD+ subclinical animals regardless of MAP infection in vitro. Vitamin D3 promoted phagocytosis in MDMs from JD- and JD+ clinical cows treated with either vitamin D3 analog. Results from this study show exogenous vitamin D3 influences macrophage M1/M2 polarization and Rab GTPase expression within MDM culture.
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Affiliation(s)
- Taylor L. T. Wherry
- Infectious Bacterial Diseases, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, IA, United States
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Rohana P. Dassanayake
- Ruminant Diseases and Immunology, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, IA, United States
| | - John P. Bannantine
- Infectious Bacterial Diseases, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, IA, United States
| | - Shankumar Mooyottu
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Judith R. Stabel
- Infectious Bacterial Diseases, National Animal Disease Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, IA, United States
- *Correspondence: Judith R. Stabel,
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14
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Taylor EN, Beckmann M, Hewinson G, Rooke D, Sinclair LA, Mur LAJ. Metabolomic changes in lactating multiparous naturally MAP-infected Holstein-Friesian dairy cows suggest changes in mitochondrial energy pathways. Res Vet Sci 2022; 152:354-363. [PMID: 36108548 DOI: 10.1016/j.rvsc.2022.09.001] [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: 01/05/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 12/01/2022]
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative organism of Johne's Disease, a chronic intestinal infection of ruminants. Infected cows begin shedding MAP within the asymptomatic, subclinical stage of infection before clinical signs, such as weight loss, diarrhoea and reduced milk yields develop within the clinical stages of disease. Herein, we examine the milk metabolomic profiles of naturally MAP-infected Holstein-Friesian cows. The study used biobanked milk samples which were collected 73.4 ± 3.79 (early lactation) and 143 ± 3.79 (mean ± SE) (mid-lactation) days post-calving from 5 MAP-infected and 5 control multiparous cows. The milk metabolome was assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) for sensitive, non-targeted metabolite fingerprinting. Metabolite fingerprinting assessments using partial least squares discriminate analyses (PLS-DA) indicated that lactation stage was a larger source of variation than MAP status. Examining each lactation stage separately for changes associated to MAP-infection status identified 45 metabolites, 33 in early lactation and 12 in mid-lactation, but only 6 metabolites were targeted in both stages of lactation. Pathway enrichment analysis suggested that MAP affected the malate-aspartate shuffle during early lactation. Pearson's correlation analysis indicated relationships between milk lactose concentrations in mid-lactation and 6 metabolites that were tentatively linked to MAP-infection status. The targeted metabolites were suggestive of wider changes in the bioenergetic metabolism that appear to be an acceleration of the effects of progressing lactation in healthy cows. Additionally, milk lactose concentrations suggest that MAP reduces the availability of lactose derivatives.
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Affiliation(s)
| | | | - G Hewinson
- Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Ceredigion, UK
| | - D Rooke
- ProTEM Services Ltd, West Sussex, UK
| | - L A Sinclair
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, UK
| | - L A J Mur
- Aberystwyth University, Ceredigion, UK.
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15
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Taylor EN, Beckmann M, Hewinson G, Rooke D, Mur LAJ, Koets AP. Metabolomic changes in polyunsaturated fatty acids and eicosanoids as diagnostic biomarkers in Mycobacterium avium ssp. paratuberculosis (MAP)-inoculated Holstein-Friesian heifers. Vet Res 2022; 53:68. [PMID: 36056402 PMCID: PMC9440510 DOI: 10.1186/s13567-022-01087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/03/2022] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative organism of Johne's disease, a chronic granulomatous enteritis of ruminants. We have previously used naturally MAP-infected heifer calves to document metabolomic changes occurring in MAP infections. Herein, we used experimentally MAP-inoculated heifer calves to identify biomarkers for MAP infections. At 2-weeks of age, 20 Holstein-Friesian (HF) calves were experimentally inoculated with MAP. These calves, along with 20 control calves, were sampled biweekly up to 13-months of age and then monthly up to 19-months of age. Sera were assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer for high throughput, sensitive, non-targeted metabolite fingerprinting. Partial least squares-discriminate analysis (PLS-DA) and hierarchical cluster analysis (HCA) discriminated between MAP-inoculated and control heifer calves. Out of 34 identified metabolites, six fatty acyls were able to differentiate between experimental groups throughout the study, including 8, 11, 14-eicosatrienoic acid and cis-8, 11, 14, 17-eicosatetraenoic acid which were also detected in our previous study and so further suggested their value as biomarkers for MAP infection. Pathway analysis highlighted the role of the alpha-linoleic acid and linoleic acid metabolism. Within these pathways, two broad types of response, with a rapid increase in some saturated fatty acids and some n-3 polyunsaturated fatty acids (PUFAs) and later n-6 PUFAs, became predominant. This could indicate an initial anti-inflammatory colonisation phase, followed by an inflammatory phase. This study demonstrates the validity of the metabolomic approach in studying MAP infections. Nevertheless, further work is required to define further key events, particularly at a cell-specific level.
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Affiliation(s)
- Emma N Taylor
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Ceredigion, SY23 3DA, UK
| | - Manfred Beckmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Ceredigion, SY23 3DA, UK
| | - Glyn Hewinson
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Ceredigion, SY23 3DA, UK.,Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Ceredigion, SY23 3DA, UK
| | - David Rooke
- ProTEM Services Ltd, Horsham, RH12 4BD, West Sussex, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Ceredigion, SY23 3DA, UK.
| | - Ad P Koets
- Wageningen Bioveterinary Research, 8221 RA, Lelystad, The Netherlands. .,Faculty of Veterinary Medicine, Population Health Systems, Utrecht University, 3584 CS, Utrecht, The Netherlands.
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16
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Agulló-Ros I, Andrada M, Pérez-Sancho M, Roy Á, Bezos J, Bonnet T, Moreno I, Paz-Sánchez Y, Domínguez M, Gómez-Villamandos JC, Domínguez L, Risalde MA. Effect of heat-inactivated Mycobacterium avium subspecies paratuberculosis (MAP) vaccine on the lesions and immunopathology developed in target tissues of naturally MAP-infected goats. Vet Microbiol 2022; 273:109543. [PMID: 36037619 DOI: 10.1016/j.vetmic.2022.109543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022]
Abstract
Paratuberculosis (PTB) is a disease caused by Mycobacterium avium subspecies paratuberculosis (MAP), which affects a broad range of hosts, including domestic and wild animals. PTB is a chronic granulomatous enteritis and lymphadenitis that compromises animal welfare and causes economic losses. The objective of this study was to evaluate the effect of a commercial heat-inactivated MAP vaccine on lesions and immunopathology developed in the target tissues of goats naturally infected with MAP. Lesions compatible with PTB in the intestine and regional lymph nodes (LNs), as well as local immune response to MAP, were evaluated and compared in Gudair®-vaccinated (n = 14) and unvaccinated (n = 11) goats from a MAP-infected farm. The percentage of animals with multifocal granulomatous lesions in the jejunal (p = 0.05) and ileocecal (p = 0.02) LNs was higher in unvaccinated animals, while a lesion score reduction of 50% was found in the LNs of vaccinated animals. Unvaccinated animals showed increased numbers and wider distribution of macrophages (MΦs, CD68 +) in histiocytic infiltrate (p = 0.0003), associated with increased numbers of mycobacteria. Increased inducible nitric oxide synthase (iNOS) expression was also reported in these animals, while M2 MΦs (CD163 +) were scarce in both groups. Vaccinated animals showed an increase in CD3 + lymphocytes, although differences in interferon gamma (IFNγ) were negligible. These results support the hypothesis that heat-inactivated MAP vaccination could reduce the severity of PTB lesions and mycobacterial load in target tissues in vaccinated adult goats.
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Affiliation(s)
- Irene Agulló-Ros
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación GISAZ, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad animal, 14014 Córdoba, Spain
| | - Marisa Andrada
- Veterinary Histology and Pathology, Institute of Animal Health and Food Safety (IUSA), Veterinary School, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain; Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Álvaro Roy
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Javier Bezos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain; Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Thomas Bonnet
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación GISAZ, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad animal, 14014 Córdoba, Spain
| | - Inmaculada Moreno
- Servicio de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Investigación Carlos III, Majadahonda, Madrid, Spain
| | - Yania Paz-Sánchez
- Veterinary Histology and Pathology, Institute of Animal Health and Food Safety (IUSA), Veterinary School, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Mercedes Domínguez
- Servicio de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Investigación Carlos III, Majadahonda, Madrid, Spain
| | - José C Gómez-Villamandos
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación GISAZ, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad animal, 14014 Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain; Dpto. de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - María A Risalde
- Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación GISAZ, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Campus de Rabanales, Edificio Sanidad animal, 14014 Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain
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17
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Heidari M, Pakdel A, Bakhtiarizadeh MR, Dehghanian F. A framework for non-preserved consensus gene module detection in Johne's disease. Front Vet Sci 2022; 9:974444. [PMID: 35968017 PMCID: PMC9363878 DOI: 10.3389/fvets.2022.974444] [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: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022] Open
Abstract
Johne's disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) is a major concern in dairy industry. Since, the pathogenesis of the disease is not clearly known, it is necessary to develop an approach to discover molecular mechanisms behind this disease with high confidence. Biological studies often suffer from issues with reproducibility. Lack of a method to find stable modules in co-expression networks from different datasets related to Johne's disease motivated us to present a computational pipeline to identify non-preserved consensus modules. Two RNA-Seq datasets related to MAP infection were analyzed, and consensus modules were detected and were subjected to the preservation analysis. The non-preserved consensus modules in both datasets were determined as they are modules whose connectivity and density are affected by the disease. Long non-coding RNAs (lncRNAs) and TF genes in the non-preserved consensus modules were identified to construct integrated networks of lncRNA-mRNA-TF. These networks were confirmed by protein-protein interactions (PPIs) networks. Also, the overlapped hub genes between two datasets were considered hub genes of the consensus modules. Out of 66 consensus modules, 21 modules were non-preserved consensus modules, which were common in both datasets and 619 hub genes were members of these modules. Moreover, 34 lncRNA and 152 TF genes were identified in 12 and 19 non-preserved consensus modules, respectively. The predicted PPIs in 17 non-preserved consensus modules were significant, and 283 hub genes were commonly identified in both co-expression and PPIs networks. Functional enrichment analysis revealed that eight out of 21 modules were significantly enriched for biological processes associated with Johne's disease including “inflammatory response,” “interleukin-1-mediated signaling pathway”, “type I interferon signaling pathway,” “cytokine-mediated signaling pathway,” “regulation of interferon-beta production,” and “response to interferon-gamma.” Moreover, some genes (hub mRNA, TF, and lncRNA) were introduced as potential candidates for Johne's disease pathogenesis such as TLR2, NFKB1, IRF1, ATF3, TREM1, CDH26, HMGB1, STAT1, ISG15, CASP3. This study expanded our knowledge of molecular mechanisms involved in Johne's disease, and the presented pipeline enabled us to achieve more valid results.
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Affiliation(s)
- Maryam Heidari
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
- *Correspondence: Abbas Pakdel
| | - Mohammad Reza Bakhtiarizadeh
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
- Mohammad Reza Bakhtiarizadeh
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18
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Mycobacterium intracellulare induces a Th17 immune response via M1-like macrophage polarization in canine peripheral blood mononuclear cells. Sci Rep 2022; 12:11818. [PMID: 35821058 PMCID: PMC9276657 DOI: 10.1038/s41598-022-16117-2] [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: 10/25/2021] [Accepted: 07/05/2022] [Indexed: 11/11/2022] Open
Abstract
Mycobacterium avium-intracellulare complex (MAC) is one of the most prevalent pathogenic nontuberculous mycobacteria that cause chronic pulmonary disease. The prevalence of MAC infection has been rising globally in a wide range of hosts, including companion animals. MAC infection has been reported in dogs; however, little is known about interaction between MAC and dogs, especially in immune response. In this study, we investigated the host immune response driven by M. intracellulare using the co-culture system of canine T helper cells and autologous monocyte-derived macrophages (MDMs). Transcriptomic analysis revealed that canine MDMs differentiated into M1-like macrophages after M. intracellulare infection and the macrophages secreted molecules that induced Th1/Th17 cell polarization. Furthermore, canine lymphocytes co-cultured with M. intracellulare-infected macrophages induced the adaptive Th17 responses after 5 days. Taken together, our results indicate that M. intracellulare elicits a Th17 response through macrophage activation in this system. Those findings might help the understanding of the canine immune response to MAC infection and diminishing the potential zoonotic risk in One Health aspect.
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19
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Wright K, Mizzi R, Plain KM, Purdie AC, de Silva K. Mycobacterium avium subsp. paratuberculosis exploits miRNA expression to modulate lipid metabolism and macrophage polarisation pathways during infection. Sci Rep 2022; 12:9681. [PMID: 35690602 PMCID: PMC9188571 DOI: 10.1038/s41598-022-13503-8] [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: 01/25/2022] [Accepted: 05/25/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogenic mycobacteria including Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease, manipulate host macrophages to persist and cause disease. In mycobacterial infection, highly plastic macrophages, shift between inflammatory M1 and permissive M2 phenotypes which alter the disease outcome and allow bacteria to survive intracellularly. Here we examine the impact of MAP infection on polarised macrophages and how increased lipid availability alters macrophage phenotype and bacterial persistence. Further, we assess if host microRNA (miRNA) are sensitive to macrophage polarisation state and how MAP can drive their expression to overcome innate responses. Using in vitro MAP infection, we find that increasing lipid availability through supplementing culture media with exogenous lipid increases cellular nitric oxide production. Lipid-associated miRs -19a, -129, -24, and -24-3p are differentially expressed following macrophage polarisation and lipid supplementation and are further regulated during MAP infection. Collectively, our results highlight the importance of host lipid metabolism in MAP infection and demonstrate control of miRNA expression by MAP to favour intracellular persistence.
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Affiliation(s)
- Kathryn Wright
- Sydney School of Veterinary Science, The University of Sydney, Faculty of Science, Sydney, NSW, Australia
| | - Rachel Mizzi
- Sydney School of Veterinary Science, The University of Sydney, Faculty of Science, Sydney, NSW, Australia
| | - Karren M Plain
- Sydney School of Veterinary Science, The University of Sydney, Faculty of Science, Sydney, NSW, Australia
| | - Auriol C Purdie
- Sydney School of Veterinary Science, The University of Sydney, Faculty of Science, Sydney, NSW, Australia
| | - Kumudika de Silva
- Sydney School of Veterinary Science, The University of Sydney, Faculty of Science, Sydney, NSW, Australia.
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20
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Louis TJ, Qasem A, Naser SA. Attenuation of Excess TNF-α Release in Crohn’s Disease by Silencing of iRHOMs 1/2 and the Restoration of TGF-β Mediated Immunosuppression Through Modulation of TACE Trafficking. Front Immunol 2022; 13:887830. [PMID: 35585977 PMCID: PMC9108260 DOI: 10.3389/fimmu.2022.887830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
TNFα converting enzyme (TACE) is a transmembrane metalloprotease that sheds an assortment of signaling receptors, cytokines, growth factors, and pro-inflammatory mediators. In Crohn’s disease (CD), TACE activity is upregulated, resulting in a marked increase of TNFα secretion and inflammation. Although treatment of CD with TNFα monoclonal antibodies is beneficial, many patients are at risk for acquiring opportunistic infections, and the treatment efficacy of TNFα monoclonal antibodies typically decreases over time. This study investigated an alternative approach for mitigating TNFα release by knocking down TACE membrane translocation in macrophages via inhibitory rhomboid proteins 1 and 2 (iRHOMs 1/2) siRNA treatment. First we measured TGFβRII shedding in ex vivo plasma samples collected from CD patients and healthy control subjects (N=40 per group). Then, we measured TGFβRII shedding and the expression and production of TGFβ ligand, TNFα, IL-6, IL-1β, IL-10, and total versus membranous TACE in vitro with THP-1 derived macrophage infected with Mycobacterium avium subspecies paratuberculosis (MAP), a highly studied CD-related pathogen. We determined that TGFβRII shedding was significantly higher in CD patients compared to healthy controls [515.52 ± 54.23 pg/mL vs 310.81 ± 43.16 pg/mL, respectively], and MAP-infected CD plasma samples had significantly more TGFβRII shedding (601.83 ± 49.56 pg/mL) than MAP-negative CD samples (430.37 ± 45.73 pg/mL). Moreover, we also determined that TACE production; TGFβ ligand expression and production; and TGFβRII shedding were also higher in MAP-infected THP-1 macrophages. Nevertheless, once we transfected the MAP infected macrophages with iRHOM siRNA, TACE production and membrane localization were significantly decreased, resulting in a significant decrease in TGFβRII shedding; an increase in Smad3 phosphorylation; a decrease in the expression and production of pro-inflammatory cytokines; and a decrease in the expression and production of stricture-associated factor, plasminogen activator inhibitor-1 (PAI-1). Our data clearly demonstrates that the regression of TACE trafficking, via iRHOM 1/2 silencing, significantly reduces the release of TNFα and restores the immunosuppressive capabilities of TGFβ signaling, which ultimately reverses inflammatory tissue damage. Accordingly, this study may provide a framework for the creation of newer, safer therapeutic options designed to treat inflammatory autoimmune diseases such as CD and rheumatoid arthritis.
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21
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RNA Microarray-Based Comparison of Innate Immune Phenotypes between Human THP-1 Macrophages Stimulated with Two BCG Strains. Int J Mol Sci 2022; 23:ijms23094525. [PMID: 35562916 PMCID: PMC9103163 DOI: 10.3390/ijms23094525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 12/10/2022] Open
Abstract
Currently, the only available vaccine against tuberculosis is Mycobacterium bovis Bacille Calmette-Guérin (BCG). Pulmonary tuberculosis protection provided by the vaccine varies depending on the strain, the patient’s age and the evaluated population. Although the adaptive immune responses induced by different BCG strains have been widely studied, little conclusive data is available regarding innate immune responses, especially in macrophages. Here, we aimed to characterize the innate immune responses of human THP-1-derived macrophages at the transcriptional level following a challenge with either the BCG Mexico (M.BCG) or Phipps (P.BCG) strains. After a brief in vitro characterization of the bacterial strains and the innate immune responses, including nitric oxide production and cytokine profiles, we analyzed the mRNA expression patterns and performed pathway enrichment analysis using RNA microarrays. Our results showed that multiple biological processes were enriched, especially those associated with innate inflammatory and antimicrobial responses, including tumor necrosis factor (TNF)-α, type I interferon (IFN-I) and IFN-γ. However, four DEGs were identified in macrophages infected with M.BCG compared to P. BCG. These findings indicated the proinflammatory stimulation of macrophages induced by both BCG strains, at the cytokine level and in terms of gene expression, suggesting a differential expression pattern of innate immune transcripts depending on the mycobacterial strain.
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22
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Ibeagha-Awemu EM, Bissonnette N, Do DN, Dudemaine PL, Wang M, Facciuolo A, Griebel P. Regionally Distinct Immune and Metabolic Transcriptional Responses in the Bovine Small Intestine and Draining Lymph Nodes During a Subclinical Mycobacterium avium subsp. paratuberculosis Infection. Front Immunol 2022; 12:760931. [PMID: 34975852 PMCID: PMC8714790 DOI: 10.3389/fimmu.2021.760931] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative infectious agent of Johne’s disease (JD), an incurable granulomatous enteritis affecting domestic livestock and other ruminants around the world. Chronic MAP infections usually begin in calves with MAP uptake by Peyer’s patches (PP) located in the jejunum (JE) and ileum (IL). Determining host responses at these intestinal sites can provide a more complete understanding of how MAP manipulates the local microenvironment to support its long-term survival. We selected naturally infected (MAPinf, n=4) and naive (MAPneg, n=3) cows and transcriptionally profiled the JE and IL regions of the small intestine and draining mesenteric lymph nodes (LN). Differentially expressed (DE) genes associated with MAP infection were identified in the IL (585), JE (218), jejunum lymph node (JELN) (205), and ileum lymph node (ILLN) (117). Three DE genes (CD14, LOC616364 and ENSBTAG00000027033) were common to all MAPinf versus MAPneg tissues. Functional enrichment analysis revealed immune/disease related biological processes gene ontology (GO) terms and pathways predominated in IL tissue, indicative of an activated immune response state. Enriched GO terms and pathways in JE revealed a distinct set of host responses from those detected in IL. Regional differences were also identified between the mesenteric LNs draining each intestinal site. More down-regulated genes (52%) and fewer immune/disease pathways (n=5) were found in the ILLN compared to a higher number of up-regulated DE genes (56%) and enriched immune/disease pathways (n=13) in the JELN. Immunohistochemical staining validated myeloid cell transcriptional changes with increased CD172-positive myeloid cells in IL and JE tissues and draining LNs of MAPinf versus MAPneg cows. Several genes, GO terms, and pathways related to metabolism were significantly DE in IL and JE, but to a lesser extent (comparatively fewer enriched metabolic GO terms and pathways) in JELN suggesting distinct regional metabolic changes in IL compared to JE and JELN in response to MAP infection. These unique tissue- and regional-specific differences provides novel insight into the dichotomy in host responses to MAP infection that occur throughout the small intestine and mesenteric LN of chronically MAP infected cows.
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Affiliation(s)
- Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Duy N Do
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Philip Griebel
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
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23
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Ibeagha-Awemu EM, Bissonnette N, Bhattarai S, Wang M, Dudemaine PL, McKay S, Zhao X. Whole Genome Methylation Analysis Reveals Role of DNA Methylation in Cow's Ileal and Ileal Lymph Node Responses to Mycobacterium avium subsp. paratuberculosis Infection. Front Genet 2021; 12:797490. [PMID: 34992636 PMCID: PMC8724574 DOI: 10.3389/fgene.2021.797490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/22/2021] [Indexed: 12/27/2022] Open
Abstract
Johne's Disease (JD), caused by Mycobacterium avium subsp paratuberculosis (MAP), is an incurable disease of ruminants and other animal species and is characterized by an imbalance of gut immunity. The role of MAP infection on the epigenetic modeling of gut immunity during the progression of JD is still unknown. This study investigated the DNA methylation patterns in ileal (IL) and ileal lymph node (ILLN) tissues from cows diagnosed with persistent subclinical MAP infection over a one to 4 years period. DNA samples from IL and ILLN tissues from cows negative (MAPneg) (n = 3) or positive for MAP infection (MAPinf) (n = 4) were subjected to whole genome bisulfite sequencing. A total of 11,263 and 62,459 differentially methylated cytosines (DMCs), and 1259 and 8086 differentially methylated regions (DMRs) (FDR<0.1) were found between MAPinf and MAPneg IL and ILLN tissues, respectively. The DMRs were found on 394 genes (denoted DMR genes) in the IL and on 1305 genes in the ILLN. DMR genes with hypermethylated promoters/5'UTR [3 (IL) and 88 (ILLN)] or hypomethylated promoters/5'UTR [10 (IL) and 25 (ILLN)] and having multiple functions including response to stimulus/immune response (BLK, BTC, CCL21, AVPR1A, CHRNG, GABRA4, TDGF1), cellular processes (H2AC20, TEX101, GLA, NCKAP5L, RBM27, SLC18A1, H2AC20BARHL2, NLGN3, SUV39H1, GABRA4, PPA1, UBE2D2) and metabolic processes (GSTO2, H2AC20, SUV39H1, PPA1, UBE2D2) are potential DNA methylation candidate genes of MAP infection. The ILLN DMR genes were enriched for more biological process (BP) gene ontology (GO) terms (n = 374), most of which were related to cellular processes (27.6%), biological regulation (16.6%), metabolic processes (15.4%) and response to stimulus/immune response (8.2%) compared to 75 BP GO terms (related to cellular processes, metabolic processes and transport, and system development) enriched for IL DMR genes. ILLN DMR genes were enriched for more pathways (n = 47) including 13 disease pathways compared with 36 enriched pathways, including 7 disease/immune pathways for IL DMR genes. In conclusion, the results show tissue specific responses to MAP infection with more epigenetic changes (DMCs and DMRs) in the ILLN than in the IL tissue, suggesting that the ILLN and immune processes were more responsive to regulation by methylation of DNA relative to IL tissue. Our data is the first to demonstrate a potential role for DNA methylation in the pathogenesis of MAP infection in dairy cattle.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Suraj Bhattarai
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, United States
| | - Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Stephanie McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, United States
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-Be-Bellevue, QC, Canada
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24
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Choi SW, Kim S, Park HT, Park HE, Choi JS, Yoo HS. MicroRNA profiling in bovine serum according to the stage of Mycobacterium avium subsp. paratuberculosis infection. PLoS One 2021; 16:e0259539. [PMID: 34735546 PMCID: PMC8568169 DOI: 10.1371/journal.pone.0259539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), and it causes diarrhea and weakness in cattle. During a long subclinical stage, infected animals without clinical signs shed pathogens through feces. For this reason, the diagnosis of JD during the subclinical stage is very important. Circulating miRNAs are attracting attention as useful biomarkers in various veterinary diseases because of their expression changes depending on the state of the disease. Based on current knowledge, circulating miRNAs extracted from bovine serum were used to develop a diagnostic tool for JD. In this study, the animals were divided into 4 groups according to fecal shedding, the presence of antibodies, and clinical signs. Gene expression was analyzed by performing miRNA sequencing for each group, and it was identified that the miRNA expression changed more as the MAP infection progressed. The eight miRNAs that were differentially expressed in all infected groups were selected as biomarker candidates based on their significant differences compared to the control group. These biomarker candidates were validated by qRT-PCR. Considering the sequencing data, two upregulated miRNAs and two downregulated miRNAs showed the same trend in the validation results. Network analysis was also conducted and the results showed that mRNAs (IL-10, TGF-β1) associated with regulatory T cells were predicted to be activated in the subclinical stage. Taken together, our data suggest that two miRNAs (bta-miR-374b, bta-miR-2887) may play major roles in the immune response to MAP infection during the subclinical stage.
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Affiliation(s)
- Sung-Woon Choi
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Suji Kim
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hong-Tae Park
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Eui Park
- Department of Microbiology, Research Institute of Life Science, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Soo Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Disease, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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25
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Canive M, Badia-Bringué G, Vázquez P, González-Recio O, Fernández A, Garrido JM, Juste RA, Alonso-Hearn M. Identification of loci associated with pathological outcomes in Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis using whole-genome sequence data. Sci Rep 2021; 11:20177. [PMID: 34635747 PMCID: PMC8505495 DOI: 10.1038/s41598-021-99672-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 12/03/2022] Open
Abstract
Bovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous enteritis that affects cattle worldwide. According to their severity and extension, PTB-associated histological lesions have been classified into the following groups; focal, multifocal, and diffuse. It is unknown whether these lesions represent sequential stages or divergent outcomes. In the current study, the associations between host genetic and pathology were explored by genotyping 813 Spanish Holstein cows with no visible lesions (N = 373) and with focal (N = 371), multifocal (N = 33), and diffuse (N = 33) lesions in gut tissues and regional lymph nodes. DNA from peripheral blood samples of these animals was genotyped with the bovine EuroG MD Bead Chip, and the corresponding genotypes were imputed to whole-genome sequencing (WGS) data using the 1000 Bull genomes reference population. A genome-wide association study (GWAS) was performed using the WGS data and the presence or absence of each type of histological lesion in a case–control approach. A total of 192 and 92 single nucleotide polymorphisms (SNPs) defining 13 and 9 distinct quantitative trait loci (QTLs) were highly-associated (P ≤ 5 × 10−7) with the multifocal (heritability = 0.075) and the diffuse (heritability = 0.189) lesions, respectively. No overlap was seen in the SNPs controlling these distinct pathological outcomes. The identified QTLs overlapped with some QTLs previously associated with PTB susceptibility, bovine tuberculosis susceptibility, clinical mastitis, somatic cell score, bovine respiratory disease susceptibility, tick resistance, IgG level, and length of productive life. Pathway analysis with candidate genes overlapping the identified QTLs revealed a significant enrichment of the keratinization pathway and cholesterol metabolism in the animals with multifocal and diffuse lesions, respectively. To test whether the enrichment of SNP variants in candidate genes involved in the cholesterol metabolism was associated with the diffuse lesions; the levels of total cholesterol were measured in plasma samples of cattle with focal, multifocal, or diffuse lesions or with no visible lesions. Our results showed reduced levels of plasma cholesterol in cattle with diffuse lesions. Taken together, our findings suggested that the variation in MAP-associated pathological outcomes might be, in part, genetically determined and indicative of distinct host responses.
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Affiliation(s)
- Maria Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,Doctoral Program in Immunology, Microbiology and Parasitology, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Gerard Badia-Bringué
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain.,Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria, Madrid, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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26
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Mallikarjunappa S, Brito LF, Pant SD, Schenkel FS, Meade KG, Karrow NA. Johne's Disease in Dairy Cattle: An Immunogenetic Perspective. Front Vet Sci 2021; 8:718987. [PMID: 34513975 PMCID: PMC8426623 DOI: 10.3389/fvets.2021.718987] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Johne's disease (JD), also known as paratuberculosis, is a severe production-limiting disease with significant economic and welfare implications for the global cattle industry. Caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP), JD manifests as chronic enteritis in infected cattle. In addition to the economic losses and animal welfare issues associated with JD, MAP has attracted public health concerns with potential association with Crohn's disease, a human inflammatory bowel disease. The lack of effective treatment options, such as a vaccine, has hampered JD control resulting in its increasing global prevalence. The disease was first reported in 1895, but in recognition of its growing economic impact, extensive recent research facilitated by a revolution in technological approaches has led to significantly enhanced understanding of the immunological, genetic, and pathogen factors influencing disease pathogenesis. This knowledge has been derived from a variety of diverse models to elucidate host-pathogen interactions including in vivo and in vitro experimental infection models, studies measuring immune parameters in naturally-infected animals, and by studies conducted at the population level to enable the estimation of genetic parameters, and the identification of genetic markers and quantitative trait loci (QTL) putatively associated with susceptibility or resistance to JD. The main objectives of this review are to summarize these recent developments from an immunogenetics perspective and attempt to extract the principal and common findings emerging from this wealth of recent information. Based on these analyses, and in light of emerging technologies such as gene-editing, we conclude by discussing potential future avenues for effectively mitigating JD in cattle.
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Affiliation(s)
- Sanjay Mallikarjunappa
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Sameer D Pant
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Kieran G Meade
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
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27
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Heidari M, Pakdel A, Bakhtiarizadeh MR, Dehghanian F. Integrated Analysis of lncRNAs, mRNAs, and TFs to Identify Regulatory Networks Underlying MAP Infection in Cattle. Front Genet 2021; 12:668448. [PMID: 34290737 PMCID: PMC8287970 DOI: 10.3389/fgene.2021.668448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Johne’s disease is a chronic infection of ruminants that burdens dairy herds with a significant economic loss. The pathogenesis of the disease has not been revealed clearly due to its complex nature. In order to achieve deeper biological insights into molecular mechanisms involved in MAP infection resulting in Johne’s disease, a system biology approach was used. As far as is known, this is the first study that considers lncRNAs, TFs, and mRNAs, simultaneously, to construct an integrated gene regulatory network involved in MAP infection. Weighted gene coexpression network analysis (WGCNA) and functional enrichment analysis were conducted to explore coexpression modules from which nonpreserved modules had altered connectivity patterns. After identification of hub and hub-hub genes as well as TFs and lncRNAs in the nonpreserved modules, integrated networks of lncRNA-mRNA-TF were constructed, and cis and trans targets of lncRNAs were identified. Both cis and trans targets of lncRNAs were found in eight nonpreserved modules. Twenty-one of 47 nonpreserved modules showed significant biological processes related to the immune system and MAP infection. Some of the MAP infection’s related pathways in the most important nonpreserved modules comprise “positive regulation of cytokine-mediated signaling pathway,” “negative regulation of leukocyte migration,” “T-cell differentiation,” “neutrophil activation,” and “defense response.” Furthermore, several genes were identified in these modules, including SLC11A1, MAPK8IP1, HMGCR, IFNGR1, CMPK2, CORO1A, IRF1, LDLR, BOLA-DMB, and BOLA-DMA, which are potentially associated with MAP pathogenesis. This study not only enhanced our knowledge of molecular mechanisms behind MAP infection but also highlighted several promising hub and hub-hub genes involved in macrophage-pathogen interaction.
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Affiliation(s)
- Maryam Heidari
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Abbas Pakdel
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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28
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Marete A, Ariel O, Ibeagha-Awemu E, Bissonnette N. Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression. Front Vet Sci 2021; 8:639053. [PMID: 33969037 PMCID: PMC8100051 DOI: 10.3389/fvets.2021.639053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.
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Affiliation(s)
- Andrew Marete
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Olivier Ariel
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.,Faculty of Science, Sherbrooke University, Sherbrooke, QC, Canada
| | - Eveline Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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29
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Ariel O, Brouard JS, Marete A, Miglior F, Ibeagha-Awemu E, Bissonnette N. Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle 'in vitro' experimentally infected macrophages. BMC Genomics 2021; 22:162. [PMID: 33678157 PMCID: PMC7938594 DOI: 10.1186/s12864-021-07487-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 02/26/2021] [Indexed: 12/22/2022] Open
Abstract
Background Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, or Johne’s disease (JD), an incurable bovine disease. The evidence for susceptibility to MAP disease points to multiple interacting factors, including the genetic predisposition to a dysregulation of the immune system. The endemic situation in cattle populations can be in part explained by a genetic susceptibility to MAP infection. In order to identify the best genetic improvement strategy that will lead to a significant reduction of JD in the population, we need to understand the link between genetic variability and the biological systems that MAP targets in its assault to dominate macrophages. MAP survives in macrophages where it disseminates. We used next-generation RNA (RNA-Seq) sequencing to study of the transcriptome in response to MAP infection of the macrophages from cows that have been naturally infected and identified as positive for JD (JD (+); n = 22) or negative for JD (healthy/resistant, JD (−); n = 28). In addition to identifying genetic variants from RNA-seq data, SNP variants were also identified using the Bovine SNP50 DNA chip. Results The complementary strategy allowed the identification of 1,356,248 genetic variants, including 814,168 RNA-seq and 591,220 DNA chip variants. Annotation using SnpEff predicted that the 2435 RNA-seq genetic variants would produce high functional effect on known genes in comparison to the 33 DNA chip variants. Significant variants from JD(+/−) macrophages were identified by genome-wide association study and revealed two quantitative traits loci: BTA4 and 11 at (P < 5 × 10− 7). Using BovineMine, gene expression levels together with significant genomic variants revealed pathways that potentially influence JD susceptibility, notably the energy-dependent regulation of mTOR by LKB1-AMPK and the metabolism of lipids. Conclusion In the present study, we succeeded in identifying genetic variants in regulatory pathways of the macrophages that may affect the susceptibility of cows that are healthy/resistant to MAP infection. RNA-seq provides an unprecedented opportunity to investigate gene expression and to link the genetic variations to biological pathways that MAP normally manipulate during the process of killing macrophages. A strategy incorporating functional markers into genetic selection may have a considerable impact in improving resistance to an incurable disease. Integrating the findings of this research into the conventional genetic selection program may allow faster and more lasting improvement in resistance to bovine paratuberculosis in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07487-4.
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Affiliation(s)
- Olivier Ariel
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Jean-Simon Brouard
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Andrew Marete
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Filippo Miglior
- Center of Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - Eveline Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada.
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Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages. Antibiotics (Basel) 2021; 10:antibiotics10020097. [PMID: 33498280 PMCID: PMC7909288 DOI: 10.3390/antibiotics10020097] [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: 11/28/2020] [Revised: 12/28/2020] [Accepted: 01/14/2021] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) is still a leading cause of death worldwide. Treatments remain unsatisfactory due to an incomplete understanding of the underlying host–pathogen interactions during infection. In the present study, weighted gene co-expression network analysis (WGCNA) was conducted to identify key macrophage modules and hub genes associated with mycobacterial infection. WGCNA was performed combining our own transcriptomic results using Mycobacterium aurum-infected human monocytic macrophages (THP1) with publicly accessible datasets obtained from three types of macrophages infected with seven different mycobacterial strains in various one-to-one combinations. A hierarchical clustering tree of 11,533 genes was built from 198 samples, and 47 distinct modules were revealed. We identified a module, consisting of 226 genes, which represented the common response of host macrophages to different mycobacterial infections that showed significant enrichment in innate immune stimulation, bacterial pattern recognition, and leukocyte chemotaxis. Moreover, by network analysis applied to the 74 genes with the best correlation with mycobacteria infection, we identified the top 10 hub-connecting genes: NAMPT, IRAK2, SOCS3, PTGS2, CCL20, IL1B, ZC3H12A, ABTB2, GFPT2, and ELOVL7. Interestingly, apart from the well-known Toll-like receptor and inflammation-associated genes, other genes may serve as novel TB diagnosis markers and potential therapeutic targets.
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Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression. Sci Rep 2021; 11:313. [PMID: 33432064 PMCID: PMC7801378 DOI: 10.1038/s41598-020-79619-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Although genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with the susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection, only a few functional mutations for bovine paratuberculosis (PTB) have been characterized. Expression quantitative trait loci (eQTLs) are genetic variants typically located in gene regulatory regions that alter gene expression in an allele-specific manner. eQTLs can be considered as functional links between genomic variants, gene expression, and ultimately phenotype. In the current study, peripheral blood (PB) and ileocecal valve (ICV) gene expression was quantified by RNA-Seq from fourteen Holstein cattle with no lesions and with PTB-associated histopathological lesions in gut tissues. Genotypes were generated from the Illumina LD EuroG10K BeadChip. The associations between gene expression levels (normalized read counts) and genetic variants were analyzed by a linear regression analysis using R Matrix eQTL 2.2. This approach allowed the identification of 192 and 48 cis-eQTLs associated with the expression of 145 and 43 genes in the PB and ICV samples, respectively. To investigate potential relationships between these cis-eQTLs and MAP infection, a case–control study was performed using the genotypes for all the identified cis-eQTLs and phenotypical data (histopathology, ELISA for MAP-antibodies detection, tissue PCR, and bacteriological culture) of 986 culled cows. Our results suggested that the heterozygous genotype in the cis-eQTL-rs43744169 (T/C) was associated with the up-regulation of the MDS1 and EVI1 complex (MECOM) expression, with positive ELISA, PCR, and bacteriological culture results, and with increased risk of progression to clinical PTB. As supporting evidence, the presence of the minor allele was associated with higher MECOM levels in plasma samples from infected cows and with increased MAP survival in an ex-vivo macrophage killing assay. Moreover, the presence of the two minor alleles in the cis-eQTL-rs110345285 (C/C) was associated with the dysregulation of the eukaryotic elongation factor 1-α2 (eEF1A2) expression and with increased ELISA (OD) values. Finally, the presence of the minor allele in the cis-eQTL rs109859270 (C/T) was associated with the up-regulation of the U1 spliceosomal RNA expression and with an increased risk of progression to clinical PTB. The introduction of these novel functional variants into marker-assisted breeding programs is expected to have a relevant effect on PTB control.
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Epithelial processed Mycobacterium avium subsp. paratuberculosis induced prolonged Th17 response and suppression of phagocytic maturation in bovine peripheral blood mononuclear cells. Sci Rep 2020; 10:21048. [PMID: 33273606 PMCID: PMC7713309 DOI: 10.1038/s41598-020-78113-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
Johne’s disease (JD) caused by Mycobacterium avium subsp. paratuberculosis (MAP) is a chronic, wasting infectious disease in ruminants that causes enormous economic losses to the dairy and beef cattle industries. Understanding the mechanism of persistency of MAP is key to produce novel ideas for the development of new diagnostic methods or prevention techniques. We sought interactions between the host and MAP using epithelial passage model, which mimic initial stage of infection. From the transcriptomic analysis of bovine immune cells (PBMCs), it was suggested that infection through the epithelial cells elicited prolonged Th17-derived immune response, as indicated by upregulation of IL-17A, IL-17F and RORC until 120 h p.i., compared to directly infected PBMCs. Global downregulation of gene expression was observed after 72 h p.i., especially for genes encoding cell surface receptors of phagocytic cells, such as Toll-like receptors and MHC class II molecules. In addition, the cholesterol efflux transporters ABCA1, ABCG1, and APOE, which are regulated by the LXR/RXR pathway, were downregulated. In summary, it would be suggested that the host initiate immune response to activate Th17-derived cytokines, and MAP survives persistently by altering the host adaptive immune response by suppressing surface receptors and manipulating lipid metabolism in phagocytic cells.
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Zhang X, Lv X, Li X, Wang Y, Lin H, Zhang J, Peng C. Dysregulated circulating SOCS3 and haptoglobin expression associated with stable coronary artery disease and acute coronary syndrome: An integrated study based on bioinformatics analysis and case-control validation. Anatol J Cardiol 2020; 24:160-174. [PMID: 32870172 PMCID: PMC7585973 DOI: 10.14744/anatoljcardiol.2020.56346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE To extensively use blood transcriptome analysis to identify potential diagnostic and therapeutic targets for cardiovascular diseases. METHODS Two gene expression datasets (GSE59867 and GSE62646) were downloaded from GEO DataSets to identify altered blood transcriptomes in patients with ST-segment elevation myocardial infarction (STEMI) compared to stable coronary artery disease (CAD). Thereafter, several computational approaches were taken to determine functional roles and regulatory networks of differentially expressed genes (DEGs). Finally, the expression of dysregulated two hub genes-suppressor of cytokine signaling 3 (SOCS3) and haptoglobin (HP)-were validated in a case-control study. RESULTS A total of 119 DEGs were identified in the discovery phase, consisting of 71 downregulated genes and 48 upregulated genes; two hub modules consisting of two hub genes-SOCS3 and HP-were identified. In the validation phase, both SOCS3 and HP were significantly downregulated in the stable CAD and acute coronary syndrome (ACS) patients when compared with healthy controls. Meanwhile, HP was significantly upregulated in STEMI patients when compared with stable CAD patients (p=0.041). Logistic regression analysis indicated that: downregulated expression of HP correlated with increased risk of CAD [odds ratio (OR)=0.52, 95% confidence interval (CI)=0.31~0.87, p=0.013]; and downregulated expression of SOCS3 correlated with increased risk of ACS (OR=0.66, 95% CI=0.46~0.94, p=0.023) when age, gender, history of hyperlipidemia, diabetes and hypertension were included as covariates. CONCLUSION Future clarification of how SOCS3 and HP influence the pathogenesis of disease may pave the way for the development of novel diagnostic and therapeutic methods.
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Affiliation(s)
- Xunnan Zhang
- Postgraduate Training Basement of Jinzhou Medicical University, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
| | - Xi Lv
- Postgraduate Training Basement of Jinzhou Medicical University, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
| | - Xiandong Li
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
| | - Yaping Wang
- Postgraduate Training Basement of Jinzhou Medicical University, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
| | - Haoyu Lin
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Shantou University Medical College; Guangdong-P.R. China
| | - Jicai Zhang
- Postgraduate Training Basement of Jinzhou Medicical University, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
| | - Chunyan Peng
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine; Hubei-P.R. China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine; Hubei-P.R. China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Hubei-P.R. China
- Address for correspondence: Chunyan Peng, MD, Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Renming road 32# Shiyan, 442000, Hubei-P.R. China Phone: +86 13636 254788 E-mail:
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