1
|
Hasankhani A, Bahrami A, Mackie S, Maghsoodi S, Alawamleh HSK, Sheybani N, Safarpoor Dehkordi F, Rajabi F, Javanmard G, Khadem H, Barkema HW, De Donato M. In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection. Front Microbiol 2022; 13:1041314. [PMID: 36532492 PMCID: PMC9748370 DOI: 10.3389/fmicb.2022.1041314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
Collapse
Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Shayan Mackie
- Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Sairan Maghsoodi
- Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Heba Saed Kariem Alawamleh
- Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Farhad Safarpoor Dehkordi
- Halal Research Center of IRI, FDA, Tehran, Iran
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hosein Khadem
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Marcos De Donato
- Regional Department of Bioengineering, Tecnológico de Monterrey, Monterrey, Mexico
| |
Collapse
|
2
|
Alvarez AH. Revisiting tuberculosis screening: An insight to complementary diagnosis and prospective molecular approaches for the recognition of the dormant TB infection in human and cattle hosts. Microbiol Res 2021; 252:126853. [PMID: 34536677 DOI: 10.1016/j.micres.2021.126853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 12/17/2022]
Abstract
Tuberculosis (TB) is defined as a chronic infection in both human and cattle hosts and many subclinical cases remain undetected. After the pathogen is inhaled by a host, phagocyted bacilli can persist inside macrophages surviving intracellularly. Hosts develop granulomatous lesions in the lungs or lymph nodes, limiting infection. However, bacilli become persister cells. Immunological diagnosis of TB is performed basically by routine tuberculin skin test (TST), and in some cases, by ancillary interferon-gamma release assay (IGRA). The concept of human latent TB infection (LTBI) by M. tuberculosis is recognized in cohorts without symptoms by routine clinical diagnostic tests, and nowadays IGRA tests are used to confirm LTBI with either active or latent specific antigens of M. tuberculosis. On the other hand, dormant infection in cattle by M. bovis has not been described by TST or IGRA testing as complications occur by cross-reactive immune responses to homolog antigens of environmental mycobacteria or a false-negative test by anergic states of a wained bovine immunity, evidencing the need for deciphering more specific biomarkers by new-generation platforms of analysis for detection of M. bovis dormant infection. The study and description of bovine latent TB infection (boLTBI) would permit the recognition of hidden animal infection with an increase in the sensitivity of routine tests for an accurate estimation of infected dairy cattle. Evidence of immunological and experimental analysis of LTBI should be taken into account to improve the study and the description of the still neglected boLTBI.
Collapse
Affiliation(s)
- Angel H Alvarez
- Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco A.C. (CIATEJ), Consejo Nacional de Ciencia y Tecnología (CONACYT), Av. Normalistas 800 C.P. 44270, Guadalajara, Jalisco, Mexico.
| |
Collapse
|
3
|
Hervet C, Boullier J, Guiadeur M, Michel L, Brun-Lafleur L, Aupiais A, Zhu J, Mounaix B, Meurens F, Renois F, Assié S. Appeasing Pheromones against Bovine Respiratory Complex and Modulation of Immune Transcript Expressions. Animals (Basel) 2021; 11:ani11061545. [PMID: 34070477 PMCID: PMC8229285 DOI: 10.3390/ani11061545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022] Open
Abstract
Bovine respiratory disease is still a major concern and has major economic impact. Another consequence of respiratory infections is the use of antimicrobial molecules to control bacterial pathogens. This can participate in the emergence and shedding of antimicrobial resistance that can threaten animal as well as human health. Appeasing pheromones with their capacity to reduce stress and thus their ability to preserve the functions of the immune system have been proposed to reduce the use of antimicrobial substances. In this study, we assessed the effect of appeasing pheromone administration on bovine health and performance during the fattening period. Zootechnical and health parameters and whole blood immune transcript expressions were measured over four weeks in bulls to determine the effect of the pheromone. We observed increased clinical signs on Day 8 (D8) and decreased clinical signs on D30 in bulls who received the pheromone and a higher expression of interleukin 8 transcripts in this group than in the control group on D8. Our results are overall in line with previous reports in livestock species. Further studies are needed to shed more light on the effect of appeasing pheromones and decipher their exact mechanisms of action.
Collapse
Affiliation(s)
- Caroline Hervet
- BIOEPAR, INRAE, Oniris, 44307 Nantes, France; (C.H.); (J.B.); (F.R.); (S.A.)
| | - Justine Boullier
- BIOEPAR, INRAE, Oniris, 44307 Nantes, France; (C.H.); (J.B.); (F.R.); (S.A.)
- Institut de l’Élevage, 14310 Villers-Bocage, France;
| | | | - Léa Michel
- TERRENA Innovation, La Noëlle, 20199 Ancenis, France;
| | | | - Anne Aupiais
- Institut de l’Élevage, 35652 Le Rheu, France; (L.B.-L.); (A.A.); (B.M.)
| | - Jianzhong Zhu
- College of Veterinary Medicine, Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, China
| | - Béatrice Mounaix
- Institut de l’Élevage, 35652 Le Rheu, France; (L.B.-L.); (A.A.); (B.M.)
| | - François Meurens
- BIOEPAR, INRAE, Oniris, 44307 Nantes, France; (C.H.); (J.B.); (F.R.); (S.A.)
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, Saskatoon, SK S7N5E3, Canada
- Correspondence: ; Tel.: +33-240-68-77-02
| | - Fanny Renois
- BIOEPAR, INRAE, Oniris, 44307 Nantes, France; (C.H.); (J.B.); (F.R.); (S.A.)
| | - Sébastien Assié
- BIOEPAR, INRAE, Oniris, 44307 Nantes, France; (C.H.); (J.B.); (F.R.); (S.A.)
| |
Collapse
|
4
|
Catozzi C, Zamarian V, Marziano G, Costa ED, Martucciello A, Serpe P, Vecchio D, Lecchi C, De Carlo E, Ceciliani F. The effects of intradermal M. bovis and M. avium PPD test on immune-related mRNA and miRNA in dermal oedema exudates of water buffaloes (Bubalus bubalis). Trop Anim Health Prod 2021; 53:250. [PMID: 33825069 PMCID: PMC8024229 DOI: 10.1007/s11250-021-02696-1] [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: 12/21/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB) is a zoonotic disease primarily caused by pathogens belonging to the genus of Mycobacterium. Programs of control and eradication for bovine TB include a screening using single intradermal tuberculin (SIT) test with Mycobacterium bovis (M. bovis)-purified protein derivatives (PPD-B) single or concurrent with Mycobacterium avium (M. avium)-purified protein derivatives (PPD-A). This study aimed to determine the effects of intradermal PPD-B and PPD-A test on immune-related mRNA and microRNAs in dermal oedema exudates of water buffaloes (Bubalus bubalis). The investigation was carried out on RNA extracted from dermal oedema exudates of 36 animals, of which 24 were M. bovis positive (M. bovis+) and 12 M. avium positive (M. avium+). The lymphocyte polarization toward Th1, Th2, TReg, and Th17 lineages was addressed by measuring the abundance of the respective cytokines and transcription factors, namely TBET, STAT4, IFNγ, and IL1β for Th1; STAT5B, and IL4 for Th2; FOXP3 and IL10 for TReg; and RORC, STAT3, and IL17A for Th17. Due to the very low abundance of Th17-related genes, a digital PCR protocol was also applied. The abundance of microRNAs involved in the immune response against PPDs, including miR-122-5p, miR-148a-3p, miR30a, and miR-455-5p, was equally measured. Results showed that IFNγ (fold change = 2.54; p = 0.037) and miR-148a-3p (fold change = 2.54; p = 0.03) were upregulated in M. bovis+ as compared to M. avium+ samples. Our preliminary results supported the pivotal role of IFNγ in the local immune response related to PPD-B and highlighted the differential expression of miR-148a-3p, which downregulates the proinflammatory cytokines and the TLR4-mediated NF-κB activation, providing an anti-inflammation modulator in responses to mycobacterial infection.
Collapse
Affiliation(s)
- Carlotta Catozzi
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Valentina Zamarian
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Gabriele Marziano
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Emanuela Dalla Costa
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Alessandra Martucciello
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, 27, 84131, Salerno, Italy
| | - Paola Serpe
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, 27, 84131, Salerno, Italy
| | - Domenico Vecchio
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, 27, 84131, Salerno, Italy
| | - Cristina Lecchi
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Esterina De Carlo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, National Reference Centre for Hygiene and Technologies of Water Buffalo Farming and Productions, Via delle Calabrie, 27, 84131, Salerno, Italy
| | - Fabrizio Ceciliani
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.
| |
Collapse
|
5
|
Wiarda JE, Boggiatto PM, Bayles DO, Waters WR, Thacker TC, Palmer MV. Severity of bovine tuberculosis is associated with innate immune-biased transcriptional signatures of whole blood in early weeks after experimental Mycobacterium bovis infection. PLoS One 2020; 15:e0239938. [PMID: 33166313 PMCID: PMC7652326 DOI: 10.1371/journal.pone.0239938] [Citation(s) in RCA: 5] [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: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium bovis, the causative agent of bovine tuberculosis, is a pathogen that impacts both animal and human health. Consequently, there is a need to improve understanding of disease dynamics, identification of infected animals, and characterization of the basis of immune protection. This study assessed the transcriptional changes occurring in cattle during the early weeks following a M. bovis infection. RNA-seq analysis of whole blood-cell transcriptomes revealed two distinct transcriptional clusters of infected cattle at both 4- and 10-weeks post-infection that correlated with disease severity. Cattle exhibiting more severe disease were transcriptionally divergent from uninfected animals. At 4-weeks post-infection, 25 genes had commonly increased expression in infected cattle compared to uninfected cattle regardless of disease severity. Ten weeks post-infection, differential gene expression was only observed when severely-affected cattle were compared to uninfected cattle. This indicates a transcriptional divergence based on clinical status following infection. In cattle with more severe disease, biological processes and cell type enrichment analyses revealed overrepresentation of innate immune-related processes and cell types in infected animals. Collectively, our findings demonstrate two distinct transcriptional profiles occur in cattle following M. bovis infection, which correlate to clinical status.
Collapse
Affiliation(s)
- Jayne E. Wiarda
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
- Immunobiology Graduate Program, Iowa State University, Ames, IA, United States of America
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United States of America
| | - Paola M. Boggiatto
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - Darrell O. Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - W. Ray Waters
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - Tyler C. Thacker
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| | - Mitchell V. Palmer
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States of America
| |
Collapse
|
6
|
Abstract
Paratuberculosis and bovine tuberculosis are two mycobacterial diseases of ruminants which have a considerable impact on livestock health, welfare, and production. These are chronic "iceberg" diseases which take years to manifest and in which many subclinical cases remain undetected. Suggested biomarkers to detect infected or diseased animals are numerous and include cytokines, peptides, and expression of specific genes; however, these do not provide a strong correlation to disease. Despite these advances, disease detection still relies heavily on dated methods such as detection of pathogen shedding, skin tests, or serology. Here we review the evidence for suitable biomarkers and their mechanisms of action, with a focus on identifying animals that are resilient to disease. A better understanding of these factors will help establish new strategies to control the spread of these diseases.
Collapse
|
7
|
Wood kraft pulp supplementation alters the rumen fermentation characteristics and epithelial transcriptomes in Holstein cattle during the high-grain diet challenge. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2019.114292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
8
|
RNA-Seq analysis of ileocecal valve and peripheral blood from Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis revealed dysregulation of the CXCL8/IL8 signaling pathway. Sci Rep 2019; 9:14845. [PMID: 31619718 PMCID: PMC6795908 DOI: 10.1038/s41598-019-51328-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/23/2019] [Indexed: 12/18/2022] Open
Abstract
Paratuberculosis is chronic granulomatous enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). Whole RNA-sequencing (RNA-Seq) is a promising source of novel biomarkers for early MAP infection and disease progression in cattle. Since the blood transcriptome is widely used as a source of biomarkers, we analyzed whether it recapitulates, at least in part, the transcriptome of the ileocecal valve (ICV), the primary site of MAP colonization. Total RNA was prepared from peripheral blood (PB) and ICV samples, and RNA-Seq was used to compare gene expression between animals with focal or diffuse histopathological lesions in gut tissues versus control animals with no detectable signs of infection. Our results demonstrated both shared, and PB and ICV-specific gene expression in response to a natural MAP infection. As expected, the number of differentially expressed (DE) genes was larger in the ICV than in the PB samples. Among the DE genes in the PB and ICV samples, there were some common genes irrespective of the type of lesion including the C-X-C motif chemokine ligand 8 (CXCL8/IL8), apolipoprotein L (APOLD1), and the interferon inducible protein 27 (IFI27). The biological processes (BP) enriched in the PB gene expression profiles from the cows with diffuse lesions included the killing of cells of other organism, defense response, immune response and the regulation of neutrophil chemotaxis. Two of these BP, the defense and immune response, were also enriched in the ICV from the cows with diffuse lesions. Metabolic analysis of the DE genes revealed that the N-glycan biosynthesis, bile secretion, one-carbon pool by folate and purine metabolism were significantly enriched in the ICV from the cows with focal lesions. In the ICV from cows with diffuse lesions; the valine, leucine and isoleucine degradation route, purine metabolism, vitamin digestion and absorption and the cholesterol routes were enriched. Some of the identified DE genes, BP and metabolic pathways will be studied further to develop novel diagnostic tools, vaccines and immunotherapeutics.
Collapse
|