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Quirino DF, Marcondes MI, de Oliveira KR, Guimarães SEF, da Silva JS, Suen G, Rossi LE, Cunha CS, Mantovani HC, Rotta PP. Comparison of ruminal microbiota, IL-1β gene variation, and tick incidence between Holstein × Gyr and Holstein heifers in grazing system. Front Microbiol 2024; 15:1132151. [PMID: 38468851 PMCID: PMC10925795 DOI: 10.3389/fmicb.2024.1132151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The variation in bacterial communities among breeds has been previously reported and may be one of the reasons why Holstein × Gyr dairy heifers have better development in grazing systems in tropical conditions. This study aimed to explore the ruminal microbiota composition, the IL-1β gene variation, tick incidence, and blood parameters of Holstein × Gyr (½ Holstein × ½ Gyr) and Holstein heifers grazing intensely managed Guinea grass (Panicum maximum Jacq. cv. Mombaça). Methods Sixteen heifers were divided into two groups consisting of 8 Holstein × Gyr and 8 Holstein heifers. The experimental period was comprised of 3 periods of 21 days. Ruminal samples were taken via the stomach tube technique. The sequencing of the V4 hypervariable region of the 16S rRNA gene was performed using the Illumina MiSeq platform. Counting and collection of ticks were conducted each 21 days. Blood and skeletal muscle tissue biopsies were performed at the end of the experiment. Results Firmicutes were the most abundant phyla present in both breed rumen samples and Bacteroidota showed differences in relative abundance between breed groups, with greater values for Holstein heifers (p < 0.05 with FDR correction). The 10 most abundant unique OTUs identified in each breed included several OTUs of the genus Prevotella. Holstein heifers had a greater tick count and weight (9.8 ticks/animal and 1.6 g/animal, respectively) than Holstein × Gyr (2.56 ticks/animal and 0.4 g/animal, respectively). We found nucleotide substitutions in the IL-1β gene that might be related to adaptation and resistance phenotypes to tick infestation in Holstein × Gyr heifers. Blood concentrations of urea, albumin, insulin-like growth factor 1, triiodothyronine, and thyroxine were greater in Holstein × Gyr than in Holstein heifers. Conclusion Adaptations in Holstein × Gyr heifers such as ruminal microbiota, tick resistance, nucleotide substitutions in IL-1β gene, and hormone concentration suggest a better energy metabolism and thermoregulation resulting in better performance in tropical grazing systems.
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Affiliation(s)
| | | | | | | | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Letícia Elisa Rossi
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila Soares Cunha
- School of Veterinary Medicine and Animal Science, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Polyana Pizzi Rotta
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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2
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Nickles MA, Huang K, Chang YS, Tsoukas MM, Sweiss NJ, Perkins DL, Finn PW. Gene Co-expression Networks Identifies Common Hub Genes Between Cutaneous Sarcoidosis and Discoid Lupus Erythematosus. Front Med (Lausanne) 2020; 7:606461. [PMID: 33324666 PMCID: PMC7724034 DOI: 10.3389/fmed.2020.606461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/28/2020] [Indexed: 11/18/2022] Open
Abstract
In this study we analyzed gene co-expression networks of three immune-related skin diseases: cutaneous sarcoidosis (CS), discoid lupus erythematosus (DLE), and psoriasis. We propose that investigation of gene co-expression networks may provide insights into underlying disease mechanisms. Microarray expression data from two cohorts of patients with CS, DLE, or psoriasis skin lesions were analyzed. We applied weighted gene correlation network analysis (WGCNA) to construct gene-gene similarity networks and cluster genes into modules based on similar expression profiles. A module of interest that was preserved between datasets and corresponded with case/control status was identified. This module was related to immune activation, specifically leukocyte activation, and was significantly increased in both CS lesions and DLE lesions compared to their respective controls. Protein-protein interaction (PPI) networks constructed for this module revealed seven common hub genes between CS lesions and DLE lesions: TLR1, ITGAL, TNFRSF1B, CD86, SPI1, BTK, and IL10RA. Common hub genes were highly upregulated in CS lesions and DLE lesions compared to their respective controls in a differential expression analysis. Our results indicate common gene expression patterns in the immune processes of CS and DLE, which may have indications for future therapeutic targets and serve as Th1-mediated disease biomarkers. Additionally, we identified hub genes unique to CS and DLE, which can help differentiate these diseases from one another and may serve as unique therapeutic targets and biomarkers. Notably, we find common gene expression patterns in the immune processes of CS and DLE through utilization of WGCNA.
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Affiliation(s)
- Melissa A. Nickles
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Kai Huang
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Yi-Shin Chang
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Maria M. Tsoukas
- Department of Dermatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Nadera J. Sweiss
- Division of Rheumatology, University of Illinois at Chicago, Chicago, IL, United States
| | - David L. Perkins
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Patricia W. Finn
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
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Roy Chattopadhyay N, Chatterjee K, Tiwari N, Chakrabarti S, Sahu SK, Deb Roy S, Ghosh A, Reddy RR, Das P, Mal S, Karnar BB, Das AK, Tsering S, Riba K, Puii Z, Zomawia E, Singh YI, Suryawanshi AR, Kumar A, Ganguly D, Goswami C, Choudhuri T. TLR9 Polymorphisms Might Contribute to the Ethnicity Bias for EBV-Infected Nasopharyngeal Carcinoma. iScience 2020; 23:100937. [PMID: 32179470 PMCID: PMC7068130 DOI: 10.1016/j.isci.2020.100937] [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: 01/17/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is endemic in some ethnic groups. The association of NPC with the Epstein-Barr virus (EBV) is firmly established; however, the mechanism is still unclear. TLR9 is well known for its essential role in viral pathogen recognition and activation of innate immunity. Here, we report a set of TLR9 polymorphisms in the TIR-2 domain of the TLR9 protein collected from the EBV-infected NPC samples from northeast Indian populations sharing the aforesaid ethnicity. The occurrence of mutations is significantly high in these samples as we found a p value of <0.0001 at a significance level of 0.05. These might play an important role for the lack of function of TLR9 and thus for the higher occurrence of EBV-mediated NPC in such ethnic groups. EBV-associated nasopharyngeal carcinoma (NPC) is endemic in Mongoloids TLR9 is essential for virus recognition and immunity against cancers Polymorphisms are common in TLR9 protein in EBV-infected Mongoloids with NPC NPC susceptibility prediction by TLR9 mutation screening in people for prevention
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Affiliation(s)
| | - Koustav Chatterjee
- Department of Biotechnology, Visva Bharati, Santiniketan, Bolpur 731235, India
| | - Nikhil Tiwari
- School of Biological Science, National Institute of Science Education and Research, Padnpur, Odisha 752050, India
| | | | - Sushil Kumar Sahu
- Depatrment of Pharmacology & Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sankar Deb Roy
- Department of Radiation Oncology, Eden Medical Center, Dimapur, Nagaland 797112, India
| | - Arijit Ghosh
- School of Biological Science, National Institute of Science Education and Research, Padnpur, Odisha 752050, India
| | - R Rajendra Reddy
- Clinical Proteomics, Institute of Life Sciences, 751023 Bhubaneswar, India
| | - Piyanki Das
- Department of Biotechnology, Visva Bharati, Santiniketan, Bolpur 731235, India
| | - Sudipa Mal
- Department of Biotechnology, Visva Bharati, Santiniketan, Bolpur 731235, India
| | - Basab Bijay Karnar
- Department of Biotechnology, Visva Bharati, Santiniketan, Bolpur 731235, India
| | - Ashok Kumar Das
- Dr B. Borooah Cancer Institute, ENT Department, Guwahati, Assam 781016, India
| | - Sam Tsering
- Tertiary Cancer Center, TomoRiba Institute of Health and Medical Sciences, Naharlagun, Arunachal Pradesh 791110, India
| | - Komri Riba
- Tertiary Cancer Center, TomoRiba Institute of Health and Medical Sciences, Naharlagun, Arunachal Pradesh 791110, India
| | - Zoreng Puii
- State Referral Hospital, Falkawn, Mizoram 796005, India
| | - Eric Zomawia
- State Referral Hospital, Falkawn, Mizoram 796005, India
| | - Y Indibar Singh
- Department of Radiotherapy, Regional Institute of Medical Sciences, Imphal, Manipur 795004, India
| | | | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, 560100 Bangalore, India; Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Dipyaman Ganguly
- Dendritic Cell Laboratory, Cancer Biology and Inflammatory Disorder, Indian Institute of Chemical Biology, 700032 Kolkata, India
| | - Chandan Goswami
- School of Biological Science, National Institute of Science Education and Research, Padnpur, Odisha 752050, India
| | - Tathagata Choudhuri
- Department of Biotechnology, Visva Bharati, Santiniketan, Bolpur 731235, India.
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Gomez-Chamorro A, Battilotti F, Cayol C, Mappes T, Koskela E, Boulanger N, Genné D, Sarr A, Voordouw MJ. Susceptibility to infection with Borrelia afzelii and TLR2 polymorphism in a wild reservoir host. Sci Rep 2019; 9:6711. [PMID: 31040326 PMCID: PMC6491475 DOI: 10.1038/s41598-019-43160-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2019] [Indexed: 12/14/2022] Open
Abstract
The study of polymorphic immune genes in host populations is critical for understanding genetic variation in susceptibility to pathogens. Controlled infection experiments are necessary to separate variation in the probability of exposure from genetic variation in susceptibility to infection, but such experiments are rare for wild vertebrate reservoir hosts and their zoonotic pathogens. The bank vole (Myodes glareolus) is an important reservoir host of Borrelia afzelii, a tick-borne spirochete that causes Lyme disease. Bank vole populations are polymorphic for Toll-like receptor 2 (TLR2), an innate immune receptor that recognizes bacterial lipoproteins. To test whether the TLR2 polymorphism influences variation in the susceptibility to infection with B. afzelii, we challenged pathogen-free, lab-born individuals of known TLR2 genotype with B. afzelii-infected ticks. We measured the spirochete load in tissues of the bank voles. The susceptibility to infection with B. afzelii following an infected tick bite was very high (95%) and did not differ between TLR2 genotypes. The TLR2 polymorphism also had no effect on the spirochete abundance in the tissues of the bank voles. Under the laboratory conditions of our study, we did not find that the TLR2 polymorphism in bank voles influenced variation in the susceptibility to B. afzelii infection.
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Affiliation(s)
| | | | - Claire Cayol
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Esa Koskela
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Nathalie Boulanger
- Facultés de Médecine et de Pharmacie, Université de Strasbourg, Strasbourg, France
| | - Dolores Genné
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Anouk Sarr
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Maarten Jeroen Voordouw
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
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Parthasarathy G, Philipp MT. Receptor tyrosine kinases play a significant role in human oligodendrocyte inflammation and cell death associated with the Lyme disease bacterium Borrelia burgdorferi. J Neuroinflammation 2017; 14:110. [PMID: 28558791 PMCID: PMC5450372 DOI: 10.1186/s12974-017-0883-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/18/2017] [Indexed: 12/28/2022] Open
Abstract
Background In previous studies, human oligodendrocytes were demonstrated to undergo apoptosis in the presence of Borrelia burgdorferi under an inflammatory milieu. Subsequently, we determined that the MEK/ERK pathway played a significant role in triggering downstream inflammation as well as apoptosis. However, the identity of receptors triggered by exposure to B. burgdorferi and initiating signaling events was unknown. Methods In this study, we explored the role of several TLR and EGFR/FGFR/PDGFR tyrosine kinase pathways in inducing inflammation in the presence of B. burgdorferi, using siRNA and/or inhibitors, in MO3.13 human oligodendrocytes. Cell death and apoptosis assays were also carried out in the presence or absence of specific receptor inhibitors along with the bacteria to determine the role of these receptors in apoptosis induction. The expression pattern of specific receptors with or without B. burgdorferi was also determined. Results TLRs 2 and 5 had a minimal role in inducing inflammation, particularly IL-6 production. Rather, their effect was mostly inhibitory, with TLR2 downregulation significantly upregulating CXCL8, and CXCL (1,2,3) levels, and TLR5 likely having a similar role in CXCL8, CXCL(1,2,3), and CCL5 levels. TLR4 contributed mostly towards CCL5 production. On the other hand, inhibition of all three EGF/FGF/PDGF receptors significantly downregulated all five of the inflammatory mediators tested even in the presence of B. burgdorferi. Their inhibition also downregulated overall cell death and apoptosis levels. The expression pattern of these receptors, as assessed by immunohistochemistry indicated that the PDGFRβ receptor was the most predominantly expressed receptor, followed by FGFR, although no significant differences were discernible between presence and absence of bacteria. Interestingly, inhibition of individual EGFR, FGFR, or PDGFR receptors did not indicate an individual role for any of these receptors in the overall downregulation of pathogenesis. Contrarily, suppression of FGFR signaling alone in the presence of bacteria significantly upregulated inflammatory mediator levels indicating that it might control an inhibitory pathway when triggered individually. Conclusions Unlike TLRs, EGF/FGF/PDGF receptors collectively play a significant role in the inflammation and apoptosis of human oligodendrocytes as mediated by B. burgdorferi. It is likely that these three receptors need to be triggered simultaneously to achieve this effect.
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Affiliation(s)
- Geetha Parthasarathy
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Tulane University, 18703, Three Rivers Road, Covington, LA, 70433, USA
| | - Mario T Philipp
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Tulane University, 18703, Three Rivers Road, Covington, LA, 70433, USA.
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Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions. J Immunol Res 2017; 2017:2197615. [PMID: 28321417 PMCID: PMC5340944 DOI: 10.1155/2017/2197615] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/19/2017] [Indexed: 12/26/2022] Open
Abstract
Pathogens have evolved unique mechanisms to breach the cell surface barrier and manipulate the host immune response to establish a productive infection. Proteins exposed to the extracellular environment, both cell surface-expressed receptors and secreted proteins, are essential targets for initial invasion and play key roles in pathogen recognition and subsequent immunoregulatory processes. The identification of the host and pathogen extracellular molecules and their interaction networks is fundamental to understanding tissue tropism and pathogenesis and to inform the development of therapeutic strategies. Nevertheless, the characterization of the proteins that function in the host-pathogen interface has been challenging, largely due to the technical challenges associated with detection of extracellular protein interactions. This review discusses available technologies for the high throughput study of extracellular protein interactions between pathogens and their hosts, with a focus on mammalian viruses and bacteria. Emerging work illustrates a rich landscape for extracellular host-pathogen interaction and points towards the evolution of multifunctional pathogen-encoded proteins. Further development and application of technologies for genome-wide identification of extracellular protein interactions will be important in deciphering functional host-pathogen interaction networks, laying the foundation for development of novel therapeutics.
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Badawi A. The Potential of Omics Technologies in Lyme Disease Biomarker Discovery and Early Detection. Infect Dis Ther 2016; 6:85-102. [PMID: 27900646 PMCID: PMC5336413 DOI: 10.1007/s40121-016-0138-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 12/31/2022] Open
Abstract
Lyme borreliosis (LB) is the most prevalent arthropod-borne infectious disease in North America and many countries of the temperate Northern Hemisphere. It is associated with local and systemic manifestations and has persistent post-treatment health complications in some individuals. Innate and acquired immunity-related inflammation is likely to play a critical role in both host defense against Borrelia burgdorferi and disease severity. Large-scale analytical approaches to quantify gene expression (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in LB have recently emerged with a potential to advance the development of disease biomarkers in early, disseminated and posttreatment disease stages. These technologies may permit defining the disease stage and facilitate its early detection to improve diagnosis. They will also likely allow elucidating the underlying molecular pathways to aid in identifying molecular targets for therapy. This article reviews the findings within the field of omics relevant to LB and its prospective utility in developing an array of biomarkers that can be employed in LB diagnosis and detection particularly at the early disease stages.
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Affiliation(s)
- Alaa Badawi
- Public Health Risk Sciences Division, Public Health Agency of Canada, 180 Queen Street West, Toronto, ON, Canada. .,Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, FitzGerald Building, 150 College Street, Toronto, ON, Canada.
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