Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus

Johnston, Dayle; Earley, Bernadette; McCabe, Matthew S.; Kim, Jae-Woo; Taylor, Jeremy F.; Lemon, Ken; McMenamy, Michael; Duffy, Catherine; Cosby, S. L.; Waters, Sinéad M.

doi:10.3389/fgene.2021.633125

Cited by 6 publications

(16 citation statements)

References 54 publications

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“…In agreement with the previous studies, functional terms including “VEGF signaling pathway,” “T-cell receptor signaling pathway” ( Tizioto et al, 2015 ), and “C-type lectin receptor signaling pathway” as well as hub–hub genes including LCK ( Smirnova et al, 2009 ), TLR3 ( Marin et al, 2016 ), TIA1 ( Johnston et al, 2021b ), TNF ( El-Deeb et al, 2020 ), and STAT5A hub–hub TF ( Lin et al, 2015 ) demonstrate the importance of the red module during BRD. Furthermore, the salmon module was mainly enriched in “cellular defense response,” “regulation of immune response,” “leukocyte cell–cell adhesion,” and “natural killer cell-mediated cytotoxicity.” Recent studies have demonstrated that some of the hub–hub genes in the salmon module, such as CCR5 ( Salem et al, 2019 ), CCR8 ( Amat et al, 2019 ; Lopez et al, 2020 ), CX3CR1 ( Scott et al, 2021 ), ITGAL , IL12RB2 ( Neupane et al, 2018 ), NCR1 ( Osman and Griebel, 2017 ), CCL5 ( N’jai et al, 2013 ), and PRF1 ( Johnston et al, 2021a ) tend to participate in BRD.…”

Section: Discussionsupporting

confidence: 89%

“…In agreement with the previous studies, functional terms including "VEGF signaling pathway," "T-cell receptor signaling pathway" (Tizioto et al, 2015), and "C-type lectin receptor signaling pathway" as well as hub-hub genes including LCK (Smirnova et al, 2009), TLR3 (Marin et al, 2016), TIA1 (Johnston et al, 2021b), TNF (El-Deeb et al, 2020, and STAT5A hub-hub TF (Lin et al, 2015) demonstrate the importance of the red module during BRD. Furthermore, the salmon module was mainly enriched in "cellular defense response," "regulation of immune response," "leukocyte cell-cell adhesion," and "natural killer cell-mediated cytotoxicity."…”

Section: Module Preservation Analysissupporting

confidence: 89%

“…Research has shown that MicroRNA-26b induces the NF-kB signaling pathway by directly targeting PTEN , which exacerbates inflammation in the lungs during infection with Gram-negative bacteria ( Zhang et al, 2015 ). Moreover, other hub–hub genes in the greenyellow module including ADAM10 ( Neupane et al, 2018 ), MGAT4A ( Johnston et al, 2021b ), and GSK3B ( Chao et al, 2019 ) were identified as important genes involved in BRD.…”

Section: Discussionmentioning

confidence: 99%

“…The yellow module showed that its genes were enriched in some important biological processes and KEGG pathways associated with BRD such as “neutrophil activation involved in immune response,” “regulation of inflammatory response,” “positive regulation of T-cell proliferation,” “MAPK signaling pathway,” “NF-kappa B signaling pathway,” “apoptosis,” “TNF signaling pathway,” “JAK-STAT signaling pathway,” and “Cytokine-cytokine receptor interaction.” Furthermore, examination of the relationship between the hub–hub genes of this module and BRD showed that many of these genes, such as IL1B ( Behura et al, 2017 ), IL15 ( Leach et al, 2012 ; Amat et al, 2019 ), CD68 ( Buchenau et al, 2010 ; Hermeyer et al, 2011 ), SOCS3 ( Ye et al, 2015 ; Zheng et al, 2015 ), NFKBIA , RAF1 , SGK1 ( Chao et al, 2019 ), ANXA1 ( Mitchell et al, 2008 ), MYD88 ( Dubbert et al, 2013 ), FAS ( Xu et al, 2012 ), CCR1 ( Lindholm-Perry et al, 2018 ), IFNAR2 ( Schlender et al, 2000 ), NFAM1 , NUDT3 ( Johnston et al, 2021b ), and SLC2A3 ( N’jai et al, 2013 ) as well as DDIT3 hub–hub TF ( Wang S. et al, 2020 ) have important effects on the interaction between the host and the pathogen. For example, stressful stimuli directly increase the expression level of the SGK1 (hub–hub gene), and consequently an upregulation in the expression of this gene leads to stimulate BoHV-1 and HSV-1 replication ( Kook and Jones, 2016 ; Zhu et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

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Integrated Network Analysis to Identify Key Modules and Potential Hub Genes Involved in Bovine Respiratory Disease: A Systems Biology Approach

et al. 2021

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Background: Bovine respiratory disease (BRD) is the most common disease in the beef and dairy cattle industry. BRD is a multifactorial disease resulting from the interaction between environmental stressors and infectious agents. However, the molecular mechanisms underlying BRD are not fully understood yet. Therefore, this study aimed to use a systems biology approach to systematically evaluate this disorder to better understand the molecular mechanisms responsible for BRD.Methods: Previously published RNA-seq data from whole blood of 18 healthy and 25 BRD samples were downloaded from the Gene Expression Omnibus (GEO) and then analyzed. Next, two distinct methods of weighted gene coexpression network analysis (WGCNA), i.e., module–trait relationships (MTRs) and module preservation (MP) analysis were used to identify significant highly correlated modules with clinical traits of BRD and non-preserved modules between healthy and BRD samples, respectively. After identifying respective modules by the two mentioned methods of WGCNA, functional enrichment analysis was performed to extract the modules that are biologically related to BRD. Gene coexpression networks based on the hub genes from the candidate modules were then integrated with protein–protein interaction (PPI) networks to identify hub–hub genes and potential transcription factors (TFs).Results: Four significant highly correlated modules with clinical traits of BRD as well as 29 non-preserved modules were identified by MTRs and MP methods, respectively. Among them, two significant highly correlated modules (identified by MTRs) and six nonpreserved modules (identified by MP) were biologically associated with immune response, pulmonary inflammation, and pathogenesis of BRD. After aggregation of gene coexpression networks based on the hub genes with PPI networks, a total of 307 hub–hub genes were identified in the eight candidate modules. Interestingly, most of these hub–hub genes were reported to play an important role in the immune response and BRD pathogenesis. Among the eight candidate modules, the turquoise (identified by MTRs) and purple (identified by MP) modules were highly biologically enriched in BRD. Moreover, STAT1, STAT2, STAT3, IRF7, and IRF9 TFs were suggested to play an important role in the immune system during BRD by regulating the coexpressed genes of these modules. Additionally, a gene set containing several hub–hub genes was identified in the eight candidate modules, such as TLR2, TLR4, IL10, SOCS3, GZMB, ANXA1, ANXA5, PTEN, SGK1, IFI6, ISG15, MX1, MX2, OAS2, IFIH1, DDX58, DHX58, RSAD2, IFI44, IFI44L, EIF2AK2, ISG20, IFIT5, IFITM3, OAS1Y, HERC5, and PRF1, which are potentially critical during infection with agents of bovine respiratory disease complex (BRDC).Conclusion: This study not only helps us to better understand the molecular mechanisms responsible for BRD but also suggested eight candidate modules along with several promising hub–hub genes as diagnosis biomarkers and therapeutic targets for BRD.

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Section: Discussionsupporting

confidence: 89%

Section: Module Preservation Analysissupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Integrated Network Analysis to Identify Key Modules and Potential Hub Genes Involved in Bovine Respiratory Disease: A Systems Biology Approach

et al. 2021

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“…Exosomes are membrane-bound small vesicles that have become the highlight of research in infectious diseases [1][2][3][4][5][6][7][8][9][10][11][12] . Several viruses perhaps use exosomes [small extracellular vesicles (EVs) of 30-120 nm, with infectious cargo] for transmission of viral RNA/proteins to the naïve recipient host cells [2][3][4][13][14][15][16][17][18][19][20][21][22] . Our previous studies have shown that arthropod-borne flavivirus full-length RNA genomes and proteins [such as Envelope protein, Non-Structural protein 1 (NS1) and/or polyprotein] are transmitted to the vertebrate host cells via arthropod exosomes [1,3,4,23] .…”

Section: Introductionmentioning

confidence: 99%

Alterations in arthropod and neuronal exosomes reduce virus transmission and replication in recipient cells

Fasae¹,

Neelakanta²,

Sultana³

2022

Extracell Vesicles Circ Nucleic Acids

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Aim: Targeting the modes of pathogen shedding/transmission via exosomes or extracellular vesicles has been envisioned as the best approach to control vector-borne diseases. This study is focused on altering exosomes stability to affect the pathogen transmission from infected to naïve recipient cells. Methods: In this study, neuronal or arthropod exosomes were treated at different temperatures or with different salts or pH conditions to analyze their ability and efficiency in the transmission of tick-borne Langat virus (LGTV) from infected to naïve recipient cells. Results: Quantitative real-time PCR (qRT-PCR) and immunoblotting analyses revealed that treatment of neuronal or tick exosomes at warmer temperatures of 37 °C or 23 °C, respectively, or with sulfate salts such as Magnesium or Ammonium sulfates or with highly alkaline pH of 9 or 11.5, dramatically reduced transmission of LGTV via infectious exosomes (human or tick cells-derived) to human neuronal (SH-SY5Y) cells or skin keratinocytes (HaCaT cells), respectively. Conclusion: Overall, this study suggests that exosome-mediated viral transmission of vector-borne pathogens to the vertebrate host or the viral dissemination and replication within or between the mammalian host can be reduced by altering the ability of exosomes with basic changes in temperatures, salts or pH conditions.

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Nanosensors for animal infectious disease detection

Rios,

Maximiano,

Feitosa

et al. 2024

Sensing and Bio-Sensing Research

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Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus

Cited by 6 publications

References 54 publications

Integrated Network Analysis to Identify Key Modules and Potential Hub Genes Involved in Bovine Respiratory Disease: A Systems Biology Approach

Integrated Network Analysis to Identify Key Modules and Potential Hub Genes Involved in Bovine Respiratory Disease: A Systems Biology Approach

Alterations in arthropod and neuronal exosomes reduce virus transmission and replication in recipient cells

Nanosensors for animal infectious disease detection

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