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      Transcriptional Response of Ovine Lung to Infection with Jaagsiekte Sheep Retrovirus

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          Abstract

          Ovine pulmonary adenocarcinoma is a chronic respiratory disease of sheep caused by jaagsiekte sheep retrovirus (JSRV). OPA is a significant economic problem for sheep farmers in many countries and is a valuable animal model for some forms of human lung cancer. Here, we examined the changes in host gene expression that occur in the lung in response to JSRV infection. We identified a large number of genes with altered expression in infected lung, including factors with roles in cancer and immune system function. We also compared the data from OPA to previously published data from human lung adenocarcinoma and found a large degree of overlap in the genes that were dysregulated. The results of this study provide exciting new avenues for future studies of OPA and may have comparative relevance for understanding human lung cancer.

          ABSTRACT

          Jaagsiekte sheep retrovirus (JSRV) is the etiologic agent of ovine pulmonary adenocarcinoma (OPA), a neoplastic lung disease of sheep. OPA is an important economic and welfare issue for sheep farmers and a valuable naturally occurring animal model for human lung adenocarcinoma. Here, we used RNA sequencing to study the transcriptional response of ovine lung tissue to infection by JSRV. We identified 1,971 ovine genes differentially expressed in JSRV-infected lung compared to noninfected lung, including many genes with roles in carcinogenesis and immunomodulation. The differential expression of selected genes was confirmed using immunohistochemistry and reverse transcription-quantitative PCR. A key finding was the activation of anterior gradient 2, yes-associated protein 1, and amphiregulin in OPA tumor cells, indicating a role for this oncogenic pathway in OPA. In addition, there was differential expression of genes related to innate immunity, including genes encoding cytokines, chemokines, and complement system proteins. In contrast, there was little evidence for the upregulation of genes involved in T-cell immunity. Many genes related to macrophage function were also differentially expressed, reflecting the increased abundance of these cells in OPA-affected lung tissue. Comparison of the genes differentially regulated in OPA with the transcriptional changes occurring in human lung cancer revealed important similarities and differences between OPA and human lung adenocarcinoma. This study provides valuable new information on the pathogenesis of OPA and strengthens the use of this naturally occurring animal model for human lung adenocarcinoma.

          IMPORTANCE Ovine pulmonary adenocarcinoma is a chronic respiratory disease of sheep caused by jaagsiekte sheep retrovirus (JSRV). OPA is a significant economic problem for sheep farmers in many countries and is a valuable animal model for some forms of human lung cancer. Here, we examined the changes in host gene expression that occur in the lung in response to JSRV infection. We identified a large number of genes with altered expression in infected lung, including factors with roles in cancer and immune system function. We also compared the data from OPA to previously published data from human lung adenocarcinoma and found a large degree of overlap in the genes that were dysregulated. The results of this study provide exciting new avenues for future studies of OPA and may have comparative relevance for understanding human lung cancer.

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          Macrophages are prominent in the stromal compartment of virtually all types of malignancy. These highly versatile cells respond to the presence of stimuli in different parts of tumors with the release of a distinct repertoire of growth factors, cytokines, chemokines, and enzymes that regulate tumor growth, angiogenesis, invasion, and/or metastasis. The distinct microenvironments where tumor-associated macrophages (TAM) act include areas of invasion where TAMs promote cancer cell motility, stromal and perivascular areas where TAMs promote metastasis, and avascular and perinecrotic areas where hypoxic TAMs stimulate angiogenesis. This review will discuss the evidence for differential regulation of TAMs in these microenvironments and provide an overview of current attempts to target or use TAMs for therapeutic purposes.
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            Following pathogen infection or tissue damage, the stimulation of pattern recognition receptors on the cell surface and in the cytoplasm of innate immune cells activates members of each of the major mitogen-activated protein kinase (MAPK) subfamilies--the extracellular signal-regulated kinase (ERK), p38 and Jun N-terminal kinase (JNK) subfamilies. In conjunction with the activation of nuclear factor-κB and interferon-regulatory factor transcription factors, MAPK activation induces the expression of multiple genes that together regulate the inflammatory response. In this Review, we discuss our current knowledge about the regulation and the function of MAPKs in innate immunity, as well as the importance of negative feedback loops in limiting MAPK activity to prevent host tissue damage. We also examine how pathogens have evolved complex mechanisms to manipulate MAPK activation to increase their virulence. Finally, we consider the potential of the pharmacological targeting of MAPK pathways to treat autoimmune and inflammatory diseases.
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              It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.

              RNA sequencing (RNA-seq) is widely used to profile transcriptional activity in biological systems. Here we present an analysis pipeline for differential expression analysis of RNA-seq experiments using the Rsubread and edgeR software packages. The basic pipeline includes read alignment and counting, filtering and normalization, modelling of biological variability and hypothesis testing. For hypothesis testing, we describe particularly the quasi-likelihood features of edgeR. Some more advanced downstream analysis steps are also covered, including complex comparisons, gene ontology enrichment analyses and gene set testing. The code required to run each step is described, along with an outline of the underlying theory. The chapter includes a case study in which the pipeline is used to study the expression profiles of mammary gland cells in virgin, pregnant and lactating mice.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                J Virol
                J. Virol
                jvi
                jvi
                JVI
                Journal of Virology
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                0022-538X
                1098-5514
                21 August 2019
                15 October 2019
                1 November 2019
                15 October 2019
                : 93
                : 21
                : e00876-19
                Affiliations
                [a ]Moredun Research Institute, Edinburgh, United Kingdom
                [b ]Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
                Ulm University Medical Center
                Author notes
                Address correspondence to David J. Griffiths, david.griffiths@ 123456moredun.ac.uk .
                [*]

                Present address: Anna Eleonora Karagianni, Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush, Midlothian, United Kingdom; Henny M. Martineau, Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom.

                Citation Karagianni AE, Vasoya D, Finlayson J, Martineau HM, Wood AR, Cousens C, Dagleish MP, Watson M, Griffiths DJ. 2019. Transcriptional response of ovine lung to infection with jaagsiekte sheep retrovirus. J Virol 93:e00876-19. https://doi.org/10.1128/JVI.00876-19.

                Author information
                https://orcid.org/0000-0003-4211-0358
                https://orcid.org/0000-0001-9160-0770
                Article
                00876-19
                10.1128/JVI.00876-19
                6803282
                31434729
                6de7c476-773d-4fc8-a2ba-e1577a98acc6
                Copyright © 2019 Karagianni et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 28 May 2019
                : 10 August 2019
                Page count
                supplementary-material: 6, Figures: 9, Tables: 3, Equations: 0, References: 81, Pages: 21, Words: 11957
                Funding
                Funded by: Scottish Government, https://doi.org/10.13039/100012095;
                Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Funded by: UK Research and Innovation | Biotechnology and Biological Sciences Research Council (BBSRC), https://doi.org/10.13039/501100000268;
                Award ID: BB/L009129/1
                Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Funded by: UK Research and Innovation | Biotechnology and Biological Sciences Research Council (BBSRC), https://doi.org/10.13039/501100000268;
                Award ID: BB/L008505/1
                Award Recipient : Award Recipient :
                Categories
                Pathogenesis and Immunity
                Custom metadata
                November 2019

                Microbiology & Virology
                jsrv,jaagsiekte,rna-seq,lung adenocarcinoma,sheep,cancer,ovine pulmonary adenocarcinoma,lung infection

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