1
|
Salamat MKF, Gossner A, Bradford B, Hunter N, Hopkins J, Houston F. Scrapie infection and endogenous retroviral expression in sheep lymphoid tissues. Vet Immunol Immunopathol 2021; 233:110194. [PMID: 33530020 DOI: 10.1016/j.vetimm.2021.110194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/28/2020] [Accepted: 01/08/2021] [Indexed: 01/09/2023]
Abstract
Transmissible spongiform encephalopathies, or prion diseases, are fatal neurodegenerative diseases affecting humans and animals. Although many host tissues express PrPC (essential for prion replication), relatively few cell types accumulate significant levels of infectivity, including neurons and other cell types in the nervous system, and follicular dendritic cells in secondary lymphoid organs. This suggests that tissue or cell-specific receptors or cofactors could play a role in controlling differential susceptibility to infection. Endogenous retroviruses (ERV), the remnants of ancient retroviral integration into the host germline, may represent one such cofactor. We examined the effect of scrapie infection on expression of three ovine ERV families (enJSRV/β1-OERV, γ1-OERV, γ2-OERV) in secondary lymphoid tissues of sheep at different time points following subcutaneous inoculation, using RT-qPCR. These OERVs were constitutively expressed in the prescapular lymph node and spleen of uninfected sheep. However, we were unable to find convincing evidence of specific differential expression of OERV in the same tissues following scrapie infection, in contrast to previous studies of ERV expression in brains of prion-infected mice and macaques. This study is the first to quantify the expression of potentially functional OERV transcripts in sheep lymphoid tissues, opening up interesting questions about the consequences for host immune function.
Collapse
Affiliation(s)
- M K F Salamat
- Division of Infection and Immunity, The Roslin Institute, R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - A Gossner
- Division of Infection and Immunity, The Roslin Institute, R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - B Bradford
- Division of Infection and Immunity, The Roslin Institute, R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - N Hunter
- Division of Infection and Immunity, The Roslin Institute, R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - J Hopkins
- Division of Infection and Immunity, The Roslin Institute, R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - F Houston
- Division of Infection and Immunity, The Roslin Institute, R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| |
Collapse
|
2
|
Muñoz-Gutiérrez JF, Aguilar Pierlé S, Schneider DA, Baszler TV, Stanton JB. Transcriptomic Determinants of Scrapie Prion Propagation in Cultured Ovine Microglia. PLoS One 2016; 11:e0147727. [PMID: 26807844 PMCID: PMC4726464 DOI: 10.1371/journal.pone.0147727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/07/2016] [Indexed: 12/22/2022] Open
Abstract
Susceptibility to infection by prions is highly dependent on the amino acid sequence and host expression of the cellular prion protein (PrPC); however, cellular expression of a genetically susceptible PrPC is insufficient. As an example, it has been shown in cultured cells that permissive and resistant sublines derived from the same parental population often have similar expression levels of PrPC. Thus, additional cellular factors must influence susceptibility to prion infection. The aim of this study was to elucidate the factors associated with relative permissiveness and resistance to scrapie prions in cultured cells derived from a naturally affected species. Two closely related ovine microglia clones with different prion susceptibility, but no detectable differences in PrPC expression levels, were inoculated with either scrapie-positive or scrapie-negative sheep brainstem homogenates. Five passages post-inoculation, the transcriptional profiles of mock and infected clones were sequenced using Illumina technology. Comparative transcriptional analyses identified twenty-two differentially transcribed genes, most of which were upregulated in poorly permissive microglia. This included genes encoding for selenoprotein P, endolysosomal proteases, and proteins involved in extracellular matrix remodeling. Furthermore, in highly permissive microglia, transforming growth factor β–induced, retinoic acid receptor response 1, and phosphoserine aminotranspherase 1 gene transcripts were upregulated. Gene Set Enrichment Analysis identified proteolysis, translation, and mitosis as the most affected pathways and supported the upregulation trend of several genes encoding for intracellular proteases and ribosomal proteins in poorly permissive microglia. This study identifies new genes potentially involved in scrapie prion propagation, corroborates results from other studies, and extends those results into another cell culture model.
Collapse
Affiliation(s)
- Juan F. Muñoz-Gutiérrez
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- * E-mail: (JFMG); (JBS)
| | - Sebastián Aguilar Pierlé
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - David A. Schneider
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- United States Department of Agriculture, Agricultural Research Service, Pullman, Washington, United States of America
| | - Timothy V. Baszler
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - James B. Stanton
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (JFMG); (JBS)
| |
Collapse
|
3
|
The effect of PrP(Sc) accumulation on inflammatory gene expression within sheep peripheral lymphoid tissue. Vet Microbiol 2015; 181:204-11. [PMID: 26507419 PMCID: PMC4678288 DOI: 10.1016/j.vetmic.2015.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/27/2015] [Accepted: 10/13/2015] [Indexed: 11/22/2022]
Abstract
Arrays quantified gene expression in peripheral LNs during sheep scrapie. Disease progression associated with alterations of inflammatory gene expression. Lymph node response contrasts with response of CNS. Step changes to gene expression after the detection of PrPSc in peripheral LNs.
Accumulation of the misfolded prion protein, PrPSc in the central nervous system (CNS) is strongly linked to progressive neurodegenerative disease. For many transmissible spongiform encephalopathies (TSEs), peripheral lymphoid tissue is an important site of PrPSc amplification but without gross immunological consequence. Susceptible VRQ homozygous New Zealand Cheviot sheep were infected with SSBP/1 scrapie by inoculation in the drainage area of the prescapular lymph nodes. The earliest time that PrPSc was consistently detected by immunohistology in these nodes was D50 post infection. This transcriptomic study of lymph node taken before (D10) and after (D50) the detection of PrPSc, aimed to identify the genes and physiological pathways affected by disease progression within the nodes as assessed by PrPSc detection. Affymetrix Ovine Gene arrays identified 75 and 80 genes as differentially-expressed at D10 and D50, respectively, in comparison with control sheep inoculated with uninfected brain homogenate. Approximately 70% of these were repressed at each time point. RT-qPCR analysis of seven genes showed statistically significant correlation with the array data, although the results for IL1RN and TGIF were different between the two technologies. The ingenuity pathway analysis (IPA) and general low level of repression of gene expression in lymphoid tissue, including many inflammatory genes, contrasts with the pro-inflammatory and pro-apoptotic events that occur within the CNS at equivalent stages of disease progression as assessed by PrPSc accumulation.
Collapse
|
4
|
Qiu X, Wu S, Hilchey SP, Thakar J, Liu ZP, Welle SL, Henn AD, Wu H, Zand MS. Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice. PLoS One 2015; 10:e0138110. [PMID: 26413862 PMCID: PMC4586376 DOI: 10.1371/journal.pone.0138110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/26/2015] [Indexed: 01/23/2023] Open
Abstract
Current approaches to study transcriptional profiles post influenza infection typically rely on tissue sampling from one or two sites at a few time points, such as spleen and lung in murine models. In this study, we infected female C57/BL6 mice intranasally with mouse-adapted H3N2/Hong Kong/X31 avian influenza A virus, and then analyzed the gene expression profiles in four different compartments (blood, lung, mediastinal lymph nodes, and spleen) over 11 consecutive days post infection. These data were analyzed by an advanced statistical procedure based on ordinary differential equation (ODE) modeling. Vastly different lists of significant genes were identified by the same statistical procedure in each compartment. Only 11 of them are significant in all four compartments. We classified significant genes in each compartment into co-expressed modules based on temporal expression patterns. We then performed functional enrichment analysis on these co-expression modules and identified significant pathway and functional motifs. Finally, we used an ODE based model to reconstruct gene regulatory network (GRN) for each compartment and studied their network properties.
Collapse
Affiliation(s)
- Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
| | - Shuang Wu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
| | - Shannon P. Hilchey
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642 United States of America
| | - Zhi-Ping Liu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- Department of Biomedical Engineering, Shandong University, Jinan, Shandong, China
| | - Stephen L. Welle
- Functional Genomics Center, University of Rochester, Rochester, NY, 14642, United States of America
| | - Alicia D. Henn
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642 United States of America
| | - Hulin Wu
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, United States of America
- * E-mail: (HW); (MSZ)
| | - Martin S. Zand
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- * E-mail: (HW); (MSZ)
| |
Collapse
|
5
|
Gossner AG, Hopkins J. Transcriptome analysis of CNS immediately before and after the detection of PrP(Sc) in SSBP/1 sheep scrapie. Vet Microbiol 2014; 173:201-7. [PMID: 25183238 PMCID: PMC4206282 DOI: 10.1016/j.vetmic.2014.07.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/25/2014] [Accepted: 07/27/2014] [Indexed: 11/18/2022]
Abstract
Arrays and DGE-tags quantified gene expression in the CNS during sheep scrapie. Neurological receptors were increased with disease progression. Clues to basis of psychiatric changes. Step changes to gene expression after the detection of PrPSc in CNS.
Sheep scrapie is a transmissible spongiform encephalopathy (TSE), progressive and fatal neurodegenerative diseases of the central nervous system (CNS) linked to the accumulation of misfolded prion protein, PrPSc. New Zealand Cheviot sheep, homozygous for the VRQ genotype of the PRNP gene are most susceptible with an incubation period of 193 days with SSBP/1 scrapie. However, the earliest time point that PrPSc can be detected in the CNS is 125 days (D125). The aim of this study was to quantify changes to the transcriptome of the thalamus and obex (medulla) at times immediately before (D75) and after (D125) PrPSc was detected. Affymetrix gene arrays were used to quantify gene expression in the thalamus and Illumina DGE-tag profiling for obex. Ingenuity Pathway Analysis was used to help describe the biological processes of scrapie pathology. Neurological disease and Cancer were common Bio Functions in each tissue at D75; inflammation and cell death were major processes at D125. Several neurological receptors were significantly increased at D75 (e.g. CHRNA6, GRM1, HCN2), which might be clues to the molecular basis of psychiatric changes associated with TSEs. No genes were significantly differentially expressed at both D75 and D125 and there was no progression of events from earlier to later time points. This implies that there is no simple linear progression of pathological or molecular events. There seems to be a step-change between D75 and D125, correlating with the detection of PrPSc, resulting in the involvement of different pathological processes in later TSE disease.
Collapse
Affiliation(s)
- Anton G Gossner
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, UK
| | - John Hopkins
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, UK.
| |
Collapse
|
6
|
Filali H, Martín-Burriel I, Harders F, Varona L, Hedman C, Mediano DR, Monzón M, Bossers A, Badiola JJ, Bolea R. Gene expression profiling of mesenteric lymph nodes from sheep with natural scrapie. BMC Genomics 2014; 15:59. [PMID: 24450868 PMCID: PMC3906094 DOI: 10.1186/1471-2164-15-59] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 01/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prion diseases are characterized by the accumulation of the pathogenic PrPSc protein, mainly in the brain and the lymphoreticular system. Although prions multiply/accumulate in the lymph nodes without any detectable pathology, transcriptional changes in this tissue may reflect biological processes that contribute to the molecular pathogenesis of prion diseases. Little is known about the molecular processes that occur in the lymphoreticular system in early and late stages of prion disease. We performed a microarray-based study to identify genes that are differentially expressed at different disease stages in the mesenteric lymph node of sheep naturally infected with scrapie. Oligo DNA microarrays were used to identify gene-expression profiles in the early/middle (preclinical) and late (clinical) stages of the disease. RESULTS In the clinical stage of the disease, we detected 105 genes that were differentially expressed (≥2-fold change in expression). Of these, 43 were upregulated and 62 downregulated as compared with age-matched negative controls. Fewer genes (50) were differentially expressed in the preclinical stage of the disease. Gene Ontology enrichment analysis revealed that the differentially expressed genes were largely associated with the following terms: glycoprotein, extracellular region, disulfide bond, cell cycle and extracellular matrix. Moreover, some of the annotated genes could be grouped into 3 specific signaling pathways: focal adhesion, PPAR signaling and ECM-receptor interaction. We discuss the relationship between the observed gene expression profiles and PrPSc deposition and the potential involvement in the pathogenesis of scrapie of 7 specific differentially expressed genes whose expression levels were confirmed by real time-PCR. CONCLUSIONS The present findings identify new genes that may be involved in the pathogenesis of natural scrapie infection in the lymphoreticular system, and confirm previous reports describing scrapie-induced alterations in the expression of genes involved in protein misfolding, angiogenesis and the oxidative stress response. Further studies will be necessary to determine the role of these genes in prion replication, dissemination and in the response of the organism to this disease.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rosa Bolea
- Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain.
| |
Collapse
|
7
|
Komolka K, Ponsuksili S, Schwerin M. Healthy sheep that differ in scrapie associated PRNP genotypes exhibit significant differences of expression pattern associated with immune response and cell-to-cell signalling in retropharyngeal lymph nodes. Vet Immunol Immunopathol 2013; 152:370-80. [PMID: 23428361 DOI: 10.1016/j.vetimm.2013.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 01/14/2013] [Accepted: 01/21/2013] [Indexed: 11/28/2022]
Abstract
The present study was conducted to test the hypothesis whether prion protein gene (PRNP) associated scrapie susceptibility is connected with physiological changes in tissue involved in pathogen uptake, migration and propagation. Jejunum, ileal Peyer's patches, retropharyngeal lymph nodes, brain stem and liver of healthy and non scrapie-infected sheep with PRNP genotypes representing the scrapie risk class R1 (scrapie-resistant) and R5 (scrapie-susceptible), respectively, were comparatively analysed by microarray technology and quantitative reverse transcriptase polymerase chain reaction (RT qPCR). Significantly higher expression levels of genes involved in immune response and cell communication pathways in retropharyngeal lymph nodes of R1 sheep in comparison with R5 animals strongly suggest PRNP associated physiological processes with impact as an early barrier in pathogen defence. Equal expression patterns in brain stem suggest no physiological differences in brain of healthy R1 and R5 animals. In addition, similar expression pattern in liver indicates that there are no transcriptional differences in genes of the hepatic energy metabolism between animals of scrapie classes R1 and R5.
Collapse
Affiliation(s)
- Katrin Komolka
- Research Group Functional Genomics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | | | | |
Collapse
|
8
|
Basu U, Guan LL, Moore SS. Functional genomics approach for identification of molecular processes underlying neurodegenerative disorders in prion diseases. Curr Genomics 2013; 13:369-78. [PMID: 23372423 PMCID: PMC3401894 DOI: 10.2174/138920212801619223] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 12/11/2022] Open
Abstract
Prion diseases or transmissible spongiform encephalopathies (TSEs) are infectious neurodegenerative disorders leading to death. These include Cresutzfeldt-Jakob disease (CJD), familial, sporadic and variant CJD and kuru in humans; and animal TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) of mule deer and elk, and transmissible mink encephalopathy. All these TSEs share common pathological features such as accumulation of mis-folded prion proteins in the central nervous system leading to cellular dysfunction and cell death. It is important to characterize the molecular pathways and events leading to prion induced neurodegeneration. Here we discuss the impact of the functional genomics approaches including microarrays, subtractive hybridization and microRNA profiling in elucidating transcriptional cascades at different stages of disease. Many of these transcriptional changes have been observed in multiple neurodegenerative diseases which may aid in identification of biomarkers for disease. A comprehensive characterization of expression profiles implicated in neurodegenerative disorders will undoubtedly advance our understanding on neuropathology and dysfunction during prion disease and other neurodegenerative disorders. We also present an outlook on the future work which may focus on analysis of structural genetic variation, genome and transcriptome sequencing using next generation sequencing with an integrated approach on animal and human TSE related studies.
Collapse
Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | | | | |
Collapse
|
9
|
Bradford BM, Mabbott NA. Prion disease and the innate immune system. Viruses 2012; 4:3389-419. [PMID: 23342365 PMCID: PMC3528271 DOI: 10.3390/v4123389] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/14/2012] [Accepted: 11/22/2012] [Indexed: 02/06/2023] Open
Abstract
Prion diseases or transmissible spongiform encephalopathies are a unique category of infectious protein-misfolding neurodegenerative disorders. Hypothesized to be caused by misfolding of the cellular prion protein these disorders possess an infectious quality that thrives in immune-competent hosts. While much has been discovered about the routing and critical components involved in the peripheral pathogenesis of these agents there are still many aspects to be discovered. Research into this area has been extensive as it represents a major target for therapeutic intervention within this group of diseases. The main focus of pathological damage in these diseases occurs within the central nervous system. Cells of the innate immune system have been proven to be critical players in the initial pathogenesis of prion disease, and may have a role in the pathological progression of disease. Understanding how prions interact with the host innate immune system may provide us with natural pathways and mechanisms to combat these diseases prior to their neuroinvasive stage. We present here a review of the current knowledge regarding the role of the innate immune system in prion pathogenesis.
Collapse
Affiliation(s)
- Barry M Bradford
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | | |
Collapse
|