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Mercer RCC, Harris DA. Mechanisms of prion-induced toxicity. Cell Tissue Res 2022; 392:81-96. [PMID: 36070155 DOI: 10.1007/s00441-022-03683-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/30/2022] [Indexed: 11/02/2022]
Abstract
Prion diseases are devastating neurodegenerative diseases caused by the structural conversion of the normally benign prion protein (PrPC) to an infectious, disease-associated, conformer, PrPSc. After decades of intense research, much is known about the self-templated prion conversion process, a phenomenon which is now understood to be operative in other more common neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide the current state of knowledge concerning a relatively poorly understood aspect of prion diseases: mechanisms of neurotoxicity. We provide an overview of proposed functions of PrPC and its interactions with other extracellular proteins in the central nervous system, in vivo and in vitro models used to delineate signaling events downstream of prion propagation, the application of omics technologies, and the emerging appreciation of the role played by non-neuronal cell types in pathogenesis.
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Affiliation(s)
- Robert C C Mercer
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
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Mice Treated Subcutaneously with Mouse LPS-Converted PrP res or LPS Alone Showed Brain Gene Expression Profiles Characteristic of Prion Disease. Vet Sci 2021; 8:vetsci8090200. [PMID: 34564594 PMCID: PMC8473295 DOI: 10.3390/vetsci8090200] [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: 08/02/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
Previously, we showed that bacterial lipopolysaccharide (LPS) converts mouse PrPC protein to a beta-rich isoform (moPrPres) resistant to proteinase K. In this study, we aimed to test if the LPS-converted PrPres is infectious and alters the expression of genes related to prion pathology in brains of terminally sick mice. Ninety female FVB/N mice at 5 weeks of age were randomly assigned to 6 groups treated subcutaneously (sc) for 6 weeks either with: (1) Saline (CTR); (2) LPS from Escherichia coli 0111:B4 (LPS), (3) one-time sc administration of de novo generated mouse recombinant prion protein (moPrP; 29-232) rich in beta-sheet by incubation with LPS (moPrPres), (4) LPS plus one-time sc injection of moPrPres, (5) one-time sc injection of brain homogenate from Rocky Mountain Lab (RLM) scrapie strain, and (6) LPS plus one-time sc injection of RML. Results showed that all treatments altered the expression of various genes related to prion disease and neuroinflammation starting at 11 weeks post-infection and more profoundly at the terminal stage. In conclusion, sc administration of de novo generated moPrPres, LPS, and a combination of moPrPres with LPS were able to alter the expression of multiple genes typical of prion pathology and inflammation.
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Transcriptional signature of prion-induced neurotoxicity in a Drosophila model of transmissible mammalian prion disease. Biochem J 2020; 477:833-852. [PMID: 32108870 PMCID: PMC7054746 DOI: 10.1042/bcj20190872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/14/2020] [Accepted: 01/31/2020] [Indexed: 12/11/2022]
Abstract
Prion diseases are fatal transmissible neurodegenerative conditions of humans and animals that arise through neurotoxicity induced by PrP misfolding. The cellular and molecular mechanisms of prion-induced neurotoxicity remain undefined. Understanding these processes will underpin therapeutic and control strategies for human and animal prion diseases, respectively. Prion diseases are difficult to study in their natural hosts and require the use of tractable animal models. Here we used RNA-Seq-based transcriptome analysis of prion-exposed Drosophila to probe the mechanism of prion-induced neurotoxicity. Adult Drosophila transgenic for pan neuronal expression of ovine PrP targeted to the plasma membrane exhibit a neurotoxic phenotype evidenced by decreased locomotor activity after exposure to ovine prions at the larval stage. Pathway analysis and quantitative PCR of genes differentially expressed in prion-infected Drosophila revealed up-regulation of cell cycle activity and DNA damage response, followed by down-regulation of eIF2 and mTOR signalling. Mitochondrial dysfunction was identified as the principal toxicity pathway in prion-exposed PrP transgenic Drosophila. The transcriptomic changes we observed were specific to PrP targeted to the plasma membrane since these prion-induced gene expression changes were not evident in similarly treated Drosophila transgenic for cytosolic pan neuronal PrP expression, or in non-transgenic control flies. Collectively, our data indicate that aberrant cell cycle activity, repression of protein synthesis and altered mitochondrial function are key events involved in prion-induced neurotoxicity, and correlate with those identified in mammalian hosts undergoing prion disease. These studies highlight the use of PrP transgenic Drosophila as a genetically well-defined tractable host to study mammalian prion biology.
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Lathe R, Darlix JL. Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy. Arch Virol 2020; 165:535-556. [PMID: 32025859 PMCID: PMC7024060 DOI: 10.1007/s00705-020-04529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022]
Abstract
The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh School of Medicine, Edinburgh, UK. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Moscow Region, Russia.
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Laboratory of Bioimaging and Pathologies (Unité Mixte de Recherche 7021), Université de Strasbourg, Illkirch, France.
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5
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Region-specific glial homeostatic signature in prion diseases is replaced by a uniform neuroinflammation signature, common for brain regions and prion strains with different cell tropism. Neurobiol Dis 2020; 137:104783. [PMID: 32001329 DOI: 10.1016/j.nbd.2020.104783] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 02/08/2023] Open
Abstract
Chronic neuroinflammation is recognized as a major neuropathological hallmark in a broad spectrum of neurodegenerative diseases including Alzheimer's, Parkinson's, Frontal Temporal Dementia, Amyotrophic Lateral Sclerosis, and prion diseases. Both microglia and astrocytes exhibit region-specific homeostatic transcriptional identities, which under chronic neurodegeneration, transform into reactive phenotypes in a region- and disease-specific manner. Little is known about region-specific identity of glia in prion diseases. The current study was designed to determine whether the region-specific homeostatic signature of glia changes with the progression of prion diseases, and whether these changes occur in a region-dependent or universal manner. Also of interest was whether different prion strains give rise to different reactive phenotypes. To answer these questions, we analyzed gene expression in the thalamus, cortex, hypothalamus and hippocampus of mice infected with 22L and ME7 prion strains using a Nanostring Neuroinflammation panel at the subclinical, early clinical and advanced stages of the disease. We found that at the preclinical stage of the disease, the region-specific homeostatic identities were preserved. However, with the appearance of clinical signs, the region-specific signatures were partially lost and replaced with a neuroinflammation signature. While the same sets of genes were activated by both prion strains, the timing of neuroinflammation and the degree of activation in different brain regions was strain-specific. Changes in astrocyte function scored at the top of the activated pathways. Moreover, clustering analysis suggested that the astrocyte function pathway responded to prion infection prior to the Activated Microglia or Neuron and Neurotransmission pathways. The current work established neuroinflammation gene expression signature associated with prion diseases. Our results illustrate that with the disease progression, the region-specific homeostatic transcriptome signatures are replaced by the region-independent neuroinflammation signature, which is common for prion strains with different cell tropism. The prion-associated neuroinflammation signature identified in the current study overlapped only partially with the microglia degenerative phenotype and the disease-associated microglia phenotype reported for animal models of other neurodegenerative diseases.
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Abstract
Complex diseases involve dynamic perturbations of pathophysiological processes during disease progression. Transcriptional programs underlying such perturbations are unknown in many diseases. Here, we present core transcriptional regulatory circuits underlying early and late perturbations in prion disease. We first identified cellular processes perturbed early and late using time-course gene expression data from three prion-infected mouse strains. We then built a transcriptional regulatory network (TRN) describing regulation of early and late processes. We found over-represented feed-forward loops (FFLs) comprising transcription factor (TF) pairs and target genes in the TRN. Using gene expression data of brain cell types, we further selected active FFLs where TF pairs and target genes were expressed in the same cell type and showed correlated temporal expression changes in the brain. We finally determined core transcriptional regulatory circuits by combining these active FFLs. These circuits provide insights into transcriptional programs for early and late pathophysiological processes in prion disease.
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Abstract
Prion diseases are fatal neurodegenerative disorders characterized by rapidly progressive dementia. Sporadic Creutzfeldt–Jakob disease (sCJD) is the most prevalent. We report that, specific gene-expression alterations utilizing a reliable in vivo mouse model (tg340-PRNP129MM) with sCJD MM1 subtype, correlate with human disease manifestations in the brain cortex related to disease progression. RNA-editing functions mediated by the APOBEC and ADAR deaminases possibly affecting protein expression necessary for normal brain function, are altered in disease stages. Our data provide powerful evidence, derived from a humanized sCJD mouse model and human autopsy material, discerning the critical role of gene expression and RNA-editing signatures, introducing disease-associated targets that can be extrapolated in other neurodegenerative disorders with common clinical and molecular features. Prion diseases are fatal neurodegenerative disorders caused by misfolding of the normal prion protein into an infectious cellular pathogen. Clinically characterized by rapidly progressive dementia and accounting for 85% of human prion disease cases, sporadic Creutzfeldt–Jakob disease (sCJD) is the prevalent human prion disease. Although sCJD neuropathological hallmarks are well-known, associated molecular alterations are elusive due to rapid progression and absence of preclinical stages. To investigate transcriptome alterations during disease progression, we utilized tg340-PRNP129MM mice infected with postmortem material from sCJD patients of the most susceptible genotype (MM1 subtype), a sCJD model that faithfully recapitulates the molecular and pathological alterations of the human disease. Here we report that transcriptomic analyses from brain cortex in the context of disease progression, reveal epitranscriptomic alterations (specifically altered RNA edited pathway profiles, eg., ER stress, lysosome) that are characteristic and possibly protective mainly for preclinical and clinical disease stages. Our results implicate regulatory epitranscriptomic mechanisms in prion disease neuropathogenesis, whereby RNA-editing targets in a humanized sCJD mouse model were confirmed in pathological human autopsy material.
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Bistaffa E, Rossi M, De Luca CMG, Cazzaniga F, Carletta O, Campagnani I, Tagliavini F, Legname G, Giaccone G, Moda F. Prion Efficiently Replicates in α-Synuclein Knockout Mice. Mol Neurobiol 2019; 56:7448-7457. [PMID: 31041657 DOI: 10.1007/s12035-019-1602-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 10/26/2022]
Abstract
Prion diseases are a group of neurodegenerative disorders associated with the conformational conversion of the cellular prion protein (PrPC) into an abnormal misfolded form named PrPSc. Other than accumulating in the brain, PrPSc can bind PrPC and force it to change conformation to PrPSc. The exact mechanism which underlies the process of PrPC/PrPSc conversion still needs to be defined and many molecules or cofactors might be involved. Several studies have documented an important role of PrPC to act as receptor for abnormally folded forms of α-synuclein which are responsible of a group of diseases known as synucleinopathies. The presence of PrPC was required to promote efficient internalization and spreading of abnormal α-synuclein between cells. In this work, we have assessed whether α-synuclein exerts any role in PrPSc conversion and propagation either in vitro or in vivo. Indeed, understanding the mechanism of PrPC/PrPSc conversion and the identification of cofactors involved in this process is crucial for developing new therapeutic strategies. Our results showed that PrPSc was able to efficiently propagate in the brain of animals even in the absence of α-synuclein thus suggesting that this protein did not act as key modulator of prion propagation. Thus, α-synuclein might take part in this process but is not specifically required for sustaining prion conversion and propagation.
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Affiliation(s)
- Edoardo Bistaffa
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Martina Rossi
- Department of Neuroscience, Laboratory of Prion Biology, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Chiara Maria Giulia De Luca
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Neuroscience, Laboratory of Prion Biology, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Federico Cazzaniga
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Olga Carletta
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Ilaria Campagnani
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Fabrizio Tagliavini
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giuseppe Legname
- Department of Neuroscience, Laboratory of Prion Biology, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Giorgio Giaccone
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Fabio Moda
- Unit of Neuropathology and Neurology 5, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
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Neuroinflammation, Microglia, and Cell-Association during Prion Disease. Viruses 2019; 11:v11010065. [PMID: 30650564 PMCID: PMC6356204 DOI: 10.3390/v11010065] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Prion disorders are transmissible diseases caused by a proteinaceous infectious agent that can infect the lymphatic and nervous systems. The clinical features of prion diseases can vary, but common hallmarks in the central nervous system (CNS) are deposition of abnormally folded protease-resistant prion protein (PrPres or PrPSc), astrogliosis, microgliosis, and neurodegeneration. Numerous proinflammatory effectors expressed by astrocytes and microglia are increased in the brain during prion infection, with many of them potentially damaging to neurons when chronically upregulated. Microglia are important first responders to foreign agents and damaged cells in the CNS, but these immune-like cells also serve many essential functions in the healthy CNS. Our current understanding is that microglia are beneficial during prion infection and critical to host defense against prion disease. Studies indicate that reduction of the microglial population accelerates disease and increases PrPSc burden in the CNS. Thus, microglia are unlikely to be a foci of prion propagation in the brain. In contrast, neurons and astrocytes are known to be involved in prion replication and spread. Moreover, certain astrocytes, such as A1 reactive astrocytes, have proven neurotoxic in other neurodegenerative diseases, and thus might also influence the progression of prion-associated neurodegeneration.
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Carroll JA, Race B, Williams K, Chesebro B. Toll-like receptor 2 confers partial neuroprotection during prion disease. PLoS One 2018; 13:e0208559. [PMID: 30596651 PMCID: PMC6312208 DOI: 10.1371/journal.pone.0208559] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Neuroinflammation and neurodegeneration are common during prion infection, but the mechanisms that underlie these pathological features are not well understood. Several components of innate immunity, such as Toll-like receptor (TLR) 4 and Complement C1q, have been shown to influence prion disease. To identify additional components of innate immunity that might impact prion disease within the central nervous system (CNS), we screened RNA from brains of pre-clinical and clinical 22L-infected mice for alterations in genes associated with innate immunity. Transcription of several genes encoding damage-associated molecular pattern (DAMP) proteins and receptors were increased in the brains of prion-infected mice. To investigate the role of some of these proteins in prion disease of the CNS, we infected mice deficient in DAMP receptor genes Tlr2, C3ar1, and C5ar1 with 22L scrapie. Elimination of TLR2 accelerated disease by a median of 10 days, while lack of C3aR1 or C5aR1 had no effect on disease tempo. Histopathologically, all knockout mouse strains tested were similar to infected control mice in gliosis, vacuolation, and PrPSc deposition. Analysis of proinflammatory markers in the brains of infected knockout mice indicated only a few alterations in gene expression suggesting that C5aR1 and TLR2 signaling did not act synergistically in the brains of prion-infected mice. These results indicate that signaling through TLR2 confers partial neuroprotection during prion infection.
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Affiliation(s)
- James A. Carroll
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Brent Race
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Katie Williams
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Bruce Chesebro
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
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Vanni S, Zattoni M, Moda F, Giaccone G, Tagliavini F, Haïk S, Deslys JP, Zanusso G, Ironside JW, Carmona M, Ferrer I, Kovacs GG, Legname G. Hemoglobin mRNA Changes in the Frontal Cortex of Patients with Neurodegenerative Diseases. Front Neurosci 2018; 12:8. [PMID: 29403351 PMCID: PMC5786544 DOI: 10.3389/fnins.2018.00008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023] Open
Abstract
Background: Hemoglobin is the major protein found in erythrocytes, where it acts as an oxygen carrier molecule. In recent years, its expression has been reported also in neurons and glial cells, although its role in brain tissue remains still unknown. Altered hemoglobin expression has been associated with various neurodegenerative disorders. Here, we investigated hemoglobin mRNA levels in brains of patients affected by variant, iatrogenic, and sporadic forms of Creutzfeldt-Jakob disease (vCJD, iCJD, sCJD, respectively) and in different genetic forms of prion diseases (gPrD) in comparison to Alzheimer's disease (AD) subjects and age-matched controls. Methods: Total RNA was obtained from the frontal cortex of vCJD (n = 20), iCJD (n = 11), sCJD (n = 23), gPrD (n = 30), and AD (n = 14) patients and age-matched controls (n = 30). RT-qPCR was performed for hemoglobin transcripts HBB and HBA1/2 using four reference genes for normalization. In addition, expression analysis of the specific erythrocyte marker ALAS2 was performed in order to account for blood contamination of the tissue samples. Hba1/2 and Hbb protein expression was then investigated with immunofluorescence and confocal microscope analysis. Results: We observed a significant up-regulation of HBA1/2 in vCJD brains together with a significant down-regulation of HBB in iCJD. In addition, while in sporadic and genetic forms of prion disease hemoglobin transcripts did not shown any alterations, both chains display a strong down-regulation in AD brains. These results were confirmed also at a protein level. Conclusions: These data indicate distinct hemoglobin transcriptional responses depending on the specific alterations occurring in different neurodegenerative diseases. In particular, the initial site of misfolding event (central nervous system vs. peripheral tissue)-together with specific molecular and conformational features of the pathological agent of the disease-seem to dictate the peculiar hemoglobin dysregulation found in prion and non-prion neurodegenerative disorders. In addition, these results suggest that gene expression of HBB and HBA1/2 in brain tissue is differentially affected by distinct prion and prion-like aggregating protein strains. Validation of these results in more accessible tissues could prompt the development of novel diagnostic tests for neurodegenerative disorders.
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Affiliation(s)
- Silvia Vanni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Marco Zattoni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Fabio Moda
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Giorgio Giaccone
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Fabrizio Tagliavini
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Stéphane Haïk
- UPMC Univ Paris 06 UMR S 1127 and Centre National de la Recherche Scientifique UMR 7225, ICM, Sorbonne Universités, Paris, France
| | | | - Gianluigi Zanusso
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - James W Ironside
- National CJD Research and Surveillance Unit, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Margarita Carmona
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Isidre Ferrer
- Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Bellvitge University Hospital (CIBERNED), Hospitalet de LLobregat, Spain
| | - Gabor G Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
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Abstract
Prion diseases are unique neurodegenerative pathologies that can occur with sporadic, genetic, and acquired etiologies. Human and animal prion diseases can be recapitulated in laboratory animals with good reproducibility providing highly controlled models for studying molecular mechanisms of neurodegeneration. In this chapter the overall area of omics research in prion diseases is described. The term omics includes all fields of studies that employ a comprehensive, unbiased, and high-throughput approach to areas of research such as functional genomics, transcriptomics, and proteomics. These kind of approaches can be extremely helpful in identifying disease susceptibility factors and pathways that are dysregulated upon the onset and the progression of the disease. Herein, the most important research about the various forms of prion pathologies in human and in models of prion diseases in animals is presented and discussed.
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13
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The role of extracellular vesicles in neurodegenerative diseases. Biochem Biophys Res Commun 2017; 483:1178-1186. [DOI: 10.1016/j.bbrc.2016.09.090] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/08/2016] [Accepted: 09/18/2016] [Indexed: 01/09/2023]
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Alibhai J, Blanco RA, Barria MA, Piccardo P, Caughey B, Perry VH, Freeman TC, Manson JC. Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration. PLoS Biol 2016; 14:e1002579. [PMID: 27880767 PMCID: PMC5120774 DOI: 10.1371/journal.pbio.1002579] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022] Open
Abstract
Protein misfolding is common across many neurodegenerative diseases, with misfolded proteins acting as seeds for "prion-like" conversion of normally folded protein to abnormal conformations. A central hypothesis is that misfolded protein accumulation, spread, and distribution are restricted to specific neuronal populations of the central nervous system and thus predict regions of neurodegeneration. We examined this hypothesis using a highly sensitive assay system for detection of misfolded protein seeds in a murine model of prion disease. Misfolded prion protein (PrP) seeds were observed widespread throughout the brain, accumulating in all brain regions examined irrespective of neurodegeneration. Importantly, neither time of exposure nor amount of misfolded protein seeds present determined regions of neurodegeneration. We further demonstrate two distinct microglia responses in prion-infected brains: a novel homeostatic response in all regions and an innate immune response restricted to sites of neurodegeneration. Therefore, accumulation of misfolded prion protein alone does not define targeting of neurodegeneration, which instead results only when misfolded prion protein accompanies a specific innate immune response. The distribution of misfolded prion protein seeding activity alone does not predict regions of neurodegeneration in prion disease; rather, a complex microglial response appears to determine selective vulnerability and provides new strategies for therapy. Normal brain function requires tight regulation of protein folding; when this goes wrong, proteins can fold into abnormal conformations, which have severe impacts on brain performance, leading to conditions like dementia. Previous studies show that abnormally folded proteins are found in restricted parts of the brain, and neuronal cells in these specific brain regions have been shown to undergo degeneration. Recent technological advances have enhanced the detection of abnormally folded prion protein (PrP) during disease; we used these technologies to test whether distribution of abnormally folded proteins is indeed restricted to regions of the brain undergoing degeneration. Surprisingly, we observed abnormally folded proteins throughout the brain, demonstrating that these proteins can accumulate in parts of the brain that do not show degeneration. Thus, the distribution of abnormally folded protein, by itself, is not sufficient for neuronal degeneration. In addition, we found that microglia (one of the nonneuronal cell types in the brain) change their response during prion disease in two different ways; one response is associated with resilient brain regions, and the second, an inflammatory response is associated with regions susceptible to degeneration. Thus, the microglial response appears to be important in determining the outcome of disease.
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Affiliation(s)
- James Alibhai
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard A. Blanco
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Marcelo A. Barria
- The National CJD Research and Surveillance Unit, Centre for Clinical Brain Sciences, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Pedro Piccardo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - V. Hugh Perry
- Centre for Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Tom C. Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jean C. Manson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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15
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Xerxa E, Barbisin M, Chieppa MN, Krmac H, Vallino Costassa E, Vatta P, Simmons M, Caramelli M, Casalone C, Corona C, Legname G. Whole Blood Gene Expression Profiling in Preclinical and Clinical Cattle Infected with Atypical Bovine Spongiform Encephalopathy. PLoS One 2016; 11:e0153425. [PMID: 27073865 PMCID: PMC4830546 DOI: 10.1371/journal.pone.0153425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022] Open
Abstract
Prion diseases, such as bovine spongiform encephalopathies (BSE), are transmissible neurodegenerative disorders affecting humans and a wide variety of mammals. Variant Creutzfeldt-Jakob disease (vCJD), a prion disease in humans, has been linked to exposure to BSE prions. This classical BSE (cBSE) is now rapidly disappearing as a result of appropriate measures to control animal feeding. Besides cBSE, two atypical forms (named H- and L-type BSE) have recently been described in Europe, Japan, and North America. Here we describe the first wide-spectrum microarray analysis in whole blood of atypical BSE-infected cattle. Transcriptome changes in infected animals were analyzed prior to and after the onset of clinical signs. The microarray analysis revealed gene expression changes in blood prior to the appearance of the clinical signs and during the progression of the disease. A set of 32 differentially expressed genes was found to be in common between clinical and preclinical stages and showed a very similar expression pattern in the two phases. A 22-gene signature showed an oscillating pattern of expression, being differentially expressed in the preclinical stage and then going back to control levels in the symptomatic phase. One gene, SEL1L3, was downregulated during the progression of the disease. Most of the studies performed up to date utilized various tissues, which are not suitable for a rapid analysis of infected animals and patients. Our findings suggest the intriguing possibility to take advantage of whole blood RNA transcriptional profiling for the preclinical identification of prion infection. Further, this study highlighted several pathways, such as immune response and metabolism that may play an important role in peripheral prion pathogenesis. Finally, the gene expression changes identified in the present study may be further investigated as a fingerprint for monitoring the progression of disease and for developing targeted therapeutic interventions.
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Affiliation(s)
- Elena Xerxa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Maura Barbisin
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Maria Novella Chieppa
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Helena Krmac
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Elena Vallino Costassa
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Paolo Vatta
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
| | - Marion Simmons
- Pathology Department, Animal and Plant Health Agency (Weybridge), New Haw, Addlestone, United Kingdom
| | - Maria Caramelli
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Cristina Casalone
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Cristiano Corona
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
| | - Giuseppe Legname
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Functional and Structural Genomics sector, Trieste, Italy
- * E-mail:
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Carroll JA, Striebel JF, Rangel A, Woods T, Phillips K, Peterson KE, Race B, Chesebro B. Prion Strain Differences in Accumulation of PrPSc on Neurons and Glia Are Associated with Similar Expression Profiles of Neuroinflammatory Genes: Comparison of Three Prion Strains. PLoS Pathog 2016; 12:e1005551. [PMID: 27046083 PMCID: PMC4821575 DOI: 10.1371/journal.ppat.1005551] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
Misfolding and aggregation of host proteins are important features of the pathogenesis of neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia and prion diseases. In all these diseases, the misfolded protein increases in amount by a mechanism involving seeded polymerization. In prion diseases, host prion protein is misfolded to form a pathogenic protease-resistant form, PrPSc, which accumulates in neurons, astroglia and microglia in the CNS. Here using dual-staining immunohistochemistry, we compared the cell specificity of PrPSc accumulation at early preclinical times post-infection using three mouse scrapie strains that differ in brain regional pathology. PrPSc from each strain had a different pattern of cell specificity. Strain 22L was mainly associated with astroglia, whereas strain ME7 was mainly associated with neurons and neuropil. In thalamus and cortex, strain RML was similar to 22L, but in substantia nigra, RML was similar to ME7. Expression of 90 genes involved in neuroinflammation was studied quantitatively using mRNA from thalamus at preclinical times. Surprisingly, despite the cellular differences in PrPSc accumulation, the pattern of upregulated genes was similar for all three strains, and the small differences observed correlated with variations in the early disease tempo. Gene upregulation correlated with activation of both astroglia and microglia detected in early disease prior to vacuolar pathology or clinical signs. Interestingly, the profile of upregulated genes in scrapie differed markedly from that seen in two acute viral CNS diseases (LaCrosse virus and BE polytropic Friend retrovirus) that had reactive gliosis at levels similar to our prion-infected mice. Accumulation of aggregates of misfolded protein in brain is a common feature of the damage seen in several neurodegenerative diseases including prion disease, Alzheimer’s disease and Parkinson’s disease. In the present work three strains of prion disease differed in accumulation of the disease-associated prion protein (PrPSc) on neurons and astroglial cells. These patterns were first detectable in the thalamus at 40–60 days after inoculation. This coincided with initial detection of gliosis and PrPSc deposition, but was far in advance of clinical signs or spongiform pathology. In spite of the different patterns of cellular PrPSc deposition, these three strains had similar patterns of expression of a large number of genes known to be active during neuroinflammatory responses and gliosis. However, the gene upregulation in scrapie differed markedly from that seen in two neurovirulent viral diseases, which also had abundant glial responses similar to those observed with prion infection.
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Affiliation(s)
- James A. Carroll
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - James F. Striebel
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Alejandra Rangel
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Tyson Woods
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Katie Phillips
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Karin E. Peterson
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brent Race
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Bruce Chesebro
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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Newaz K, Sriram K, Bera D. Identification of Major Signaling Pathways in Prion Disease Progression Using Network Analysis. PLoS One 2015; 10:e0144389. [PMID: 26646948 PMCID: PMC4672924 DOI: 10.1371/journal.pone.0144389] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/17/2015] [Indexed: 12/27/2022] Open
Abstract
Prion diseases are transmissible neurodegenerative diseases that arise due to conformational change of normal, cellular prion protein (PrPC) to protease-resistant isofrom (rPrPSc). Deposition of misfolded PrpSc proteins leads to an alteration of many signaling pathways that includes immunological and apoptotic pathways. As a result, this culminates in the dysfunction and death of neuronal cells. Earlier works on transcriptomic studies have revealed some affected pathways, but it is not clear which is (are) the prime network pathway(s) that change during the disease progression and how these pathways are involved in crosstalks with each other from the time of incubation to clinical death. We perform network analysis on large-scale transcriptomic data of differentially expressed genes obtained from whole brain in six different mouse strain-prion strain combination models to determine the pathways involved in prion diseases, and to understand the role of crosstalks in disease propagation. We employ a notion of differential network centrality measures on protein interaction networks to identify the potential biological pathways involved. We also propose a crosstalk ranking method based on dynamic protein interaction networks to identify the core network elements involved in crosstalk with different pathways. We identify 148 DEGs (differentially expressed genes) potentially related to the prion disease progression. Functional association of the identified genes implicates a strong involvement of immunological pathways. We extract a bow-tie structure that is potentially dysregulated in prion disease. We also propose an ODE model for the bow-tie network. Predictions related to diseased condition suggests the downregulation of the core signaling elements (PI3Ks and AKTs) of the bow-tie network. In this work, we show using transcriptomic data that the neuronal dysfunction in prion disease is strongly related to the immunological pathways. We conclude that these immunological pathways occupy influential positions in the PFNs (protein functional networks) that are related to prion disease. Importantly, this functional network involvement is prevalent in all the five different mouse strain-prion strain combinations that we studied. We also conclude that the dysregulation of the core elements of the bow-tie structure, which belongs to PI3K-Akt signaling pathway, leads to dysregulation of the downstream components corresponding to other biological pathways.
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Affiliation(s)
- Khalique Newaz
- Department of Computer Science, IIIT Delhi, New Delhi, India
| | - K. Sriram
- Center for Computational Biology, IIIT Delhi, New Delhi, India
| | - Debajyoti Bera
- Department of Computer Science, IIIT Delhi, New Delhi, India
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18
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Abstract
Prion diseases are a heterogeneous class of fatal neurodegenerative disorders associated with misfolding of host cellular prion protein (PrP(C)) into a pathological isoform, termed PrP(Sc). Prion diseases affect various mammals, including humans, and effective treatments are not available. Prion diseases are distinguished from other protein misfolding disorders - such as Alzheimer's or Parkinson's disease - in that they are infectious. Prion diseases occur sporadically without any known exposure to infected material, and hereditary cases resulting from rare mutations in the prion protein have also been documented. The mechanistic underpinnings of prion and other neurodegenerative disorders remain poorly understood. Various proteomics techniques have been instrumental in early PrP(Sc) detection, biomarker discovery, elucidation of PrP(Sc) structure and mapping of biochemical pathways affected by pathogenesis. Moving forward, proteomics approaches will likely become more integrated into the clinical and research settings for the rapid diagnosis and characterization of prion pathogenesis.
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Affiliation(s)
- Roger A Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIH,NIAID, Hamilton, MT 59840, USA
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19
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Abstract
Background Prions diseases are fatal neurodegenerative diseases of mammals. While the molecular responses to prion infection have been extensively characterized in the laboratory mouse, little is known in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage beginning with mouse RML prions. Results We describe the accumulation of rat prions, associated pathology and the transcriptional impact throughout the disease course. Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular and cellular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated by prion infection in mice are not affected in rats. Conclusion Our findings detail the molecular responses to prion disease in the rat and highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1884-7) contains supplementary material, which is available to authorized users.
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20
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Majer A, Booth SA. Microdissection and transcriptional profiling: a window into the pathobiology of preclinical prion disease. Prion 2015; 8:67-74. [PMID: 24406429 DOI: 10.4161/pri.27729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Prion diseases share common features on a sub-cellular level with many neurodegenerative diseases including Alzheimer disease; the most prevalent neurodegenerative disease world-wide. The most obvious similarity is the accumulation of misfolded forms of the host proteins which forms aggregates in the brains of patients. Remarkably, one of the earliest pathological changes detected in degenerating brain tissue, well before clinical symptoms are observed, is synaptic dysfunction and loss. This pathology was recently shown to be reversible in early stages of mouse prion disease suggesting that synaptic regeneration and reestablishment of neuronal function is possible. Determination of the molecular events that underlie synapse degeneration and how this eventually results in neuronal loss is therefore a research priority that may contribute to the search for new therapeutic interventions for neurodegenerative disorders. Functional genomic studies using unbiased whole genome expression analyses represent one method that can provide insights into these perplexing processes. However, transcriptional profiles from brain tissues are representative of a heterogeneous mixture of cell types that effectively mask the expression of low abundance transcripts, or molecular changes that occur only in a small population of affected neurons. One method that was recently applied to address these challenges was laser capture microdissection which was used to effectively isolate the CA1 neuronal rich region of the hippocampus prior to RNA extraction. Profiling of both mRNAs and microRNAs revealed previously unidentified neuronal-specific genes and expression signatures that are relevant to understanding the pathophysiological processes involved in preclinical stages of prion disease. In this review we will highlight these molecular signatures and discuss their implications with respect to prion-induced neurodegeneration.
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21
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Prion infection of mouse brain reveals multiple new upregulated genes involved in neuroinflammation or signal transduction. J Virol 2014; 89:2388-404. [PMID: 25505076 DOI: 10.1128/jvi.02952-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Gliosis is often a preclinical pathological finding in neurodegenerative diseases, including prion diseases, but the mechanisms facilitating gliosis and neuronal damage in these diseases are not understood. To expand our knowledge of the neuroinflammatory response in prion diseases, we assessed the expression of key genes and proteins involved in the inflammatory response and signal transduction in mouse brain at various times after scrapie infection. In brains of scrapie-infected mice at pre- and postclinical stages, we identified 15 previously unreported differentially expressed genes related to inflammation or activation of the STAT signal transduction pathway. Levels for the majority of differentially expressed genes increased with time postinfection. In quantitative immunoblotting experiments of STAT proteins, STAT1α, phosphorylated-STAT1α (pSTAT1α), and pSTAT3 were increased between 94 and 131 days postinfection (p.i.) in brains of mice infected with strain 22L. Furthermore, a select group of STAT-associated genes was increased preclinically during scrapie infection, suggesting early activation of the STAT signal transduction pathway. Comparison of inflammatory markers between mice infected with scrapie strains 22L and RML indicated that the inflammatory responses and gene expression profiles in the brains were strikingly similar, even though these scrapie strains infect different brain regions. The endogenous interleukin-1 receptor antagonist (IL-1Ra), an inflammatory marker, was newly identified as increasing preclinically in our model and therefore might influence scrapie pathogenesis in vivo. However, in IL-1Ra-deficient or overexpressor transgenic mice inoculated with scrapie, neither loss nor overexpression of IL-1Ra demonstrated any observable effect on gliosis, protease-resistant prion protein (PrPres) formation, disease tempo, pathology, or expression of the inflammatory genes analyzed. IMPORTANCE Prion infection leads to PrPres deposition, gliosis, and neuroinflammation in the central nervous system before signs of clinical illness. Using a scrapie mouse model of prion disease to assess various time points postinoculation, we identified 15 unreported genes that were increased in the brains of scrapie-infected mice and were associated with inflammation and/or JAK-STAT activation. Comparison of mice infected with two scrapie strains (22L and RML), which have dissimilar neuropathologies, indicated that the inflammatory responses and gene expression profiles in the brains were similar. Genes that increased prior to clinical signs might be involved in controlling scrapie infection or in facilitating damage to host tissues. We tested the possible role of the endogenous IL-1Ra, which was increased at 70 days p.i. In scrapie-infected mice deficient in or overexpressing IL-1Ra, there was no observable effect on gliosis, PrPres formation, disease tempo, pathology, or expression of inflammatory genes analyzed.
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22
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Söderberg KL, Guterstam P, Langel U, Gräslund A. Targeting prion propagation using peptide constructs with signal sequence motifs. Arch Biochem Biophys 2014; 564:254-61. [PMID: 25447819 DOI: 10.1016/j.abb.2014.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 12/25/2022]
Abstract
Synthetic peptides with sequences derived from the cellular prion protein (PrP(C)) unprocessed N-terminus are able to counteract the propagation of proteinase K resistant prions (PrP(Res), indicating the presence of the prion isoform of the prion protein) in cell cultures (Löfgren et al., 2008). The anti-prion peptides have characteristics like cell penetrating peptides (CPPs) and consist of the prion protein hydrophobic signal sequence followed by a polycationic motif (residues KKRPKP), in mouse PrP(C) corresponding to residues 1-28. Here we analyze the sequence elements required for the anti-prion effect of KKRPKP-conjugates. Neuronal GT1-1 cells were infected with either prion strain RML or 22L. Variable peptide constructs originating from the mPrP1-28 sequence were analyzed for anti-prion effects, measured as disappearance of proteinase K resistant prions (PrP(Res)) in the infected cell cultures. We find that even a 5 amino acid N-terminal shortening of the signal peptide abolishes the anti-prion effect. We show that the signal peptide from PrP(C) can be replaced with the signal peptide from the Neural cell adhesion molecule-1; NCAM11-19, with a retained capacity to reduce PrP(Res) levels. The anti-prion effect is lost if the polycationic N-terminal PrP(C)-motif is conjugated to any conventional CPP, such as TAT48-60, transportan-10 or penetratin. We propose a mechanism by which a signal peptide from a secretory or cell surface protein acts to promote the transport of a prion-binding polycationic PrP(C)-motif to a subcellular location where prion conversion occurs (most likely the Endosome Recycling Compartment), thereby targeting prion propagation.
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Affiliation(s)
- Kajsa Löfgren Söderberg
- The Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Peter Guterstam
- The Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ulo Langel
- The Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Astrid Gräslund
- The Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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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.
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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.
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24
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Shott RH, Appanah C, Grenier C, Tremblay G, Roucou X, Schang LM. Development of kinomic analyses to identify dysregulated signaling pathways in cells expressing cytoplasmic PrP. Virol J 2014; 11:175. [PMID: 25280966 PMCID: PMC4283144 DOI: 10.1186/1743-422x-11-175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/26/2014] [Indexed: 12/20/2022] Open
Abstract
Background Dysregulated protein kinase signaling is involved in the pathogenesis of many chronic diseases. However, the dysregulated signaling pathways critical to prion pathogenesis remain incompletely characterized. Global analyses of signaling pathways may be useful to better characterize these pathways. We therefore set out to develop such global assays. To this end, we used as a model cytoplasmic mutants of the cellular prion protein (PrPC), which are toxic to N2a neuroblastoma cells. We tested the global assays for their sensitivity to detect changes in signaling pathways in cells expressing cytoplasmic PrP mutants. Methods We developed a targeted proteomics (kinomics) approach using multiplex Western blots to identify signaling pathways dysregulated in chronic neurological pathologies. We tested the approach for its potential ability to detect signaling changes in N2a cells expressing cytoplasmic PrP mutants. Results Multiplex Western blots were designed to quantitate the expression levels of 137 protein kinases in a single membrane and using only 1.2 mg of sample. The response of the blots was sensitive and linear to changes of 6% in protein levels. Hierarchical and functional clustering of the relative expression levels identified an mTOR signaling pathway as potentially dysregulated in N2a cells expressing cytoplasmic PrP. The mTOR signaling pathway regulates global protein synthesis, which is inhibited in cells expressing cytoplasmic PrP. The levels of proteins involved in the Akt1/p70S6K branch of mTOR signaling changed in synchrony with time of cytoplasmic PrP expression. Three kinases in this pathway, Akt, p70S6K, and eIF4B were in their inactive states, as evaluated by phosphorylation of their regulatory sites. Conclusion The results presented are consistent with the previously reported inhibition of Akt/p70S6K/eIF4B signaling as mediating pathogenesis of cytoplasmic PrP. We conclude that the kinomic analyses are sensitive and specific to detect signaling pathways dysregulated in a simple in vitro model of PrP pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-175) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Luis M Schang
- Department of Biochemistry and Centre for Prions and Protein Folding Diseases (CPPFD), University of Alberta, Edmonton, AB T6G 2E1, Canada.
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Moore RA, Sturdevant DE, Chesebro B, Priola SA. Proteomics analysis of amyloid and nonamyloid prion disease phenotypes reveals both common and divergent mechanisms of neuropathogenesis. J Proteome Res 2014; 13:4620-34. [PMID: 25140793 PMCID: PMC4227561 DOI: 10.1021/pr500329w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Prion
diseases are a heterogeneous group of neurodegenerative disorders
affecting various mammals including humans. Prion diseases are characterized
by a misfolding of the host-encoded prion protein (PrPC) into a pathological isoform termed PrPSc. In wild-type
mice, PrPC is attached to the plasma membrane by a glycosylphosphatidylinositol
(GPI) anchor and PrPSc typically accumulates in diffuse
nonamyloid deposits with gray matter spongiosis. By contrast, when
mice lacking the GPI anchor are infected with the same prion inoculum,
PrPSc accumulates in dense perivascular amyloid plaques
with little or no gray matter spongiosis. In order to evaluate whether
different host biochemical pathways were implicated in these two phenotypically
distinct prion disease models, we utilized a proteomics approach.
In both models, infected mice displayed evidence of a neuroinflammatory
response and complement activation. Proteins involved in cell death
and calcium homeostasis were also identified in both phenotypes. However,
mitochondrial pathways of apoptosis were implicated only in the nonamyloid
form, whereas metal binding and synaptic vesicle transport were more
disrupted in the amyloid phenotype. Thus, following infection with
a single prion strain, PrPC anchoring to the plasma membrane
correlated not only with the type of PrPSc deposition but
also with unique biochemical pathways associated with pathogenesis.
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Affiliation(s)
- Roger A Moore
- Laboratory of Persistent Viral Diseases and ‡Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases , Hamilton, Montana 59840, United States
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Barbisin M, Vanni S, Schmädicke AC, Montag J, Motzkus D, Opitz L, Salinas-Riester G, Legname G. Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques. BMC Genomics 2014; 15:434. [PMID: 24898206 PMCID: PMC4061447 DOI: 10.1186/1471-2164-15-434] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prion diseases are fatal neurodegenerative disorders whose pathogenesis mechanisms are not fully understood. In this context, the analysis of gene expression alterations occurring in prion-infected animals represents a powerful tool that may contribute to unravel the molecular basis of prion diseases and therefore discover novel potential targets for diagnosis and therapeutics. Here we present the first large-scale transcriptional profiling of brains from BSE-infected cynomolgus macaques, which are an excellent model for human prion disorders. RESULTS The study was conducted using the GeneChip® Rhesus Macaque Genome Array and revealed 300 transcripts with expression changes greater than twofold. Among these, the bioinformatics analysis identified 86 genes with known functions, most of which are involved in cellular development, cell death and survival, lipid homeostasis, and acute phase response signaling. RT-qPCR was performed on selected gene transcripts in order to validate the differential expression in infected animals versus controls. The results obtained with the microarray technology were confirmed and a gene signature was identified. In brief, HBB and HBA2 were down-regulated in infected macaques, whereas TTR, APOC1 and SERPINA3 were up-regulated. CONCLUSIONS Some genes involved in oxygen or lipid transport and in innate immunity were found to be dysregulated in prion infected macaques. These genes are known to be involved in other neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Our results may facilitate the identification of potential disease biomarkers for many neurodegenerative diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
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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.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rosa Bolea
- Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain.
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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.
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Affiliation(s)
- Katrin Komolka
- Research Group Functional Genomics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
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Filali H, Vidal E, Bolea R, Márquez M, Marco P, Vargas A, Pumarola M, Martin-Burriel I, Badiola JJ. Gene and protein patterns of potential prion-related markers in the central nervous system of clinical and preclinical infected sheep. Vet Res 2013; 44:14. [PMID: 23497022 PMCID: PMC3608070 DOI: 10.1186/1297-9716-44-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/05/2013] [Indexed: 12/15/2022] Open
Abstract
The molecular pathogenic mechanisms of prion diseases are far from clear. Genomic analyses have revealed genetic biomarkers potentially involved in prion neuropathology in naturally scrapie-infected sheep, a good animal model of infectious prionopathies. However, these biomarkers must be validated in independent studies at different stages of the disease. The gene and protein expression profiles and protein distribution of six potential genetic biomarkers (i.e., CAPN6, COL1A2, COL3A1, GALA1, MT2A and MTNR1B) are presented here for both the early and terminal stages of scrapie in five different brain regions. Gene transcription changes were confirmed in the medulla oblongata, and the expression profiles were generally similar in other central nervous system regions. The changes were more substantial in clinical animals compared to preclinical animals. The expression of the CAPN6 protein increased in the spinal cord and cerebellum of the clinical and preclinical brains. The distribution of the GALA1 was identified in glial cells from the cerebellum of scrapie-infected animals, GALA1 protein expression was increased in clinical animals in the majority of regions, and the increase of MT2A was in agreement with previous reports. The downregulation of MTNR1B was especially marked in the Purkinje cells. Finally, although collagen genes were downregulated the protein immunostaining did not reveal significant changes between the scrapie-infected and control animals. In conclusion, this study of gene transcription and protein expression and distribution confirm CAPN6, GALA1, MTNR1B and MT2A as potential targets for further prion disease research.
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Affiliation(s)
- Hicham Filali
- Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain.
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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.
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Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
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Rubenstein R. Proteomic analysis of prion diseases: creating clarity or causing confusion? Electrophoresis 2012; 33:3631-43. [PMID: 23161058 DOI: 10.1002/elps.201200310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 06/25/2012] [Accepted: 07/04/2012] [Indexed: 11/10/2022]
Abstract
Prion diseases, or transmissible spongiform encephalopathies, are progressive, fatal neurodegenerative diseases. There are both human and animal forms of the disease and all are associated with the conversion of a normal host-coded cellular prion protein (PrP(C) ) into an abnormal protease-resistant isoform (PrP(Sc) ). Although methodologies are sensitive and specific for postmortem disease diagnosis, the use of PrP(Sc) as a preclinical or general biomarker for surveillance is difficult, due to the fact that it is present in extremely small amounts in accessible tissues or body fluids such as blood, urine, saliva, and cerebrospinal fluid. Recently, amplification techniques have been developed, which have enabled increased sensitivity for PrP(Sc) detection. However, it has recently been reported that proteinase K sensitive, pathological isoforms of PrP may have a significant role in the pathogenesis of some prion diseases. Accordingly, the development of new diagnostic tests that do not rely on PrP(Sc) and proteinase K digestion is desirable. The search for biomarkers (other than PrP(Sc) ) as tools for diagnosis of prion diseases has a long history. Ideally biomarkers able to detect all transmissible spongiform encephalopathies, even at preclinical stages of infection are desirable but not yet possible due to the heterogeneity of the disease and lengthy disease progression. Recent advances in neuroproteomics have led to an overwhelming amount of information, which may offer insight on protein-protein interactions. While the amount of data obtained is impressive, the ability to relate it to the disease and validating its usefulness in diagnostic biomarker development remains a formidable challenge.
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Affiliation(s)
- Richard Rubenstein
- Department of Neurology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.
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Majer A, Medina SJ, Niu Y, Abrenica B, Manguiat KJ, Frost KL, Philipson CS, Sorensen DL, Booth SA. Early mechanisms of pathobiology are revealed by transcriptional temporal dynamics in hippocampal CA1 neurons of prion infected mice. PLoS Pathog 2012; 8:e1003002. [PMID: 23144617 PMCID: PMC3493483 DOI: 10.1371/journal.ppat.1003002] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/13/2012] [Indexed: 12/23/2022] Open
Abstract
Prion diseases typically have long pre-clinical incubation periods during which time the infectious prion particle and infectivity steadily propagate in the brain. Abnormal neuritic sprouting and synaptic deficits are apparent during pre-clinical disease, however, gross neuronal loss is not detected until the onset of the clinical phase. The molecular events that accompany early neuronal damage and ultimately conclude with neuronal death remain obscure. In this study, we used laser capture microdissection to isolate hippocampal CA1 neurons and determined their pre-clinical transcriptional response during infection. We found that gene expression within these neurons is dynamic and characterized by distinct phases of activity. We found that a major cluster of genes is altered during pre-clinical disease after which expression either returns to basal levels, or alternatively undergoes a direct reversal during clinical disease. Strikingly, we show that this cluster contains a signature highly reminiscent of synaptic N-methyl-D-aspartic acid (NMDA) receptor signaling and the activation of neuroprotective pathways. Additionally, genes involved in neuronal projection and dendrite development were also altered throughout the disease, culminating in a general decline of gene expression for synaptic proteins. Similarly, deregulated miRNAs such as miR-132-3p, miR-124a-3p, miR-16-5p, miR-26a-5p, miR-29a-3p and miR-140-5p follow concomitant patterns of expression. This is the first in depth genomic study describing the pre-clinical response of hippocampal neurons to early prion replication. Our findings suggest that prion replication results in the persistent stimulation of a programmed response that is mediated, at least in part, by synaptic NMDA receptor activity that initially promotes cell survival and neurite remodelling. However, this response is terminated prior to the onset of clinical symptoms in the infected hippocampus, seemingly pointing to a critical juncture in the disease. Manipulation of these early neuroprotective pathways may redress the balance between degeneration and survival, providing a potential inroad for treatment. Neurodegenerative diseases affect an ever-increasing proportion of the population; therefore, there is an urgent need to develop treatments. Prion disorders belong to this group of diseases and although rare and uniquely transmissible, share many features on a sub-cellular level. Central to disease is progressive synaptic impairment that invariably leads to the irreversible loss of neurons. Understanding this process is undoubtedly essential for rational drug discovery. In this study we looked at neurons very early in disease, when prions are barely detectable and there are no clinical symptoms observed. Specifically, we performed a comprehensive analysis of transcriptional changes within a particularly dense area of neurons, the CA1 hippocampus region, from prion-infected and control mice. In this way we were able to enrich our data for molecular changes unique to neurons and minimize those changes characteristic of support cells such as astrocytes and microglia. We detected the activation of a transcriptional program indicative of a protective mechanism within these neurons early in disease. This mechanism diminished as disease progressed and was lost altogether, concurrently with the onset of clinical symptoms. These findings demonstrate the ability of neurons to mount an initial neuroprotective response to prions that could be exploited for therapy development.
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Affiliation(s)
- Anna Majer
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sarah J. Medina
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yulian Niu
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Bernard Abrenica
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kathy J. Manguiat
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kathy L. Frost
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Clark S. Philipson
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Debra L. Sorensen
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Stephanie A. Booth
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Filali H, Martin-Burriel I, Harders F, Varona L, Serrano C, Acín C, Badiola JJ, Bossers A, Bolea R. Medulla oblongata transcriptome changes during presymptomatic natural scrapie and their association with prion-related lesions. BMC Genomics 2012; 13:399. [PMID: 22897917 PMCID: PMC3495657 DOI: 10.1186/1471-2164-13-399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/06/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pathogenesis of natural scrapie and other prion diseases is still poorly understood. Determining the variations in the transcriptome in the early phases of the disease might clarify some of the molecular mechanisms of the prion-induced pathology and allow for the development of new biomarkers for diagnosis and therapy. This study is the first to focus on the identification of genes regulated during the preclinical phases of natural scrapie in the ovine medulla oblongata (MO) and the association of these genes with prion deposition, astrocytosis and spongiosis. RESULTS A custom microarray platform revealed that 86 significant probes had expression changes greater than 2-fold. From these probes, we identified 32 genes with known function; the highest number of regulated genes was included in the phosphoprotein-encoding group. Genes encoding extracellular marker proteins and those involved in the immune response and apoptosis were also differentially expressed. In addition, we investigated the relationship between the gene expression profiles and the appearance of the main scrapie-associated brain lesions. Quantitative Real-time PCR was used to validate the expression of some of the regulated genes, thus showing the reliability of the microarray hybridization technology. CONCLUSIONS Genes involved in protein and metal binding and oxidoreductase activity were associated with prion deposition. The expression of glial fibrillary acidic protein (GFAP) was associated with changes in the expression of genes encoding proteins with oxidoreductase and phosphatase activity, and the expression of spongiosis was related to genes encoding extracellular matrix components or transmembrane transporters. This is the first genome-wide expression study performed in naturally infected sheep with preclinical scrapie. As in previous studies, our findings confirm the close relationship between scrapie and other neurodegenerative diseases.
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Affiliation(s)
- Hicham Filali
- Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
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Basu U, Almeida LM, Dudas S, Graham CE, Czub S, Moore SS, Guan LL. Gene expression alterations in Rocky Mountain elk infected with chronic wasting disease. Prion 2012; 6:282-301. [PMID: 22561165 DOI: 10.4161/pri.19915] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chronic wasting disease (CWD) is an invariably fatal neurologic disease that naturally infects mule deer, white tailed deer and elk. The understanding of CWD neurodegeneration at a molecular level is very limited. In this study, microarray analysis was performed to determine changes in the gene expression profiles in six different tissues including brain, midbrain, thalamus, spleen, RPLN and tonsil of CWD-infected elk in comparison to non-infected healthy elk, using 24,000 bovine specific oligo probes. In total, 329 genes were found to be differentially expressed (> 2.0-fold) between CWD negative and positive brain tissues, with 132 genes upregulated and 197 genes downregulated. There were 249 DE genes in the spleen (168 up- and 81 downregulated), 30 DE genes in the retropharyngeal lymph node (RPLN) (18 up- and 12 downregulated), and 55 DE genes in the tonsil (21 up- and 34 downregulated). Using Gene Ontology (GO), the DE genes were assigned to functional groups associated with cellular process, biological regulation, metabolic process, and regulation of biological process. For all brain tissues, the highest ranking networks for DE genes identified by Ingenuity Pathway Analysis (IPA) were associated with neurological disease, cell morphology, cellular assembly and organization. Quantitative real-time PCR (qRT-PCR) validated the expression of DE genes primarily involved in different regulatory pathways, including neuronal signaling and synapse function, calcium signaling, apoptosis and cell death and immune cell trafficking and inflammatory response. This is the first study to evaluate altered gene expression in multiple organs including brain from orally infected elk and the results will improve our understanding of CWD neurodegeneration at the molecular level.
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Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB, Canada
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35
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Llorens F, Del Río JA. Unraveling the neuroprotective mechanisms of PrP (C) in excitotoxicity. Prion 2012; 6:245-51. [PMID: 22437735 DOI: 10.4161/pri.19639] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Knowledge of the natural roles of cellular prion protein (PrP (C) ) is essential to an understanding of the molecular basis of prion pathologies. This GPI-anchored protein has been described in synaptic contacts, and loss of its synaptic function in complex systems may contribute to the synaptic loss and neuronal degeneration observed in prionopathy. In addition, Prnp knockout mice show enhanced susceptibility to several excitotoxic insults, GABAA receptor-mediated fast inhibition was weakened, LTP was modified and cellular stress increased. Although little is known about how PrP (C) exerts its function at the synapse or the downstream events leading to PrP (C) -mediated neuroprotection against excitotoxic insults, PrP (C) has recently been reported to interact with two glutamate receptor subunits (NR2D and GluR6/7). In both cases the presence of PrP (C) blocks the neurotoxicity induced by NMDA and Kainate respectively. Furthermore, signals for seizure and neuronal cell death in response to Kainate in Prnp knockout mouse are associated with JNK3 activity, through enhancing the interaction of GluR6 with PSD-95. In combination with previous data, these results shed light on the molecular mechanisms behind the role of PrP (C) in excitotoxicity. Future experimental approaches are suggested and discussed.
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Affiliation(s)
- Franc Llorens
- Molecular and Cellular Neurobiotechnology Group, Institut de Bioenginyeria de Catalunya (IBEC), Parc Científic de Barcelona, Barcelona, Spain.
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Hasebe R, Raymond GJ, Horiuchi M, Caughey B. Reaction of complement factors varies with prion strains in vitro and in vivo. Virology 2012; 423:205-13. [PMID: 22222213 DOI: 10.1016/j.virol.2011.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/21/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022]
Abstract
Roles of complement factors in prion infection of the central nervous system remain unclear. In this study, we assessed the strain-dependent reactivity of complement factors in prion infections of Neuro2a (N2a) cells and mouse brains. N2a cells persistently infected with either Chandler or 22L scrapie strains were cultured in the presence of normal mouse serum (NMS), followed by staining with phosphatidylserine binding protein and early apoptosis marker Annexin V. The proportion of Annexin V positive cells was increased both in Chandler- and 22L-infected cells. Preincubation of NMS with anti-C1q, C3 and/or C9 antibodies reduced Annexin V positive cells in Chandler-infected cells, while only anti-C3 antibodies were effective on 22L-infected cells. The immunohistochemistry showed that deposition of C1q and C3 was different between Chandler- and 22L-infected mouse brains. These results indicate that the reactivity of complement factors differs between prion strains both in vitro and in vivo.
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Affiliation(s)
- Rie Hasebe
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT 59840, USA.
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Tortosa R, Castells X, Vidal E, Costa C, Ruiz de Villa MDC, Sánchez A, Barceló A, Torres JM, Pumarola M, Ariño J. Central nervous system gene expression changes in a transgenic mouse model for bovine spongiform encephalopathy. Vet Res 2011; 42:109. [PMID: 22035425 PMCID: PMC3225326 DOI: 10.1186/1297-9716-42-109] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 10/28/2011] [Indexed: 12/04/2022] Open
Abstract
Gene expression analysis has proven to be a very useful tool to gain knowledge of the factors involved in the pathogenesis of diseases, particularly in the initial or preclinical stages. With the aim of finding new data on the events occurring in the Central Nervous System in animals affected with Bovine Spongiform Encephalopathy, a comprehensive genome wide gene expression study was conducted at different time points of the disease on mice genetically modified to model the bovine species brain in terms of cellular prion protein. An accurate analysis of the information generated by microarray technique was the key point to assess the biological relevance of the data obtained in terms of Transmissible Spongiform Encephalopathy pathogenesis. Validation of the microarray technique was achieved by RT-PCR confirming the RNA change and immunohistochemistry techniques that verified that expression changes were translated into variable levels of protein for selected genes. Our study reveals changes in the expression of genes, some of them not previously associated with prion diseases, at early stages of the disease previous to the detection of the pathological prion protein, that might have a role in neuronal degeneration and several transcriptional changes showing an important imbalance in the Central Nervous System homeostasis in advanced stages of the disease. Genes whose expression is altered at early stages of the disease should be considered as possible therapeutic targets and potential disease markers in preclinical diagnostic tool development. Genes non-previously related to prion diseases should be taken into consideration for further investigations.
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Affiliation(s)
- Raül Tortosa
- Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain.
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38
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Moore RA, Timmes AG, Wilmarth PA, Safronetz D, Priola SA. Identification and removal of proteins that co-purify with infectious prion protein improves the analysis of its secondary structure. Proteomics 2011; 11:3853-65. [PMID: 21805638 DOI: 10.1002/pmic.201100253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 05/30/2011] [Accepted: 06/27/2011] [Indexed: 12/13/2022]
Abstract
Prion diseases are neurodegenerative disorders associated with the accumulation of an abnormal isoform of the mammalian prion protein (PrP). Fourier transform infrared spectroscopy (FTIR) has previously been used to show that the conformation of aggregated, infectious PrP (PrP(Sc) ) varies between prion strains and these unique conformations may determine strain-specific disease phenotypes. However, the relative amounts of α-helix, β-sheet and other secondary structures have not always been consistent between studies, suggesting that other proteins might be confounding the analysis of PrP(Sc) secondary structure. We have used FTIR and LC-MS/MS to analyze enriched PrP(Sc) from mouse and hamster prion strains both before and after the removal of protein contaminants that commonly co-purify with PrP(Sc) . Our data show that non-PrP proteins do contribute to absorbances that have been associated with α-helical, loop, turn and β-sheet structures attributed to PrP(Sc) . The major contaminant, the α-helical protein ferritin, absorbs strongly at 1652 cm(-1) in the FTIR spectrum associated with PrP(Sc) . However, even the removal of more than 99% of the ferritin from PrP(Sc) did not completely abolish absorbance at 1652 cm(-1) . Our results show that contaminating proteins alter the FTIR spectrum attributed to PrP(Sc) and suggest that the α-helical, loop/turn and β-sheet secondary structure that remains following their removal are derived from PrP(Sc) itself.
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Affiliation(s)
- Roger A Moore
- Rocky Mountain Laboratories/Laboratory of Persistent Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S. 4th St., Hamilton, MT 59840, USA.
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Gossner A, Roupaka S, Foster J, Hunter N, Hopkins J. Transcriptional profiling of peripheral lymphoid tissue reveals genes and networks linked to SSBP/1 scrapie pathology in sheep. Vet Microbiol 2011; 153:218-28. [PMID: 21684093 DOI: 10.1016/j.vetmic.2011.05.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 05/10/2011] [Accepted: 05/16/2011] [Indexed: 12/30/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) are slow and progressive neurodegenerative diseases of humans and animals. The major target organ for all TSEs is the brain but some TSE agents are associated with prior accumulation within the peripheral lymphoid system. Many studies have examined the effects of scrapie infection on the expression of central nervous system (CNS) genes, but this study examines the progression of scrapie pathology in the peripheral lymphoid system and how scrapie infection affects the transcriptome of the lymph nodes and spleen. Infection of sheep with SSBP/1 scrapie resulted in PrP(Sc) deposition in the draining prescapular lymph node (PSLN) by 25 days post infection (dpi) in VRQ/VRQ genotype sheep and 75 dpi in tonsils and spleen. Progression of PrP(Sc) deposition in VRQ/ARR animals was 25 dpi later in the PSLN and 250 dpi later in spleen. Microarray analysis of 75 dpi tissues from VRQ/VRQ sheep identified 52 genes in PSLN and 37 genes in spleen cells that showed significant difference (P ≤ 0.05) between scrapie-infected and mock-infected animals. Transcriptional pathway analysis highlighted immunological disease, cell death and neurological disease as the biological pathways associated with scrapie pathogenesis in the peripheral lymphoid system. PrP(Sc) accumulation of lymphoid tissue resulted in the repression of genes linked to inflammation and oxidative stress, and the up-regulation of genes related to apoptosis.
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Affiliation(s)
- Anton Gossner
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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40
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Gene expression profiling and association with prion-related lesions in the medulla oblongata of symptomatic natural scrapie animals. PLoS One 2011; 6:e19909. [PMID: 21629698 PMCID: PMC3101219 DOI: 10.1371/journal.pone.0019909] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/06/2011] [Indexed: 02/04/2023] Open
Abstract
The pathogenesis of natural scrapie and other prion diseases remains unclear. Examining transcriptome variations in infected versus control animals may highlight new genes potentially involved in some of the molecular mechanisms of prion-induced pathology. The aim of this work was to identify disease-associated alterations in the gene expression profiles of the caudal medulla oblongata (MO) in sheep presenting the symptomatic phase of natural scrapie. The gene expression patterns in the MO from 7 sheep that had been naturally infected with scrapie were compared with 6 controls using a Central Veterinary Institute (CVI) custom designed 4×44K microarray. The microarray consisted of a probe set on the previously sequenced ovine tissue library by CVI and was supplemented with all of the Ovis aries transcripts that are currently publicly available. Over 350 probe sets displayed greater than 2-fold changes in expression. We identified 148 genes from these probes, many of which encode proteins that are involved in the immune response, ion transport, cell adhesion, and transcription. Our results confirm previously published gene expression changes that were observed in murine models with induced scrapie. Moreover, we have identified new genes that exhibit differential expression in scrapie and could be involved in prion neuropathology. Finally, we have investigated the relationship between gene expression profiles and the appearance of the main scrapie-related lesions, including prion protein deposition, gliosis and spongiosis. In this context, the potential impacts of these gene expression changes in the MO on scrapie development are discussed.
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Almeida LM, Basu U, Khaniya B, Taniguchi M, Williams JL, Moore SS, Guan LL. Gene expression in the medulla following oral infection of cattle with bovine spongiform encephalopathy. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:110-126. [PMID: 21218340 DOI: 10.1080/15287394.2011.529061] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The identification of variations in gene expression in response to bovine spongiform encephalopathy (BSE) may help to elucidate the mechanisms of neuropathology and prion replication and discover biomarkers for disease. In this study, genes that are differentially expressed in the caudal medulla tissues of animals infected with different doses of PrP(BSE) at 12 and 45 mo post infection were compared using array containing 24,000 oligonucleotide probes. Data analysis identified 966 differentially expressed (DE) genes between control and infected animals. Genes identified in at least two of four experiments (control versus 1-g infected animals at 12 and 45-mo; control versus 100-g infected animals at 12 and 45 mo) were considered to be the genes that may be associated with BSE disease. From the 176 DE genes associated with BSE, 84 had functions described in the Gene Ontology (GO) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 14 genes revealed that prion infection may cause dysfunction of several different networks, including extracellular matrix (ECM), cell adhesion, neuroactive ligand-receptor interaction, complement and coagulation cascades, MAPK signaling, neurodegenerative disorder, SNARE interactions in vesicular transport, and the transforming growth factor (TGF) beta signaling pathways. The identification of DE genes will contribute to a better understanding of the molecular mechanisms of neuropathology in bovine species. Additional studies on larger number of animals are in progress in our laboratory to investigate the roles of these DE genes in pathogenesis of BSE.
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Affiliation(s)
- Luciane M Almeida
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Moody LR, Herbst AJ, Aiken JM. Upregulation of interferon-gamma-induced genes during prion infection. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:146-153. [PMID: 21218343 PMCID: PMC4621959 DOI: 10.1080/15287394.2011.529064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Global gene expression analysis allows for the identification of transcripts that are differentially regulated during a disease state. Many groups, including our own, have identified hundreds of genes differentially regulated in response to prion infection. Eleven transcripts, upregulated in the brains of prion-infected animals, which were classified in the literature as stimulated by the cytokine interferon-gamma (IFN-γ), were identified. This is intriguing, as IFN-γ has recently been detected in the brains of prion-infected animals. Quantitation of several genes, categorized as IFN-γ inducible, by quantitative real-time polymerase chain reaction (qRT-PCR) confirms that these transcripts are upregulated. Future approaches for delineating the role of IFN-γ-induced transcripts and their function in prion infection are described.
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Affiliation(s)
- Laura R. Moody
- Cellular and Molecular Biology Graduate Program; Department of Comparative Biosciences; University of Wisconsin, Madison, Wisconsin, USA
| | - Allen J. Herbst
- Centre for Prions and Protein Folding Diseases, Edmonton, Alberta, Canada
| | - Judd M. Aiken
- Centre for Prions and Protein Folding Diseases, Edmonton, Alberta, Canada
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Gene expression analysis in distinct regions of the central nervous system during the development of SSBP/1 sheep scrapie. Vet Microbiol 2011; 147:42-8. [DOI: 10.1016/j.vetmic.2010.05.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 05/25/2010] [Accepted: 05/28/2010] [Indexed: 11/24/2022]
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Wong M, Toth J, Haney S, Krewski D, Leighton FA, Ricketts M, Westaway D, Cashman N. PrioNet Canada: a network of centres of excellence for research on prion diseases--ongoing and future research directions. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:73-87. [PMID: 21218336 DOI: 10.1080/15287394.2011.529056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It is PrioNet's vision to build a network that shapes and sustains prion research in Canada, translating basic science into accessible socioeconomic benefits for global betterment. PrioNet's research is developing surveillance measures, diagnostic tools, vaccines, and potential therapies and determining the various impacts of prion diseases on people. PrioNet seeks to integrate scientifically informed risk management strategies and to use this knowledge to address ongoing problems posed by bovine spongiform encephalopathy (BSE), the gathering crisis of chronic wasting disease (CWD), emerging issues of human prion disease, and basic scientific understanding of the nature of prions. PrioNet is strategically responding to prion threats by focusing its network of highly accomplished researchers and trainees to implement integrated risk management strategies that could not be supported by other mechanisms.
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Affiliation(s)
- Michelle Wong
- PrioNet Canada, 200-2386 East Mall, Vancouver, British Columbia, Canada
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Basu U, Almeida L, Olson NE, Meng Y, Williams JL, Moore SS, Guan LL. Transcriptome analysis of the medulla tissue from cattle in response to bovine spongiform encephalopathy using digital gene expression tag profiling. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:127-137. [PMID: 21218341 DOI: 10.1080/15287394.2011.529062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Bovine spongiform encephalopathy (BSE) is a transmissible, fatal neurodegenerative disorder of cattle produced by prions. The use of excessive parallel sequencing for comparison of gene expression in bovine control and infected tissues may help to elucidate the molecular mechanisms associated with this disease. In this study, tag profiling Solexa sequencing was used for transcriptome analysis of bovine brain tissues. Replicate libraries were prepared from mRNA isolated from control and infected (challenged with 100 g of BSE-infected brain) medulla tissues 45 mo after infection. For each library, 5-6 million sequence reads were generated and approximately 67-70% of the reads were mapped against the Bovine Genome database to approximately 13,700-14,120 transcripts (each having at least one read). About 42-47% of the total reads mapped uniquely. Using the GeneSifter software package, 190 differentially expressed (DE) genes were identified (>2.0-fold change, p < .01): 73 upregulated and 117 downregulated. Seventy-nine DE genes had functions described in the Gene Ontology (GO) database and 16 DE genes were involved in 38 different pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Digital analysis expression by tag profiling may be a powerful approach to comprehensive transcriptome analysis to identify changes associated with disease progression, leading to a better understanding of the underlying mechanism of pathogenesis of BSE.
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Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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Huzarewich RLCH, Medina S, Robertson C, Parchaliuk D, Booth SA. Transcriptional modulation in a leukocyte-depleted splenic cell population during prion disease. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2011; 74:1504-1520. [PMID: 22043911 DOI: 10.1080/15287394.2011.618979] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Prion replication in the periphery precedes neuroinvasion in many experimental rodent scrapie models, and in natural sheep scrapie and chronic wasting disease (CWD) in cervids. Prions propagate in the germinal centers of secondary lymphoid organs and are strongly associated with follicular dendritic cells (FDC) and possibly circulating dendritic cells and macrophages. Given the importance of lymphoid organs in prion disease transmission and pathogenesis, gene expression studies may reveal host factors or biological pathways related to prion replication and accumulation. A procedure was developed to enrich for FDC, dendritic cells, and macrophages prior to the investigation of transcriptional alterations in murine splenic cells during prion pathogenesis. In total, 1753 transcripts exhibited fold changes greater than three (false discovery rates less than 2%) in this population isolated from spleens of prion-infected versus uninfected mice. The gene for the small leucine-rich proteoglycan decorin (DCN) was one of the genes most overexpressed in infected mice, and the splenic protein levels mirrored this in mice infected with scrapie as well as bovine spongiform encephalopathy (BSE) and variant Creutzfeldt-Jakob disease (vCJD). A number of groups of functionally related genes were also significantly decreased in infected spleens. These included genes related to iron metabolism and homeostasis, pathways that have also been implicated in prion pathogenesis in the brain. These gene expression alterations provide insights into the molecular mechanisms underlying prion disease pathogenesis and may serve as a pool of potential surrogate markers for the early detection and diagnosis of some prion diseases.
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Affiliation(s)
- Rhiannon L C H Huzarewich
- Molecular PathoBiology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Tang Y, Xiang W, Terry L, Kretzschmar HA, Windl O. Transcriptional analysis implicates endoplasmic reticulum stress in bovine spongiform encephalopathy. PLoS One 2010; 5:e14207. [PMID: 21151970 PMCID: PMC2997050 DOI: 10.1371/journal.pone.0014207] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 11/01/2010] [Indexed: 11/18/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE) is a fatal, transmissible, neurodegenerative disease of cattle. To date, the disease process is still poorly understood. In this study, brain tissue samples from animals naturally infected with BSE were analysed to identify differentially regulated genes using Affymetrix GeneChip Bovine Genome Arrays. A total of 230 genes were shown to be differentially regulated and many of these genes encode proteins involved in immune response, apoptosis, cell adhesion, stress response and transcription. Seventeen genes are associated with the endoplasmic reticulum (ER) and 10 of these 17 genes are involved in stress related responses including ER chaperones, Grp94 and Grp170. Western blotting analysis showed that another ER chaperone, Grp78, was up-regulated in BSE. Up-regulation of these three chaperones strongly suggests the presence of ER stress and the activation of the unfolded protein response (UPR) in BSE. The occurrence of ER stress was also supported by changes in gene expression for cytosolic proteins, such as the chaperone pair of Hsp70 and DnaJ. Many genes associated with the ubiquitin-proteasome pathway and the autophagy-lysosome system were differentially regulated, indicating that both pathways might be activated in response to ER stress. A model is presented to explain the mechanisms of prion neurotoxicity using these ER stress related responses. Clustering analysis showed that the differently regulated genes found from the naturally infected BSE cases could be used to predict the infectious status of the samples experimentally infected with BSE from the previous study and vice versa. Proof-of-principle gene expression biomarkers were found to represent BSE using 10 genes with 94% sensitivity and 87% specificity.
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Affiliation(s)
- Yue Tang
- Department of Molecular Pathogenesis and Genetics, Veterinary Laboratories Agency, Surrey, United Kingdom
- * E-mail: (YT); (OW)
| | - Wei Xiang
- Institute of Biochemistry, Emil-Fischer-Center, University Erlangen-Nuernberg, Erlangen, Germany
| | - Linda Terry
- Department of Molecular Pathogenesis and Genetics, Veterinary Laboratories Agency, Surrey, United Kingdom
| | - Hans A. Kretzschmar
- Institute of Neuropathology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Otto Windl
- Department of Molecular Pathogenesis and Genetics, Veterinary Laboratories Agency, Surrey, United Kingdom
- * E-mail: (YT); (OW)
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Shinkai-Ouchi F, Yamakawa Y, Hara H, Tobiume M, Nishijima M, Hanada K, Hagiwara K. Identification and structural analysis of C-terminally truncated collapsin response mediator protein-2 in a murine model of prion diseases. Proteome Sci 2010; 8:53. [PMID: 20961402 PMCID: PMC2978134 DOI: 10.1186/1477-5956-8-53] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 10/20/2010] [Indexed: 12/16/2022] Open
Abstract
Background Prion diseases are fatal neurodegenerative disorders that accompany an accumulation of the disease-associated form(s) of prion protein (PrPSc) in the central nervous system. The neuropathological changes in the brain begin with focal deposits of PrPSc, followed by pathomorphological abnormalities of axon terminal degeneration, synaptic loss, atrophy of dendritic trees, and eventual neuronal cell death in the lesions. However, the underlying molecular basis for these neuropathogenic abnormalities is not fully understood. Results In a proteomic analysis of soluble proteins in the brains of mice challenged intracerebrally with scrapie prion (Obihiro I strain), we found that the amount of the full-length form of collapsin response mediator protein-2 (CRMP-2; 61 kDa) decreased in the late stages of the disease, while the amount of its truncated form (56 kDa) increased to comparable levels observed for the full-length form. Detailed analysis by liquid chromatography-electrospray ionization-tandem mass spectrometry showed that the 56-kDa form (named CRMP-2-ΔC) lacked the sequence from serine518 to the C-terminus, including the C-terminal phosphorylation sites important for the regulation of axonal growth and axon-dendrite specification in developing neurons. The invariable size of the mRNA transcript in Northern blot analysis suggested that the truncation was due to post-translational proteolysis. By overexpression of CRMP-2-ΔC in primary cultured neurons, we observed the augmentation of the development of neurite branch tips to the same levels as for CRMP-2T514A/T555A, a non-phosphorylated mimic of the full-length protein. This suggests that the increased level of CRMP-2-ΔC in the brain modulates the integrity of neurons, and may be involved in the pathogenesis of the neuronal abnormalities observed in the late stages of the disease. Conclusions We identified the presence of CRMP-2-ΔC in the brain of a murine model of prion disease. Of note, C-terminal truncations of CRMP-2 have been recently observed in models for neurodegenerative disorders such as ischemia, traumatic brain injury, and Wallerian degeneration. While the structural identity of CRMP-2-ΔC in those models remains unknown, the present study should provide clues to the molecular pathology of degenerating neurons in prion diseases in connection with other neurodegenerative disorders.
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Affiliation(s)
- Fumiko Shinkai-Ouchi
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Moore RA, Timmes A, Wilmarth PA, Priola SA. Comparative profiling of highly enriched 22L and Chandler mouse scrapie prion protein preparations. Proteomics 2010; 10:2858-69. [PMID: 20518029 PMCID: PMC3742083 DOI: 10.1002/pmic.201000104] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 05/16/2010] [Indexed: 12/11/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) or prion diseases are characterized by the accumulation of an aggregated isoform of the prion protein (PrP). This pathological isoform, termed PrP(Sc), appears to be the primary component of the TSE infectious agent or prion. However, it is not clear to what extent other protein cofactors may be involved in TSE pathogenesis or whether there are PrP(Sc)-associated proteins which help to determine TSE strain-specific disease phenotypes. We enriched PrP(Sc) from the brains of mice infected with either 22L or Chandler TSE strains and examined the protein content of these samples using nanospray LC-MS/MS. These samples were compared with "mock" PrP(Sc) preparations from uninfected brains. PrP was the major component of the infected samples and ferritin was the most abundant impurity. Mock enrichments contained no detectable PrP but did contain a significant amount of ferritin. Of the total proteins identified, 32% were found in both mock and infected samples. The similarities between PrP(Sc) samples from 22L and Chandler TSE strains suggest that the non-PrP(Sc) protein components found in standard enrichment protocols are not strain specific.
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Affiliation(s)
- Roger A Moore
- Rocky Mountain Laboratories, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
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Chadi S, Young R, Le Guillou S, Tilly G, Bitton F, Martin-Magniette ML, Soubigou-Taconnat L, Balzergue S, Vilotte M, Peyre C, Passet B, Béringue V, Renou JP, Le Provost F, Laude H, Vilotte JL. Brain transcriptional stability upon prion protein-encoding gene invalidation in zygotic or adult mouse. BMC Genomics 2010; 11:448. [PMID: 20649983 PMCID: PMC3091645 DOI: 10.1186/1471-2164-11-448] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 07/22/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The physiological function of the prion protein remains largely elusive while its key role in prion infection has been expansively documented. To potentially assess this conundrum, we performed a comparative transcriptomic analysis of the brain of wild-type mice with that of transgenic mice invalidated at this locus either at the zygotic or at the adult stages. RESULTS Only subtle transcriptomic differences resulting from the Prnp knockout could be evidenced, beside Prnp itself, in the analyzed adult brains following microarray analysis of 24 109 mouse genes and QPCR assessment of some of the putatively marginally modulated loci. When performed at the adult stage, neuronal Prnp disruption appeared to sequentially induce a response to an oxidative stress and a remodeling of the nervous system. However, these events involved only a limited number of genes, expression levels of which were only slightly modified and not always confirmed by RT-qPCR. If not, the qPCR obtained data suggested even less pronounced differences. CONCLUSIONS These results suggest that the physiological function of PrP is redundant at the adult stage or important for only a small subset of the brain cell population under classical breeding conditions. Following its early reported embryonic developmental regulation, this lack of response could also imply that PrP has a more detrimental role during mouse embryogenesis and that potential transient compensatory mechanisms have to be searched for at the time this locus becomes transcriptionally activated.
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Affiliation(s)
- Sead Chadi
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, F-78350, Jouy-en-Josas, France
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