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A V, Kumar A, Mahala S, Chandra Janga S, Chauhan A, Mehrotra A, Kumar De A, Ranjan Sahu A, Firdous Ahmad S, Vempadapu V, Dutt T. Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds. Gene 2024; 893:147950. [PMID: 37918549 DOI: 10.1016/j.gene.2023.147950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.
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Affiliation(s)
- Vani A
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Sudarshan Mahala
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, IUPUI, Indianapolis, IN, USA
| | - Anuj Chauhan
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Arun Kumar De
- Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Amiya Ranjan Sahu
- Central Coastal Agricultural Research Institute, Old Goa, Goa, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Varshini Vempadapu
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
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Sola D, Betancor M, Marco Lorente PA, Pérez Lázaro S, Barrio T, Sevilla E, Marín B, Moreno B, Monzón M, Acín C, Bolea R, Badiola JJ, Otero A. Diagnosis in Scrapie: Conventional Methods and New Biomarkers. Pathogens 2023; 12:1399. [PMID: 38133284 PMCID: PMC10746075 DOI: 10.3390/pathogens12121399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Scrapie, a naturally occurring prion disease affecting goats and sheep, comprises classical and atypical forms, with classical scrapie being the archetype of transmissible spongiform encephalopathies. This review explores the challenges of scrapie diagnosis and the utility of various biomarkers and their potential implications for human prion diseases. Understanding these biomarkers in the context of scrapie may enable earlier prion disease diagnosis in humans, which is crucial for effective intervention. Research on scrapie biomarkers bridges the gap between veterinary and human medicine, offering hope for the early detection and improved management of prion diseases.
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Affiliation(s)
- Diego Sola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Marina Betancor
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Paula A. Marco Lorente
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Sonia Pérez Lázaro
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Tomás Barrio
- Unité Mixte de Recherche de l’Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement1225 Interactions Hôtes-Agents Pathogènes, École Nationale Vétérinaire de Toulouse, 31076 Toulouse, France
| | - Eloisa Sevilla
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Belén Marín
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Bernardino Moreno
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Marta Monzón
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Cristina Acín
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Rosa Bolea
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Juan J. Badiola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
| | - Alicia Otero
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, IA2, Universidad de Zaragoza, 50013 Zaragoza, Spain; (D.S.)
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Discovering novel clues of natural selection on four worldwide goat breeds. Sci Rep 2023; 13:2110. [PMID: 36747064 PMCID: PMC9902602 DOI: 10.1038/s41598-023-27490-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/03/2023] [Indexed: 02/08/2023] Open
Abstract
In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose. However, and despite the intensity of artificial selection, natural selection continues acting, possibly leaving a more diluted contribution over time, whose traces may be more difficult to capture. In order to explore selection footprints as response of environmental adaptation, we analysed a total of 993 goats from four transboundary goats breeds (Angora, Boer, Nubian and Saanen) genotyped with the SNP chip 50 K using outlier detection, runs of homozygosity and haplotype-based detection methods. Our results showed that all methods identified footprints on chromosome 6 (from 30 to 49 Mb) for two specific populations of Nubian goats sampled in Egypt. In Angora and Saanen breeds, we detected two selective sweeps using HapFLK, on chromosome 21 (from 52 to 55 Mb) and chromosome 25 (from 1 to 5 Mb) respectively. The analysis of runs of homozygosity showed some hotspots in all breeds. The overall investigation of the selected regions detected combining the different approaches and the gene ontology exploration revealed both novel and well-known loci related to adaptation, especially for heat stress. Our findings can help to better understand the balance between the two selective pressures in commercial goat breeds providing new insights on the molecular mechanisms of adaptation.
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Kang X, Liu Y, Zhang J, Xu Q, Liu C, Fang M. Characteristics and Expression Profile of KRT71 Screened by Suppression Subtractive Hybridization cDNA Library in Curly Fleece Chinese Tan Sheep. DNA Cell Biol 2017; 36:552-564. [PMID: 28509589 DOI: 10.1089/dna.2017.3718] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As an important commercial trait for sheep, curly fleece has a great economic impact on production costs and efficiency in sheep industry. To identify genes that are important for curly fleece formation in mammals, a suppression subtractive hybridization analysis was performed on the shoulder skin tissues exposed to two different growth stages of Chinese Tan sheep with different phenotypes (curly fleece and noncurling fleece). BLAST analysis identified 67 differentially expressed genes, of which 31 were expressed lower and 36 were expressed higher in lambs than in adult sheep. Differential expressions of seven randomly selected genes were verified using quantitative real-time polymerase chain reaction (qRT-PCR). KRT71 gene was selected for further study due to its high correlation with the curly hair phenotype in various mammal species. Semi-qPCR showed distinctively high expression of KRT71 in skin tissues. Moreover, qPCR result showed a significantly higher expression of KRT71 in curly fleece than noncurling Tan sheep. The luciferase assay and electrophoresis mobility shift assay showed that there were transcription factor binding sites in the promoter region of KRT71 related to the differential expression of KRT71 at the two growth stages of Tan sheep. Online bioinformation tools predicted MFZ1 as a transcriptional factor that regulates the expression of KRT71. These studies on KRT71 gene revealed some mechanisms underlying the relationship between the KRT71 gene and the curly fleece phenotype of Tan sheep.
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Affiliation(s)
- Xiaolong Kang
- 1 National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University , Beijing, People's Republic of China .,2 College of Agriculture, Ningxia University , Yinchuan, People's Republic of China
| | - Yufang Liu
- 1 National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University , Beijing, People's Republic of China
| | - Jibin Zhang
- 3 Department of Animal Science, Iowa State University , Ames, Iowa
| | - Qinqin Xu
- 1 National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University , Beijing, People's Republic of China
| | - Chengkun Liu
- 1 National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University , Beijing, People's Republic of China
| | - Meiying Fang
- 1 National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University , Beijing, People's Republic of China .,4 Beijing Key Laboratory for Animal Genetic Improvement, Beijing, People's Republic of China
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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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Campisi E, Cardone F, Graziano S, Galeno R, Pocchiari M. Role of proteomics in understanding prion infection. Expert Rev Proteomics 2013; 9:649-66. [PMID: 23256675 DOI: 10.1586/epr.12.58] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Transmissible spongiform encephalopathies or prion diseases are fatal neurodegenerative pathologies characterized by the autocatalytic misfolding and polymerization of a cellular glycoprotein (cellular prion protein [PrP(C)]) that accumulates in the CNS and leads to neurodegeneration. The detailed mechanics of PrP(C) conversion to its pathological isoform (PrP(TSE)) are unclear but one or more exogenous factors are likely involved in the process of PrP misfolding. In the last 20 years, proteomic investigations have identified several endogenous proteins that interact with PrP(C), PrP(TSE) or both, which are possibly involved in the prion pathogenetic process. However, current approaches have not yet produced convincing conclusions on the biological value of such PrP interactors. Future advancements in the comprehension of the molecular pathogenesis of prion diseases, in experimental techniques and in data analysis procedures, together with a boost in more productive international collaborations, are therefore needed to improve the understanding on the role of PrP interactors. Finally, the advancement of 'omics' techniques in prion diseases will contribute to the development of novel diagnostic tests and effective drugs.
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Affiliation(s)
- Edmondo Campisi
- Department of Cell Biology and Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
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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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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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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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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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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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Application of "omics" to prion biomarker discovery. J Biomed Biotechnol 2010; 2010:613504. [PMID: 20224650 PMCID: PMC2833310 DOI: 10.1155/2010/613504] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 12/03/2009] [Accepted: 12/30/2009] [Indexed: 02/01/2023] Open
Abstract
The advent of genomics and proteomics has been a catalyst for the discovery of biomarkers able to discriminate biological processes such as the pathogenesis of complex diseases. Prompt detection of prion diseases is particularly desirable given their transmissibility, which is responsible for a number of human health risks stemming from exogenous sources of prion protein. Diagnosis relies on the ability to detect the biomarker PrPSc, a pathological isoform of the host protein PrPC, which is an essential component of the infectious prion. Immunochemical detection of PrPSc is specific and sensitive enough for antemortem testing of brain tissue, however, this is not the case in accessible biological fluids or for the detection of recently identified novel prions with unique biochemical properties. A complementary approach to the detection of PrPSc itself is to identify alternative, “surrogate” gene or protein biomarkers indicative of disease. Biomarkers are also useful to track the progress of disease, especially important in the assessment of therapies, or to identify individuals “at risk”. In this review we provide perspective on current progress and pitfalls in the use of “omics” technologies to screen body fluids and tissues for biomarker discovery in prion diseases.
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Benetti F, Gasperini L, Zampieri M, Legname G. Gene expression profiling to identify druggable targets in prion diseases. Expert Opin Drug Discov 2010; 5:177-202. [PMID: 22822917 DOI: 10.1517/17460440903544449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
IMPORTANCE OF THE FIELD Despite many recent advances in prion research, the molecular mechanisms by which prions cause neurodegeneration have not been established. In fact, the complexity and the novelty characterizing this class of disorders pose a huge challenge to drug discovery. Pharmacogenomics has recently adopted high-throughput transcriptome analyses to predict potential drug target candidates, with promising results in various fields of medicine. AREAS COVERED IN THIS REVIEW The present work offers an overview of the transcriptional alterations induced by prion infection in different biological systems. Hereafter, therapeutic approaches are discussed in light of the identified altered processes. WHAT THE READER WILL GAIN This review offers readers a detailed overview on microarray analyses, taking into account their advantages and limitations. Our work can help readers, from many research areas, to design a suitable microarray experiment. TAKE HOME MESSAGE So far, drugs acting on the pathways identified by microarray analysis have not been found to be effective in prion diseases therapy. An integration of gene expression profiling, proteomics and physiology should be applied to pursue this aim.
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Affiliation(s)
- Federico Benetti
- Laboratory of Prion Biology, Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati-International School of Advanced Studies (SISSA-ISAS), Edificio Q1, Basovizza, Trieste, Italy
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Nieznanski K. Interactions of prion protein with intracellular proteins: so many partners and no consequences? Cell Mol Neurobiol 2009; 30:653-66. [PMID: 20041289 DOI: 10.1007/s10571-009-9491-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 12/18/2009] [Indexed: 10/20/2022]
Abstract
Prion protein (PrP) plays a key role in the pathogenesis of transmissible spongiform encephalopathies (TSEs)--fatal diseases of the central nervous system. Its physiological function as well as exact role in neurodegeneration remain unclear, hence screens for proteins interacting with PrP seem to be the most promising approach to elucidating these issues. PrP is mostly a plasma membrane-anchored extracellular glycoprotein and only a small fraction resides inside the cell, yet the number of identified intracellular partners of PrP is comparable to that of its membranal or extracellular interactors. Since some TSEs are accompanied by significantly increased levels of cytoplasmic PrP and this fraction of the protein has been found to be neurotoxic, it is of particular interest to characterize the intracellular interactome of PrP. It seems reasonable that at elevated cytoplasmic levels, PrP may exert cytotoxic effect by affecting the physiological functions of its intracellular interactors. This review is focused on the cytoplasmic partners of PrP along with possible consequences of their binding.
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Affiliation(s)
- Krzysztof Nieznanski
- Department of Biochemistry, Polish Academy of Sciences, Nencki Institute of Experimental Biology, 3 Pasteur St, Warsaw 02093, Poland.
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Giorgi A, Di Francesco L, Principe S, Mignogna G, Sennels L, Mancone C, Alonzi T, Sbriccoli M, De Pascalis A, Rappsilber J, Cardone F, Pocchiari M, Maras B, Schininà ME. Proteomic profiling of PrP27-30-enriched preparations extracted from the brain of hamsters with experimental scrapie. Proteomics 2009; 9:3802-14. [DOI: 10.1002/pmic.200900085] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Lathe R, Harris A. Differential display detects host nucleic acid motifs altered in scrapie-infected brain. J Mol Biol 2009; 392:813-22. [PMID: 19631225 DOI: 10.1016/j.jmb.2009.07.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Revised: 07/08/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
Abstract
The transmissible spongiform encephalopathies (TSEs) including scrapie have been attributed to an infectious protein or prion. Infectivity is allied to conversion of the endogenous nucleic-acid-binding protein PrP to an infectious modified form known as PrP(sc). The protein-only theory does not easily explain the enigmatic properties of the agent including strain variation. It was previously suggested that a short nucleic acid, perhaps host-encoded, might contribute to the pathoetiology of the TSEs. No candidate host molecules that might explain transmission of strain differences have yet been put forward. Differential display is a robust technique for detecting nucleic acid differences between two populations. We applied this technique to total nucleic acid preparations from scrapie-infected and control brain. Independent RNA preparations from eight normal and eight scrapie-infected (strain 263K) hamster brains were randomly amplified and visualized in parallel. Though the nucleic acid patterns were generally identical in scrapie-infected versus control brain, some rare bands were differentially displayed. Molecular species consistently overrepresented (or underrepresented) in all eight infected brain samples versus all eight controls were excised from the display, sequenced, and assembled into contigs. Only seven ros contigs (RNAs over- or underrepresented in scrapie) emerged, representing <4 kb from the transcriptome. All contained highly stable regions of secondary structure. The most abundant scrapie-only ros sequence was homologous to a repetitive transposable element (LINE; long interspersed nuclear element). Other ros sequences identified cellular RNA 7SL, clathrin heavy chain, visinin-like protein-1, and three highly specific subregions of ribosomal RNA (ros1-3). The ribosomal ros sequences accurately corresponded to LINE; retrotransposon insertion sites in ribosomal DNA (p<0.01). These differential motifs implicate specific host RNAs in the pathoetiology of the TSEs.
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Stanton JB, Knowles DP, Call DR, Mathison BA, Baszler TV. Limited transcriptional response of ovine microglia to prion accumulation. Biochem Biophys Res Commun 2009; 386:345-50. [PMID: 19523453 DOI: 10.1016/j.bbrc.2009.06.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/08/2009] [Indexed: 01/22/2023]
Abstract
The conversion of normal cellular prion protein to disease-associated prion protein (PrP(Sc)) is a fundamental component of prion disease pathogenesis. The molecular mechanisms contributing to prion conversion and the impact of PrP(Sc) accumulation on cellular biology are not fully understood. To further define the molecular changes associated with PrP(Sc) accumulation in cultured cells, the transcriptional profile of PrP(Sc)-accumulating primary ovine microglia was compared to the profile of PrP(Sc)-lacking microglia using the Affymetrix Bovine Genome Array. The experimental design included three biological replicates, each with three technical replicates, and samples that were collected at the point of near maximal PrP(Sc) accumulation levels as measured by ELISA. The array analysis revealed only 19 upregulated genes and 30 downregulated genes in PrP(Sc)-accumulating microglia. The results support the hypothesis that chronic PrP(Sc) accumulation in cultured microglia results in a limited transcriptional response.
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Affiliation(s)
- James B Stanton
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040, USA.
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Guillerme-Bosselut F, Forestier L, Jayat-Vignoles C, Vilotte JL, Popa I, Portoukalian J, Le Dur A, Laude H, Julien R, Gallet PF. Glycosylation-related gene expression profiling in the brain and spleen of scrapie-affected mouse. Glycobiology 2009; 19:879-89. [PMID: 19386898 DOI: 10.1093/glycob/cwp062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A central event in the formation of infectious prions is the conformational change of a host-encoded glycoprotein, PrP(C), into a pathogenic isoform, PrP(Sc). The molecular requirements for efficient PrP conversion remain unknown. Altered glycosylation has been linked to various pathologies and the N-glycans harbored by two prion protein isoforms are different. In order to search for glycosylation-related genes that could mark prion infection, we used a glycosylation-dedicated microarray that allowed the simultaneous analysis of the expression of 165 glycosylation-related genes encoding proteins of the glycosyltransferase, glycosidase, lectin, and sulfotransferase families to compare the gene expression profiles of normal and scrapie-infected mouse brain and spleen. Eight genes were found upregulated in "scrapie brain" at the final state of the disease. In the spleen, five genes presented a modified expression. Three genes were also upregulated in the spleen of infected mice, and two (Pigq and St3gal5) downregulated. All changes were confirmed by qPCR and biochemical analyses applied to Pigq and St3gal5 proteins.
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Deletion of the SCN gene cluster on 2q24.4 is associated with severe epilepsy: an array-based genotype-phenotype correlation and a comprehensive review of previously published cases. Epilepsy Res 2008; 81:69-79. [PMID: 18539002 DOI: 10.1016/j.eplepsyres.2008.04.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 03/13/2008] [Accepted: 04/22/2008] [Indexed: 01/01/2023]
Abstract
PURPOSE To characterize a deletion of chromosome 2q at the molecular level in a patient suffering from severe epilepsy resembling severe myoclonic epilepsy of infancy/Dravet's syndrome (SMEI/DS) and to correlate other cases harboring deletions in the same region to morphological and clinical data. METHODS Array-based comparative genomic hybridization (array CGH) was performed on DNA from the patient. Forty-three previously published cases reporting deletions within region 2q21-q31 were collected and analyzed regarding their cytogenetic and clinical data. RESULTS A del(2)(q24.3q31.1) was detected in the patient, spanning a 10.4-megabase (Mb) region between 165.18 and 175.58Mb, harboring 47 genes. FISH analysis was performed, confirming this deletion. Twenty-two of the 43 previously published cases were seizure-positive. The most common dysmorphic features were ear abnormalities, microcephaly, micrognathia and brachysyndactyly for all patients as well as for solely the seizure-positive and -negative ones. For the 22 seizure-positive cases chromosome subband 2q24.3 constituted the smallest commonly deleted region among the majority of the cases, where subbands 2q22.1 and 2q33.3 represented the most proximal and distal breakpoint, respectively. CONCLUSIONS Based on the early age of presentation and the severity of the epilepsy reported for the majority of the seizure-positive cases it was concluded that SMEI/DS could be the epileptic encephalopathy associated with deletions within the 2q22.1-q33.3 region, due to haploinsuffiency of SCN1A and/or complete or partial deletion of other voltage-gated sodium channel genes caused by the aberration. Furthermore, our study supports that array CGH is a competent technique for screening SCN1A mutation-negative patients diagnosed with SMEI/DS-like epilepsies and dysmorphic features, generating rapid and high-resolution data of genomic imbalances present in the patients.
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