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Bergasa-Caceres F, Rabitz HA. Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic. Int J Mol Sci 2021; 22:ijms22168619. [PMID: 34445324 PMCID: PMC8395309 DOI: 10.3390/ijms22168619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
The initial steps of the folding pathway of the C-terminal domain of the murine prion protein mPrP(90–231) are predicted based on the sequential collapse model (SCM). A non-local dominant contact is found to form between the connecting region between helix 1 and β-sheet 1 and the C-terminal region of helix 3. This non-local contact nucleates the most populated molten globule-like intermediate along the folding pathway. A less stable early non-local contact between segments 120–124 and 179–183, located in the middle of helix 2, promotes the formation of a less populated molten globule-like intermediate. The formation of the dominant non-local contact constitutes an example of the postulated Nature’s Shortcut to the prion protein collapse into the native structure. The possible role of the less populated molten globule-like intermediate is explored as the potential initiation point for the folding for three pathogenic mutants (T182A, I214V, and Q211P in mouse prion numbering) of the prion protein.
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Zhang X, Ma X, Gan T, Shi Y, Wang Y, Liu Q. Secondary Chemical Bonding between Insoluble Calcium Oxalate and Carbonyl Oxygen Atoms of GLY and VAL Residues Triggers the Formation of Aβ Aggregates and Their Deposition in the Brain. ACS Chem Neurosci 2020; 11:4007-4011. [PMID: 33271013 DOI: 10.1021/acschemneuro.0c00662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite intense efforts, the cause of Alzheimer's disease is still not fully understood. A chemical and biochemical perspective could shed light on this disorder. Secondary chemical bonding between calcium and carbonyl oxygen atoms of glycine and valine might give rise to aggregates in the brain, which may later result in cell senescence. The decrease of solubility caused by amino acid substitutions in specific risk factors compounds insolubility issue and likely triggers early-onset Alzheimer's disease. Occasionally the enhancement of hydrogen bonding by amino acid replacements can reinforce the aggregates. Therefore, secondary chemical bonding to cations can generate cellular stresses in patients with Alzheimer's disease in addition to other chemical and biochemical interactions such as salt bridge. The distinction between early-onset and late-onset Alzheimer's disease risk factors may lie in the total capacity of a protein or local potency of a protein fragment to bind calcium or/and oxalate as calcium oxalate is highly insoluble and stressful.
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Affiliation(s)
- Xiaoxiao Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Xiaoqian Ma
- The Third Xiang Ya Hospital of Central South University, Changsha 410006, China
| | - Tao Gan
- School of Basic Medicine, Gannan Medical University, Ganzhou 34100, Jiangxi, China
| | - Yunfan Shi
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuan Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qiuyun Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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3
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Lee J, Chang I, Yu W. Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein. Sci Rep 2019; 9:19144. [PMID: 31844149 PMCID: PMC6915724 DOI: 10.1038/s41598-019-55661-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Destabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC). Hydrophobic interaction is the main driving force for protein folding, and critically affects the stability and solvability. To examine the importance of the hydrophobic core in the PrP, we chose six amino acids (V176, V180, T183, V210, I215, and Y218) that make up the hydrophobic core at the middle of the H2-H3 bundle. A few pathological mutants of these amino acids have been reported, such as V176G, V180I, T183A, V210I, I215V, and Y218N. We focused on how these pathologic mutations affect the hydrophobic core and thermostability of PrP. For this, we ran a temperature-based replica-exchange molecular dynamics (T-REMD) simulation, with a cumulative simulation time of 28 μs, for extensive ensemble sampling. From the T-REMD ensemble, we calculated the protein folding free energy difference between wild-type and mutant PrP using the thermodynamic integration (TI) method. Our results showed that pathological mutants V176G, T183A, I215V, and Y218N decrease the PrP stability. At the atomic level, we examined the change in pair-wise hydrophobic interactions from valine-valine to valine-isoleucine (and vice versa), which is induced by mutation V180I, V210I (I215V) at the 180th-210th (176th-215th) pair. Finally, we investigated the importance of the π-stacking between Y218 and F175.
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Affiliation(s)
- Juhwan Lee
- Center for Proteome Biophysics, DGIST, Daegu, 42988, Korea.
- Department of Emerging Material Sciences, DGIST, Daegu, 42988, Korea.
- Core Protein Resources Center, DGIST, Daegu, 42988, Korea.
- Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
| | - Iksoo Chang
- Center for Proteome Biophysics, DGIST, Daegu, 42988, Korea
- Core Protein Resources Center, DGIST, Daegu, 42988, Korea
- Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea
| | - Wookyung Yu
- Core Protein Resources Center, DGIST, Daegu, 42988, Korea.
- Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea.
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Baiardi S, Rossi M, Capellari S, Parchi P. Recent advances in the histo-molecular pathology of human prion disease. Brain Pathol 2019; 29:278-300. [PMID: 30588685 DOI: 10.1111/bpa.12695] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/11/2018] [Indexed: 02/06/2023] Open
Abstract
Prion diseases are progressive neurodegenerative disorders affecting humans and other mammalian species. The term prion, originally put forward to propose the concept that a protein could be infectious, refers to PrPSc , a misfolded isoform of the cellular prion protein (PrPC ) that represents the pathogenetic hallmark of these disorders. The discovery that other proteins characterized by misfolding and seeded aggregation can spread from cell to cell, similarly to PrPSc , has increased interest in prion diseases. Among neurodegenerative disorders, however, prion diseases distinguish themselves for the broader phenotypic spectrum, the fastest disease progression and the existence of infectious forms that can be transmitted through the exposure to diseased tissues via ingestion, injection or transplantation. The main clinicopathological phenotypes of human prion disease include Creutzfeldt-Jakob disease, by far the most common, fatal insomnia, variably protease-sensitive prionopathy, and Gerstmann-Sträussler-Scheinker disease. However, clinicopathological manifestations extend even beyond those predicted by this classification. Because of their transmissibility, the phenotypic diversity of prion diseases can also be propagated into syngenic hosts as prion strains with distinct characteristics, such as incubation period, pattern of PrPSc distribution and regional severity of histopathological changes in the brain. Increasing evidence indicates that different PrPSc conformers, forming distinct ordered aggregates, encipher the phenotypic variants related to prion strains. In this review, we summarize the most recent advances concerning the histo-molecular pathology of human prion disease focusing on the phenotypic spectrum of the disease including co-pathologies, the characterization of prion strains by experimental transmission and their correlation with the physicochemical properties of PrPSc aggregates.
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Affiliation(s)
- Simone Baiardi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marcello Rossi
- IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Sabina Capellari
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy.,IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Piero Parchi
- IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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5
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Bagyinszky E, Kang MJ, Pyun J, Giau VV, An SSA, Kim S. Early-onset Alzheimer's disease patient with prion (PRNP) p.Val180Ile mutation. Neuropsychiatr Dis Treat 2019; 15:2003-2013. [PMID: 31410005 PMCID: PMC6645694 DOI: 10.2147/ndt.s215277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 01/04/2023] Open
Abstract
Background: In this study, a known PRNP mutation, Val180Ile (c.G538A), was reported in a 58 years old female patient, clinically diagnosed with Alzheimer's disease (AD). Case report: The patient presented slowly progressive cognitive decline in memory and visuospatial domain. Neuroimaging showed hippocampal atrophy in MRI and mild amyloid positivity in PET scan. Even though her cerebrospinal fluid (CSF) was positive for 14-3-3 protein, no sign of Creutzfeldt-Jakob diseases symptoms was observed. In addition, reduced Aβ42 and elevated total-Tau and phospho-Tau in CSF also proved the AD diagnosis. The mutation may disturb the hydrophobic core of prion protein, and result in abnormal intramolecular interactions. Due to 23andMe, PRNP Val180Ile could not be categorized either as a mutation with complete penetrance, or as neutral variant, and could have a possible role in neurodegeneration. Pathological overlap was observed between prion diseases and other neurodegenerative diseases, including AD or frontotemporal dementia. Conclusion: Whole exome sequencing and pathway analysis of patient revealed rare or possible risk variants in AD associated genes, such as SORL1 or ABCA7. Along with PRNP, AD risk genes may play a role in negative regulation of amyloid formation. Dysfunctions in these genes could possibly be associated in reduced neuroprotection and amyloid clearance.
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Affiliation(s)
- Eva Bagyinszky
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnamsi 461-701, Republic of Korea
| | - Min Ju Kang
- Department of Neurology, Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Jungmin Pyun
- Department of Neurology, Seoul National University College of Medicine and Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
| | - Vo Van Giau
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnamsi 461-701, Republic of Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Medical Research Institute, Gachon University, Sungnamsi 461-701, Republic of Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, 463-707, Republic of Korea
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6
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Abstract
Genetic prion diseases (gPrDs) caused by mutations in the prion protein gene (PRNP) have been classified as genetic Creutzfeldt-Jakob disease, Gerstmann-Sträussler-Scheinker disease, or fatal familial insomnia. Mutations in PRNP can be missense, nonsense, and/or octapeptide repeat insertions or, possibly, deletions. These mutations can produce diverse clinical features. They may also show varying ancillary testing results and neuropathological findings. Although the majority of gPrDs have a rapid progression with a short survival time of a few months, many also present as ataxic or parkinsonian disorders, which have a slower decline over a few to several years. A few very rare mutations manifest as neuropsychiatric disorders, with systemic symptoms that include gastrointestinal disorders and neuropathy; these forms can progress over years to decades. In this review, we classify gPrDs as rapid, slow, or mixed types based on their typical rate of progression and duration, and we review the broad spectrum of phenotypes manifested by these diseases.
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Affiliation(s)
- Mee-Ohk Kim
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, California 94158
| | - Leonel T Takada
- Cognitive and Behavioral Neurology Unit, Department of Neurology, University of São Paulo, São Paulo, 05403-900, Brazil
| | - Katherine Wong
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, California 94158
| | - Sven A Forner
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, California 94158
| | - Michael D Geschwind
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, California 94158
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Abstract
Genetic Creutzfeldt-Jakob disease (CJD) is associated with mutations in the human PrP gene (PRNP) on chromosome 20p12-pter. Pathogenic mutations have been identified in 10-15% of all CJD patients, who often have a family history of autosomal-dominant pattern of inheritance and variable penetrance. However, the use of genetic tests implemented by surveillance networks all over the world increasingly identifies unexpectedly PRNP mutations in persons apparently presenting with a sporadic form of CJD. A high phenotypic variability was reported in genetic prion diseases, which partly overlap with the features of sporadic CJD. Here we review recent advances on the epidemiologic, clinical, and neuropathologic features of cases that phenotypically resemble CJD linked to point and insert mutations of the PRNP gene. Multidisciplinary studies are still required to understand the phenotypic spectrum, penetrance, and significance of PRNP mutations.
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Bagyinszky E, Giau VV, Youn YC, An SSA, Kim S. Characterization of mutations in PRNP (prion) gene and their possible roles in neurodegenerative diseases. Neuropsychiatr Dis Treat 2018; 14:2067-2085. [PMID: 30147320 PMCID: PMC6097508 DOI: 10.2147/ndt.s165445] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abnormal prion proteins are responsible for several fatal neurodegenerative diseases in humans and in animals, including Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker disease, and fatal familial insomnia. Genetics is important in prion diseases, but in the most cases, cause of diseases remained unknown. Several mutations were found to be causative for prion disorders, and the effect of mutations may be heterogeneous. In addition, different prion mutations were suggested to play a possible role in additional phenotypes, such as Alzheimer's type pathology, spongiform encephalopathy, or frontotemporal dementia. Pathogenic nature of several prion mutations remained unclear, such as M129V and E219K. These two polymorphic sites were suggested as either risk factors for different disorders, such as Alzheimer's disease (AD), variant CJD, or protease-sensitive prionopathy, and they can also be disease-modifying factors. Pathological overlap may also be possible with AD or progressive dementia, and several patients with prion mutations were initially diagnosed with AD. This review also introduces briefly the diagnosis of prion diseases and the issues with their diagnosis. Since prion diseases have quite heterogeneous phenotypes, a complex analysis, a combination of genetic screening, cerebrospinal fluid biomarker analysis and imaging technologies could improve the early disease diagnosis.
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Affiliation(s)
- Eva Bagyinszky
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, Gyeonggi-do, South Korea,
| | - Vo Van Giau
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, Gyeonggi-do, South Korea,
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, Gyeonggi-do, South Korea,
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine & Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Seongnam, South Korea
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Takada LT, Kim MO, Metcalf S, Gala II, Geschwind MD. Prion disease. HANDBOOK OF CLINICAL NEUROLOGY 2018; 148:441-464. [DOI: 10.1016/b978-0-444-64076-5.00029-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Takada LT, Kim MO, Cleveland RW, Wong K, Forner SA, Gala II, Fong JC, Geschwind MD. Genetic prion disease: Experience of a rapidly progressive dementia center in the United States and a review of the literature. Am J Med Genet B Neuropsychiatr Genet 2017; 174:36-69. [PMID: 27943639 PMCID: PMC7207989 DOI: 10.1002/ajmg.b.32505] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 12/21/2022]
Abstract
Although prion diseases are generally thought to present as rapidly progressive dementias with survival of only a few months, the phenotypic spectrum for genetic prion diseases (gPrDs) is much broader. The majority have a rapid decline with short survival, but many patients with gPrDs present as slowly progressive ataxic or parkinsonian disorders with progression over a few to several years. A few very rare mutations even present as neuropsychiatric disorders, sometimes with systemic symptoms such as gastrointestinal disorders and neuropathy, progressing over years to decades. gPrDs are caused by mutations in the prion protein gene (PRNP), and have been historically classified based on their clinicopathological features as genetic Jakob-Creutzfeldt disease (gJCD), Gerstmann-Sträussler-Scheinker (GSS), or Fatal Familial Insomnia (FFI). Mutations in PRNP can be missense, nonsense, and octapeptide repeat insertions or a deletion, and present with diverse clinical features, sensitivities of ancillary testing, and neuropathological findings. We present the UCSF gPrD cohort, including 129 symptomatic patients referred to and/or seen at UCSF between 2001 and 2016, and compare the clinical features of the gPrDs from 22 mutations identified in our cohort with data from the literature, as well as perform a literature review on most other mutations not represented in our cohort. E200K is the most common mutation worldwide, is associated with gJCD, and was the most common in the UCSF cohort. Among the GSS-associated mutations, P102L is the most commonly reported and was also the most common at UCSF. We also had several octapeptide repeat insertions (OPRI), a rare nonsense mutation (Q160X), and three novel mutations (K194E, E200G, and A224V) in our UCSF cohort. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Leonel T. Takada
- Cognitive and Behavioral Neurology Unit, Department of Neurology, University of São Paulo, São Paulo, Brazil
| | - Mee-Ohk Kim
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94107
| | - Ross W. Cleveland
- Department of Pediatrics, The University of Vermont Children’s Hospital, University of Vermont, Burlington, VT 05401
| | - Katherine Wong
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94107
| | - Sven A. Forner
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94107
| | - Ignacio Illán Gala
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jamie C. Fong
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94107
| | - Michael D. Geschwind
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94107
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de Pedro-Cuesta J, Martínez-Martín P, Rábano A, Alcalde-Cabero E, José García López F, Almazán-Isla J, Ruiz-Tovar M, Medrano MJ, Avellanal F, Calero O, Calero M. Drivers: A Biologically Contextualized, Cross-Inferential View of the Epidemiology of Neurodegenerative Disorders. J Alzheimers Dis 2016; 51:1003-22. [PMID: 26923014 PMCID: PMC4927850 DOI: 10.3233/jad-150884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Sutherland et al. (2011) suggested that, instead of risk factors for single neurodegenerative disorders (NDDs), there was a need to identify specific “drivers”, i.e., risk factors with impact on specific deposits, such as amyloid-β, tau, or α-synuclein, acting across entities. Objectives and Methods: Redefining drivers as “neither protein/gene- nor entity-specific features identifiable in the clinical and general epidemiology of conformational NDDs (CNDDs) as potential footprints of templating/spread/transfer mechanisms”, we conducted an analysis of the epidemiology of ten CNDDs, searching for patterns. Results: We identified seven potential drivers, each of which was shared by at least two CNDDs: 1) an age-at-exposure-related susceptibility to Creutzfeldt-Jakob disease (CJD) and several late-life CNDDs; 2) a relationship between age at onset, survival, and incidence; 3) shared genetic risk factors for CJD and late-life CNNDs; 4) partly shared personal (diagnostic, educational, behavioral, and social risk factors) predating clinical onset of late-life CNDDs; 5) two environmental risk factors, namely, surgery for sporadic CJD and amyotrophic lateral sclerosis, and Bordetella pertussis infection for Parkinson’s disease; 6) reticulo-endothelial system stressors or general drivers (andropause or premenopausal estrogen deficiency, APOEɛ4, and vascular risk factors) for late-life CNDDs such as dementia/Alzheimer’s disease, type-2 diabetes mellitus, and some sporadic cardiac and vascular degenerative diseases; and 7) a high, invariant incidence ratio of sporadic to genetic forms of mid- and late-life CNDDs, and type-2 diabetes mellitus. Conclusion: There might be a systematic epidemiologic pattern induced by specific proteins (PrP, TDP-43, SOD1, α-synuclein, amyloid-β, tau, Langerhans islet peptide, and transthyretin) or established combinations of these.
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Affiliation(s)
- Jesús de Pedro-Cuesta
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Pablo Martínez-Martín
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Alberto Rábano
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Enrique Alcalde-Cabero
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Fernando José García López
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Javier Almazán-Isla
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - María Ruiz-Tovar
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Maria-José Medrano
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Fuencisla Avellanal
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Olga Calero
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Chronic Disease Programme, Carlos III Institute of Health, Madrid, Spain
| | - Miguel Calero
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain.,Chronic Disease Programme, Carlos III Institute of Health, Madrid, Spain
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12
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Zhang W, Jiao B, Xiao T, Pan C, Liu X, Zhou L, Tang B, Shen L. Mutational analysis of PRNP in Alzheimer's disease and frontotemporal dementia in China. Sci Rep 2016; 6:38435. [PMID: 27910931 PMCID: PMC5133586 DOI: 10.1038/srep38435] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/09/2016] [Indexed: 12/14/2022] Open
Abstract
The prion protein (PRNP) gene is associated with prion diseases, whereas variants of the PRNP gene may also explain some cases of Alzheimer disease (AD) and frontotemporal dementia (FTD) in Caucasian populations. To determine the prevalence of the PRNP gene in patients with AD and FTD in China, we screened all exons of the PRNP gene in a cohort of 683 cases (606 AD and 77 FTD) in the Chinese Han population and we detected a novel missense mutation p.S17G in a late-onset AD (LOAD) patient. Furthermore, we analyzed the PRNP M/V polymorphism at codon 129, which was previously reported as a risk factor. However, there were no significant differences in genotype and allele frequency either in AD (OR = 0.75[0.378-1.49], P = 0.492), or FTD patients (OR = 2.046[0.265-15.783], P = 0.707). To our knowledge, this is the first study to reveal a correlation between the PRNP gene and Chinese AD and FTD patients in a large cohort. This study reports a novel p.S17G mutation in a clinically diagnosed LOAD patient, suggesting that the PRNP mutation is present in Chinese AD patients, whereas, M129V polymorphism is not a risk factor for AD or FTD in the Chinese Han population.
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Affiliation(s)
- Weiwei Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingting Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chuzheng Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lin Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,State Key Laboratory of Medical Genetics, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,State Key Laboratory of Medical Genetics, Changsha, China
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Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LPC, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TFJ, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O'Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JGJ, Ikram MA, Uitterlinden AG, van Duijn CM, Daly MJ, MacArthur DG. Quantifying prion disease penetrance using large population control cohorts. Sci Transl Med 2016; 8:322ra9. [PMID: 26791950 DOI: 10.1126/scitranslmed.aad5169] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. We assess the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. We show that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.
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Affiliation(s)
- Eric Vallabh Minikel
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA.
| | - Sonia M Vallabh
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karol Estrada
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | | | - Cory Y McLean
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Joyce Y Tung
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Linda P C Yu
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Pierluigi Gambetti
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Janis Blevins
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Shulin Zhang
- University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Yvonne Cohen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Wei Chen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Tsuyoshi Hamaguchi
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Nobuo Sanjo
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Hidehiro Mizusawa
- National Center Hospital, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Yosikazu Nakamura
- Department of Public Health, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Tetsuyuki Kitamoto
- Department of Neurological Science, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Steven J Collins
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alison Boyd
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert G Will
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Richard Knight
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Claudia Ponto
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Inga Zerr
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Sabina Eigenbrod
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Miguel Calero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Jesús de Pedro-Cuesta
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Stéphane Haïk
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Jean-Louis Laplanche
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Elodie Bouaziz-Amar
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Jean-Philippe Brandel
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Sabina Capellari
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Piero Parchi
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Anna Poleggi
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anna Ladogana
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jamie L Marshall
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio 70210, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Anna Kähler
- Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA. Karolinska Institutet, Stockholm SE-171 77, Sweden
| | | | - Shaun M Purcell
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Annemieke Rozemuller
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Casper Jansen
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | | | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands. Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | | | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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Schmitz M, Dittmar K, Llorens F, Gelpi E, Ferrer I, Schulz-Schaeffer WJ, Zerr I. Hereditary Human Prion Diseases: an Update. Mol Neurobiol 2016; 54:4138-4149. [PMID: 27324792 DOI: 10.1007/s12035-016-9918-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/03/2016] [Indexed: 01/19/2023]
Abstract
Prion diseases in humans are neurodegenerative diseases which are caused by an accumulation of abnormal, misfolded cellular prion protein known as scrapie prion protein (PrPSc). Genetic, acquired, or spontaneous (sporadic) forms are known. Pathogenic mutations in the human prion protein gene (PRNP) have been identified in 10-15 % of CJD patients. These mutations may be single point mutations, STOP codon mutations, or insertions or deletions of octa-peptide repeats. Some non-coding mutations and new mutations in the PrP gene have been identified without clear evidence for their pathogenic significance. In the present review, we provide an updated overview of PRNP mutations, which have been documented in the literature until now, describe the change in the DNA, the family history, the pathogenicity, and the number of described cases, which has not been published in this complexity before. We also provide a description of each genetic prion disease type, present characteristic histopathological features, and the PrPSc isoform expression pattern of various familial/genetic prion diseases.
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Affiliation(s)
- Matthias Schmitz
- Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany. .,Department of Neuropathology, Georg-August University, Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
| | - Kathrin Dittmar
- Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Franc Llorens
- Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Ellen Gelpi
- Neurological Tissue Bank, Biobanc-Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Barcelona, Spain
| | - Walter J Schulz-Schaeffer
- Department of Neuropathology, Georg-August University, Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Inga Zerr
- Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
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Calero M, Gómez-Ramos A, Calero O, Soriano E, Avila J, Medina M. Additional mechanisms conferring genetic susceptibility to Alzheimer's disease. Front Cell Neurosci 2015; 9:138. [PMID: 25914626 PMCID: PMC4391239 DOI: 10.3389/fncel.2015.00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/23/2015] [Indexed: 01/18/2023] Open
Abstract
Familial Alzheimer’s disease (AD), mostly associated with early onset, is caused by mutations in three genes (APP, PSEN1, and PSEN2) involved in the production of the amyloid β peptide. In contrast, the molecular mechanisms that trigger the most common late onset sporadic AD remain largely unknown. With the implementation of an increasing number of case-control studies and the upcoming of large-scale genome-wide association studies there is a mounting list of genetic risk factors associated with common genetic variants that have been associated with sporadic AD. Besides apolipoprotein E, that presents a strong association with the disease (OR∼4), the rest of these genes have moderate or low degrees of association, with OR ranging from 0.88 to 1.23. Taking together, these genes may account only for a fraction of the attributable AD risk and therefore, rare variants and epistastic gene interactions should be taken into account in order to get the full picture of the genetic risks associated with AD. Here, we review recent whole-exome studies looking for rare variants, somatic brain mutations with a strong association to the disease, and several studies dealing with epistasis as additional mechanisms conferring genetic susceptibility to AD. Altogether, recent evidence underlines the importance of defining molecular and genetic pathways, and networks rather than the contribution of specific genes.
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Affiliation(s)
- Miguel Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Chronic Disease Programme, Instituto de Salud Carlos III Madrid, Spain ; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
| | - Alberto Gómez-Ramos
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Centro de Biología Molecular Severo Ochoa CSIC-UAM Madrid, Spain
| | - Olga Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Chronic Disease Programme, Instituto de Salud Carlos III Madrid, Spain
| | - Eduardo Soriano
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; University of Barcelona Barcelona, Spain
| | - Jesús Avila
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Centro de Biología Molecular Severo Ochoa CSIC-UAM Madrid, Spain
| | - Miguel Medina
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
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Ganegoda GU, Wang J, Wu FX, Li M. Prediction of disease genes using tissue-specified gene-gene network. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 3:S3. [PMID: 25350876 PMCID: PMC4243117 DOI: 10.1186/1752-0509-8-s3-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Tissue specificity is an important aspect of many genetic diseases in the context of genetic disorders as the disorder affects only few tissues. Therefore tissue specificity is important in identifying disease-gene associations. Hence this paper seeks to discuss the impact of using tissue specificity in predicting new disease-gene associations and how to use tissue specificity along with phenotype information for a particular disease. METHODS In order to find out the impact of using tissue specificity for predicting new disease-gene associations, this study proposes a novel method called tissue-specified genes to construct tissues-specific gene-gene networks for different tissue samples. Subsequently, these networks are used with phenotype details to predict disease genes by using Katz method. The proposed method was compared with three other tissue-specific network construction methods in order to check its effectiveness. Furthermore, to check the possibility of using tissue-specific gene-gene network instead of generic protein-protein network at all time, the results are compared with three other methods. RESULTS In terms of leave-one-out cross validation, calculation of the mean enrichment and ROC curves indicate that the proposed approach outperforms existing network construction methods. Furthermore tissues-specific gene-gene networks make a more positive impact on predicting disease-gene associations than generic protein-protein interaction networks. CONCLUSIONS In conclusion by integrating tissue-specific data it enabled prediction of known and unknown disease-gene associations for a particular disease more effectively. Hence it is better to use tissue-specific gene-gene network whenever possible. In addition the proposed method is a better way of constructing tissue-specific gene-gene networks.
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Affiliation(s)
| | - JianXin Wang
- School of Information Science and Engineering, Central South University, Changsha, China
| | - Fang-Xiang Wu
- School of Information Science and Engineering, Central South University, Changsha, China
- College of Engineering, University of Saskatchewan, 57 Campus Dr., Saskatoon, SK Canada
| | - Min Li
- School of Information Science and Engineering, Central South University, Changsha, China
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