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Krokidis MG, Exarchos T, Vlamos P. Bioinformatics Approaches for Parkinson's Disease in Clinical Practice: Data-Driven Biomarkers and Pharmacological Treatment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1338:193-198. [PMID: 34973025 DOI: 10.1007/978-3-030-78775-2_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Parkinson's disease is a gradually progressive neurodegenerative disorder characterized by a selective loss of dopaminergic neurons in the midbrain area called the substantia nigra pars compacta and cytoplasmic alpha-synuclein-rich inclusions termed Lewy bodies. The etiology and pathogenesis remain incompletely understood. The development of reliable biomarkers for the early and accurate diagnosis, including biochemical, genetic, clinical, and neuroimaging markers, is crucial for unraveling the pathogenic processes of the disease as well as patients' progress surveillance. High-throughput technologies and system biology methodologies can support the identification of potent molecular fingerprints together with the establishment of dynamic network biomarkers. Emphasis is given on multi-omics datasets and dysregulated pathways associated with differentially expressed transcripts, modified protein motifs, and altered metabolic profiles. Although there is no therapy that terminates the neurodegenerative process and dopamine replacement strategy with L-DOPA represents the most effective treatment, numerous therapeutic protocols such as dopamine receptor agonists, MAO-B inhibitors, and cholinesterase inhibitors represent candidate treatments providing at the same time valuable network-based approaches to drug repositioning. Computational methodologies and bioinformatics platforms for visualization, clustering, and validating of molecular and clinical datasets provide important insights into diagnostic processing and therapeutic pipeline.
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Affiliation(s)
- Marios G Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece.
| | - Themis Exarchos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Panayiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
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2
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Chi J, Xie Q, Jia J, Liu X, Sun J, Deng Y, Yi L. Integrated Analysis and Identification of Novel Biomarkers in Parkinson's Disease. Front Aging Neurosci 2018; 10:178. [PMID: 29967579 PMCID: PMC6016006 DOI: 10.3389/fnagi.2018.00178] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/24/2018] [Indexed: 02/05/2023] Open
Abstract
Parkinson's disease (PD) is a quite common neurodegenerative disorder with a prevalence of approximately 1:800-1,000 in subjects over 60 years old. The aim of our study was to determine the candidate target genes in PD through meta-analysis of multiple gene expression arrays datasets and to further combine mRNA and miRNA expression analyses to identify more convincing biological targets and their regulatory factors. Six included datasets were obtained from the Gene Expression Omnibus database by systematical search, including five mRNA datasets (150 substantia nigra samples in total) and one miRNA dataset containing 32 peripheral blood samples. A chip meta-analysis of five microarray data was conducted by using the metaDE package and 94 differentially expressed (DE) mRNAs were comprehensively obtained. And 19 deregulated DE miRNAs were obtained through the analysis of one miRNAs dataset by Qlucore Omics Explorer software. An interaction network formed by DE mRNAs, DE miRNAs, and important pathways was discovered after we analyzed the functional enrichment, protein-protein interactions, and miRNA targetome prediction analysis. In conclusion, this study suggested that five significantly downregulated mRNAs (MAPK8, CDC42, NDUFS1, COX4I1, and SDHC) and three significantly downregulated miRNAs (miR-126-5p, miR-19-3p, and miR-29a-3p) were potentially useful diagnostic markers in clinic, and lipid metabolism (especially non-alcoholic fatty liver disease pathway) and mitochondrial dysregulation may be the keys to biochemically detectable molecular defects. However, the role of these new biomarkers and molecular mechanisms in PD requires further experiments in vivo and in vitro and further clinical evidence.
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Affiliation(s)
- Jieshan Chi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Qizhi Xie
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Jingjing Jia
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaoma Liu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jingjing Sun
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuanfei Deng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- National Clinical Research Center for Geriatric Diseases Shenzhen Center, Peking University Shenzhen Hospital, Shenzhen, China
| | - Li Yi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- National Clinical Research Center for Geriatric Diseases Shenzhen Center, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Li Yi,
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Belle K, Shabazz FS, Nuytemans K, Davis DA, Ali A, Young JL, Scott WK, Mash DC, Vance JM, Dykxhoorn DM. Generation of disease-specific autopsy-confirmed iPSCs lines from postmortem isolated Peripheral Blood Mononuclear Cells. Neurosci Lett 2016; 637:201-206. [PMID: 27826014 DOI: 10.1016/j.neulet.2016.10.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/30/2016] [Accepted: 10/31/2016] [Indexed: 12/25/2022]
Abstract
Understanding the molecular mechanisms that underlie neurodegenerative disorders has been hampered by a lack of readily available model systems that replicate the complexity of the human disease. Recent advances in stem cell technology have facilitated the derivation of patient-specific stem cells from a variety of differentiated cell types. These induced pluripotent stem cells (iPSCs) are attractive disease models since they can be grown and differentiated to produce large numbers of disease-relevant cell types. However, most iPSC lines are derived in advance of, and without the benefit of, neuropathological confirmation of the donor - the gold standard for many disease classifications and measurement of disease severity. While others have reported the generation of autopsy-confirmed iPSC lines from patient explants, these methods require outgrowth of cadaver tissue, which require additional time and is often only successful ∼50% of the time. Here we report the rapid generation of autopsy-confirmed iPSC lines from peripheral blood mononuclear cells (PBMCs) drawn postmortem. Since this approach doesn't require the propagation of previously frozen cadaver tissue, iPSC can be rapidly and efficiently produced from patients with autopsy-confirmed pathology. These matched iPSC-derived patient-specific neurons and postmortem brain tissue will support studies of specific mechanisms that drive the pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Kinsley Belle
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Francelethia S Shabazz
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - David A Davis
- Department of Neurology, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Aleena Ali
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Juan L Young
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami FL, United States; John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - William K Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami FL, United States; John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami FL, United States; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Jeffrey M Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami FL, United States; John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States
| | - Derek M Dykxhoorn
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami FL, United States; John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL, United States.
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Liu G, Boot B, Locascio JJ, Jansen IE, Winder‐Rhodes S, Eberly S, Elbaz A, Brice A, Ravina B, van Hilten JJ, Cormier‐Dequaire F, Corvol J, Barker RA, Heutink P, Marinus J, Williams‐Gray CH, Scherzer CR. Specifically neuropathic Gaucher's mutations accelerate cognitive decline in Parkinson's. Ann Neurol 2016; 80:674-685. [PMID: 27717005 PMCID: PMC5244667 DOI: 10.1002/ana.24781] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE We hypothesized that specific mutations in the β-glucocerebrosidase gene (GBA) causing neuropathic Gaucher's disease (GD) in homozygotes lead to aggressive cognitive decline in heterozygous Parkinson's disease (PD) patients, whereas non-neuropathic GD mutations confer intermediate progression rates. METHODS A total of 2,304 patients with PD and 20,868 longitudinal visits for up to 12.8 years (median, 4.1) from seven cohorts were analyzed. Differential effects of four types of genetic variation in GBA on longitudinal cognitive decline were evaluated using mixed random and fixed effects and Cox proportional hazards models. RESULTS Overall, 10.3% of patients with PD and GBA sequencing carried a mutation. Carriers of neuropathic GD mutations (1.4% of patients) had hazard ratios (HRs) for global cognitive impairment of 3.17 (95% confidence interval [CI], 1.60-6.25) and a hastened decline in Mini-Mental State Exam scores compared to noncarriers (p = 0.0009). Carriers of complex GBA alleles (0.7%) had an HR of 3.22 (95% CI, 1.18-8.73; p = 0.022). By contrast, the common, non-neuropathic N370S mutation (1.5% of patients; HR, 1.96; 95% CI, 0.92-4.18) or nonpathogenic risk variants (6.6% of patients; HR, 1.36; 95% CI, 0.89-2.05) did not reach significance. INTERPRETATION Mutations in the GBA gene pathogenic for neuropathic GD and complex alleles shift longitudinal cognitive decline in PD into "high gear." These findings suggest a relationship between specific types of GBA mutations and aggressive cognitive decline and have direct implications for improving the design of clinical trials. Ann Neurol 2016;80:674-685.
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Affiliation(s)
- Ganqiang Liu
- Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham & Women's HospitalCambridgeMA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's HospitalBostonMA
| | - Brendon Boot
- Biomarkers Program, Harvard NeuroDiscovery CenterBostonMA
- Department of NeurologyBrigham and Women's HospitalBostonMA
| | - Joseph J. Locascio
- Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham & Women's HospitalCambridgeMA
- Department of NeurologyMassachusetts General HospitalBostonMA
| | - Iris E. Jansen
- Department of Medical GenomicsVU University Medical Center, Neuroscience Campus AmsterdamAmsterdamHZThe Netherlands
- German Center for Neurodegenerative diseases (DZNE)TübingenGermany
| | - Sophie Winder‐Rhodes
- John Van Geest Centre for Brain Repair, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Shirley Eberly
- Department of Biostatistics and Computational BiologyUniversity of Rochester Medical CenterRochesterNY
| | - Alexis Elbaz
- INSERM, Centre for Research in Epidemiology and Population Health, U1018, Epidemiology of ageing and age related diseasesVillejuifFrance
- University Paris‐Sud, UMRS 1018VillejuifFrance
| | - Alexis Brice
- Sorbonne Université, Université Pierre et Marie Curie Paris 06 UMR S 1127, Institut National de Santé et en Recherche Médicale U 1127 and Centre d'Investigation Clinique 1422, Centre National de Recherche Scientifique U 7225, Institut du Cerveau et de la Moelle Epinière, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié‐SalpêtrièreParisFrance
| | | | | | - Florence Cormier‐Dequaire
- Sorbonne Université, Université Pierre et Marie Curie Paris 06 UMR S 1127, Institut National de Santé et en Recherche Médicale U 1127 and Centre d'Investigation Clinique 1422, Centre National de Recherche Scientifique U 7225, Institut du Cerveau et de la Moelle Epinière, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié‐SalpêtrièreParisFrance
| | - Jean‐Christophe Corvol
- Sorbonne Université, Université Pierre et Marie Curie Paris 06 UMR S 1127, Institut National de Santé et en Recherche Médicale U 1127 and Centre d'Investigation Clinique 1422, Centre National de Recherche Scientifique U 7225, Institut du Cerveau et de la Moelle Epinière, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié‐SalpêtrièreParisFrance
| | - Roger A. Barker
- John Van Geest Centre for Brain Repair, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Peter Heutink
- Department of Medical GenomicsVU University Medical Center, Neuroscience Campus AmsterdamAmsterdamHZThe Netherlands
- German Center for Neurodegenerative diseases (DZNE)TübingenGermany
| | - Johan Marinus
- Department of NeurologyLeiden University Medical CenterLeidenThe Netherlands
| | - Caroline H. Williams‐Gray
- John Van Geest Centre for Brain Repair, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Clemens R. Scherzer
- Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham & Women's HospitalCambridgeMA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's HospitalBostonMA
- Biomarkers Program, Harvard NeuroDiscovery CenterBostonMA
- Department of NeurologyBrigham and Women's HospitalBostonMA
- Department of NeurologyMassachusetts General HospitalBostonMA
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Mehanna R, Scherzer CR, Ding H, Locascio JJ. Unrecognized vitamin D3 deficiency is common in Parkinson disease: Harvard Biomarker study. Neurology 2014; 82:1666; discussion 1666. [PMID: 24799519 PMCID: PMC10845904 DOI: 10.1212/01.wnl.0000449750.81263.7d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Cesani M, Cavalca E, Macco R, Leoncini G, Terreni MR, Lorioli L, Furlan R, Comi G, Doglioni C, Zacchetti D, Sessa M, Scherzer CR, Biffi A. Metallothioneins as dynamic markers for brain disease in lysosomal disorders. Ann Neurol 2014; 75:127-37. [PMID: 24242821 PMCID: PMC4237725 DOI: 10.1002/ana.24053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 10/17/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To facilitate development of novel disease-modifying therapies for lysosomal storage disorder (LSDs) characterized by nervous system involvement such as metachromatic leukodystrophy (MLD), molecular markers for monitoring disease progression and therapeutic response are needed. To this end, we sought to identify blood transcripts associated with the progression of MLD. METHODS Genome-wide expression analysis was performed in primary T lymphocytes of 24 patients with MLD compared to 24 age- and sex-matched healthy controls. Genes associated with MLD were identified, confirmed on a quantitative polymerase chain reaction platform, and replicated in an independent patient cohort. mRNA and protein expression of the prioritized gene family of metallothioneins was evaluated in postmortem patient brains and in mouse models representing 6 other LSDs. Metallothionein expression during disease progression and in response to specific treatment was evaluated in 1 of the tested LSD mouse models. Finally, a set of in vitro studies was planned to dissect the biological functions exerted by this class of molecules. RESULTS Metallothionein genes were significantly overexpressed in T lymphocytes and brain of patients with MLD and generally marked nervous tissue damage in the LSDs here evaluated. Overexpression of metallothioneins correlated with measures of disease progression in mice and patients, whereas their levels decreased in mice upon therapeutic treatment. In vitro studies indicated that metallothionein expression is regulated in response to oxidative stress and inflammation, which are biochemical hallmarks of lysosomal storage diseases. INTERPRETATION Metallothioneins are potential markers of neurologic disease processes and treatment response in LSDs.
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Affiliation(s)
- Martina Cesani
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy; Neurogenomics Laboratory, Harvard Medical School and Brigham & Women's Hospital, Cambridge, MA, USA
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Mellick GD, Silburn PA, Sutherland GT, Siebert GA. Exploiting the potential of molecular profiling in Parkinson’s disease: current practice and future probabilities. Expert Rev Mol Diagn 2014; 10:1035-50. [PMID: 21080820 DOI: 10.1586/erm.10.86] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- George D Mellick
- Eskitis Institute for Cell & Molecular Therapies, School of Biomolecular & Physical Sciences, Griffith University, Brisbane, QLD 4111, Australia.
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Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas. Dev Psychopathol 2013; 24:1427-42. [PMID: 23062308 DOI: 10.1017/s0954579412000818] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of gene expression (i.e., the study of the transcriptome) in different cells and tissues allows us to understand the molecular mechanisms of their differentiation, development and functioning. In this article, we describe some studies of gene-expression profiling for the purposes of understanding developmental (age-related) changes in the brain using different technologies (e.g., DNA-Microarray) and the new and increasingly popular RNA-Seq. We focus on advancements in studies of gene expression in the human brain, which have provided data on the structure and age-related variability of the transcriptome in the brain. We present data on RNA-Seq of the transcriptome in three distinct areas of the neocortex from different ages: mature and elderly individuals. We report that most age-related transcriptional changes affect cellular signaling systems, and, as a result, the transmission of nerve impulses. In general, the results demonstrate the high potential of RNA-Seq for the study of distinctive features of gene expression among cortical areas and the changes in expression through normal and atypical development of the central nervous system.
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Johnson R, Noble W, Tartaglia GG, Buckley NJ. Neurodegeneration as an RNA disorder. Prog Neurobiol 2012; 99:293-315. [PMID: 23063563 PMCID: PMC7116994 DOI: 10.1016/j.pneurobio.2012.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/14/2012] [Accepted: 09/26/2012] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases constitute one of the single most important public health challenges of the coming decades, and yet we presently have only a limited understanding of the underlying genetic, cellular and molecular causes. As a result, no effective disease-modifying therapies are currently available, and no method exists to allow detection at early disease stages, and as a result diagnoses are only made decades after disease pathogenesis, by which time the majority of physical damage has already occurred. Since the sequencing of the human genome, we have come to appreciate that the transcriptional output of the human genome is extremely rich in non-protein coding RNAs (ncRNAs). This heterogeneous class of transcripts is widely expressed in the nervous system, and is likely to play many crucial roles in the development and functioning of this organ. Most exciting, evidence has recently been presented that ncRNAs play central, but hitherto unappreciated roles in neurodegenerative processes. Here, we review the diverse available evidence demonstrating involvement of ncRNAs in neurodegenerative diseases, and discuss their possible implications in the development of therapies and biomarkers for these conditions.
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Key Words
- neurodegeneration
- neurodegenerative disease
- non-coding rna
- alzheimer's disease
- parkinson's disease
- huntington's disease
- trinucleotide repeat disorder
- bace1
- rest
- long non-coding rna
- microrna
- har1
- sox2ot
- mir-9
- mir-132
- mir-124
- ndds, neurodegenerative disorders
- ad, alzheimer's disease
- hd, huntington's disease
- pd, parkinson's disease
- als, amyotrophic lateral sclerosis
- app, amyloid precursor protein
- cftr, cystic fibrosis
- csf, cerebrospinal fluid
- sod1, superoxide dismutase 1
- tardbp, tar dna binding protein
- psen-1, presenilin 1
- psen-2, presenilin 1
- mapt, microtubule-associated protein tau
- snca, α-synuclein
- ups, ubiquitin-proteasome system
- aββ, -amyloid
- er, endoplasmic reticulum
- ber, base excision repair
- parp-1, poly-adp ribose polymerase-1
- lncrnas, long non-coding rnas
- mirnas, microrna
- ncrna, non-coding rnas
- ngs, next generation sequencing
- pcr, polymerase chain reaction
- sars, severe acute respiratory disorder
- sca, spinal cerebellar ataxia
- dm, myotonic dystrophy
- hdl2, huntington's disease-like 2
- tnds, trinucleotide repeat disorders
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Affiliation(s)
- Rory Johnson
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain
| | - Wendy Noble
- Kings College London, Institute of Psychiatry, London, UK
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader, 88, 08003 Barcelona, Catalunya, Spain
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Potashkin JA, Santiago JA, Ravina BM, Watts A, Leontovich AA. Biosignatures for Parkinson's disease and atypical parkinsonian disorders patients. PLoS One 2012; 7:e43595. [PMID: 22952715 PMCID: PMC3428307 DOI: 10.1371/journal.pone.0043595] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/26/2012] [Indexed: 02/06/2023] Open
Abstract
Diagnosis of Parkinson' disease (PD) carries a high misdiagnosis rate due to failure to recognize atypical parkinsonian disorders (APD). Usually by the time of diagnosis greater than 60% of the neurons in the substantia nigra are dead. Therefore, early detection would be beneficial so that therapeutic intervention may be initiated early in the disease process. We used splice variant-specific microarrays to identify mRNAs whose expression is altered in peripheral blood of early-stage PD patients compared to healthy and neurodegenerative disease controls. Quantitative polymerase chain reaction assays were used to validate splice variant transcripts in independent sample sets. Here we report a PD signature used to classify blinded samples with 90% sensitivity and 94% specificity and an APD signature that resulted in a diagnosis with 95% sensitivity and 94% specificity. This study provides the first discriminant functions with coherent diagnostic signatures for PD and APD. Analysis of the PD biomarkers identified a regulatory network with nodes centered on the transcription factors HNF4A and TNF, which have been implicated in insulin regulation.
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Affiliation(s)
- Judith A Potashkin
- The Cellular and Molecular Pharmacology Department, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois, United States of America.
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Transcriptional modulator H2A histone family, member Y (H2AFY) marks Huntington disease activity in man and mouse. Proc Natl Acad Sci U S A 2011; 108:17141-6. [PMID: 21969577 DOI: 10.1073/pnas.1104409108] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Huntington disease (HD) is a progressive neurodegenerative disease that affects 30,000 individuals in North America. Treatments that slow its relentless course are not yet available, and biomarkers that can reliably measure disease activity and therapeutic response are urgently needed to facilitate their development. Here, we interrogated 119 human blood samples for transcripts associated with HD. We found that the dynamic regulator of chromatin plasticity H2A histone family, member Y (H2AFY) is specifically overexpressed in the blood and frontal cortex of patients with HD compared with controls. This association precedes the onset of clinical symptoms, was confirmed in two mouse models, and was independently replicated in cross-sectional and longitudinal clinical studies comprising 142 participants. A histone deacetylase inhibitor that suppresses neurodegeneration in animal models reduces H2AFY levels in a randomized phase II clinical trial. This study identifies the chromatin regulator H2AFY as a potential biomarker associated with disease activity and pharmacodynamic response that may become useful for enabling disease-modifying therapeutics for HD.
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Cytokines regulate neuronal gene expression: Differential effects of Th1, Th2 and monocyte/macrophage cytokines. J Neuroimmunol 2011; 238:19-33. [DOI: 10.1016/j.jneuroim.2011.06.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/16/2011] [Accepted: 06/17/2011] [Indexed: 12/19/2022]
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Quest for new genomic and proteomic biomarkers in neurology. Transl Neurosci 2011. [DOI: 10.2478/s13380-011-0005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe possibility of identifying novel biomarkers for neurodegenerative diseases has been greatly enhanced with recent advances in genomics and proteomics. Novel technologies have the potential to hasten the development of new biomarkers useful as predictors of disease etiology and outcome, as well as responsiveness to therapy. Disease-modifying new therapies are very much needed in modern approaches to treatment of neurodegenerative diseases. Current progress in the field encounters a degree of skepticism about the reliability of genomic and proteomic data and its relevance for clinical applications. Standard operating procedures covering sample collection, methodology and statistical analysis need to be fully developed and strictly adhered to in order to assure reproducible and clinically relevant results. Previous studies involving patients with neurodegenerative diseases show promise in using genomic and proteomic approaches for development of new biomarkers. Confirmation of any novel biomarker in multiple independent patient cohorts and correlation of the improvement in biomarker endpoint with clinical improvement in longitudinal patient studies remains crucial for future successful application. We propose that a combination of approaches in biomarker discovery may in the end lead to identification of promising candidates at DNA, RNA, protein and small molecule level.
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Grünblatt E, Zehetmayer S, Jacob CP, Müller T, Jost WH, Riederer P. Pilot study: peripheral biomarkers for diagnosing sporadic Parkinson's disease. J Neural Transm (Vienna) 2010; 117:1387-93. [PMID: 21069393 DOI: 10.1007/s00702-010-0509-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 10/05/2010] [Indexed: 01/26/2023]
Abstract
The need for an early and differential diagnosis of Parkinson's disease (PD) is undoubtedly one of the main quests of the century. An early biomarker would enable therapy to begin sooner and would, hopefully, slow or better prevent progression of the disease. We performed transcript profiling via quantitative RT-PCR in RNA originating from peripheral blood samples. The groups were de novo (n = 11) and medicated PD (n = 94) subjects and healthy controls (n = 34), while for negative control Alzheimer's disease (AD; n = 14) subjects were recruited as an additional neurodegenerative disease. The results were retested on a second recruitment consisting 22 medicated PD subjects versus 33 controls and 12 AD. Twelve transcripts were chosen as candidate genes, according to previous postmortem brain profiling. Multiple analyses resulted in four significant genes: proteasome (prosome, macropain) subunit-alpha type-2 (PSMA2; p = 0.0002, OR = 1.15 95% CI 1.07-1.24), laminin, beta-2 (laminin S) (LAMB2; p = 0.0078, OR = 2.26 95% CI 1.24-4.14), aldehyde dehydrogenase 1 family-member A1 (ALDH1A1; p = 0.016, OR = 1.05 95% CI 1.01-1.1), and histone cluster-1 H3e (HIST1H3E; p = 0.03, OR = 0.975 95% CI 0.953-0.998) differentiating between medicated PD subjects versus controls. Using these four biomarkers for PD diagnosis, we achieved sensitivity and specificity of more than 80%. These biomarkers might be specific for PD diagnosis, since in AD subjects no significant results were observed. In the second validation, three genes (PSMA2, LAMB2 and ALDH1A1) demonstrated high reproducibility. This result supports previous studies of gene expression profiling and may facilitate the development of biomarkers for early diagnosis of PD.
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Affiliation(s)
- Edna Grünblatt
- Clinical Neurochemistry, National Parkinson Foundation Centre of Excellence Research Laboratories, Neurochemistry Laboratory, Clinic and Policlinic for Psychiatry, Psychosomatic and Psychotherapy, University of Würzburg, Füchsleinstr 15, 97080 Würzburg, Germany.
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15
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Zheng B, Liao Z, Locascio JJ, Lesniak KA, Roderick SS, Watt ML, Eklund AC, Zhang-James Y, Kim PD, Hauser MA, Grünblatt E, Moran LB, Mandel SA, Riederer P, Miller RM, Federoff HJ, Wüllner U, Papapetropoulos S, Youdim MB, Cantuti-Castelvetri I, Young AB, Vance JM, Davis RL, Hedreen JC, Adler CH, Beach TG, Graeber MB, Middleton FA, Rochet JC, Scherzer CR. PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease. Sci Transl Med 2010; 2:52ra73. [PMID: 20926834 PMCID: PMC3129986 DOI: 10.1126/scitranslmed.3001059] [Citation(s) in RCA: 617] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Parkinson's disease affects 5 million people worldwide, but the molecular mechanisms underlying its pathogenesis are still unclear. Here, we report a genome-wide meta-analysis of gene sets (groups of genes that encode the same biological pathway or process) in 410 samples from patients with symptomatic Parkinson's and subclinical disease and healthy controls. We analyzed 6.8 million raw data points from nine genome-wide expression studies, and 185 laser-captured human dopaminergic neuron and substantia nigra transcriptomes, followed by two-stage replication on three platforms. We found 10 gene sets with previously unknown associations with Parkinson's disease. These gene sets pinpoint defects in mitochondrial electron transport, glucose utilization, and glucose sensing and reveal that they occur early in disease pathogenesis. Genes controlling cellular bioenergetics that are expressed in response to peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) are underexpressed in Parkinson's disease patients. Activation of PGC-1α results in increased expression of nuclear-encoded subunits of the mitochondrial respiratory chain and blocks the dopaminergic neuron loss induced by mutant α-synuclein or the pesticide rotenone in cellular disease models. Our systems biology analysis of Parkinson's disease identifies PGC-1α as a potential therapeutic target for early intervention.
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Affiliation(s)
- Bin Zheng
- Laboratory for Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 65 Landsdowne Street, Suite 307A, Cambridge, MA 02139, USA
| | - Zhixiang Liao
- Laboratory for Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 65 Landsdowne Street, Suite 307A, Cambridge, MA 02139, USA
| | - Joseph J. Locascio
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kristen A. Lesniak
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah S. Roderick
- Laboratory for Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 65 Landsdowne Street, Suite 307A, Cambridge, MA 02139, USA
| | - Marla L. Watt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Aron C. Eklund
- Laboratory for Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 65 Landsdowne Street, Suite 307A, Cambridge, MA 02139, USA
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Yanli Zhang-James
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Peter D. Kim
- Department of Neurosurgery, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Edna Grünblatt
- Clinical Neurochemistry, National Parkinson Foundation Centre of Excellence Research Laboratory, University of Würzburg, 97070 Würzburg, Germany
| | | | - Silvia A. Mandel
- Eve Topf and National Parkinson Foundation Centers of Excellence for Neurodegenerative Diseases, Technion-Faculty of Medicine, Haifa 31096, Israel
| | - Peter Riederer
- Clinical Neurochemistry, National Parkinson Foundation Centre of Excellence Research Laboratory, University of Würzburg, 97070 Würzburg, Germany
| | - Renee M. Miller
- Center for Neural Development and Disease, University of Rochester, Rochester, NY 14620, USA
| | - Howard J. Federoff
- Department of Neurology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Ullrich Wüllner
- Department of Neurology, Friedrich-Wilhelms-University Bonn, UKB, 53105 Bonn, Germany
| | - Spyridon Papapetropoulos
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Allergan, Irvine, CA 92623-9534, USA
| | - Moussa B. Youdim
- Eve Topf and National Parkinson Foundation Centers of Excellence for Neurodegenerative Diseases, Technion-Faculty of Medicine, Haifa 31096, Israel
- Department of Biology, Yonsei World Central University, Department of Biology, Seoul 120-749, South Korea
| | | | - Anne B. Young
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jeffery M. Vance
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Richard L. Davis
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - John C. Hedreen
- Harvard Brain Tissue Resource Center, Department of Psychiatry, McLean Hospital, Belmont, MA 02478, USA
| | - Charles H. Adler
- Mayo Division of Movement Disorders, Mayo Clinic Arizona, Scottsdale, AZ 85259, USA
| | - Thomas G. Beach
- W. H. Civin Laboratory of Neuropathology, Sun Health Research Institute, Sun City, AZ 85259, USA
| | - Manuel B. Graeber
- The Brain & Mind Research Institute, University of Sydney, Sydney, NSW 2050, Australia
| | - Frank A. Middleton
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Clemens R. Scherzer
- Laboratory for Neurogenomics, Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 65 Landsdowne Street, Suite 307A, Cambridge, MA 02139, USA
- Harvard NeuroDiscovery Center Biomarker Program, Cambridge, MA 02139, USA
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16
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Clinical trials of disease-modifying therapies for neurodegenerative diseases: the challenges and the future. Nat Med 2010; 16:1223-6. [PMID: 21052078 DOI: 10.1038/nm.2220] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease represent a crucial and exponentially increasing challenge to health care systems throughout the world. There is an urgent need for effective treatments that will both delay their onset and slow their inexorable progression. Many obstacles stand in the way of realizing these goals. It is expected that future advances will have a major impact on how and when the diagnosis will be made. It is hoped that these will eventually make it possible to initiate effective disease-modifying therapies long before the neurodegenerative process becomes established and symptomatic.
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17
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Deep sequencing of coding and non-coding RNA in the CNS. Brain Res 2010; 1338:146-54. [PMID: 20307502 DOI: 10.1016/j.brainres.2010.03.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 03/10/2010] [Accepted: 03/15/2010] [Indexed: 01/23/2023]
Abstract
Several methods now exist for identifying and quantifying many biological events in parallel and in a relatively unbiased fashion. For gene expression experiments, cloning approaches have been supplemented with microarray platforms over the past few years. The focus of this review is on deep sequencing, a new set of techniques that can be used to both identify RNA species and quantify them in a massively parallel fashion. Deep sequencing has some advantages over other methods, driven largely by the high depth of coverage for any library of nucleic acids. This allows, for example, estimates of alternative splicing and untranslated region utilization. We will discuss how deep sequencing methods are being applied to characterization of gene expression in the brain and how these technologies might develop over the next few years.
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