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Elango R, Banaganapalli B, Mujalli A, AlRayes N, Almaghrabi S, Almansouri M, Sahly A, Jadkarim GA, Malik MZ, Kutbi HI, Shaik NA, Alefishat E. Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues. Bioinform Biol Insights 2023; 17:11779322231166214. [PMID: 37153842 PMCID: PMC10155030 DOI: 10.1177/11779322231166214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 05/10/2023] Open
Abstract
The Parkinson disease (PD) is the second most common neurodegenerative disorder affecting the central nervous system and motor functions. The biological complexity of PD is yet to reveal potential targets for intervention or to slow the disease severity. Therefore, this study aimed to compare the fidelity of blood to substantia nigra (SN) tissue gene expression from PD patients to provide a systematic approach to predict role of the key genes of PD pathobiology. Differentially expressed genes (DEGs) from multiple microarray data sets of PD blood and SN tissue from GEO database are identified. Using the theoretical network approach and variety of bioinformatic tools, we prioritized the key genes from DEGs. A total of 540 and 1024 DEGs were identified in blood and SN tissue samples, respectively. Functional pathways closely related to PD such as ERK1 and ERK2 cascades, mitogen-activated protein kinase (MAPK) signaling, Wnt, nuclear factor-κB (NF-κB), and PI3K-Akt signaling were observed by enrichment analysis. Expression patterns of 13 DEGs were similar in both blood and SN tissues. Comprehensive network topological analysis and gene regulatory networks identified additional 10 DEGs functionally connected with molecular mechanisms of PD through the mammalian target of rapamycin (mTOR), autophagy, and AMP-activated protein kinase (AMPK) signaling pathways. Potential drug molecules were identified by chemical-protein network and drug prediction analysis. These potential candidates can be further validated in vitro/in vivo to be used as biomarkers and/or novel drug targets for the PD pathology and/or to arrest or delay the neurodegeneration over the years, respectively.
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Affiliation(s)
- Ramu Elango
- Department of Genetic Medicine, Faculty
of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of
Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah,
Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty
of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of
Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah,
Saudi Arabia
| | - Abdulrahman Mujalli
- Department of Laboratory Medicine,
Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi
Arabia
| | - Nuha AlRayes
- Princess Al-Jawhara Al-Brahim Center of
Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah,
Saudi Arabia
- Department of Medical Laboratory
Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah,
Saudi Arabia
| | - Sarah Almaghrabi
- Department of Medical Laboratory
Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah,
Saudi Arabia
- Center of Innovation in Personalized
Medicine (CIPM), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majid Almansouri
- Department of Clinical Biochemistry,
Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Sahly
- Princess Al-Jawhara Al-Brahim Center of
Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah,
Saudi Arabia
| | - Gada Ali Jadkarim
- Department of Genetic Medicine, Faculty
of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Md Zubbair Malik
- School of Computational and Integrative
Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Hussam Ibrahim Kutbi
- Department of Pharmacy Practice,
Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty
of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of
Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah,
Saudi Arabia
| | - Eman Alefishat
- Department of Clinical Pharmacology,
College of Medicine, Khalifa University, Abu Dhabi, United Arab Emirates
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Chang KH, Liu CH, Wang YR, Lo YS, Chang CW, Wu HC, Chen CM. Upregulation of APAF1 and CSF1R in Peripheral Blood Mononuclear Cells of Parkinson's Disease. Int J Mol Sci 2023; 24:ijms24087095. [PMID: 37108258 PMCID: PMC10139006 DOI: 10.3390/ijms24087095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Increased oxidative stress and neuroinflammation play a crucial role in the pathogenesis of Parkinson's disease (PD). In this study, the expression levels of 52 genes related to oxidative stress and inflammation were measured in peripheral blood mononuclear cells of the discovery cohort including 48 PD patients and 25 healthy controls. Four genes, including ALDH1A, APAF1, CR1, and CSF1R, were found to be upregulated in PD patients. The expression patterns of these genes were validated in a second cohort of 101 PD patients and 61 healthy controls. The results confirmed the upregulation of APAF1 (PD: 0.34 ± 0.18, control: 0.26 ± 0.11, p < 0.001) and CSF1R (PD: 0.38 ± 0.12, control: 0.33 ± 0.10, p = 0.005) in PD patients. The expression level of APAF1 was correlated with the scores of the Unified Parkinson's Disease Rating Scale (UPDRS, r = 0.235, p = 0.018) and 39-item PD questionnaire (PDQ-39, r = 0.250, p = 0.012). The expression level of CSF1R was negatively correlated with the scores of the mini-mental status examination (MMSE, r = -0.200, p = 0.047) and Montréal Cognitive Assessment (MoCA, r = -0.226, p = 0.023). These results highly suggest that oxidative stress biomarkers in peripheral blood may be useful in monitoring the progression of motor disabilities and cognitive decline in PD patients.
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Affiliation(s)
- Kuo-Hsuan Chang
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chia-Hsin Liu
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yi-Ru Wang
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yen-Shi Lo
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chun-Wei Chang
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Hsiu-Chuan Wu
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chiung-Mei Chen
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
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Xue J, Li F, Dai P. The Potential of ANK1 to Predict Parkinson's Disease. Genes (Basel) 2023; 14:genes14010226. [PMID: 36672967 PMCID: PMC9859451 DOI: 10.3390/genes14010226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The main cause of Parkinson's disease (PD) remains unknown and the pathologic changes in the brain limit rapid diagnosis. Herein, differentially expressed genes (DEGs) in the Gene Expression Omnibus (GEO) database (GSE8397 and GSE22491) were assessed using linear models for microarray analysis (limma). Ankyrin 1 (ANK1) was the only common gene differentially down-regulated in lateral substantia nigra (LSN), medial substantia nigra (MSN) and blood. Additionally, DEGs between high ANK1 and low ANK1 in GSE99039 were picked out and then uploaded to the Database for Annotation, Visualization and Integrated Discovery (DAVID) for gene ontology (GO) functional annotation analysis. GO analysis displayed that these DEGs were mainly enriched in oxygen transport, myeloid cell development and gas transport (biological process (BP)); hemoglobin complex, haptoglobin-hemoglobin complex and cortical cytoskeleton (cellular component (CC)); and oxygen transporter activity, haptoglobin binding and oxygen binding (molecular function (MF)). Receiver operating characteristic (ROC) curve analysis showed ANK1 had good diagnostic accuracy and increased the area under the curve (AUC) value when combined with other biomarkers. Consistently, intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropy-ridi-ne (MPTP) in C57BL/6J mice reduced ANK1 mRNA expression in both substantia nigra and blood compared to the control group. Thus, ANK1 may serve as a candidate biomarker for PD diagnosis.
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Shi WZ, Li W, Cheng Y, Zhang M, Niu XC, Gao QW, Lu Y, Tian T, Du S, Mi Y, Chang MZ, Tian Y. The cytoprotective role of omentin against oxidative stress-induced PC12 apoptosis. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2021; 49:483-492. [PMID: 34151664 DOI: 10.1080/21691401.2021.1892707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/15/2021] [Indexed: 10/21/2022]
Abstract
Oxidative stress has been proven to play a critical role in the pathogenesis of neuronal injury. As a novel adipocytokine, omentin is produced by visceral adipose with insulin sensitizing effects and has been revealed to possess anti-inflammatory effects. However, the possible effect of omentin on oxidative stress remains unknown. The present study aimed to detect the potential protective effect of omentin against hydrogen peroxide (H2O2)-induced cytotoxicity of PC12 cells. The results showed that no cytotoxic effect was shown in PC12 cells co-cultured with omentin alone at a concentration of 50-1000 ng/mL. The CCK8 and TUNEL assays suggested that omentin could remarkably attenuate apoptosis induced by 100 μM H2O2. The PCR and western blotting showed that the expression levels of Bax was significantly inhibited by omentin via the upregulation of miR-128-3p at its 3'-UTR. Taken together, these results indicated that omentin protects PC12 cells against H2O2-induced apoptosis, and further studies need to be conducted before utilization in the clinic for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Wen-Zhen Shi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Wu Li
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Ye Cheng
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Meng Zhang
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Xiao-Chen Niu
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Qi-Wei Gao
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
| | - Ying Lu
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Tian Tian
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Shan Du
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Yan Mi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Ming-Ze Chang
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Ye Tian
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
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Kurvits L, Lättekivi F, Reimann E, Kadastik-Eerme L, Kasterpalu KM, Kõks S, Taba P, Planken A. Transcriptomic profiles in Parkinson's disease. Exp Biol Med (Maywood) 2021; 246:584-595. [PMID: 33148011 PMCID: PMC7934142 DOI: 10.1177/1535370220967325] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Transcriptomics in Parkinson's disease offers insights into the pathogenesis of Parkinson's disease but obtaining brain tissue has limitations. In order to bypass this issue, we profile and compare differentially expressed genes and enriched pathways (KEGG) in two peripheral tissues (blood and skin) of 12 Parkinson's disease patients and 12 healthy controls using RNA-sequencing technique and validation with RT-qPCR. Furthermore, we compare our results to previous Parkinson's disease post mortem brain tissue and blood results using the robust rank aggregation method. The results show no overlapping differentially expressed genes or enriched pathways in blood vs. skin in our sample sets (25 vs. 1068 differentially expressed genes with an FDR ≤ 0.05; 1 vs. 9 pathways in blood and skin, respectively). A meta-analysis from previous transcriptomic sample sets using either microarrays or RNA-Seq yields a robust rank aggregation list of cortical gene expression changes with 43 differentially expressed genes; a list of substantia nigra changes with 2 differentially expressed genes and a list of blood changes with 1 differentially expressed gene being statistically significant at FDR ≤ 0.05. In cortex 1, KEGG pathway was enriched, four in substantia nigra and two in blood. None of the differentially expressed genes or pathways overlap between these tissues. When comparing our previously published skin transcription analysis, two differentially expressed genes between the cortex robust rank aggregation and skin overlap. In this study, for the first time a meta-analysis is applied on transcriptomic sample sets in Parkinson's disease. Simultaneously, it explores the notion that Parkinson's disease is not just a neuronal tissue disease by exploring peripheral tissues. The comparison of different Parkinson's disease tissues yields surprisingly few significant differentially expressed genes and pathways, suggesting that divergent gene expression profiles in distinct cell lineages, metabolic and possibly iatrogenic effects create too much transcriptomic noise for detecting significant signal. On the other hand, there are signs that point towards Parkinson's disease-specific changes in non-neuronal peripheral tissues in Parkinson's disease, indicating that Parkinson's disease might be a multisystem disorder.
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Affiliation(s)
- Lille Kurvits
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Department of Neurology, Charité – Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Freddy Lättekivi
- Institute of Pathophysiology, University of Tartu, Tartu 50411, Estonia
| | - Ene Reimann
- Estonian Genome Center Science Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Liis Kadastik-Eerme
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | | | - Sulev Kõks
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, University of Western Australia, QE II Medical Centre, Nedlands, WA 6009, Australia
| | - Pille Taba
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | - Anu Planken
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
- Oncology and Haematology Clinic, North-Estonian Medical Centre, Tallinn 13419, Estonia
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6
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Karaaslan Z, Kahraman ÖT, Şanlı E, Ergen HA, Ulusoy C, Bilgiç B, Yılmaz V, Tüzün E, Hanağası HA, Küçükali Cİ. Inflammation and regulatory T cell genes are differentially expressed in peripheral blood mononuclear cells of Parkinson's disease patients. Sci Rep 2021; 11:2316. [PMID: 33504893 PMCID: PMC7841172 DOI: 10.1038/s41598-021-81961-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
Our aim was to identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMC) of Parkinson’s disease (PD) patients and healthy controls by microarray technology and analysis of related molecular pathways by functional annotation. Thirty PD patients and 30 controls were enrolled. Agilent Human 8X60 K Oligo Microarray was used for gene level expression identification. Gene ontology and pathway enrichment analyses were used for functional annotation of DEGs. Protein–protein interaction analyses were performed with STRING. Expression levels of randomly selected DEGs were quantified by real time quantitative polymerase chain reaction (RT-PCR) for validation. Flow cytometry was done to determine frequency of regulatory T cells (Tregs) in PBMC. A total of 361 DEGs (143 upregulated and 218 downregulated) were identified after GeneSpring analysis. DEGs were involved in 28 biological processes, 12 cellular components and 26 molecular functions. Pathway analyses demonstrated that upregulated genes mainly enriched in p53 (CASP3, TSC2, ATR, MDM4, CCNG1) and PI3K/Akt (IL2RA, IL4R, TSC2, VEGFA, PKN2, PIK3CA, ITGA4, BCL2L11) signaling pathways. TP53 and PIK3CA were identified as most significant hub proteins. Expression profiles obtained by RT-PCR were consistent with microarray findings. PD patients showed increased proportions of CD49d+ Tregs, which correlated with disability scores. Survival pathway genes were upregulated putatively to compensate neuronal degeneration. Bioinformatics analysis showed an association between survival and inflammation genes. Increased CD49d+ Treg ratios might signify the effort of the immune system to suppress ongoing neuroinflammation.
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Affiliation(s)
- Zerrin Karaaslan
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Özlem Timirci Kahraman
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Elif Şanlı
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Hayriye Arzu Ergen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Canan Ulusoy
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Başar Bilgiç
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Vuslat Yılmaz
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Erdem Tüzün
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Haşmet Ayhan Hanağası
- Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Cem İsmail Küçükali
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen‐Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. EMBO Mol Med 2020; 12:e11942. [PMID: 32715657 PMCID: PMC7507321 DOI: 10.15252/emmm.201911942] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are brain-abundant RNAs of mostly unknown functions. To seek their roles in Parkinson's disease (PD), we generated an RNA sequencing resource of several brain region tissues from dozens of PD and control donors. In the healthy substantia nigra (SN), circRNAs accumulate in an age-dependent manner, but in the PD SN this correlation is lost and the total number of circRNAs reduced. In contrast, the levels of circRNAs are increased in the other studied brain regions of PD patients. We also found circSLC8A1 to increase in the SN of PD individuals. CircSLC8A1 carries 7 binding sites for miR-128 and is strongly bound to the microRNA effector protein Ago2. Indeed, RNA targets of miR-128 are also increased in PD individuals, suggesting that circSLC8A1 regulates miR-128 function and/or activity. CircSLC8A1 levels also increased in cultured cells exposed to the oxidative stress-inducing agent paraquat but were decreased in cells treated with the neuroprotective antioxidant regulator drug Simvastatin. Together, our work links circSLC8A1 to oxidative stress-related Parkinsonism and suggests further exploration of its molecular function in PD.
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Affiliation(s)
- Mor Hanan
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Alon Simchovitz
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Nadav Yayon
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Shani Vaknine
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Roni Cohen‐Fultheim
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Miriam Karmon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Nimrod Madrer
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Talia Miriam Rohrlich
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Moria Maman
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Estelle R Bennett
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - David S Greenberg
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Eran Meshorer
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Hermona Soreq
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Sebastian Kadener
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Biology DepartmentBrandeis UniversityWalthamMAUSA
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8
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Hu Y, Zhang K, Zhang T, Wang J, Chen F, Qin W, Tong W, Guan Q, He Y, Gu C, Chen X, Kang UJ, Sun YE, Li S, Jin L. Exercise Reverses Dysregulation of T-Cell-Related Function in Blood Leukocytes of Patients With Parkinson's Disease. Front Neurol 2020; 10:1389. [PMID: 32047471 PMCID: PMC6997272 DOI: 10.3389/fneur.2019.01389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/17/2019] [Indexed: 01/11/2023] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease with movement and balance impairments. Although studies have reported improvement of motor symptoms with physical exercise, the mechanisms by which exercise is beneficial remains poorly understood. Our study addresses the exercise-induced changes to peripheral immune cells by interrogating the transcriptome of blood-derived leukocytes in PD patients before and after exercise. Patients attended 1 h exercise classes twice a week for 12 weeks. Leukocytes were collected at the beginning and end of the study for gene expression analysis by RNA-seq or quantitative real-time PCR. We correlated differentially expressed genes after exercise with clinical measures and analyzed the potential functions of gene changes with Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analysis. Exercise improved measures of movement and balance when compared with scores before the exercise program. Among the gene changes, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analysis suggests that T-cell receptor signaling, T-cell activation, and T-cell migration pathways were downregulated, while the T-cell receptor signaling pathway was the most significantly correlated with clinical measures. To further investigate T-cell-related changes in PD leukocytes, we reanalyzed the differentially expressed genes from publicly available microarray data and found that genes in the T-cell activation, differentiation, and migration pathways were upregulated in PD samples compared to controls in a time-dependent manner. Together, our findings suggest that exercise rehabilitation may improve movement and balance in PD patients by reversing the upregulated T-cell activation pathways associated with PD. This study was registered with the Chinese Clinical Trial Registry under ChiCTR-TRC-14004707. Registered on May 27, 2014.
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Affiliation(s)
- Yong Hu
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Neurology, Department of Neuroscience and Physiology, NYU Langone Health, The Marlene and Paolo Fresco Institute for Parkinson's and Movement Disorders, Neuroscience Institute, New York, NY, United States
| | - Kunshan Zhang
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tianyu Zhang
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junbang Wang
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fei Chen
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenting Qin
- Department of Spine Surgery, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Weifang Tong
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiang Guan
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yijing He
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunya Gu
- Department of Spine Surgery, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyu Chen
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Un Jung Kang
- Department of Neurology, Department of Neuroscience and Physiology, NYU Langone Health, The Marlene and Paolo Fresco Institute for Parkinson's and Movement Disorders, Neuroscience Institute, New York, NY, United States
| | - Yi E. Sun
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siguang Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lingjing Jin
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Lu E, Sarkar S, Raymick J, Paule MG, Gu Q. Decreased Mcl-1 protein level in the striatum of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice. Brain Res 2018; 1678:432-439. [DOI: 10.1016/j.brainres.2017.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 12/15/2022]
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Affiliation(s)
- Alice S Chen-Plotkin
- Department of Neurology, University of Pennsylvania, 3 West Gates, 3400 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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Borrageiro G, Haylett W, Seedat S, Kuivaniemi H, Bardien S. A review of genome-wide transcriptomics studies in Parkinson's disease. Eur J Neurosci 2017; 47:1-16. [DOI: 10.1111/ejn.13760] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/26/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Genevie Borrageiro
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
| | - William Haylett
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
| | - Soraya Seedat
- Department of Psychiatry; Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Helena Kuivaniemi
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
- Department of Psychiatry; Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics; Department of Biomedical Sciences; Faculty of Medicine and Health Sciences; Stellenbosch University; PO Box 241 Cape Town South Africa
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12
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Shamir R, Klein C, Amar D, Vollstedt EJ, Bonin M, Usenovic M, Wong YC, Maver A, Poths S, Safer H, Corvol JC, Lesage S, Lavi O, Deuschl G, Kuhlenbaeumer G, Pawlack H, Ulitsky I, Kasten M, Riess O, Brice A, Peterlin B, Krainc D. Analysis of blood-based gene expression in idiopathic Parkinson disease. Neurology 2017; 89:1676-1683. [PMID: 28916538 DOI: 10.1212/wnl.0000000000004516] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/23/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples). METHODS Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks. RESULTS A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was identified with the training cohort and successfully replicated in both an independent validation cohort (area under the curve [AUC] = 0.79, p = 7.13E-6) and a subsequent independent test cohort (AUC = 0.74, p = 4.2E-4). Network analysis of the signature revealed gene enrichment in pathways, including metabolism, oxidation, and ubiquitination/proteasomal activity, and misregulation of mitochondria-localized genes, including downregulation of COX4I1, ATP5A1, and VDAC3. CONCLUSIONS We present a large-scale study of PD gene expression profiling. This work identifies a reliable blood-based PD signature and highlights the importance of large-scale patient cohorts in developing potential PD biomarkers.
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Affiliation(s)
- Ron Shamir
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Christine Klein
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - David Amar
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Eva-Juliane Vollstedt
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Michael Bonin
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Marija Usenovic
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Yvette C Wong
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Ales Maver
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Sven Poths
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Hershel Safer
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Jean-Christophe Corvol
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Suzanne Lesage
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Ofer Lavi
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Günther Deuschl
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Gregor Kuhlenbaeumer
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Heike Pawlack
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Meike Kasten
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Olaf Riess
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Alexis Brice
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Borut Peterlin
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel
| | - Dimitri Krainc
- From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel.
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13
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Pinho R, Guedes LC, Soreq L, Lobo PP, Mestre T, Coelho M, Rosa MM, Gonçalves N, Wales P, Mendes T, Gerhardt E, Fahlbusch C, Bonifati V, Bonin M, Miltenberger-Miltényi G, Borovecki F, Soreq H, Ferreira JJ, F. Outeiro T. Gene Expression Differences in Peripheral Blood of Parkinson's Disease Patients with Distinct Progression Profiles. PLoS One 2016; 11:e0157852. [PMID: 27322389 PMCID: PMC4913914 DOI: 10.1371/journal.pone.0157852] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
The prognosis of neurodegenerative disorders is clinically challenging due to the inexistence of established biomarkers for predicting disease progression. Here, we performed an exploratory cross-sectional, case-control study aimed at determining whether gene expression differences in peripheral blood may be used as a signature of Parkinson’s disease (PD) progression, thereby shedding light into potential molecular mechanisms underlying disease development. We compared transcriptional profiles in the blood from 34 PD patients who developed postural instability within ten years with those of 33 patients who did not develop postural instability within this time frame. Our study identified >200 differentially expressed genes between the two groups. The expression of several of the genes identified was previously found deregulated in animal models of PD and in PD patients. Relevant genes were selected for validation by real-time PCR in a subset of patients. The genes validated were linked to nucleic acid metabolism, mitochondria, immune response and intracellular-transport. Interestingly, we also found deregulation of these genes in a dopaminergic cell model of PD, a simple paradigm that can now be used to further dissect the role of these molecular players on dopaminergic cell loss. Altogether, our study provides preliminary evidence that expression changes in specific groups of genes and pathways, detected in peripheral blood samples, may be correlated with differential PD progression. Our exploratory study suggests that peripheral gene expression profiling may prove valuable for assisting in prediction of PD prognosis, and identifies novel culprits possibly involved in dopaminergic cell death. Given the exploratory nature of our study, further investigations using independent, well-characterized cohorts will be essential in order to validate our candidates as predictors of PD prognosis and to definitively confirm the value of gene expression analysis in aiding patient stratification and therapeutic intervention.
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Affiliation(s)
- Raquel Pinho
- Department of NeuroDegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Niedersachsen, Germany
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Leonor C. Guedes
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Lilach Soreq
- Department of Molecular Neuroscience, The Institute of Neurology, University College London, London, United Kingdom
| | - Patrícia P. Lobo
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Tiago Mestre
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Miguel Coelho
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Mário M. Rosa
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Nilza Gonçalves
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Pauline Wales
- Department of NeuroDegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Niedersachsen, Germany
| | - Tiago Mendes
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Ellen Gerhardt
- Department of NeuroDegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Niedersachsen, Germany
| | - Christiane Fahlbusch
- Department of NeuroDegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Niedersachsen, Germany
| | - Vincenzo Bonifati
- Department Clinical Genetics, Erasmus MC, Rotterdam, South Holland, The Netherlands
| | - Michael Bonin
- Institute of Medical Genetics and Applied Genomics, Eberhard-Karls-University Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Gabriel Miltenberger-Miltényi
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Fran Borovecki
- Department for Functional Genomics, Center for Translational and Clinical Research, University Hospital Center Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biological Chemistry, The Life Sciences Institute, Jerusalem, Israel
| | - Joaquim J. Ferreira
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
- * E-mail: (TFO); (JJF)
| | - Tiago F. Outeiro
- Department of NeuroDegeneration and Restorative Research, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Niedersachsen, Germany
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail: (TFO); (JJF)
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14
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Zhou H, Skolnick J. A knowledge-based approach for predicting gene-disease associations. Bioinformatics 2016; 32:2831-8. [PMID: 27283949 DOI: 10.1093/bioinformatics/btw358] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023] Open
Abstract
MOTIVATION Recent advances of next-generation sequence technologies have made it possible to rapidly and inexpensively identify gene variations. Knowing the disease association of these gene variations is important for early intervention to treat deadly diseases and provide possible targets to cure these diseases. Genome-wide association studies (GWAS) have identified many individual genes associated with common diseases. To exploit the large amount of data obtained from GWAS studies and leverage our understanding of common as well as rare diseases, we have developed a knowledge-based approach to predict gene-disease associations. We first derive gene-gene mutual information by utilizing the cooccurrence of genes in known gene-disease association data. Subsequently, the mutual information is combined with known protein-protein interaction networks by a boosted tree regression method. RESULTS The method called Know-GENE is compared with the method of random walking on the heterogeneous network using the same input data. For a set of 960 diseases, using the same training data in testing in 3-fold cross-validation, the average recall rate within the top ranked 100 genes by Know-GENE is 65.0% compared with 37.9% by the state of the art random walking on heterogeneous network. This significant improvement is mostly due to the inclusion of knowledge-based mutual information. AVAILABILITY AND IMPLEMENTATION Predictions for genes associated with the 960 diseases are available at http://cssb2.biology.gatech.edu/knowgene CONTACT : skolnick@gatech.edu.
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Affiliation(s)
- Hongyi Zhou
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jeffrey Skolnick
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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15
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Simchovitz A, Soreq L, Soreq H. Transcriptome profiling in Parkinson's leukocytes: from early diagnostics to neuroimmune therapeutic prospects. Curr Opin Pharmacol 2015; 26:102-9. [PMID: 26609801 DOI: 10.1016/j.coph.2015.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD) involves motor symptoms reflecting the progressive degeneration of dopaminergic neurons in the substantia nigra. However, diagnosis is only enabled late in the disease, limiting treatment to palliative assistance. Here, we review recently generated transcriptional profiling datasets from blood and brain RNA of human PD cohorts and animal models that may offer unprecedented progress in PD research. Specifically, advanced analysis techniques demonstrated functionally inter-related underlying impairments of RNA metabolism and neuroimmune signalling processes. Identifying novel biomarkers in serum and nucleated blood cells, including protein networks and non-coding RNAs can drive discovery of the molecular mechanisms involved and reveal new targets for therapeutic intervention, posing a dual diagnosis/treatment opportunity for limiting the exacerbation of neuroinflammatory events in PD.
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Affiliation(s)
- Alon Simchovitz
- Department of Biological Chemistry and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Lilach Soreq
- Department of Molecular Neuroscience, UCL Institute of Neurology (ION), Queen Square, London WC1N 3BG, UK
| | - Hermona Soreq
- Department of Biological Chemistry and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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16
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Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S. Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients. BMC Genomics 2015; 16:876. [PMID: 26510930 PMCID: PMC4625854 DOI: 10.1186/s12864-015-2058-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD. METHODS Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set"). RESULTS Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR. CONCLUSIONS Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.
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Affiliation(s)
- Raffaella Calligaris
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Mihaela Banica
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Paola Roncaglia
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. .,Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD Hinxton, Cambridge, UK.
| | - Elisa Robotti
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Sara Finaurini
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Christina Vlachouli
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Lucia Antonutti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Francesco Iorio
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy. .,Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD Hinxton, Cambridge, UK.
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy.
| | - Tatiana Cattaruzza
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Andrea Ceiner
- ITALTBS S.p.A., AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Dejan Lazarevic
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. .,CBM Scrl - Consorzio per il Centro di Biomedicina Molecolare, Area Science Park, S.S.14, km 163.5, Basovizza, 34149, Trieste, Italy.
| | - Alberto Cucca
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Nicola Pangher
- ITALTBS S.p.A., AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Emilio Marengo
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy. .,Department Computer Science & Systems, School of Engineering, University of Naples "Federico II", via Claudio 21, 80125, Naples, Italy.
| | - Gilberto Pizzolato
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
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17
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Potential Biomarkers of the Earliest Clinical Stages of Parkinson's Disease. PARKINSONS DISEASE 2015; 2015:294396. [PMID: 26483988 PMCID: PMC4592918 DOI: 10.1155/2015/294396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/04/2015] [Accepted: 09/10/2015] [Indexed: 12/15/2022]
Abstract
Parkinson's disease (PD) is a widespread neurodegenerative disorder. Despite the intensive studies of this pathology, in general, the picture of the etiopathogenesis has still not been clarified fully. To understand better the mechanisms underlying the pathogenesis of PD, we analyzed the expression of 10 genes in the peripheral blood of treated and untreated patients with PD. 35 untreated patients with PD and 12 treated patients with Parkinson's disease (Hoehn and Yahr scores 1-2) were studied. An analysis of the mRNA levels of ATP13A2, PARK2, PARK7, PINK1, LRRK2, SNCA, ALDH1A1, PDHB, PPARGC1A, and ZNF746 genes in the peripheral blood of patients was carried out using reverse transcription followed by real-time PCR. A statistically significant and specific increase by more than 1.5-fold in the expression of the ATP13A2, PARK7, and ZNF746 genes was observed in patients with PD. Based on these results, it can be suggested that the upregulation of the mRNA levels of ATP13A2, PARK7, and ZNF746 in untreated patients in the earliest clinical stages can also be observed in the preclinical stages of PD, and that these genes can be considered as potential biomarkers of the preclinical stage of PD.
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18
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Herrera AJ, Espinosa-Oliva AM, Carrillo-Jiménez A, Oliva-Martín MJ, García-Revilla J, García-Quintanilla A, de Pablos RM, Venero JL. Relevance of chronic stress and the two faces of microglia in Parkinson's disease. Front Cell Neurosci 2015; 9:312. [PMID: 26321913 PMCID: PMC4536370 DOI: 10.3389/fncel.2015.00312] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/28/2015] [Indexed: 12/26/2022] Open
Abstract
This review is aimed to highlight the importance of stress and glucocorticoids (GCs) in modulating the inflammatory response of brain microglia and hence its potential involvement in Parkinson’s disease (PD). The role of inflammation in PD has been reviewed extensively in the literature and it is supposed to play a key role in the course of the disease. Historically, GCs have been strongly associated as anti-inflammatory hormones. However, accumulating evidence from the peripheral and central nervous system have clearly revealed that, under specific conditions, GCs may promote brain inflammation including pro-inflammatory activation of microglia. We have summarized relevant data linking PD, neuroinflamamation and chronic stress. The timing and duration of stress response may be critical for delineating an immune response in the brain thus probably explain the dual role of GCs and/or chronic stress in different animal models of PD.
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Affiliation(s)
- Antonio J Herrera
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - Ana M Espinosa-Oliva
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - Alejandro Carrillo-Jiménez
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - María J Oliva-Martín
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - Juan García-Revilla
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - Alberto García-Quintanilla
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - Rocío M de Pablos
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
| | - José L Venero
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla Sevilla, Spain
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19
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Gao L, Li C, Yang RY, Lian WW, Fang JS, Pang XC, Qin XM, Liu AL, Du GH. Ameliorative effects of baicalein in MPTP-induced mouse model of Parkinson's disease: A microarray study. Pharmacol Biochem Behav 2015; 133:155-63. [PMID: 25895692 DOI: 10.1016/j.pbb.2015.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 01/17/2023]
Abstract
Baicalein, a flavonoid from Scutellaria baicalensis Georgi, has been shown to possess neuroprotective properties. The purpose of this study was to explore the effects of baicalein on motor behavioral deficits and gene expression in N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mice model of Parkinson's disease (PD). The behavioral results showed that baicalein significantly improves the abnormal behaviors in MPTP-induced mice model of PD, as manifested by shortening the total time for climbing down the pole, prolonging the latent periods of rotarod, and increasing the vertical movements. Using cDNA microarray and subsequent bioinformatic analyses, it was found that baicalein significantly promotes the biological processes including neurogenesis, neuroblast proliferation, neurotrophin signaling pathway, walking and locomotor behaviors, and inhibits dopamine metabolic process through regulation of gene expressions. Based on analysis of gene co-expression networks, the results indicated that the regulation of genes such as LIMK1, SNCA and GLRA1 by baicalein might play central roles in the network. Our results provide experimental evidence for the potential use of baicalein in the treatment of PD, and revealed gene expression profiles, biological processes and pathways influenced by baicalein in MPTP-treated mice.
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Affiliation(s)
- Li Gao
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, PR China
| | - Chao Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Ran-Yao Yang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Wen-Wen Lian
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Jian-Song Fang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Xiao-Cong Pang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Xue-Mei Qin
- Modern Research Center for Traditional Chinese Medicine of Shanxi University, Taiyuan 030006, PR China
| | - Ai-Lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; Beijing Key Laboratory of Drug Target Research and Drug Screening, Beijing 100050, PR China.
| | - Guan-Hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, PR China.
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Involvement of endocytosis and alternative splicing in the formation of the pathological process in the early stages of Parkinson's disease. BIOMED RESEARCH INTERNATIONAL 2014; 2014:718732. [PMID: 24804238 PMCID: PMC3996366 DOI: 10.1155/2014/718732] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/05/2014] [Accepted: 03/13/2014] [Indexed: 12/17/2022]
Abstract
Parkinson's disease (PD) is the one of most widespread neurodegenerative pathologies. Because of the impossibility of studying the endogenous processes that occur in the brain of patients with PD in the presymptomatic stage, the mechanisms that trigger the disease remain unknown. Thus, the identification of the processes that play an important role in the early stages of the disease in these patients is extremely difficult. In this context, we performed a whole-transcriptome analysis of the peripheral blood of untreated patients with stage 1 PD (Hoehn-Yahr scale). We demonstrated a significant change in the levels of transcripts included in the large groups of processes associated with the functioning of the immune system and cellular transport. Moreover, a significant change in the splicing of genes involved in cellular-transport processes was shown in our study.
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Soreq L, Guffanti A, Salomonis N, Simchovitz A, Israel Z, Bergman H, Soreq H. Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PLoS Comput Biol 2014; 10:e1003517. [PMID: 24651478 PMCID: PMC3961179 DOI: 10.1371/journal.pcbi.1003517] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/31/2014] [Indexed: 12/22/2022] Open
Abstract
The continuously prolonged human lifespan is accompanied by increase in neurodegenerative diseases incidence, calling for the development of inexpensive blood-based diagnostics. Analyzing blood cell transcripts by RNA-Seq is a robust means to identify novel biomarkers that rapidly becomes a commonplace. However, there is lack of tools to discover novel exons, junctions and splicing events and to precisely and sensitively assess differential splicing through RNA-Seq data analysis and across RNA-Seq platforms. Here, we present a new and comprehensive computational workflow for whole-transcriptome RNA-Seq analysis, using an updated version of the software AltAnalyze, to identify both known and novel high-confidence alternative splicing events, and to integrate them with both protein-domains and microRNA binding annotations. We applied the novel workflow on RNA-Seq data from Parkinson's disease (PD) patients' leukocytes pre- and post- Deep Brain Stimulation (DBS) treatment and compared to healthy controls. Disease-mediated changes included decreased usage of alternative promoters and N-termini, 5′-end variations and mutually-exclusive exons. The PD regulated FUS and HNRNP A/B included prion-like domains regulated regions. We also present here a workflow to identify and analyze long non-coding RNAs (lncRNAs) via RNA-Seq data. We identified reduced lncRNA expression and selective PD-induced changes in 13 of over 6,000 detected leukocyte lncRNAs, four of which were inversely altered post-DBS. These included the U1 spliceosomal lncRNA and RP11-462G22.1, each entailing sequence complementarity to numerous microRNAs. Analysis of RNA-Seq from PD and unaffected controls brains revealed over 7,000 brain-expressed lncRNAs, of which 3,495 were co-expressed in the leukocytes including U1, which showed both leukocyte and brain increases. Furthermore, qRT-PCR validations confirmed these co-increases in PD leukocytes and two brain regions, the amygdala and substantia-nigra, compared to controls. This novel workflow allows deep multi-level inspection of RNA-Seq datasets and provides a comprehensive new resource for understanding disease transcriptome modifications in PD and other neurodegenerative diseases. Long non-coding RNAs (lncRNAs) comprise a novel, fascinating class of RNAs with largely unknown biological functions. Parkinson's-disease (PD) is the most frequent motor disorder, and Deep-brain-stimulation (DBS) treatment alleviates the symptoms, but early disease biomarkers are still unknown and new future genetic interference targets are urgently needed. Using RNA-sequencing technology and a novel computational workflow for in-depth exploration of whole-transcriptome RNA-seq datasets, we detected and analyzed lncRNAs in sequenced libraries from PD patients' leukocytes pre and post-treatment and the brain, adding this full profile resource of over 7,000 lncRNAs to the few human tissues-derived lncRNA datasets that are currently available. Our study includes sample-specific database construction, detecting disease-derived changes in known and novel lncRNAs, exons and junctions and predicting corresponding changes in Polyadenylation choices, protein domains and miRNA binding sites. We report widespread transcript structure variations at the splice junction and exons levels, including novel exons and junctions and alteration of lncRNAs followed by experimental validation in PD leukocytes and two PD brain regions compared with controls. Our results suggest lncRNAs involvement in neurodegenerative diseases, and specifically PD. This comprehensive workflow will be of use to the increasing number of laboratories producing RNA-Seq data in a wide range of biomedical studies.
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Affiliation(s)
- Lilach Soreq
- Department of Medical Neurobiology, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Alessandro Guffanti
- Department of Biological Chemistry, The Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
- Genomnia srl, Lainate, Milan, Italy
| | - Nathan Salomonis
- Department of Pediatrics, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Zvi Israel
- The Center for Functional and Restorative Neurosurgery, Department of Neurosurgery, Hadassah University Hospital, Jerusalem, Israel
| | - Hagai Bergman
- Department of Medical Neurobiology, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- Department of Biological Chemistry, The Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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22
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Soreq L, Salomonis N, Bronstein M, Greenberg DS, Israel Z, Bergman H, Soreq H. Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. Front Mol Neurosci 2013; 6:10. [PMID: 23717260 PMCID: PMC3652308 DOI: 10.3389/fnmol.2013.00010] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/16/2013] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are key post transcriptional regulators of their multiple target genes. However, the detailed profile of miRNA expression in Parkinson's disease, the second most common neurodegenerative disease worldwide and the first motor disorder has not been charted yet. Here, we report comprehensive miRNA profiling by next-generation small-RNA sequencing, combined with targets inspection by splice-junction and exon arrays interrogating leukocyte RNA in Parkinson's disease patients before and after deep brain stimulation (DBS) treatment and of matched healthy control volunteers (HC). RNA-Seq analysis identified 254 miRNAs and 79 passenger strand forms as expressed in blood leukocytes, 16 of which were modified in patients pre-treatment as compared to HC. 11 miRNAs were modified following brain stimulation 5 of which were changed inversely to the disease induced changes. Stimulation cessation further induced changes in 11 miRNAs. Transcript isoform abundance analysis yielded 332 changed isoforms in patients compared to HC, which classified brain transcriptomes of 47 PD and control independent microarrays. Functional enrichment analysis highlighted mitochondrion organization. DBS induced 155 splice changes, enriched in ubiquitin homeostasis. Cellular composition analysis revealed immune cell activity pre and post treatment. Overall, 217 disease and 74 treatment alternative isoforms were predictably targeted by modified miRNAs within both 3′ and 5′ untranslated ends and coding sequence sites. The stimulation-induced network sustained 4 miRNAs and 7 transcripts of the disease network. We believe that the presented dynamic networks provide a novel avenue for identifying disease and treatment-related therapeutic targets. Furthermore, the identification of these networks is a major step forward in the road for understanding the molecular basis for neurological and neurodegenerative diseases and assessment of the impact of brain stimulation on human diseases.
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Affiliation(s)
- Lilach Soreq
- Department of Medical Neurobiology, Hadassah Faculty of Medicine, The Hebrew University of Jerusalem Jerusalem, Israel
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23
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Leal MC, Casabona JC, Puntel M, Pitossi FJ. Interleukin-1β and tumor necrosis factor-α: reliable targets for protective therapies in Parkinson's Disease? Front Cell Neurosci 2013; 7:53. [PMID: 23641196 PMCID: PMC3638129 DOI: 10.3389/fncel.2013.00053] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/10/2013] [Indexed: 12/31/2022] Open
Abstract
Neuroinflammation has received increased attention as a target for putative neuroprotective therapies in Parkinson’s Disease (PD). Two prototypic pro-inflammatory cytokines interleukin-1β (IL-1) and tumor necrosis factor-α (TNF) have been implicated as main effectors of the functional consequences of neuroinflammation on neurodegeneration in PD models. In this review, we describe that the functional interaction between these cytokines in the brain differs from the periphery (e.g., their expression is not induced by each other) and present data showing predominantly a toxic effect of these cytokines when expressed at high doses and for a sustained period of time in the substantia nigra pars compacta (SN). In addition, we highlight opposite evidence showing protective effects of these two main cytokines when conditions of duration, amount of expression or state of activation of the target or neighboring cells are changed. Furthermore, we discuss these results in the frame of previous disappointing results from anti-TNF-α clinical trials against Multiple Sclerosis, another neurodegenerative disease with a clear neuroinflammatory component. In conclusion, we hypothesize that the available evidence suggests that the duration and dose of IL-1β or TNF-α expression is crucial to predict their functional effect on the SN. Since these parameters are not amenable for measurement in the SN of PD patients, we call for an in-depth analysis to identify downstream mediators that could be common to the toxic (and not the protective) effects of these cytokines in the SN. This strategy could spare the possible neuroprotective effect of these cytokines operative in the patient at the time of treatment, increasing the probability of efficacy in a clinical setting. Alternatively, receptor-specific agonists or antagonists could also provide a way to circumvent undesired effects of general anti-inflammatory or specific anti-IL-1β or TNF-α therapies against PD.
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Affiliation(s)
- María C Leal
- Institute Leloir Fundation - IIBBA-CONICET Buenos Aires, Argentina
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24
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Soreq L, Bergman H, Goll Y, Greenberg DS, Israel Z, Soreq H. Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes. J Cell Mol Med 2012; 16:1496-507. [PMID: 21910823 PMCID: PMC3823218 DOI: 10.1111/j.1582-4934.2011.01444.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Subthalamic deep brain stimulation (DBS) reversibly modulates Parkinson's disease (PD) motor symptoms, providing an unusual opportunity to compare leucocyte transcripts in the same individuals before and after neurosurgery and 1 hr after stimulus cessation (ON- and OFF-stimulus). Here, we report DBS-induced reversibility and OFF-stimulus restoration in 12 of 16 molecular functions and 3 of 4 biological processes shown in exon microarrays to be differentially expressed between PD patients and controls, post-DBS from pre-DBS and OFF from ON states. Intriguingly, 6 of 18 inflammation and immune-related functions exhibited reversibility, and the extent of stimulus-induced changes correlated with the neurological DBS efficacy, suggesting mechanistic implications. A minimal list of 29 transcripts that changed in all three comparisons between states discriminated pre-surgery and OFF states from post-surgery and controls. Six of these transcripts were found to be able to distinguish between PD patients and both healthy controls and patients with other neurological diseases in a previously published whole blood 3’ array data study of early PD patients. Our findings support the future use of this approach for identifying targets for therapeutic intervention and assessing the efficacy of current and new treatments in this and other neurological diseases.
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Affiliation(s)
- Lilach Soreq
- Department of Medical Neurobiology (Physiology), IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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25
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Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder second only to Alzheimer's disease. Diagnosis remains clinical, based on phenotypic patterns. In the last decade many attempts to develop early differential pre-clinical markers have been reported. In this presentation, the molecular risk factors that may link between the etiopathogenesis leading to PD and peripheral markers will be discussed. Genetic variation known to be involved in familial forms of PD will be shown to be linked to sporadic cases, as for example leucine-rich repeat kinase 2 (LRRK2) that was found to regulate microRNA-mediated translation regulation. In addition postmortem microarray findings of transcription alterations will be compared to the peripheral findings of mRNA profiles. Molecular processes involved in ubiquitination and proteasome, autophagy, mitochondrial dysfunction and the nicotinic and adenosine A2 protection will be discussed. The question of what time-point should be used measuring the different markers and the course of the disease considered, and the future possibilities in exploring these techniques will be debated.
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Affiliation(s)
- Edna Grünblatt
- Hospital of Child and Adolescent Psychiatry, University of Zurich, Zurich, Switzerland.
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26
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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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27
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Inflammatory Pathways in Parkinson's Disease; A BNE Microarray Study. PARKINSONS DISEASE 2012; 2012:214714. [PMID: 22548201 PMCID: PMC3324922 DOI: 10.1155/2012/214714] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Accepted: 01/04/2012] [Indexed: 12/18/2022]
Abstract
The aetiology of Parkinson's disease (PD) is yet to be fully understood but it is becoming more and more evident that neuronal cell death may be multifactorial in essence. The main focus of PD research is to better understand substantia nigra homeostasis disruption, particularly in relation to the wide-spread deposition of the aberrant protein α-synuclein. Microarray technology contributed towards PD research with several studies to date and one gene, ALDH1A1 (Aldehyde dehydrogenase 1 family, member A1), consistently reappeared across studies including the present study, highlighting dopamine (DA) metabolism dysfunction resulting in oxidative stress and most probably leading to neuronal cell death. Neuronal cell death leads to increased inflammation through the activation of astrocytes and microglia. Using our dataset, we aimed to isolate some of these pathways so to offer potential novel neuroprotective therapeutic avenues. To that effect our study has focused on the upregulation of P2X7 (purinergic receptor P2X, ligand-gated ion channel, 7) receptor pathway (microglial activation) and on the NOS3 (nitric oxide synthase 3) pathway (angiogenesis). In summary, although the exact initiator of striatal DA neuronal cell death remains to be determined, based on our analysis, this event does not remain without consequence. Extracellular ATP and reactive astrocytes appear to be responsible for the activation of microglia which in turn release proinflammatory cytokines contributing further to the parkinsonian condition. In addition to tackling oxidative stress pathways we also suggest to reduce microglial and endothelial activation to support neuronal outgrowth.
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28
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Meta-analysis of genetic and environmental Parkinson's disease models reveals a common role of mitochondrial protection pathways. Neurobiol Dis 2012; 45:1018-30. [PMID: 22198569 DOI: 10.1016/j.nbd.2011.12.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 11/11/2011] [Accepted: 12/04/2011] [Indexed: 11/22/2022] Open
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29
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Gilboa-Geffen A, Wolf Y, Hanin G, Melamed-Book N, Pick M, Bennett ER, Greenberg DS, Lester S, Rischmueller M, Soreq H. Activation of the alternative NFκB pathway improves disease symptoms in a model of Sjogren's syndrome. PLoS One 2011; 6:e28727. [PMID: 22174879 PMCID: PMC3235165 DOI: 10.1371/journal.pone.0028727] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/14/2011] [Indexed: 11/28/2022] Open
Abstract
The purpose of our study was to understand if Toll-like receptor 9 (TLR9) activation could contribute to the control of inflammation in Sjogren's syndrome. To this end, we manipulated TLR9 signaling in non-obese diabetic (NOD) and TLR9−/− mice using agonistic CpG oligonucleotide aptamers, TLR9 inhibitors, and the in-house oligonucleotide BL-7040. We then measured salivation, inflammatory response markers, and expression of proteins downstream to NF-κB activation pathways. Finally, we labeled proteins of interest in salivary gland biopsies from Sjogren's syndrome patients, compared to Sicca syndrome controls. We show that in NOD mice BL-7040 activates TLR9 to induce an alternative NF-κB activation mode resulting in increased salivation, elevated anti-inflammatory response in salivary glands, and reduced peripheral AChE activity. These effects were more prominent and also suppressible by TLR9 inhibitors in NOD mice, but TLR9−/− mice were resistant to the salivation-promoting effects of CpG oligonucleotides and BL-7040. Last, salivary glands from Sjogren's disease patients showed increased inflammatory and decreased anti-inflammatory biomarkers, in addition to decreased levels of alternative NF-κB pathway proteins. In summary, we have demonstrated that activation of TLR9 by BL-7040 leads to non-canonical activation of NF-κB, promoting salivary functioning and down-regulating inflammation. We propose that BL-7040 could be beneficial in treating Sjogren's syndrome and may be applicable to additional autoimmune syndromes.
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Affiliation(s)
- Adi Gilboa-Geffen
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yochai Wolf
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Geula Hanin
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Naomi Melamed-Book
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marjorie Pick
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Estelle R. Bennett
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David S. Greenberg
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Susan Lester
- Rheumatology Unit, Queen Elizabeth Hospital, Woodville, Australia
| | | | - Hermona Soreq
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Edmond and Lily Safra Center of Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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30
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Greene JG. Current status and future directions of gene expression profiling in Parkinson's disease. Neurobiol Dis 2010; 45:76-82. [PMID: 21056669 DOI: 10.1016/j.nbd.2010.10.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 10/25/2010] [Accepted: 10/27/2010] [Indexed: 12/31/2022] Open
Abstract
Parkinson's disease (PD) is a common age-associated neurodegenerative disorder. Motor symptoms are the cardinal component of PD, but non-motor symptoms, such as dementia, depression, and autonomic dysfunction are being increasingly recognized. Motor symptoms are primarily caused by selective degeneration of substantia nigra dopamine (SNDA) neurons in the midbrain; non-motor symptoms may be referable to well-described pathology at multiple levels of the neuraxis. Development of symptomatic and disease-modifying therapies is dependent on an accurate and comprehensive understanding of the pathogenesis and pathophysiology of PD. Gene expression profiling has been recently employed to assess function on a broad level in the hopes of gaining greater knowledge concerning how individual mechanisms of disease fit together as a whole and to generate novel hypotheses concerning PD pathogenesis, diagnosis, and progression. So far, the majority of studies have been performed on postmortem brain samples from PD patients, but more recently, studies have targeted enriched populations of dopamine neurons and have begun to explore extra-nigral neurons and even peripheral tissues. This review will provide a brief synopsis of gene expression profiling in parkinsonism and its pitfalls to date and propose several potential future directions and uses for the technique. It will focus on the use of microarray experiments to stimulate hypotheses concerning mechanisms of neurodegeneration in PD, since the majority of studies thus far have addressed that complicated issue.
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Affiliation(s)
- James G Greene
- Department of Neurology and the Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA.
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31
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Toiber D, Azkona G, Ben-Ari S, Torán N, Soreq H, Dierssen M. Engineering DYRK1A overdosage yields Down syndrome-characteristic cortical splicing aberrations. Neurobiol Dis 2010; 40:348-59. [PMID: 20600907 DOI: 10.1016/j.nbd.2010.06.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 05/31/2010] [Accepted: 06/22/2010] [Indexed: 01/07/2023] Open
Abstract
Down syndrome (DS) associates with impaired brain functions, but the underlying mechanism(s) are yet unclear. The "gene dosage" hypothesis predicts that in DS, overexpression of a single gene can impair multiple brain functions through a signal amplification effect due to impaired regulatory mechanism(s). Here, we report findings attributing to impairments in the splicing process such a regulatory role. We have used DS fetal brain samples in search for initial evidence and employed engineered mice with MMU16 partial trisomy (Ts65Dn) or direct excess of the splicing-associated nuclear kinase Dyrk1A, overdosed in DS for further analyses. We present specific albeit modest changes in the DS brain's splicing machinery with subsequently amplified effects in target transcripts; and we demonstrate that engineered excess of Dyrk1A can largely recapitulate these changes. Specifically, in both the fetal DS brains and the Dyrk1A overdose models, we found ample modestly modified splicing-associated transcripts which apparently induced secondary enhancement in exon inclusion of key synaptic transcripts. Thus, DS-reduced levels of the dominant-negative TRKBT1 transcript, but not other TRKB mRNA transcripts, were accompanied by corresponding decreases in BDNF. In addition, the DS brains and Dyrk1A overdosage models showed selective changes in the transcripts composition of neuroligin mRNAs as well as reductions in the "synaptic" acetylcholinesterase variant AChE-S mRNA and corresponding increases in the stress-inducible AChE-R mRNA variant, yielding key synaptic proteins with unusual features. In cotransfected cells, Dyrk1A overdosage caused parallel changes in the splicing pattern of an AChE mini-gene, suggesting that Dyrk1A overdosage is both essential and sufficient to induce the observed change in the composition of AChE mRNA variants. Furthermore, the Dyrk1A overdosage animal models showed pronounced changes in the structure of neuronal nuclear speckles, where splicing events take place and in SR proteins phosphorylation known to be required for the splicing process. Together, our findings demonstrate DS-like brain splicing machinery malfunctioning in Dyrk1A overexpressing mice. Since individual splicing choices may alter cell fate determination, axon guidance, and synaptogenesis, these findings suggest the retrieval of balanced splicing as a goal for DS therapeutic manipulations early in DS development.
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Affiliation(s)
- Debra Toiber
- Department of Biological Chemistry and Interdisciplinary Center for Neuronal Computation (ICNC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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32
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Abstract
The immune system plays an important role in the development of personalized medicine for a variety of diseases including cancer, autoimmune diseases, and infectious diseases. Immunoinformatics, or computational immunology, is an emerging area that provides fundamental methodologies in the study of immunomics, that is, immune-related genomics and proteomics. The integration of immunoinformatics with systems biology approaches may lead to a better understanding of immune-related diseases at various systems levels. Such methods can contribute to translational studies that bring scientific discoveries of the immune system into better clinical practice. One of the most intensely studied areas of the immune system is immune epitopes. Epitopes are important for disease understanding, host-pathogen interaction analyses, antimicrobial target discovery, and vaccine design. The information about genetic diversity of the immune system may help define patient subgroups for individualized vaccine or drug development. Cellular pathways and host immune-pathogen interactions have a crucial impact on disease pathogenesis and immunogen design. Epigenetic studies may help understand how environmental changes influence complex immune diseases such as allergy. High-throughput technologies enable the measurements and catalogs of genes, proteins, interactions, and behavior. Such perception may contribute to the understanding of the interaction network among humans, vaccines, and drugs, to enable new insights of diseases and therapeutic responses. The integration of immunomics information may ultimately lead to the development of optimized vaccines and drugs tailored to personalized prevention and treatment. An immunoinformatics portal containing relevant resources is available at http://immune.pharmtao.com.
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33
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Meng B, Zhu S, Li S, Zeng Q, Mei B. Global view of the mechanisms of improved learning and memory capability in mice with music-exposure by microarray. Brain Res Bull 2009; 80:36-44. [PMID: 19486929 DOI: 10.1016/j.brainresbull.2009.05.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 05/05/2009] [Accepted: 05/25/2009] [Indexed: 12/29/2022]
Abstract
Music has been proved beneficial to improve learning and memory in many species including human in previous research work. Although some genes have been identified to contribute to the mechanisms, it is believed that the effect of music is manifold, behind which must concern a complex regulation network. To further understand the mechanisms, we exposed the mice to classical music for one month. The subsequent behavioral experiments showed improvement of spatial learning capability and elevation of fear-motivated memory in the mice with music-exposure as compared to the naïve mice. Meanwhile, we applied the microarray to compare the gene expression profiles of the hippocampus and cortex between the mice with music-exposure and the naïve mice. The results showed approximately 454 genes in cortex (200 genes up-regulated and 254 genes down-regulated) and 437 genes in hippocampus (256 genes up-regulated and 181 genes down-regulated) were significantly affected in music-exposing mice, which mainly involved in ion channel activity and/or synaptic transmission, cytoskeleton, development, transcription, hormone activity. Our work may provide some hints for better understanding the effects of music on learning and memory.
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Affiliation(s)
- Bo Meng
- Key Lab of Brain Functional Genomics, MOE & STCSM, Shanghai Institute of Brain Functional Genomics, East China Normal University, 3663 North Zhongshan Road, Shanghai, China.
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