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Kelly J, Xu X, Eales JM, Keavney B, Berzuini C, Tomaszewski M, Guo H. Interactive molecular causal networks of hypertension using a fast machine learning algorithm MRdualPC. BMC Med Res Methodol 2024; 24:168. [PMID: 39095705 PMCID: PMC11295895 DOI: 10.1186/s12874-024-02229-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding the complex interactions between genes and their causal effects on diseases is crucial for developing targeted treatments and gaining insight into biological mechanisms. However, the analysis of molecular networks, especially in the context of high-dimensional data, presents significant challenges. METHODS This study introduces MRdualPC, a computationally tractable algorithm based on the MRPC approach, to infer large-scale causal molecular networks. We apply MRdualPC to investigate the upstream causal transcriptomics influencing hypertension using a comprehensive dataset of kidney genome and transcriptome data. RESULTS Our algorithm proves to be 100 times faster than MRPC on average in identifying transcriptomics drivers of hypertension. Through clustering, we identify 63 modules with causal driver genes, including 17 modules with extensive causal networks. Notably, we find that genes within one of the causal networks are associated with the electron transport chain and oxidative phosphorylation, previously linked to hypertension. Moreover, the identified causal ancestor genes show an over-representation of blood pressure-related genes. CONCLUSIONS MRdualPC has the potential for broader applications beyond gene expression data, including multi-omics integration. While there are limitations, such as the need for clustering in large gene expression datasets, our study represents a significant advancement in building causal molecular networks, offering researchers a valuable tool for analyzing big data and investigating complex diseases.
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Affiliation(s)
- Jack Kelly
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Bernard Keavney
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
- Division of Cardiology and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Carlo Berzuini
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK
- Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Hui Guo
- Centre for Biostatistics, School of Health Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, UK.
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2
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Piergiorge RM, Vasconcelos ATRD, Santos-Rebouças CB. Understanding the (epi)genetic dysregulation in Parkinson's disease through an integrative brain competitive endogenous RNA network. Mech Ageing Dev 2024; 219:111942. [PMID: 38762037 DOI: 10.1016/j.mad.2024.111942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Parkinson's disease (PD) is a rapidly growing neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra pars compacta (SN) and aggregation of α-synuclein. Its aetiology involves a multifaceted interplay among genetic, environmental, and epigenetic factors. We integrated brain gene expression data from PD patients to construct a comprehensive regulatory network encompassing messenger RNAs (mRNAs), microRNAs (miRNAs), circular RNAs (circRNAs) and, for the first time, RNA binding proteins (RBPs). Expression data from the SN of PD patients and controls were systematically selected from public databases to identify combined differentially expressed genes (DEGs). Brain co-expression analysis revealed modules comprising significant DEGs that function cooperatively. The relationships among co-expressed DEGs, miRNAs, circRNAs, and RBPs revealed an intricate competitive endogenous RNA (ceRNA) network responsible for post-transcriptional dysregulation in PD. Many genes in the ceRNA network, including the TOMM20 and HMGCR genes, overlap with the most relevant genes in our previous Alzheimer's disease-associated ceRNA network, suggesting common underlying mechanisms between both conditions. Moreover, in the ceRNA subnetwork, the RBP Aly/REF export factor (ALYREF), which acts as an RNA 5-methylcytosine(m5C)-binding protein, stood out. Our data sheds new light on the potential role of brain ceRNA networks in PD pathogenesis.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil.
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Melachroinou K, Divolis G, Tsafaras G, Karampetsou M, Fortis S, Stratoulias Y, Papadopoulou G, Kriebardis AG, Samiotaki M, Vekrellis K. Endogenous Alpha-Synuclein is Essential for the Transfer of Pathology by Exosome-Enriched Extracellular Vesicles, Following Inoculation with Preformed Fibrils in vivo. Aging Dis 2024; 15:869-892. [PMID: 37548944 PMCID: PMC10917543 DOI: 10.14336/ad.2023.0614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/14/2023] [Indexed: 08/08/2023] Open
Abstract
The main pathological hallmark of Parkinson's disease (PD) and related synucleinopathies is the presence of intracellular proteinaceous aggregates, enriched in the presynaptic protein alpha-Synuclein (α-Syn). α-Syn association with exosomes has been previously documented both as a physiological process of secretion and as a pathological process of disease transmission, however, critical information about the mechanisms governing this interplay is still lacking. To address this, we utilized the α-Syn preformed fibril (PFF) mouse model of PD, as a source of brain-derived exosome-enriched extracellular vesicles (ExE-EVs) and assessed their pathogenic capacity following intrastriatal injections in host wild type (WT) mouse brain. We further investigated the impact of the fibrillar α-Syn on the exosomal cargo independent of the endogenous α-Syn, by isolating ExE-EVs from PFF-injected α-Syn knockout mice. Although PFF inoculation does not alter the morphology, size distribution, and quantity of brain-derived ExE-EVs, it triggers changes in the exosomal proteome related to synaptic and mitochondrial function, as well as metabolic processes. Importantly, we showed that the presence of the endogenous α-Syn is essential for the ExE-EVs to acquire a pathogenic capacity, allowing them to mediate disease transmission by inducing phosphorylated-α-Syn pathology. Notably, misfolded α-Syn containing ExE-EVs when injected in WT mice were able to induce astrogliosis and synaptic alterations in the host brain, at very early stages of α-Syn pathology, preceding the formation of the insoluble α-Syn accumulations. Collectively, our data suggest that exosomal cargo defines their ability to spread α-Syn pathology.
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Affiliation(s)
- Katerina Melachroinou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Georgios Divolis
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - George Tsafaras
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Mantia Karampetsou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Sotirios Fortis
- Laboratory of Reliability and Quality Control in Laboratory Hematology (HemQcR), Department of Biomedical Sciences, School of Health & Welfare Sciences, University of West Attica (UniWA), Egaleo, Greece.
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece.
| | - Yannis Stratoulias
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Gina Papadopoulou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Anastasios G Kriebardis
- Laboratory of Reliability and Quality Control in Laboratory Hematology (HemQcR), Department of Biomedical Sciences, School of Health & Welfare Sciences, University of West Attica (UniWA), Egaleo, Greece.
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
| | - Kostas Vekrellis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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Jin M, Shi R, Gao D, Wang B, Li N, Li X, Sik A, Liu K, Zhang X. ErbB2 pY -1248 as a predictive biomarker for Parkinson's disease based on research with RPPA technology and in vivo verification. CNS Neurosci Ther 2024; 30:e14407. [PMID: 37564024 PMCID: PMC10848095 DOI: 10.1111/cns.14407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023] Open
Abstract
AIMS This study aims to reveal a promising biomarker for Parkinson's disease (PD) based on research with reverse phase protein array (RPPA) technology for the first time and in vivo verification, which gains time for early intervention in PD, thus increasing the effectiveness of treatment and reducing disease morbidity. METHODS AND RESULTS We employed RPPA technology which can assess both total and post-translationally modified proteins to identify biomarker candidates of PD in a cellular PD model. As a result, the phosphorylation (pY-1248) of the epidermal growth factor receptor (EGFR) ErbB2 is a promising biomarker candidate for PD. In addition, lapatinib, an ErbB2 tyrosine kinase inhibitor, was used to verify this PD biomarker candidate in vivo. We found that lapatinib-attenuated dopaminergic neuron loss and PD-like behavior in the zebrafish PD model. Accordingly, the expression of ErbB2pY-1248 significantly increased in the MPTP-induced mouse PD model. Our results suggest that ErbB2pY-1248 is a predictive biomarker for PD. CONCLUSIONS In this study, we found that ErbB2pY-1248 is a predictive biomarker of PD by using RPPA technology and in vivo verification. It offers a new perspective on PD diagnosing and treatment, which will be essential in identifying individuals at risk of PD. In addition, this study provides new ideas for digging into biomarkers of other neurodegenerative diseases.
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Affiliation(s)
- Meng Jin
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Ruidie Shi
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
- School of PsychologyNorth China University of Science and TechnologyTang'shanChina
| | - Daili Gao
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Baokun Wang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Ning Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Xia Li
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd.Ji'nanChina
| | - Attila Sik
- Institute of Transdisciplinary Discoveries, Medical SchoolUniversity of PecsPécsHungary
- Institute of Clinical Sciences, Medical SchoolUniversity of BirminghamBirminghamUK
- Institute of Physiology, Medical SchoolUniversity of PecsPécsHungary
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences)Ji'nanChina
- Engineering Research Center of Zebrafish Models for Human Diseases and Drug Screening of Shandong ProvinceJi'nanChina
| | - Xiujun Zhang
- School of PsychologyNorth China University of Science and TechnologyTang'shanChina
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Huang J, Li B, Wei H, Li C, Liu C, Mi H, Chen S. Integrative analysis of gene expression profiles of substantia nigra identifies potential diagnosis biomarkers in Parkinson's disease. Sci Rep 2024; 14:2167. [PMID: 38272954 PMCID: PMC10810830 DOI: 10.1038/s41598-024-52276-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease whose etiology is attributed to development of Lewy bodies and degeneration of dopaminergic neurons in the substantia nigra (SN). Currently, there are no definitive diagnostic indicators for PD. In this study, we aimed to identify potential diagnostic biomarkers for PD and analyzed the impact of immune cell infiltrations on disease pathogenesis. The PD expression profile data for human SN tissue, GSE7621, GSE20141, GSE20159, GSE20163 and GSE20164 were downloaded from the Gene Expression Omnibus (GEO) database for use in the training model. After normalization and merging, we identified differentially expressed genes (DEGs) using the Robust rank aggregation (RRA) analysis. Simultaneously, DEGs after batch correction were identified. Gene interactions were determined through venn Diagram analysis. Functional analyses and protein-protein interaction (PPI) networks were used to the identify hub genes, which were visualized through Cytoscape. A Lasso Cox regression model was employed to identify the potential diagnostic genes. The GSE20292 dataset was used for validation. The proportion of infiltrating immune cells in the samples were determined via the CIBERSORT method. Sixty-two DEGs were screened in this study. They were found to be enriched in nerve conduction, dopamine (DA) metabolism, and DA biosynthesis Gene Ontology (GO) terms. The PPI network and Lasso Cox regression analysis revealed seven potential diagnostic genes, namely SLC18A2, TAC1, PCDH8, KIAA0319, PDE6H, AXIN1, and AGTR1, were subsequently validated in peripheral blood samples obtained from healthy control (HC) and PD patients, as well as in the GSE20292 dataset. The results revealed the exceptional sensitivity and specificity of these genes in PD diagnosis and monitoring. Moreover, PD patients exhibited a higher number of plasma cells, compared to HC individuals. The SLC18A2, TAC1, PCDH8, KIAA0319, PDE6H, AXIN1, and AGTR1 are potential diagnostic biomarkers for PD. Our findings also reveal the essential roles of immune cell infiltration in both disease onset and trajectory.
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Affiliation(s)
- Junming Huang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, 530000, Guangxi, China
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Bowen Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Huangwei Wei
- Department of Neurology, The People Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Chengxin Li
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Chao Liu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hua Mi
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China.
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, 530000, Guangxi, China.
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Habibzadeh A, Ostovan VR, Keshavarzian O, Kardeh S, Mahmoudi SS, Zakeri MR, Tabrizi R. Volatile organic compounds analysis as promising biomarkers for Parkinson's disease diagnosis: A systematic review and meta-analysis. Clin Neurol Neurosurg 2023; 235:108022. [PMID: 37939618 DOI: 10.1016/j.clineuro.2023.108022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023]
Abstract
OBJECTIVE Researchers are investigating the potential of volatile organic compounds (VOCs) obtained from exhaled breath and sebum as non-invasive tools for early Parkinson's disease (PD) diagnosis. The present study aims to assess the feasibility of using VOC analysis for PD diagnosis and determine the overall diagnostic accuracy of the proposed tests. METHODS We performed systematic searches based on the PRISMA guidelines to identify relevant studies on VOCs in PD diagnosis using exhaled breath or sebum samples. The selected articles were described, and meta-analysis was conducted on those that provided the sensitivity and specificity data. RESULTS Out of 1268 articles initially identified, 8 met the inclusion criteria and provided specific sensitivity and specificity data for PD, which were included in the current meta-analysis. The pooled analysis of these findings showed a mean area under the receiver operating characteristic curve of 0.85, a sensitivity of 0.81 (95% confidence interval (CI): 0.72, 0.88), and a specificity of 0.76 (95% CI: 0.66, 0.84). CONCLUSION The analysis of VOCs in exhaled breath and sebum has shown promise as a new avenue for non-invasive diagnosis of PD. VOCs' ability to distinguish PD from healthy controls suggests their potential clinical application in screening for the disease. Consequently, VOCs hold significant potential as biomarkers for PD diagnosis and offer a promising novel approach to identifying and diagnosing the condition.
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Affiliation(s)
- Adrina Habibzadeh
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran; USERN Office, Fasa University of Medical Sciences, Fasa, Iran
| | - Vahid Reza Ostovan
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Keshavarzian
- School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sina Kardeh
- Central Clinical School, Monash University, Melbourne, Australia
| | - Seyed Sasan Mahmoudi
- Student Research Committee, Department of Neurosurgery, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad-Reza Zakeri
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Tabrizi
- USERN Office, Fasa University of Medical Sciences, Fasa, Iran; Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran; Clinical Research Development Unit, Valiasr Hospital, Fasa University of Medical Sciences, Fasa, Iran.
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7
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Kelly J, Moyeed R, Carroll C, Luo S, Li X. Blood biomarker-based classification study for neurodegenerative diseases. Sci Rep 2023; 13:17191. [PMID: 37821485 PMCID: PMC10567903 DOI: 10.1038/s41598-023-43956-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
As the population ages, neurodegenerative diseases are becoming more prevalent, making it crucial to comprehend the underlying disease mechanisms and identify biomarkers to allow for early diagnosis and effective screening for clinical trials. Thanks to advancements in gene expression profiling, it is now possible to search for disease biomarkers on an unprecedented scale.Here we applied a selection of five machine learning (ML) approaches to identify blood-based biomarkers for Alzheimer's (AD) and Parkinson's disease (PD) with the application of multiple feature selection methods. Based on ROC AUC performance, one optimal random forest (RF) model was discovered for AD with 159 gene markers (ROC-AUC = 0.886), while one optimal RF model was discovered for PD (ROC-AUC = 0.743). Additionally, in comparison to traditional ML approaches, deep learning approaches were applied to evaluate their potential applications in future works. We demonstrated that convolutional neural networks perform consistently well across both the Alzheimer's (ROC AUC = 0.810) and Parkinson's (ROC AUC = 0.715) datasets, suggesting its potential in gene expression biomarker detection with increased tuning of their architecture.
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Affiliation(s)
- Jack Kelly
- Faculty of Medicine, Biology and Health, Centre for Biostatistics, School of Health Sciences, University of Manchester, Manchester, UK.
- Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK.
| | - Rana Moyeed
- Faculty of Science and Engineering, University of Plymouth, Plymouth, PL6 8BU, UK
| | - Camille Carroll
- Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK
| | - Shouqing Luo
- Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK
| | - Xinzhong Li
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK.
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8
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Yadav SK, Jauhari A, Singh N, Pandey A, Sarkar S, Pandey S, Garg RK, Parmar D, Yadav S. Transcriptomics and Proteomics Approach for the Identification of Altered Blood microRNAs and Plasma Proteins in Parkinson's Disease. Cell Mol Neurobiol 2023; 43:3527-3553. [PMID: 37219663 DOI: 10.1007/s10571-023-01362-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by the selective destruction of dopaminergic neurons (DA-nergic). Clinically, PD is diagnosed based on developing signs and symptoms. A neurological and physical examination and sometimes medical and family history also help in the diagnosis of PD. However, most of these features are visible when more than 80% of the dopaminergic neurons have degenerated. An understanding of the selective degeneration process at the cellular and molecular level and the development of new biomarkers are required for effective PD management. Several studies have been carried out using a selected set of miRNAs/ mRNAs and proteins to develop biomarkers of PD; however, an unbiased and combined miRNA-protein profiling study was required to identify the markers of progressive and selected degeneration of dopaminergic neurons in PD patients. In the present study, we have carried out global protein profiling through LC-MS/MS and miRNA profiling by using a "brain-specific" miRNA array panel of 112 miRNAs in PD patients and healthy controls to find the unprejudiced group of proteins and miRNAs that are deregulating in PD. In the whole blood samples of PD patients compared to healthy controls, the expression of 23 miRNAs and 289 proteins was significantly increased, whereas the expression of 4 miRNAs and 132 proteins was considerably downregulated. Network analysis, functional enrichment, annotation, and analysis of miRNA-protein interactions were also performed as part of the bioinformatics investigation of the discovered miRNAs and proteins revealing several pathways that lead to PD development and pathogenesis. Based on the analysis of miRNA and protein profiling, we have identified four miRNAs (hsa-miR-186-5p, miR-29b, miR-139 & has-miR-150-5p) and four proteins (YWHAZ, PSMA4, HYOU1, & SERPINA1), which can be targeted for the development of new biomarkers of PD. In vitro studies have identified the role of miR-186-5p in regulating the levels of the YWHAZ/YWHAB & CALM2 gene, which has shown maximum downregulation in PD patients and is known for its role in neuroprotection from apoptotic cell death & calcium regulation. In conclusion, our research has identified a group of miRNA-proteins that can be developed as PD biomarkers; however, future studies on the release of these miRNAs and proteins in extracellular vesicles circulating in the blood of PD patients can further validate these as specific biomarkers of PD.
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Affiliation(s)
- Sanjeev Kumar Yadav
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
- Department of Neuroscience, UConn Health, Farmington, CT, 06032, USA
| | - Abhishek Jauhari
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Nishant Singh
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
- Department of Molecular Medicine, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Anuj Pandey
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Sana Sarkar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Shweta Pandey
- Department of Neurology, King George's Medical University, Lucknow, 226003, UP, India
| | - Ravindra K Garg
- Department of Neurology, King George's Medical University, Lucknow, 226003, UP, India
| | - Devendra Parmar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
| | - Sanjay Yadav
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India.
- Department of Biochemistry, All India Institute of Medical Sciences, Munshiganj, Raebareli, 229405, Uttar Pradesh, India.
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Zeighami Y, Bakken TE, Nickl-Jockschat T, Peterson Z, Jegga AG, Miller JA, Schulkin J, Evans AC, Lein ES, Hawrylycz M. A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. PLoS Biol 2023; 21:e3002058. [PMID: 37079537 PMCID: PMC10118126 DOI: 10.1371/journal.pbio.3002058] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/02/2023] [Indexed: 04/21/2023] Open
Abstract
Genes associated with risk for brain disease exhibit characteristic expression patterns that reflect both anatomical and cell type relationships. Brain-wide transcriptomic patterns of disease risk genes provide a molecular-based signature, based on differential co-expression, that is often unique to that disease. Brain diseases can be compared and aggregated based on the similarity of their signatures which often associates diseases from diverse phenotypic classes. Analysis of 40 common human brain diseases identifies 5 major transcriptional patterns, representing tumor-related, neurodegenerative, psychiatric and substance abuse, and 2 mixed groups of diseases affecting basal ganglia and hypothalamus. Further, for diseases with enriched expression in cortex, single-nucleus data in the middle temporal gyrus (MTG) exhibits a cell type expression gradient separating neurodegenerative, psychiatric, and substance abuse diseases, with unique excitatory cell type expression differentiating psychiatric diseases. Through mapping of homologous cell types between mouse and human, most disease risk genes are found to act in common cell types, while having species-specific expression in those types and preserving similar phenotypic classification within species. These results describe structural and cellular transcriptomic relationships of disease risk genes in the adult brain and provide a molecular-based strategy for classifying and comparing diseases, potentially identifying novel disease relationships.
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Affiliation(s)
- Yashar Zeighami
- Douglas Research Centre, Department of Psychiatry, McGill University, Montreal, Canada
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Trygve E. Bakken
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Thomas Nickl-Jockschat
- Department of Psychiatry, Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Zeru Peterson
- Department of Psychiatry, Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Jay Schulkin
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Alan C. Evans
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Michael Hawrylycz
- Allen Institute for Brain Science, Seattle, Washington, United States of America
- University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America
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Lee RMQ, Koh TW. Genetic modifiers of synucleinopathies-lessons from experimental models. OXFORD OPEN NEUROSCIENCE 2023; 2:kvad001. [PMID: 38596238 PMCID: PMC10913850 DOI: 10.1093/oons/kvad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2024]
Abstract
α-Synuclein is a pleiotropic protein underlying a group of progressive neurodegenerative diseases, including Parkinson's disease and dementia with Lewy bodies. Together, these are known as synucleinopathies. Like all neurological diseases, understanding of disease mechanisms is hampered by the lack of access to biopsy tissues, precluding a real-time view of disease progression in the human body. This has driven researchers to devise various experimental models ranging from yeast to flies to human brain organoids, aiming to recapitulate aspects of synucleinopathies. Studies of these models have uncovered numerous genetic modifiers of α-synuclein, most of which are evolutionarily conserved. This review discusses what we have learned about disease mechanisms from these modifiers, and ways in which the study of modifiers have supported ongoing efforts to engineer disease-modifying interventions for synucleinopathies.
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Affiliation(s)
- Rachel Min Qi Lee
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Tong-Wey Koh
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Block S3 #05-01, 16 Science Drive 4, Singapore, 117558, Singapore
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Roshan SA, Elangovan G, Gunaseelan D, Jayachandran SK, Kandasamy M, Anusuyadevi M. Pathogenomic Signature and Aberrant Neurogenic Events in Experimental Cerebral Ischemic Stroke: A Neurotranscriptomic-Based Implication for Dementia. J Alzheimers Dis 2023; 94:S289-S308. [PMID: 36776051 PMCID: PMC10473090 DOI: 10.3233/jad-220831] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2022] [Indexed: 02/12/2023]
Abstract
BACKGROUND Cerebral ischemic stroke is caused due to neurovascular damage or thrombosis, leading to neuronal dysfunction, neuroinflammation, neurodegeneration, and regenerative failure responsible for neurological deficits and dementia. The valid therapeutic targets against cerebral stroke remain obscure. Thus, insight into neuropathomechanisms resulting from the aberrant expression of genes appears to be crucial. OBJECTIVE In this study, we have elucidated how neurogenesis-related genes are altered in experimental stroke brains from the available transcriptome profiles in correlation with transcriptome profiles of human postmortem stroke brain tissues. METHODS The transcriptome datasets available on the middle cerebral artery occlusion (MCAo) rat brains were obtained from the Gene Expression Omnibus, National Center for Biotechnology Information. Of the available datasets, 97 samples were subjected to the meta-analysis using the network analyst tool followed by Cytoscape-based enrichment mapping analysis. The key differentially expressed genes (DEGs) were validated and compared with transcriptome profiling of human stroke brains. RESULTS Results revealed 939 genes are differently expressed in the brains of the MCAo rat model of stroke, in which 30 genes are key markers of neural stem cells, and regulators of neurogenic processes. Its convergence with DEGs from human stroke brains has revealed common targets. CONCLUSION This study has established a panel of highly important DEGs to signify the potential therapeutic targets for neuroregenerative strategy against pathogenic events associated with cerebral stroke. The outcome of the findings can be translated to mitigate neuroregeneration failure seen in various neurological and metabolic disease manifestations with neurocognitive impairments.
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Affiliation(s)
- Syed Aasish Roshan
- Molecular Neuro-Gerontology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Gayathri Elangovan
- Molecular Neuro-Gerontology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Dharani Gunaseelan
- Molecular Neuro-Gerontology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Swaminathan K. Jayachandran
- Drug Discovery and Molecular Cardiology Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Mahesh Kandasamy
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- University Grants Commission-Faculty Recharge Program (UGC-FRP), New Delhi, India
| | - Muthuswamy Anusuyadevi
- Molecular Neuro-Gerontology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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12
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Zhao Y, Zhang K, Pan H, Wang Y, Zhou X, Xiang Y, Xu Q, Sun Q, Tan J, Yan X, Li J, Guo J, Tang B, Liu Z. Genetic Analysis of Six Transmembrane Protein Family Genes in Parkinson's Disease in a Large Chinese Cohort. Front Aging Neurosci 2022; 14:889057. [PMID: 35860667 PMCID: PMC9289399 DOI: 10.3389/fnagi.2022.889057] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Parkinson's disease (PD) is a neurodegenerative disorder with the manifestation of motor symptoms and non-motor symptoms. Previous studies have indicated the role of several transmembrane (TMEM) protein family genes in PD pathogenesis. Materials and Methods In order to better investigate the genetic role of PD-related TMEM protein family genes in PD, including TMEM230, TMEM59, TMEM108, TMEM163, TMEM175, and TMEM229B, 1,917 sporadic early onset PD (sEOPD) or familial PD (FPD) patients and 1,652 healthy controls were analyzed by whole-exome sequencing (WES) while 1,962 sporadic late-onset PD (sLOPD) and 1,279 healthy controls were analyzed by whole-genome sequencing (WGS). Rare and common variants for each gene were included in the analysis. Results One hundred rare damaging or loss of function variants of six genes were found at the threshold of MAF < 0.1%. Three rare Dmis variants of TMEM230 were specifically identified in PD. Rare missense variants of TMEM59 were statistically significantly associated with PD in the WES cohort, indicating the role of TMEM59 in FPD and sEOPD. Rare missense variants of TMEM108 were suggestively associated with PD in the WGS cohort, indicating the potential role of TMEM108 in sLOPD. The rare variant of the other three genes and common variants of six genes were not significantly associated with PD. Conclusion We performed a large case-control study to systematically investigate the role of several PD-related TMEM protein family genes in PD. We identified three PD-specific variants in TMEM230, the significant association of TMEM59 with FPD, and sEOPD and the suggestive association of TMEM108 with sLOPD.
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Affiliation(s)
- Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Kailin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yige Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxia Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yaqin Xiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiying Sun
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Jieqiong Tan
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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13
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Cukier HN, Kim H, Griswold AJ, Codreanu SG, Prince LM, Sherrod SD, McLean JA, Dykxhoorn DM, Ess KC, Hedera P, Bowman AB, Neely MD. Genomic, transcriptomic, and metabolomic profiles of hiPSC-derived dopamine neurons from clinically discordant brothers with identical PRKN deletions. NPJ Parkinsons Dis 2022; 8:84. [PMID: 35768426 PMCID: PMC9243035 DOI: 10.1038/s41531-022-00346-3] [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: 11/07/2021] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
We previously reported on two brothers who carry identical compound heterozygous PRKN mutations yet present with significantly different Parkinson's Disease (PD) clinical phenotypes. Juvenile cases demonstrate that PD is not necessarily an aging-associated disease. Indeed, evidence for a developmental component to PD pathogenesis is accumulating. Thus, we hypothesized that the presence of additional genetic modifiers, including genetic loci relevant to mesencephalic dopamine neuron development, could potentially contribute to the different clinical manifestations of the two brothers. We differentiated human-induced pluripotent stem cells (hiPSCs) derived from the two brothers into mesencephalic neural precursor cells and early postmitotic dopaminergic neurons and performed wholeexome sequencing and transcriptomic and metabolomic analyses. No significant differences in the expression of canonical dopamine neuron differentiation markers were observed. Yet our transcriptomic analysis revealed a significant downregulation of the expression of three neurodevelopmentally relevant cell adhesion molecules, CNTN6, CNTN4 and CHL1, in the cultures of the more severely affected brother. In addition, several HLA genes, known to play a role in neurodevelopment, were differentially regulated. The expression of EN2, a transcription factor crucial for mesencephalic dopamine neuron development, was also differentially regulated. We further identified differences in cellular processes relevant to dopamine metabolism. Lastly, wholeexome sequencing, transcriptomics and metabolomics data all revealed differences in glutathione (GSH) homeostasis, the dysregulation of which has been previously associated with PD. In summary, we identified genetic differences which could potentially, at least partially, contribute to the discordant clinical PD presentation of the two brothers.
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Affiliation(s)
- Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hyunjin Kim
- School of Health Sciences, Purdue University, West Lafayette, Indiana, IN, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Simona G Codreanu
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Lisa M Prince
- School of Health Sciences, Purdue University, West Lafayette, Indiana, IN, USA
| | - Stacy D Sherrod
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kevin C Ess
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Peter Hedera
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, University of Louisville, Louisville, KY, USA
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, Indiana, IN, USA.
| | - M Diana Neely
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
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14
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Ruffini N, Klingenberg S, Heese R, Schweiger S, Gerber S. The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Front Aging Neurosci 2022; 14:866886. [PMID: 35832065 PMCID: PMC9271745 DOI: 10.3389/fnagi.2022.866886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
The common features of all neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease, are the accumulation of aggregated and misfolded proteins and the progressive loss of neurons, leading to cognitive decline and locomotive dysfunction. Still, they differ in their ultimate manifestation, the affected brain region, and the kind of proteinopathy. In the last decades, a vast number of processes have been described as associated with neurodegenerative diseases, making it increasingly harder to keep an overview of the big picture forming from all those data. In this meta-study, we analyzed genomic, transcriptomic, proteomic, and epigenomic data of the aforementioned diseases using the data of 234 studies in a network-based approach to study significant general coherences but also specific processes in individual diseases or omics levels. In the analysis part, we focus on only some of the emerging findings, but trust that the meta-study provided here will be a valuable resource for various other researchers focusing on specific processes or genes contributing to the development of neurodegeneration.
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Affiliation(s)
- Nicolas Ruffini
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Leibniz Institute for Resilience Research, Leibniz Association, Mainz, Germany
| | - Susanne Klingenberg
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Raoul Heese
- Fraunhofer Institute for Industrial Mathematics (ITWM), Kaiserslautern, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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15
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Identification of Novel Noninvasive Diagnostics Biomarkers in the Parkinson’s Diseases and Improving the Disease Classification Using Support Vector Machine. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5009892. [PMID: 35342758 PMCID: PMC8941533 DOI: 10.1155/2022/5009892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022]
Abstract
Background Parkinson's disease (PD) is a neurological disorder that is marked by the deficit of neurons in the midbrain that changes motor and cognitive function. In the substantia nigra, the selective demise of dopamine-producing neurons was the main cause of this disease. The purpose of this research was to discover genes involved in PD development. Methods In this study, the microarray dataset (GSE22491) provided by GEO was used for further analysis. The Limma package under R software was used to examine and assess gene expression and identify DEGs. The DAVID online tool was used to accomplish GO enrichment analysis and KEGG pathway for DEGs. Furthermore, the PPI network of these DEGs was depicted using the STRING database and analyzed through the Cytoscape to identify hub genes. Support vector machine (SVM) classifier was subsequently employed to predict the accuracy of genes. Result PPI network consisted of 264 nodes as well as 502 edges was generated using the DEGs recognized from the Limma package under the R software. Moreover, three genes were identified as hubs: GNB5, GNG11, and ELANE. By using 3-gene combination, SVM found that prediction accuracy of 88% can be achieved. Conclusion According to the findings of the study, the 3 hub genes GNB5, GNG11, and ELANE may be used as PD detection biomarkers. Moreover, the results obtained from SVM with high accuracy can be considered as PD biomarkers in further investigations.
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16
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Pedrero-Prieto CM, Frontiñán-Rubio J, Alcaín FJ, Durán-Prado M, Peinado JR, Rabanal-Ruiz Y. Biological Significance of the Protein Changes Occurring in the Cerebrospinal Fluid of Alzheimer's Disease Patients: Getting Clues from Proteomic Studies. Diagnostics (Basel) 2021; 11:1655. [PMID: 34573996 PMCID: PMC8467255 DOI: 10.3390/diagnostics11091655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/18/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
The fact that cerebrospinal fluid (CSF) deeply irrigates the brain together with the relative simplicity of sample extraction from patients make this biological fluid the best target for biomarker discovery in neurodegenerative diseases. During the last decade, biomarker discovery has been especially fruitful for the identification new proteins that appear in the CSF of Alzheimer's disease (AD) patients together with amyloid-β (Aβ42), total tau (T-tau), and phosphorylated tau (P-tau). Thus, several proteins have been already stablished as important biomarkers, due to an increase (i.e., CHI3L1) or a decrease (i.e., VGF) in AD patients' CSF. Notwithstanding this, only a deep analysis of a database generated with all the changes observed in CSF across multiple proteomic studies, and especially those using state-of-the-art methodologies, may expose those components or metabolic pathways disrupted at different levels in AD. Deep comparative analysis of all the up- and down-regulated proteins across these studies revealed that 66% of the most consistent protein changes in CSF correspond to intracellular proteins. Interestingly, processes such as those associated to glucose metabolism or RXR signaling appeared inversely represented in CSF from AD patients in a significant manner. Herein, we discuss whether certain cellular processes constitute accurate indicators of AD progression by examining CSF. Furthermore, we uncover new CSF AD markers, such as ITAM, PTPRZ or CXL16, identified by this study.
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Affiliation(s)
- Cristina M. Pedrero-Prieto
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, CRIB, University of Castilla-La Mancha (UCLM), Paseo de Moledores SN, 13071 Ciudad Real, Spain; (C.M.P.-P.); (J.F.-R.); (F.J.A.); (M.D.-P.)
- Neuroplasticity and Neurodegeneration Laboratory, Ciudad Real Medical School, CRIB, University of Castilla-La Mancha (UCLM), 13005 Ciudad Real, Spain
| | - Javier Frontiñán-Rubio
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, CRIB, University of Castilla-La Mancha (UCLM), Paseo de Moledores SN, 13071 Ciudad Real, Spain; (C.M.P.-P.); (J.F.-R.); (F.J.A.); (M.D.-P.)
| | - Francisco J. Alcaín
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, CRIB, University of Castilla-La Mancha (UCLM), Paseo de Moledores SN, 13071 Ciudad Real, Spain; (C.M.P.-P.); (J.F.-R.); (F.J.A.); (M.D.-P.)
| | - Mario Durán-Prado
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, CRIB, University of Castilla-La Mancha (UCLM), Paseo de Moledores SN, 13071 Ciudad Real, Spain; (C.M.P.-P.); (J.F.-R.); (F.J.A.); (M.D.-P.)
| | - Juan R. Peinado
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, CRIB, University of Castilla-La Mancha (UCLM), Paseo de Moledores SN, 13071 Ciudad Real, Spain; (C.M.P.-P.); (J.F.-R.); (F.J.A.); (M.D.-P.)
| | - Yoana Rabanal-Ruiz
- Department of Medical Sciences, Ciudad Real Medical School, Oxidative Stress and Neurodegeneration Group, CRIB, University of Castilla-La Mancha (UCLM), Paseo de Moledores SN, 13071 Ciudad Real, Spain; (C.M.P.-P.); (J.F.-R.); (F.J.A.); (M.D.-P.)
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Reelin Alleviates Mesenchymal Stem Cell Senescence and Reduces Pathological α-Synuclein Expression in an In Vitro Model of Parkinson's Disease. Genes (Basel) 2021; 12:genes12071066. [PMID: 34356083 PMCID: PMC8308051 DOI: 10.3390/genes12071066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 02/08/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative diseases. The mechanisms underlying PD remain to be fully elucidated, and research into treatments for this condition is ongoing. Recent advances in genetic research have shed light on the mechanisms underlying PD. In this study, we used PD and control mesenchymal stem cells (MSCs) obtained from adipose tissues to confirm the differences between groups at the cellular and molecular levels. The results revealed that in PD MSCs, cell viability was clearly lower, and the rate of cell senescence was higher compared to the controls. Next, to compare the gene expression in PD and control cells, transcriptome analysis was performed. Genes in pathways, including extracellular matrix (ECM) receptor interaction, P53 signaling, and focal adhesion, were down-regulated in PD. Among genes related to ECM receptor interaction, RELN gene expression was markedly decreased in PD cells; however, after being treated with recombinant Reelin protein, a significant increase in cell viability and a decrease in α-Synuclein aggregation and cell senescence were observed. In conclusion, Reelin affects PD by positively influencing the cell characteristics. Our findings will facilitate research into new treatments for PD.
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Motyl JA, Strosznajder JB, Wencel A, Strosznajder RP. Recent Insights into the Interplay of Alpha-Synuclein and Sphingolipid Signaling in Parkinson's Disease. Int J Mol Sci 2021; 22:ijms22126277. [PMID: 34207975 PMCID: PMC8230587 DOI: 10.3390/ijms22126277] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/22/2023] Open
Abstract
Molecular studies have provided increasing evidence that Parkinson’s disease (PD) is a protein conformational disease, where the spread of alpha-synuclein (ASN) pathology along the neuraxis correlates with clinical disease outcome. Pathogenic forms of ASN evoke oxidative stress (OS), neuroinflammation, and protein alterations in neighboring cells, thereby intensifying ASN toxicity, neurodegeneration, and neuronal death. A number of evidence suggest that homeostasis between bioactive sphingolipids with opposing function—e.g., sphingosine-1-phosphate (S1P) and ceramide—is essential in pro-survival signaling and cell defense against OS. In contrast, imbalance of the “sphingolipid biostat” favoring pro-oxidative/pro-apoptotic ceramide-mediated changes have been indicated in PD and other neurodegenerative disorders. Therefore, we focused on the role of sphingolipid alterations in ASN burden, as well as in a vast range of its neurotoxic effects. Sphingolipid homeostasis is principally directed by sphingosine kinases (SphKs), which synthesize S1P—a potent lipid mediator regulating cell fate and inflammatory response—making SphK/S1P signaling an essential pharmacological target. A growing number of studies have shown that S1P receptor modulators, and agonists are promising protectants in several neurological diseases. This review demonstrates the relationship between ASN toxicity and alteration of SphK-dependent S1P signaling in OS, neuroinflammation, and neuronal death. Moreover, we discuss the S1P receptor-mediated pathways as a novel promising therapeutic approach in PD.
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Affiliation(s)
- Joanna A. Motyl
- Department of Hybrid Microbiosystems Engineering, Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Ks. Trojdena 4 St., 02-109 Warsaw, Poland; (J.A.M.); (A.W.)
| | - Joanna B. Strosznajder
- Department of Cellular Signalling, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego St., 02-106 Warsaw, Poland;
| | - Agnieszka Wencel
- Department of Hybrid Microbiosystems Engineering, Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Ks. Trojdena 4 St., 02-109 Warsaw, Poland; (J.A.M.); (A.W.)
| | - Robert P. Strosznajder
- Laboratory of Preclinical Research and Environmental Agents, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego St., 02-106 Warsaw, Poland
- Correspondence:
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Seefelder M, Kochanek S. A meta-analysis of transcriptomic profiles of Huntington's disease patients. PLoS One 2021; 16:e0253037. [PMID: 34111223 PMCID: PMC8191979 DOI: 10.1371/journal.pone.0253037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Description of robust transcriptomic alterations in Huntington’s disease is essential to identify targets for biochemical studies and drug development. We analysed publicly available transcriptome data from the brain and blood of 220 HD patients and 241 healthy controls and identified 737 and 661 genes with robustly altered mRNA levels in the brain and blood of HD patients, respectively. In the brain, a subnetwork of 320 genes strongly correlated with HD and was enriched in transport-related genes. Bioinformatical analysis of this subnetwork highlighted CDC42, PAK1, YWHAH, NFY, DLX1, HMGN3, and PRMT3. Moreover, we found that CREB1 can regulate 78.0% of genes whose mRNA levels correlated with HD in the blood of patients. Alterations in protein transport, metabolism, transcriptional regulation, and CDC42-mediated functions are likely central features of HD. Further our data substantiate the role of transcriptional regulators that have not been reported in the context of HD (e.g. DLX1, HMGN3 and PRMT3) and strongly suggest dysregulation of NFY and its target genes across tissues. A large proportion of the identified genes such as CDC42 were also altered in Parkinson’s (PD) and Alzheimer’s disease (AD). The observed dysregulation of CDC42 and YWHAH in samples from HD, AD and PD patients indicates that those genes and their upstream regulators may be interesting therapeutic targets.
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, Ulm, Germany
- * E-mail:
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Salman MM, Al-Obaidi Z, Kitchen P, Loreto A, Bill RM, Wade-Martins R. Advances in Applying Computer-Aided Drug Design for Neurodegenerative Diseases. Int J Mol Sci 2021; 22:4688. [PMID: 33925236 PMCID: PMC8124449 DOI: 10.3390/ijms22094688] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases (NDs) including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease are incurable and affect millions of people worldwide. The development of treatments for this unmet clinical need is a major global research challenge. Computer-aided drug design (CADD) methods minimize the huge number of ligands that could be screened in biological assays, reducing the cost, time, and effort required to develop new drugs. In this review, we provide an introduction to CADD and examine the progress in applying CADD and other molecular docking studies to NDs. We provide an updated overview of potential therapeutic targets for various NDs and discuss some of the advantages and disadvantages of these tools.
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Affiliation(s)
- Mootaz M. Salman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3QX, UK;
- Oxford Parkinson’s Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Zaid Al-Obaidi
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Alkafeel, Najaf 54001, Iraq;
- Department of Chemistry and Biochemistry, College of Medicine, University of Kerbala, Karbala 56001, Iraq
| | - Philip Kitchen
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (P.K.); (R.M.B.)
| | - Andrea Loreto
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3QX, UK;
- John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Roslyn M. Bill
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (P.K.); (R.M.B.)
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3QX, UK;
- Oxford Parkinson’s Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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21
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Anirudhan A, Angulo-Bejarano PI, Paramasivam P, Manokaran K, Kamath SM, Murugesan R, Sharma A, Ahmed SSSJ. RPL6: A Key Molecule Regulating Zinc- and Magnesium-Bound Metalloproteins of Parkinson's Disease. Front Neurosci 2021; 15:631892. [PMID: 33790735 PMCID: PMC8006920 DOI: 10.3389/fnins.2021.631892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease with no definite molecular markers for diagnosis. Metal exposure may alter cellular proteins that contribute to PD. Exploring the cross-talk between metal and its binding proteins in PD could reveal a new strategy for PD diagnosis. We performed a meta-analysis from different PD tissue microarray datasets to identify differentially expressed genes (DEGs) common to the blood and brain. Among common DEGs, we extracted 280 metalloprotein-encoding genes to construct protein networks describing the regulation of metalloproteins in the PD blood and brain. From the metalloprotein network, we identified three important functional hubs. Further analysis shows 60S ribosomal protein L6 (RPL6), a novel intermediary molecule connecting the three hubs of the metalloproteins network. Quantitative real-time PCR analysis showed that RPL6 was downregulated in PD peripheral blood mononuclear cell (PBMC) samples. Simultaneously, trace element analysis revealed altered serum zinc and magnesium concentrations in PD samples. The Pearson's correlation analysis shows that serum zinc and magnesium regulate the RPL6 gene expression in PBMC. Thus, metal-regulating RPL6 acts as an intermediary molecule connecting the three hubs that are functionally associated with PD. Overall our study explores the understanding of metal-mediated pathogenesis in PD, which provides a serum metal environment regulating the cellular gene expression that may light toward metal and gene expression-based biomarkers for PD diagnosis.
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Affiliation(s)
- Athira Anirudhan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
| | | | - Prabu Paramasivam
- Department of Neurology, School of Medicine, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM, United States
| | - Kalaivani Manokaran
- Department of Medical Laboratory Technology, Manipal College of Health Professions, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - S Manjunath Kamath
- Department of Pharmacology, Saveetha Dental College (SDC), Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Ram Murugesan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Ashutosh Sharma
- School of Engineering and Sciences, Centre of Bioengineering, Tecnologico de Monterrey, Queretaro, Mexico
| | - Shiek S S J Ahmed
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, India
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22
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Vitic Z, Safory H, Jovanovic VM, Sarusi Y, Stavsky A, Kahn J, Kuzmina A, Toker L, Gitler D, Taube R, Friedel RH, Engelender S, Brodski C. BMP5/7 protect dopaminergic neurons in an α-synuclein mouse model of Parkinson's disease. Brain 2021; 144:e15. [PMID: 33253359 PMCID: PMC7940172 DOI: 10.1093/brain/awaa368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Zagorka Vitic
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Hazem Safory
- Department of Biochemistry, The B. Rappaport Faculty of Medicine and Institute of Medical Research, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Vukasin M Jovanovic
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Yael Sarusi
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Alexandra Stavsky
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Joy Kahn
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Alona Kuzmina
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Lilah Toker
- Neuro-SysMed Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
| | - Daniel Gitler
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Ran Taube
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
| | - Roland H Friedel
- Departments of Neuroscience and Neurosurgery, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simone Engelender
- Department of Biochemistry, The B. Rappaport Faculty of Medicine and Institute of Medical Research, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Claude Brodski
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Be'er Sheva, Israel
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23
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Krokidis MG, Exarchos TP, Vlamos P. Data-driven biomarker analysis using computational omics approaches to assess neurodegenerative disease progression. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:1813-1832. [PMID: 33757212 DOI: 10.3934/mbe.2021094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The complexity of biological systems suggests that current definitions of molecular dysfunctions are essential distinctions of a complex phenotype. This is well seen in neurodegenerative diseases (ND), such as Alzheimer's disease (AD) and Parkinson's disease (PD), multi-factorial pathologies characterized by high heterogeneity. These challenges make it necessary to understand the effectiveness of candidate biomarkers for early diagnosis, as well as to obtain a comprehensive mapping of how selective treatment alters the progression of the disorder. A large number of computational methods have been developed to explain network-based approaches by integrating individual components for modeling a complex system. In this review, high-throughput omics methodologies are presented for the identification of potent biomarkers associated with AD and PD pathogenesis as well as for monitoring the response of dysfunctional molecular pathways incorporating multilevel clinical information. In addition, principles for efficient data analysis pipelines are being discussed that can help address current limitations during the experimental process by increasing the reproducibility of benchmarking studies.
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Affiliation(s)
- Marios G Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
| | - Themis P Exarchos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
| | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
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24
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Hendrickx DM, Garcia P, Ashrafi A, Sciortino A, Schmit KJ, Kollmus H, Nicot N, Kaoma T, Vallar L, Buttini M, Glaab E. A New Synuclein-Transgenic Mouse Model for Early Parkinson's Reveals Molecular Features of Preclinical Disease. Mol Neurobiol 2021; 58:576-602. [PMID: 32997293 PMCID: PMC8219584 DOI: 10.1007/s12035-020-02085-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
Understanding Parkinson's disease (PD), in particular in its earliest phases, is important for diagnosis and treatment. However, human brain samples are collected post-mortem, reflecting mainly end-stage disease. Because brain samples of mouse models can be collected at any stage of the disease process, they are useful in investigating PD progression. Here, we compare ventral midbrain transcriptomics profiles from α-synuclein transgenic mice with a progressive, early PD-like striatal neurodegeneration across different ages using pathway, gene set, and network analysis methods. Our study uncovers statistically significant altered genes across ages and between genotypes with known, suspected, or unknown function in PD pathogenesis and key pathways associated with disease progression. Among those are genotype-dependent alterations associated with synaptic plasticity and neurotransmission, as well as mitochondria-related genes and dysregulation of lipid metabolism. Age-dependent changes were among others observed in neuronal and synaptic activity, calcium homeostasis, and membrane receptor signaling pathways, many of which linked to G-protein coupled receptors. Most importantly, most changes occurred before neurodegeneration was detected in this model, which points to a sequence of gene expression events that may be relevant for disease initiation and progression. It is tempting to speculate that molecular changes similar to those changes observed in our model happen in midbrain dopaminergic neurons before they start to degenerate. In other words, we believe we have uncovered molecular changes that accompany the progression from preclinical to early PD.
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Affiliation(s)
- Diana M. Hendrickx
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Laboratoire National de Santé (LNS), Neuropathology Unit, Dudelange, Luxembourg
| | - Amer Ashrafi
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Present Address: Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Kristopher J. Schmit
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Tony Kaoma
- Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
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25
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Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. Neurobiol Dis 2020; 149:105225. [PMID: 33347974 PMCID: PMC7856076 DOI: 10.1016/j.nbd.2020.105225] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Lewy body diseases (LBD), and the amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) spectrum are defined by the accumulation of specific misfolded protein aggregates. However, the mechanisms by which each proteinopathy leads to neurodegeneration remain elusive. We hypothesized that there is a common "pan-neurodegenerative" gene expression signature driving pathophysiology across these clinically and pathologically diverse proteinopathies. To test this hypothesis, we performed a systematic review of human CNS transcriptomics datasets from AD, LBD, and ALS-FTD patients and age-matched controls in the Gene Expression Omnibus (GEO) and ArrayExpress databases, followed by consistent processing of each dataset, meta-analysis, pathway enrichment, and overlap analyses. After applying pre-specified eligibility criteria and stringent data pre-processing, a total of 2600 samples from 26 AD, 21 LBD, and 13 ALS-FTD datasets were included in the meta-analysis. The pan-neurodegenerative gene signature is characterized by an upregulation of innate immunity, cytoskeleton, and transcription and RNA processing genes, and a downregulation of the mitochondrial electron transport chain. Pathway enrichment analyses also revealed the upregulation of neuroinflammation (including Toll-like receptor, TNF, and NFκB signaling) and phagocytosis, and the downregulation of mitochondrial oxidative phosphorylation, lysosomal acidification, and ubiquitin-proteasome pathways. Our findings suggest that neuroinflammation and a failure in both neuronal energy metabolism and protein degradation systems are consistent features underlying neurodegenerative diseases, despite differences in the extent of neuronal loss and brain regions involved.
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26
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Phung DM, Lee J, Hong S, Kim YE, Yoon J, Kim YJ. Meta-Analysis of Differentially Expressed Genes in the Substantia Nigra in Parkinson's Disease Supports Phenotype-Specific Transcriptome Changes. Front Neurosci 2020; 14:596105. [PMID: 33390883 PMCID: PMC7775392 DOI: 10.3389/fnins.2020.596105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 01/26/2023] Open
Abstract
Background Studies regarding differentially expressed genes (DEGs) in Parkinson’s disease (PD) have focused on common upstream regulators or dysregulated pathways or ontologies; however, the relationships between DEGs and disease-related or cell type-enriched genes have not been systematically studied. Meta-analysis of DEGs (meta-DEGs) are expected to overcome the limitations, such as replication failure and small sample size of previous studies. Purpose Meta-DEGs were performed to investigate dysregulated genes enriched with neurodegenerative disorder causative or risk genes in a phenotype-specific manner. Methods Six microarray datasets from PD patients and controls, for which substantia nigra sample transcriptome data were available, were downloaded from the NINDS data repository. Meta-DEGs were performed using two methods, combining p-values and combing effect size, and common DEGs were used for secondary analyses. Gene sets of cell type-enriched or disease-related genes for PD, Alzheimer’s disease (AD), and hereditary progressive ataxia were constructed by curation of public databases and/or published literatures. Results Our meta-analyses revealed 449 downregulated and 137 upregulated genes. Overrepresentation analyses with cell type-enriched genes were significant in neuron-enriched genes but not in astrocyte- or microglia-enriched genes. Meta-DEGs were significantly enriched in causative genes for hereditary disorders accompanying parkinsonism but not in genes associated with AD or hereditary progressive ataxia. Enrichment of PD-related genes was highly significant in downregulated DEGs but insignificant in upregulated genes. Conclusion Downregulated meta-DEGs were associated with PD-related genes, but not with other neurodegenerative disorder genes. These results highlight disease phenotype-specific changes in dysregulated genes in PD.
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Affiliation(s)
- Duong My Phung
- Department of Biomedical Gerontology, Ilsong Institute of Life and Science, Hallym University, Anyang, South Korea
| | - Jinwoo Lee
- Department of Computer Engineering, Hallym University, Chuncheon, South Korea
| | - SangKyoon Hong
- Hallym Institute of Translational Genomics and Bioinformatics, Anyang, South Korea
| | - Young Eun Kim
- Laboratory of Parkinson's Disease and Neurogenetics, Department of Neurology, Hallym University, Anyang, South Korea
| | - Jeehee Yoon
- Department of Computer Engineering, Hallym University, Chuncheon, South Korea
| | - Yun Joong Kim
- Department of Neurology, Yonsei University College of Medicine, Yongin, South Korea.,Department of Neurology, Yongin Severance Hospital, Yonsei University Health System, Yongin, South Korea
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27
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Lin TK, Lin KJ, Lin KL, Liou CW, Chen SD, Chuang YC, Wang PW, Chuang JH, Wang TJ. When Friendship Turns Sour: Effective Communication Between Mitochondria and Intracellular Organelles in Parkinson's Disease. Front Cell Dev Biol 2020; 8:607392. [PMID: 33330511 PMCID: PMC7733999 DOI: 10.3389/fcell.2020.607392] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease with pathological hallmarks including progressive neuronal loss from the substantia nigra pars compacta and α-synuclein intraneuronal inclusions, known as Lewy bodies. Although the etiology of PD remains elusive, mitochondrial damage has been established to take center stage in the pathogenesis of PD. Mitochondria are critical to cellular energy production, metabolism, homeostasis, and stress responses; the association with PD emphasizes the importance of maintenance of mitochondrial network integrity. To accomplish the pleiotropic functions, mitochondria are dynamic not only within their own network but also in orchestrated coordination with other organelles in the cellular community. Through physical contact sites, signal transduction, and vesicle transport, mitochondria and intracellular organelles achieve the goals of calcium homeostasis, redox homeostasis, protein homeostasis, autophagy, and apoptosis. Herein, we review the finely tuned interactions between mitochondria and surrounding intracellular organelles, with focus on the nucleus, endoplasmic reticulum, Golgi apparatus, peroxisomes, and lysosomes. Participants that may contribute to the pathogenic mechanisms of PD will be highlighted in this review.
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Affiliation(s)
- Tsu-Kung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Jung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Lieh Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shang-Der Chen
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yao-Chung Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Wen Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Metabolism, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jiin-Haur Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Pediatric Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tzu-Jou Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Pediatric, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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28
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Spen modulates lipid droplet content in adult Drosophila glial cells and protects against paraquat toxicity. Sci Rep 2020; 10:20023. [PMID: 33208773 PMCID: PMC7674452 DOI: 10.1038/s41598-020-76891-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
Glial cells are early sensors of neuronal injury and can store lipids in lipid droplets under oxidative stress conditions. Here, we investigated the functions of the RNA-binding protein, SPEN/SHARP, in the context of Parkinson’s disease (PD). Using a data-mining approach, we found that SPEN/SHARP is one of many astrocyte-expressed genes that are significantly differentially expressed in the substantia nigra of PD patients compared with control subjects. Interestingly, the differentially expressed genes are enriched in lipid metabolism-associated genes. In a Drosophila model of PD, we observed that flies carrying a loss-of-function allele of the ortholog split-ends (spen) or with glial cell-specific, but not neuronal-specific, spen knockdown were more sensitive to paraquat intoxication, indicating a protective role for Spen in glial cells. We also found that Spen is a positive regulator of Notch signaling in adult Drosophila glial cells. Moreover, Spen was required to limit abnormal accumulation of lipid droplets in glial cells in a manner independent of its regulation of Notch signaling. Taken together, our results demonstrate that Spen regulates lipid metabolism and storage in glial cells and contributes to glial cell-mediated neuroprotection.
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29
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Kelm-Nelson CA, Gammie S. Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout rats. BMC Genomics 2020; 21:625. [PMID: 32942992 PMCID: PMC7495669 DOI: 10.1186/s12864-020-07037-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background Parkinson’s disease (PD) is a degenerative disease with early-stage pathology hypothesized to manifest in brainstem regions. Vocal deficits, including soft, monotone speech, result in significant clinical and quality of life issues and are present in 90% of PD patients; yet the underlying pathology mediating these significant voice deficits is unknown. The Pink1−/− rat is a valid model of early-onset PD that presents with analogous vocal communication deficits. Previous work shows abnormal α-synuclein protein aggregation in the periaqueductal gray (PAG), a brain region critical and necessary to the modulation of mammalian vocal behavior. In this study, we used high-throughput RNA sequencing to examine gene expression within the PAG of both male and female Pink1−/− rats as compared to age-matched wildtype controls. We used a bioinformatic approach to (1) test the hypothesis that loss of Pink1 in the PAG will influence the differential expression of genes that interact with Pink1, (2) highlight other key genes that relate to this type of Mendelian PD, and (3) catalog molecular targets that may be important for the production of rat vocalizations. Results Knockout of the Pink1 gene resulted in differentially expressed genes for both male and female rats that also mapped to human PD datasets. Pathway analysis highlighted several significant metabolic pathways. Weighted gene co-expression network analysis (WGCNA) was used to identify gene nodes and their interactions in (A) males, (B) females, and (C) combined-sexes datasets. For each analysis, within the module containing the Pink1 gene, Pink1 itself was the central node with the highest number of interactions with other genes including solute carriers, glutamate metabotropic receptors, and genes associated with protein localization. Strong connections between Pink1 and Krt2 and Hfe were found in both males and female datasets. In females a number of modules were significantly correlated with vocalization traits. Conclusions Overall, this work supports the premise that gene expression changes in the PAG may contribute to the vocal deficits observed in this PD rat model. Additionally, this dataset identifies genes that represent new therapeutic targets for PD voice disorders.
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Affiliation(s)
- Cynthia A Kelm-Nelson
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of Wisconsin-Madison, 1300 University Avenue, 483 Medical Sciences Center, Madison, WI, 53706, USA.
| | - Stephen Gammie
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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30
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Vavougios GD. SARS-CoV-2 dysregulation of PTBP1 and YWHAE/Z gene expression: A primer of neurodegeneration. Med Hypotheses 2020; 144:110212. [PMID: 33254518 PMCID: PMC7448818 DOI: 10.1016/j.mehy.2020.110212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2 neurotropism has been increasingly recognized by its imaging and syndromic manifestations in the literature. The purpose of this report is to explore the limited yet salient current evidence that SARS-CoV-2′s host genomic targets PTBP1 and the 14-3-3 protein isoform encoding genes YWHAE and YWHAZ may be hold the key to understanding how neurotropism triggers neurodegeneration and how it may contribute to the onset of neurodegenerative disease. Considering that PTBP1 silencing in particular has recently been shown to reverse clinical parkinsonism and induce neurogenesis, as well as the known interactions of PTBP1 and YWHAE/Z with coronaviruses – most notably 14-3-3 and SARS-CoV, recent studies reinvigorate the infectious etiology hypotheses on major neurodegenerative disease such as AD and iPD. Considering that human coronaviruses with definite neurotropism have been shown to achieve long-term latency within the mammalian CNS as a result of specific accommodating mutations, the corroboration of genomic-level evidence with neuroimaging has vast potential implications for neurodegenerative disease.
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Affiliation(s)
- George D Vavougios
- Department of Neurology, Athens Naval Hospital, P.C. 115 21, Athens, Greece; Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C. 41500 Larissa, Greece; Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 - 4, P.C. 35 131 - Galaneika, Lamia, Greece.
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Hendrickx DM, Glaab E. Comparative transcriptome analysis of Parkinson's disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes. BMC Med Genomics 2020; 13:114. [PMID: 32811487 PMCID: PMC7437934 DOI: 10.1186/s12920-020-00761-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Parkinson's Disease (PD) and Hutchinson-Gilford Progeria Syndrome (HGPS) are two heterogeneous disorders, which both display molecular and clinical alterations associated with the aging process. However, similarities and differences between molecular changes in these two disorders have not yet been investigated systematically at the level of individual biomolecules and shared molecular network alterations. METHODS Here, we perform a comparative meta-analysis and network analysis of human transcriptomics data from case-control studies for both diseases to investigate common susceptibility genes and sub-networks in PD and HGPS. Alzheimer's disease (AD) and primary melanoma (PM) were included as controls to confirm that the identified overlapping susceptibility genes for PD and HGPS are non-generic. RESULTS We find statistically significant, overlapping genes and cellular processes with significant alterations in both diseases. Interestingly, the majority of these shared affected genes display changes with opposite directionality, indicating that shared susceptible cellular processes undergo different mechanistic changes in PD and HGPS. A complementary regulatory network analysis also reveals that the altered genes in PD and HGPS both contain targets controlled by the upstream regulator CDC5L. CONCLUSIONS Overall, our analyses reveal a significant overlap of affected cellular processes and molecular sub-networks in PD and HGPS, including changes in aging-related processes that may reflect key susceptibility factors associated with age-related risk for PD.
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Affiliation(s)
- Diana M. Hendrickx
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, Belvaux, L- 4367 Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, Belvaux, L- 4367 Luxembourg
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Huff K, Suárez-Trujillo A, Kuang S, Plaut K, Casey T. One-to-one relationships between milk miRNA content and protein abundance in neonate duodenum support the potential for milk miRNAs regulating neonate development. Funct Integr Genomics 2020; 20:645-656. [PMID: 32458191 DOI: 10.1007/s10142-020-00743-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/08/2020] [Accepted: 05/13/2020] [Indexed: 10/24/2022]
Abstract
Breast milk plays an essential role for offspring development; however, there lacks evidence of how specific milk components like nucleic acids mechanistically function to regulate neonate development. Previously, we found that maternal high-fat diet (HFD) not only significantly affected mRNA and miRNA content of the secreted milk transcriptome in mice but also affected the duodenal proteome of suckling pups. Here, we hypothesized that nucleic acids differentially expressed in milk of HFD fed dams are related to differentially abundant proteins in offspring duodenum nursed by HFD dams. We tested this hypothesis by analyzing one-to-one relationships in RNA-seq data of milk transcriptomes from control (10% kcal fat) and HFD (60% kcal fat) fed mice and liquid chromatography-tandem mass spectrometry (LC-MS/MS) duodenal proteome data from pups exposed to milk. Ten percent of differentially abundant duodenal proteins between controls and HFD-exposed pups had predicted upregulation or downregulation based on differential milk RNA content. Of these, 76% were targets of upregulated miRNA, and linear regression analysis indicated relationships (p < 0.05) between multiple milk miRNA counts and duodenal protein abundance. Duodenal proteins that were potential targets of milk miRNA enriched Gene Ontology (GO) terms and KEGG pathways related to cytoskeletal structure and neural development, suggesting potential regulation of pup enteric nervous system. One-to-one relationships between milk miRNA content and protein abundance in neonate duodenum support the potential for milk miRNAs regulating neonate development. Identification of milk miRNAs that changed in response to maternal diet will enable design of mechanistic studies that test effects on neonate.
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Affiliation(s)
- Katelyn Huff
- Biological & Biomedical Sciences Program, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Aridany Suárez-Trujillo
- Department of Animal Sciences, Purdue University, 175 South University Street, West Lafayette, IN, 47907-2063, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, 175 South University Street, West Lafayette, IN, 47907-2063, USA
| | - Karen Plaut
- Department of Animal Sciences, Purdue University, 175 South University Street, West Lafayette, IN, 47907-2063, USA
| | - Theresa Casey
- Department of Animal Sciences, Purdue University, 175 South University Street, West Lafayette, IN, 47907-2063, USA.
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Kelly J, Moyeed R, Carroll C, Luo S, Li X. Genetic networks in Parkinson's and Alzheimer's disease. Aging (Albany NY) 2020; 12:5221-5243. [PMID: 32205467 PMCID: PMC7138567 DOI: 10.18632/aging.102943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Parkinson’s disease (PD) and Alzheimer’s disease (AD) are the most common neurodegenerative diseases and there is increasing evidence that they share common physiological and pathological links. Here we have conducted the largest network analysis of PD and AD based on their gene expressions in blood to date. We identified modules that were not preserved between disease and healthy control (HC) networks, and important hub genes and transcription factors (TFs) in these modules. We highlighted that the PD module not preserved in HCs was associated with insulin resistance, and HDAC6 was identified as a hub gene in this module which may have the role of influencing tau phosphorylation and autophagic flux in neurodegenerative disease. The AD module associated with regulation of lipolysis in adipocytes and neuroactive ligand-receptor interaction was not preserved in healthy and mild cognitive impairment networks and the key hubs TRPC5 and BRAP identified as potential targets for therapeutic treatments of AD. Our study demonstrated that PD and AD share common disrupted genetics and identified novel pathways, hub genes and TFs that may be new areas for mechanistic study and important targets in both diseases.
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Affiliation(s)
- Jack Kelly
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Rana Moyeed
- Faculty of Science and Engineering, Plymouth University, Plymouth PL6 8BU, UK
| | - Camille Carroll
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Shouqing Luo
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Xinzhong Li
- School of Science, Engineering and Design, Teesside University, Middlesbrough TS1 3BX, UK
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Keo A, Mahfouz A, Ingrassia AMT, Meneboo JP, Villenet C, Mutez E, Comptdaer T, Lelieveldt BPF, Figeac M, Chartier-Harlin MC, van de Berg WDJ, van Hilten JJ, Reinders MJT. Transcriptomic signatures of brain regional vulnerability to Parkinson's disease. Commun Biol 2020; 3:101. [PMID: 32139796 PMCID: PMC7058608 DOI: 10.1038/s42003-020-0804-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/28/2020] [Indexed: 01/11/2023] Open
Abstract
The molecular mechanisms underlying caudal-to-rostral progression of Lewy body pathology in Parkinson's disease remain poorly understood. Here, we identified transcriptomic signatures across brain regions involved in Braak Lewy body stages in non-neurological adults from the Allen Human Brain Atlas. Among the genes that are indicative of regional vulnerability, we found known genetic risk factors for Parkinson's disease: SCARB2, ELOVL7, SH3GL2, SNCA, BAP1, and ZNF184. Results were confirmed in two datasets of non-neurological subjects, while in two datasets of Parkinson's disease patients we found altered expression patterns. Co-expression analysis across vulnerable regions identified a module enriched for genes associated with dopamine synthesis and microglia, and another module related to the immune system, blood-oxygen transport, and endothelial cells. Both were highly expressed in regions involved in the preclinical stages of the disease. Finally, alterations in genes underlying these region-specific functions may contribute to the selective regional vulnerability in Parkinson's disease brains.
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Affiliation(s)
- Arlin Keo
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ahmed Mahfouz
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Angela M T Ingrassia
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Jean-Pascal Meneboo
- University Lille, Plate-forme de génomique fonctionnelle et Structurale, F-59000, Lille, France
- University lille. Bilille, F-59000, Lille, France
| | - Celine Villenet
- University Lille, Plate-forme de génomique fonctionnelle et Structurale, F-59000, Lille, France
| | - Eugénie Mutez
- University Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
- Inserm, UMR-S 1172, Early Stages of Parkinson's Disease, F-59000, Lille, France
- University Lille, Service de Neurologie et Pathologie du mouvement, centre expert Parkinson, F-59000, Lille, France
| | - Thomas Comptdaer
- University Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France
- Inserm, UMR-S 1172, Early Stages of Parkinson's Disease, F-59000, Lille, France
| | - Boudewijn P F Lelieveldt
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martin Figeac
- University Lille, Plate-forme de génomique fonctionnelle et Structurale, F-59000, Lille, France
- University lille. Bilille, F-59000, Lille, France
| | - Marie-Christine Chartier-Harlin
- University Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, F-59000, Lille, France.
- Inserm, UMR-S 1172, Early Stages of Parkinson's Disease, F-59000, Lille, France.
| | - Wilma D J van de Berg
- Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands.
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Marcel J T Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
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Toro-Domínguez D, Villatoro-García JA, Martorell-Marugán J, Román-Montoya Y, Alarcón-Riquelme ME, Carmona-Sáez P. A survey of gene expression meta-analysis: methods and applications. Brief Bioinform 2020; 22:1694-1705. [PMID: 32095826 DOI: 10.1093/bib/bbaa019] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing use of high-throughput gene expression quantification technologies over the last two decades and the fact that most of the published studies are stored in public databases has triggered an explosion of studies available through public repositories. All this information offers an invaluable resource for reuse to generate new knowledge and scientific findings. In this context, great interest has been focused on meta-analysis methods to integrate and jointly analyze different gene expression datasets. In this work, we describe the main steps in the gene expression meta-analysis, from data preparation to the state-of-the art statistical methods. We also analyze the main types of applications and problems that can be approached in gene expression meta-analysis studies and provide a comparative overview of the available software and bioinformatics tools. Moreover, a practical guide for choosing the most appropriate method in each case is also provided.
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Affiliation(s)
- Daniel Toro-Domínguez
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Juan Antonio Villatoro-García
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Jordi Martorell-Marugán
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
| | - Yolanda Román-Montoya
- Department of Statistics and Operations Research, University of Granada, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain.,Unit of Inflammatory Diseases, Department of Environmental Medicine, Karolinska Institute, 171 67, Solna, Sweden
| | - Pedro Carmona-Sáez
- GENYO (Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016 Granada, Spain
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Meta-Analysis of Gene Expression Changes in the Blood of Patients with Mild Cognitive Impairment and Alzheimer's Disease Dementia. Int J Mol Sci 2019; 20:ijms20215403. [PMID: 31671574 PMCID: PMC6862214 DOI: 10.3390/ijms20215403] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Dementia is a major public health concern affecting approximately 47 million people worldwide. Mild cognitive impairment (MCI) is one form of dementia that affects an individual’s memory with or without affecting their daily life. Alzheimer’s disease dementia (ADD) is a more severe form of dementia that usually affects elderly individuals. It remains unclear whether MCI is a distinct disorder from or an early stage of ADD. Methods: Gene expression data from blood were analyzed to identify potential biomarkers that may be useful for distinguishing between these two forms of dementia. Results: A meta-analysis revealed 91 genes dysregulated in individuals with MCI and 387 genes dysregulated in ADD. Pathway analysis identified seven pathways shared between MCI and ADD and nine ADD-specific pathways. Fifteen transcription factors were associated with MCI and ADD, whereas seven transcription factors were specific for ADD. Mir-335-5p was specific for ADD, suggesting that it may be useful as a biomarker. Diseases that are associated with MCI and ADD included developmental delays, cognition impairment, and movement disorders. Conclusion: These results provide a better molecular understanding of peripheral changes that occur in MCI and ADD patients and may be useful in the identification of diagnostic and prognostic biomarkers.
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Ghorbani S, Szigetvari PD, Haavik J, Kleppe R. Serine 19 phosphorylation and 14‐3‐3 binding regulate phosphorylation and dephosphorylation of tyrosine hydroxylase on serine 31 and serine 40. J Neurochem 2019; 152:29-47. [DOI: 10.1111/jnc.14872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Sadaf Ghorbani
- Department of Biomedicine K.G. Jebsen Centre for Research on Neuropsychiatric Disorders University of Bergen Bergen Norway
| | - Peter D. Szigetvari
- Department of Biomedicine K.G. Jebsen Centre for Research on Neuropsychiatric Disorders University of Bergen Bergen Norway
| | - Jan Haavik
- Department of Biomedicine K.G. Jebsen Centre for Research on Neuropsychiatric Disorders University of Bergen Bergen Norway
- Division of Psychiatry Haukeland University Hospital Bergen Norway
| | - Rune Kleppe
- Division of Psychiatry Haukeland University Hospital Bergen Norway
- Computational Biology Unit Department of Informatics University of Bergen Bergen Norway
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