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Klokkaris A, Migdalska-Richards A. An Overview of Epigenetic Changes in the Parkinson's Disease Brain. Int J Mol Sci 2024; 25:6168. [PMID: 38892355 PMCID: PMC11172855 DOI: 10.3390/ijms25116168] [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: 05/05/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disorder, predominantly of the motor system. Although some genetic components and cellular mechanisms of Parkinson's have been identified, much is still unknown. In recent years, emerging evidence has indicated that non-DNA-sequence variation (in particular epigenetic mechanisms) is likely to play a crucial role in the development and progression of the disease. Here, we present an up-to-date overview of epigenetic processes including DNA methylation, DNA hydroxymethylation, histone modifications and non-coding RNAs implicated in the brain of those with Parkinson's disease. We will also discuss the limitations of current epigenetic research in Parkinson's disease, the advantages of simultaneously studying genetics and epigenetics, and putative novel epigenetic therapies.
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Affiliation(s)
| | - Anna Migdalska-Richards
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK;
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2
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Musgrove MRB, Mikhaylova M, Bredy TW. Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: Non-coding RNAs spanning learning, memory and adaptive immunity. J Neurochem 2024; 168:961-976. [PMID: 38339812 DOI: 10.1111/jnc.16071] [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: 10/30/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs (ncRNAs) are highly plastic RNA molecules that can sequester cellular proteins and other RNAs, serve as transporters of cellular cargo and provide spatiotemporal feedback to the genome. Mounting evidence indicates that ncRNAs are central to biology, and are critical for neuronal development, metabolism and intra- and intercellular communication in the brain. Their plasticity arises from state-dependent dynamic structure states that can be influenced by cell type and subcellular environment, which can subsequently enable the same ncRNA with discrete functions in different contexts. Here, we highlight different classes of brain-enriched ncRNAs, including microRNA, long non-coding RNA and other enigmatic ncRNAs, that are functionally important for both learning and memory and adaptive immunity, and describe how they may promote cross-talk between these two evolutionarily ancient biological systems.
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Affiliation(s)
- Mason R B Musgrove
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Marina Mikhaylova
- AG Optobiologie, Institute für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Timothy W Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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3
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Fröhlich A, Pfaff AL, Middlehurst B, Hughes LS, Bubb VJ, Quinn JP, Koks S. Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson's disease progression. Sci Rep 2024; 14:10932. [PMID: 38740892 DOI: 10.1038/s41598-024-61753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are transposable elements which represent a source of genetic variation. We previously demonstrated that the presence/absence of a human-specific SVA, termed SVA_67, correlated with the progression of Parkinson's disease (PD). In the present study, we demonstrate that SVA_67 acts as expression quantitative trait loci, thereby exhibiting a strong regulatory effect across the genome using whole genome and transcriptomic data from the Parkinson's progression markers initiative cohort. We further show that SVA_67 is polymorphic for its variable number tandem repeat domain which correlates with both regulatory properties in a luciferase reporter gene assay in vitro and differential expression of multiple genes in vivo. Additionally, this variation's utility as a biomarker is reflected in a correlation with a number of PD progression markers. These experiments highlight the plethora of transcriptomic and phenotypic changes associated with SVA_67 polymorphism which should be considered when investigating the missing heritability of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren S Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
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4
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Anilkumar AK, Vij P, Lopez S, Leslie SM, Doxtater K, Khan MM, Yallapu MM, Chauhan SC, Maestre GE, Tripathi MK. Long Non-Coding RNAs: New Insights in Neurodegenerative Diseases. Int J Mol Sci 2024; 25:2268. [PMID: 38396946 PMCID: PMC10889599 DOI: 10.3390/ijms25042268] [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: 01/03/2024] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are gradually becoming a burden to society. The adverse effects and mortality/morbidity rates associated with these NDDs are a cause of many healthcare concerns. The pathologic alterations of NDDs are related to mitochondrial dysfunction, oxidative stress, and inflammation, which further stimulate the progression of NDDs. Recently, long non-coding RNAs (lncRNAs) have attracted ample attention as critical mediators in the pathology of NDDs. However, there is a significant gap in understanding the biological function, molecular mechanisms, and potential importance of lncRNAs in NDDs. This review documents the current research on lncRNAs and their implications in NDDs. We further summarize the potential implication of lncRNAs to serve as novel therapeutic targets and biomarkers for patients with NDDs.
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Affiliation(s)
- Adithya K. Anilkumar
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Puneet Vij
- Department of Pharmaceutical Sciences, St. John’s University, Queens, NY 11439, USA
| | - Samantha Lopez
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Sophia M. Leslie
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Kyle Doxtater
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Murali M. Yallapu
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Gladys E. Maestre
- Department of Neurosciences, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78550, USA
- South Texas Alzheimer’s Disease Research Center, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX 78550, USA
| | - Manish K. Tripathi
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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Sarıekiz FG, Tomatır AG, Tokgün PE, Bir LS. Evaluation of Long Non-coding RNA Expression Profiles in Peripheral Blood Mononuclear Cells of Patients with Parkinson's Disease. Mol Neurobiol 2023; 60:6201-6211. [PMID: 37436601 DOI: 10.1007/s12035-023-03470-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
As in many biological processes, the long non-coding RNAs (lncRNA) are currently known to have important roles in Parkinson's disease (PD). The aim of the study is to evaluate differentiated expressions of lncRNAs and their target mRNAs in the peripheral blood cells of individuals with Parkinson's disease. The peripheral blood samples were taken from 10 Parkinson's diagnosed people aging 50 years and more and from 10 healthy people as for the control group. Total RNA was isolated from peripheral blood mononuclear cells (PBMC), and a total of 5 samples were selected and evaluated by microarray analysis. lncRNAs with high fold change (fc < 1.5/fc > 1.5) were determined as a result of the analysis. Following this, the expression changes of some lncRNAs and their target mRNAs were examined by quantitative simultaneous polymerase chain reaction (qRT-PCR) in all individuals in the patient and control groups. Also, in order to determine the molecular level basic activities of lncRNAs determined by microarray analysis and which biological process and biochemical pathway they were in, Gene Ontology (GO) analysis ( http://geneontology.org/ ) database was used. Thirteen upregulated and 31 downregulated lncRNAs whose expression changes were determined by microarray analysis and confirmed by qRT-PCR method were found in Parkinson's patients. As they were evaluated by GO analysis, lncRNAs were expressed differently in patient and control groups and they are found to be related with the processes such as macromolecule metabolic processes, immune system, gene expression, cell activation, ATPase activity, DNA packaging complex, signal receptor activity, immune receptor activity, and protein binding were found to be significant.
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Affiliation(s)
- Fatma Gizem Sarıekiz
- Department of Medical Biology, Faculty of Medicine, Pamukkale University, Kınıklı/Denizli, Turkey.
| | - Ayşe Gaye Tomatır
- Department of Medical Biology, Faculty of Medicine, Pamukkale University, Kınıklı/Denizli, Turkey
| | - Pervin Elvan Tokgün
- Department of Medical Genetics, Faculty of Medicine, Pamukkale University, Denizli, Turkey
| | - Levent Sinan Bir
- Department of Neurology, Faculty of Medicine, Pamukkale University, Denizli, Turkey
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Fu F, Du K, Li YS, Li LS, Xin Y, Wang D, Lei TY, Deng Q, Yu QX, Liao C. Identification of Alternative Splicing and LncRNA Genes in Brain Tissues of Fetal Mice at Different Developmental Stages. Comb Chem High Throughput Screen 2023; 26:58-82. [PMID: 35400338 DOI: 10.2174/1386207325666220408091206] [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: 07/09/2021] [Revised: 01/12/2022] [Accepted: 01/27/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Brain development is an extremely complex and precisely regulated process, with about one-third of genes expressed and precisely regulated during brain development. OBJECTIVE This study aims to explore the molecular mechanisms involved in brain development. METHODS We first established the expression profile of long non-coding RNAs (lncRNAs) and mRNAs in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d through high-throughput sequencing. Second, the associated functions, pathways, and networks of the co-differentially expressed lncRNAs and mRNAs were identified via Gene Ontology (GO), pathway analysis, and PPI network. After bioinformatic analysis and screening, 8 differentially expressed lncRNAs and mRNAs with the same genetic origin were verified by RT-qPCR analysis in brain tissues of fetal mice at different developmental stages. RESULTS The data revealed that there were 972 co-differentially expressed lncRNAs and 992 codifferentially expressed mRNAs in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d. And we discovered 125 differentially expressed lncRNAs and mRNAs, which have the same genetic origin, in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d through sequencing results and bioinformatics analysis. Besides, we proved that 8 lncRNAs, which have had the same genetic origin as differentially expressed mRNAs, were prominently downregulated, while their maternal genes were upregulated during brain development in fetal mice. CONCLUSION Our results preliminarily illustrated the differentially expressed lncRNAs and mRNAs, both of which were derived from the same parent genes, during brain development in fetal mice, which suggests that alternative splicing of lncRNA exists during brain development. Besides, our study provides a perspective on critical genes for brain development, which might be the underlying therapeutic targets for developmental brain diseases in children.
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Affiliation(s)
- Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Kun Du
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Ying-Si Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Lu-Shan Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yang Xin
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Dan Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Ting-Ying Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Qiong Deng
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Qiu-Xia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
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Huang T, Zhao JY, Pan RR, Jiang T, Fu XX, Huang Q, Wang XX, Gong PY, Tian YY, Zhang YD. Dysregulation of Circulatory Levels of lncRNAs in Parkinson's Disease. Mol Neurobiol 2023; 60:317-328. [PMID: 36264433 DOI: 10.1007/s12035-022-03086-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 10/05/2022] [Indexed: 12/30/2022]
Abstract
Emerging evidence suggested that long non-coding RNAs (lncRNAs) were involved in Parkinson's disease (PD) pathogenesis. Herein, we used gene expression profiles from GEO database to construct a PD-specific ceRNA network. Functional enrichment analysis suggested that ceRNA network might participate in the development of PD. PPI networks were constructed, and the ceRNA subnetwork based on five hub genes was set up. In a cohort of 32 PD patients and 31 healthy controls, the expression of 10 DElncRNAs (TTC3-AS1, LINC01259, ZMYND10-AS1, CHRM3-AS1, MYO16-AS1, AGBL5-IT1, HOTAIRM1, RABGAP1L-IT1, HLCS-IT1, and LINC00393) were further verified. Consistent with the microarray data, LINC01259 expression was significantly lower in PD patients compared with controls (P = 0.008). Intriguingly, such a difference was only observed among male patients and male controls when dividing study participants based on their gender (P = 0.016). However, the expression of other lncRNAs did not differ significantly between the two groups. Receiver operating characteristic (ROC) curve analysis revealed that the diagnostic power of LINC01259 was 0.694 for PD and 0.677 for early-stage PD. GSEA enrichment analysis revealed that LINC01259 was mainly enriched in biological processes associated with immune function and inflammatory response. Moreover, LINC01259 expression was not correlated with age of patients, disease duration, disease stage, MDS-UPDRS score, MDS-UPDRS III score, MMSE score, and MOCA score. The current study provides further evidence for the dysregulation of lncRNAs in circulating leukocytes of PD patients, revealing that LINC01259 has clinical potential as a novel immune and inflammatory biomarker for PD and early-stage PD diagnosis.
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Affiliation(s)
- Ting Huang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - Jin-Ying Zhao
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - Rong-Rong Pan
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - Teng Jiang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - Xin-Xin Fu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 210000, China
| | - Qing Huang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - Xi-Xi Wang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - Peng-Yu Gong
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China
| | - You-Yong Tian
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China.
| | - Ying-Dong Zhang
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210000, China.
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Canseco-Rodriguez A, Masola V, Aliperti V, Meseguer-Beltran M, Donizetti A, Sanchez-Perez AM. Long Non-Coding RNAs, Extracellular Vesicles and Inflammation in Alzheimer's Disease. Int J Mol Sci 2022; 23:13171. [PMID: 36361952 PMCID: PMC9654199 DOI: 10.3390/ijms232113171] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 08/10/2023] Open
Abstract
Alzheimer's Disease (AD) has currently no effective treatment; however, preventive measures have the potential to reduce AD risk. Thus, accurate and early prediction of risk is an important strategy to alleviate the AD burden. Neuroinflammation is a major factor prompting the onset of the disease. Inflammation exerts its toxic effect via multiple mechanisms. Amongst others, it is affecting gene expression via modulation of non-coding RNAs (ncRNAs), such as miRNAs. Recent evidence supports that inflammation can also affect long non-coding RNA (lncRNA) expression. While the association between miRNAs and inflammation in AD has been studied, the role of lncRNAs in neurodegenerative diseases has been less explored. In this review, we focus on lncRNAs and inflammation in the context of AD. Furthermore, since plasma-isolated extracellular vesicles (EVs) are increasingly recognized as an effective monitoring strategy for brain pathologies, we have focused on the studies reporting dysregulated lncRNAs in EVs isolated from AD patients and controls. The revised literature shows a positive association between pro-inflammatory lncRNAs and AD. However, the reports evaluating lncRNA alterations in EVs isolated from the plasma of patients and controls, although still limited, confirm the value of specific lncRNAs associated with AD as reliable biomarkers. This is an emerging field that will open new avenues to improve risk prediction and patient stratification, and may lead to the discovery of potential novel therapeutic targets for AD.
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Affiliation(s)
- Ania Canseco-Rodriguez
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
| | - Valeria Masola
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Maria Meseguer-Beltran
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Ana María Sanchez-Perez
- Neurobiotecnology Group, Faculty of Health Science, Institute of Advanced Materials (INAM), University of Jaume I, 12006 Castellon, Spain
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Na C, Wen-Wen C, Li W, Ao-Jia Z, Ting W. Significant Role of Long Non-coding RNAs in Parkinson's Disease. Curr Pharm Des 2022; 28:3085-3094. [PMID: 36154598 DOI: 10.2174/1381612828666220922110551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/27/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disease in the world, with clinical manifestations of resting tremor, akinesia (or bradykinesia), rigidity, and postural instability. However, the molecular pathogenesis of PD is still unclear, and its effective treatments are limited. Substantial evidence demonstrates that long non-coding RNAs (lncRNAs) have important functions in various human diseases, such as cancer, cardiovascular disease, and neurodegenerative diseases. Therefore, the main purpose of this study is to review the role of lncRNAs in the pathogenesis of PD. METHODS The role of lncRNAs in the pathogenesis of PD is summarized by reviewing Pubmed. RESULTS Thirty different lncRNAs are aberrantly expressed in PD and promote or inhibit PD by mediating ubiquitin-proteasome system, autophagy-lysosomal pathway, dopamine (DA) neuronal apoptosis, mitochondrial function, oxidative stress, and neuroinflammation. CONCLUSION In this direction, lncRNA may contribute to the treatment of PD as a diagnostic and therapeutic target for PD.
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Affiliation(s)
- Chen Na
- Department of Pharmacy, Institute of Advanced Pharmaceutical Technology, College of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Chen Wen-Wen
- Department of Pharmacy, Institute of Advanced Pharmaceutical Technology, College of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Wang Li
- Department of Pharmacy, Institute of Advanced Pharmaceutical Technology, College of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Zhou Ao-Jia
- Department of Pharmacy, Institute of Advanced Pharmaceutical Technology, College of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Wang Ting
- Department of Pharmacy, Institute of Advanced Pharmaceutical Technology, College of Medicine, Wuhan University of Science and Technology, Wuhan 430065, China.,Academy of Nutrition and Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan 430065, China
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10
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Abrishamdar M, Jalali MS, Rashno M. MALAT1 lncRNA and Parkinson's Disease: The role in the Pathophysiology and Significance for Diagnostic and Therapeutic Approaches. Mol Neurobiol 2022; 59:5253-5262. [PMID: 35665903 DOI: 10.1007/s12035-022-02899-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/24/2022] [Indexed: 12/25/2022]
Abstract
Parkinson's disease (PD) is the second most common age-related neurodegenerative disorder. PD is characterized by progressive loss of dopamine-producing neurons in the substantia nigra (SN) region of brain tissue followed by the α-synuclein-based Lewy bodies' formation. These conditions are manifested by various motor and non-motor symptoms such as resting tremor, limb rigidity, bradykinesia and posture instability, cognitive impairment, sleep disorders, and emotional and memory dysfunctions. Long non-coding RNAs (lncRNAs) are closely related to protein-coding genes and are involved in various biological processes. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) lncRNA is involved in different pathways, including alternative splicing, transcriptional regulation, and post-transcriptional regulation, and also interacts with RNAs as a miRNA sponge. MALAT1 is highly expressed in brain tissues and several lines of evidence suggested it is probably involved in synapse generation and other neurophysiological pathways. This narrative review discussed all aspects of MALAT1-associated mechanisms involved in the PD pathogenesis, i.e., perturbed α-synuclein homeostasis, apoptosis and autophagy, and neuro-inflammation. Lastly, the possible applications of MALAT1 as a diagnostic biomarker and its importance to developing therapeutic strategies were highlighted. The literature search was conducted using neurodegeneration, neurodegenerative disorders, Parkinson's disease, lncRNA, and MALAT1 as search items in Google Scholar, Web of Knowledge, PubMed, and Scopus up to December 2021.
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Affiliation(s)
| | - M S Jalali
- Persian Gulf Physiology Research Center, Department of Physiology, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - M Rashno
- Department of Immunulogy, Cellular and Molecular Research Center, Medicine Faculty, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Wu L, Xu Q, Zhou M, Chen Y, Jiang C, Jiang Y, Lin Y, He Q, Zhao L, Dong Y, Liu J, Chen W. Plasma miR-153 and miR-223 Levels as Potential Biomarkers in Parkinson’s Disease. Front Neurosci 2022; 16:865139. [PMID: 35655754 PMCID: PMC9152100 DOI: 10.3389/fnins.2022.865139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/23/2022] [Indexed: 12/15/2022] Open
Abstract
Background Small molecule RNAs (miRNAs) could induce downregulation of α-synuclein (SNCA) expression by binding the 3’ untranslated region of SNCA, thus playing an important role in the pathogenesis of Parkinson’s disease (PD). Recent studies suggest that SNCA-related miRNAs in saliva are promising PD biomarkers. Research on those miRNAs in plasma is rare in patients with PD. Objective To detect the plasma expression levels of three SNCA related miRNAs (miR-7, miR-153, and miR-223) in PD, and to explore their diagnostic value and associations with clinical phenotype. Methods MiR-7, miR-153, and miR-223 levels were detected in the plasma of 75 PD patients and 73 normal controls (NCs) via real-time quantitative polymerase chain reaction. The receiver operating characteristic (ROC) curves were delineated to evaluate their diagnostic value in PD. In addition, their associations with demographic, key motor, and non-motor symptoms were explored by serial scales. Results The expression levels of plasma miR-153 and miR-223 were significantly decreased in patients with PD relative to NCs. The area under the ROC curve separating PD from NCs was 63.1% for miR-153 and 86.2% for miR-223, respectively. The plasma miR-153 level in de novo PD was lower than that in treated patients (p = 0.006), its level increased gradually with disease duration (r = 0.358, p = 0.002) and Unified Parkinson’s Disease Rating Scale Part III score (r = 0.264, p = 0.022). Plasma miR-223 level was decreased in patients with clinical possible rapid eye movement sleep behavior disorder (cpRBD) compared with those without cpRBD (p < 0.001), and its level was negatively associated with RBDSQ score (r = -0.334, p = 0.003). Multiple linear regression analysis revealed that disease duration (p = 0.049) was the independently associated factor of miR-153 level; whereas, RBDSQ (p = 0.009) was related to miR-223 level in PD. Conclusion Plasma miR-153 and miR-223 levels could be potential biomarkers of PD.
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Pantaleo E, Monaco A, Amoroso N, Lombardi A, Bellantuono L, Urso D, Lo Giudice C, Picardi E, Tafuri B, Nigro S, Pesole G, Tangaro S, Logroscino G, Bellotti R. A Machine Learning Approach to Parkinson’s Disease Blood Transcriptomics. Genes (Basel) 2022; 13:genes13050727. [PMID: 35627112 PMCID: PMC9141063 DOI: 10.3390/genes13050727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/23/2022] Open
Abstract
The increased incidence and the significant health burden associated with Parkinson’s disease (PD) have stimulated substantial research efforts towards the identification of effective treatments and diagnostic procedures. Despite technological advancements, a cure is still not available and PD is often diagnosed a long time after onset when irreversible damage has already occurred. Blood transcriptomics represents a potentially disruptive technology for the early diagnosis of PD. We used transcriptome data from the PPMI study, a large cohort study with early PD subjects and age matched controls (HC), to perform the classification of PD vs. HC in around 550 samples. Using a nested feature selection procedure based on Random Forests and XGBoost we reached an AUC of 72% and found 493 candidate genes. We further discussed the importance of the selected genes through a functional analysis based on GOs and KEGG pathways.
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Affiliation(s)
- Ester Pantaleo
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Dipartimento Interateneo di Fisica M. Merlin, Università degli Studi di Bari Aldo Moro, Via G. Amendola 173, 70125 Bari, Italy
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy
| | - Angela Lombardi
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento Interateneo di Fisica M. Merlin, Università degli Studi di Bari Aldo Moro, Via G. Amendola 173, 70125 Bari, Italy
- Correspondence:
| | - Loredana Bellantuono
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Daniele Urso
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, De Crespigny Park, London SE5 8AF, UK
| | - Claudio Lo Giudice
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy; (C.L.G.); (E.P.); (G.P.)
| | - Ernesto Picardi
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy; (C.L.G.); (E.P.); (G.P.)
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Benedetta Tafuri
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
| | - Salvatore Nigro
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
- Istituto di Nanotecnologia (NANOTEC), Consiglio Nazionale delle Ricerche, Via Monteroni, 73100 Lecce, Italy
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy; (C.L.G.); (E.P.); (G.P.)
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Sabina Tangaro
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via A. Orabona 4, 70125 Bari, Italy
| | - Giancarlo Logroscino
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Centro per le Malattie Neurodegenerative e l’Invecchiamento Cerebrale, Dipartimento di Ricerca Clinica in Neurologia, Università degli Studi di Bari Aldo Moro, Pia Fondazione Cardinale G. Panico, 73039 Tricase, Italy; (D.U.); (B.T.); (S.N.)
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Via A. Orabona 4, 70125 Bari, Italy; (E.P.); (A.M.); (N.A.); (L.B.); (S.T.); (R.B.)
- Dipartimento Interateneo di Fisica M. Merlin, Università degli Studi di Bari Aldo Moro, Via G. Amendola 173, 70125 Bari, Italy
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13
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Dana S, Ghaedi K, Peymani M, Esfahani MHN. MiR-141-3p Expression Profiling in MPP Treated Differentiated SH-SY5Y Cells: A Model of Parkinson’s Disease. NEUROCHEM J+ 2022. [DOI: 10.1134/s1819712422010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Zhang P, Rasheed M, Liang J, Wang C, Feng L, Chen Z. Emerging Potential of Exosomal Non-coding RNA in Parkinson’s Disease: A Review. Front Aging Neurosci 2022; 14:819836. [PMID: 35360206 PMCID: PMC8960858 DOI: 10.3389/fnagi.2022.819836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Exosomes are extracellular vesicles that are released by cells and circulate freely in body fluids. Under physiological and pathological conditions, they serve as cargo for various biological substances such as nucleotides (DNA, RNA, ncRNA), lipids, and proteins. Recently, exosomes have been revealed to have an important role in the pathophysiology of several neurodegenerative illnesses, including Parkinson’s disease (PD). When secreted from damaged neurons, these exosomes are enriched in non-coding RNAs (e.g., miRNAs, lncRNAs, and circRNAs) and display wide distribution characteristics in the brain and periphery, bridging the gap between normal neuronal function and disease pathology. However, the current status of ncRNAs carried in exosomes regulating neuroprotection and PD pathogenesis lacks a systematic summary. Therefore, this review discussed the significance of ncRNAs exosomes in maintaining the normal neuron function and their pathogenic role in PD progression. Additionally, we have emphasized the importance of ncRNAs exosomes as potential non-invasive diagnostic and screening agents for the early detection of PD. Moreover, bioengineered exosomes are proposed to be used as drug carriers for targeted delivery of RNA interference molecules across the blood-brain barrier without immune system interference. Overall, this review highlighted the diverse characteristics of ncRNA exosomes, which may aid researchers in characterizing future exosome-based biomarkers for early PD diagnosis and tailored PD medicines.
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Affiliation(s)
- Peng Zhang
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China
| | - Madiha Rasheed
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Junhan Liang
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Chaolei Wang
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Lin Feng
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China
- *Correspondence: Lin Feng,
| | - Zixuan Chen
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
- Zixuan Chen,
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15
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Policarpo R, d’Ydewalle C. Missing lnc(RNAs) in Alzheimer's Disease? Genes (Basel) 2021; 13:39. [PMID: 35052379 PMCID: PMC8774680 DOI: 10.3390/genes13010039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
With the ongoing demographic shift towards increasingly elderly populations, it is estimated that approximately 150 million people will live with Alzheimer's disease (AD) by 2050. By then, AD will be one of the most burdensome diseases of this and potentially next centuries. Although its exact etiology remains elusive, both environmental and genetic factors play crucial roles in the mechanisms underlying AD neuropathology. Genome-wide association studies (GWAS) identified genetic variants associated with AD susceptibility in more than 40 different genomic loci. Most of these disease-associated variants reside in non-coding regions of the genome. In recent years, it has become clear that functionally active transcripts arise from these non-coding loci. One type of non-coding transcript, referred to as long non-coding RNAs (lncRNAs), gained significant attention due to their multiple roles in neurodevelopment, brain homeostasis, aging, and their dysregulation or dysfunction in neurological diseases including in AD. Here, we will summarize the current knowledge regarding genetic variations, expression profiles, as well as potential functions, diagnostic or therapeutic roles of lncRNAs in AD. We postulate that lncRNAs may represent the missing link in AD pathology and that unraveling their role may open avenues to better AD treatments.
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Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium;
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, 3000 Leuven, Belgium
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., 2340 Beerse, Belgium
| | - Constantin d’Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., 2340 Beerse, Belgium
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16
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Manna I, Quattrone A, De Benedittis S, Iaccino E, Quattrone A. Roles of Non-Coding RNAs as Novel Diagnostic Biomarkers in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2021; 11:1475-1489. [PMID: 34334422 PMCID: PMC8609715 DOI: 10.3233/jpd-212726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 02/06/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder, affecting 5%of the elderly population. Currently, the diagnosis of PD is mainly based on clinical features and no definitive diagnostic biomarkers have been identified. The discovery of biomarkers at the earliest stages of PD is of extreme interest. This review focuses on the current findings in the field of circulating non-coding RNAs in PD. We briefly describe the more established circulating biomarkers in PD and provide a more thorough review of non-coding RNAs, in particular microRNAs, long non-coding RNAs and circular RNAs, differentially expressed in PD, highlighting their potential for being considered as biomarkers for diagnosis. Together, these studies hold promise for the use of peripheral biomarkers for the diagnosis of PD.
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Affiliation(s)
- Ida Manna
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Section of Germaneto, Catanzaro, Italy
| | - Andrea Quattrone
- Department of Medical and Surgical Sciences, Institute of Neurology, University “Magna Graecia, ” Germaneto, Catanzaro, Italy
| | - Selene De Benedittis
- Department of Medical and Surgical Sciences, University “Magna Graecia, ” Germaneto, Catanzaro, Italy
| | - Enrico Iaccino
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Aldo Quattrone
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Section of Germaneto, Catanzaro, Italy
- Neuroscience Research Center, University “Magna Graecia”, Catanzaro, Italy
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17
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Zhang L, Shao Y, Tang C, Liu Z, Tang D, Hu C, Liang X, Hu Z, Luo G. Identification of Novel Biomarkers in Platelets for Diagnosing Parkinson's Disease. Eur Neurol 2021; 85:122-131. [PMID: 34875658 DOI: 10.1159/000520102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Parkinson's disease (PD) is a common neurodegenerative disease affecting the elderly, but there is no blood test for PD diagnosis in the clinic currently. This study aimed to explore promising biomarkers in platelets (PLTs) for PD diagnosis. METHODS PLTs were isolated from whole blood samples of PD patients and healthy controls (HCs), and RNA was extracted for sequencing. RNA-seq was performed on the Illumina HiSeq platform. RESULTS A total of 2,221 genes with differential transcript levels (GDTLs) were identified between PD patients and HCs, 1,041 of which are upregulated genes and 1,180 of which are downregulated genes. WASH5P was the most upregulated gene and AC114491.1 was the most downregulated gene. Among the top 12 most relevant genes, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), eukaryotic elongation factor 1A (EEF1A1), and cathepsin S (CTSS) were reported to be associated with PD. Furthermore, gene ontology analysis showed that the most significant term in biological processes was neutrophil degranulation; the most enriched term in cellular components was cytoplasmic vesicle lumen; and tumor necrosis factor receptor superfamily binding was the most significant term in molecular functions. In the Kyoto Encyclopedia of Genes and Genomes enrichment analysis, inflammation-related pathway accounts for the majority. CONCLUSION Our findings demonstrated WASH5P, MALAT1, EEF1A1, and CTSS may be promising biomarkers in PD, which may contribute to improving the effectiveness and accuracy of diagnosis for PD in the future.
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Affiliation(s)
- Lei Zhang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China,
| | - Yiye Shao
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunlei Tang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Zhen Liu
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Dingzhong Tang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Canfang Hu
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Xuelin Liang
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
| | - Zhaoyang Hu
- Fun-Med Pharmaceutical Technology (Shanghai) Co., Ltd., Shanghai, China
| | - Guojun Luo
- Department of Neurology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai, China
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18
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Guo Y, Liu Y, Wang H, Liu P. Long noncoding RNA SRY-box transcription factor 2 overlapping transcript participates in Parkinson's disease by regulating the microRNA-942-5p/nuclear apoptosis-inducing factor 1 axis. Bioengineered 2021; 12:8570-8582. [PMID: 34607512 PMCID: PMC8806952 DOI: 10.1080/21655979.2021.1987126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 01/20/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder. Studies have shown that long noncoding RNA SRY-box transcription factor 2 overlapping transcript (lncRNA SOX2-OT) is highly expressed in PD patients, but its specific functions and mechanisms require further research. To address this gap, this study utilized an in vitro PD cell model induced by 1-methyl-4-phenylpyridinium (MPP+). Cell viability, apoptosis, lactate dehydrogenase (LDH) activity, inflammatory factor secretion, and oxidative stress indicators were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-dipheyltetrazolium bromide assay, LDH assay, flow cytometry, enzyme linked immunosorbent assay (ELISA), and corresponding kits, respectively. Gene and protein expression were measured using quantitative real-time-PCR and western blotting, respectively. The results indicated that microRNA-942-5p (miR-942-5p) was a direct target of lncRNA SOX2-OT and nuclear apoptosis-inducing factor 1 (NAIF1) was a direct target of miR-942-5p. The expression levels of lncRNA SOX2-OT and NAIF1 were increased, and miR-942-5p expression was decreased in SH-SY5Y cells following MPP+ treatment. In addition, MPP+ treatment reduced SH-SY5Y cell viability, increased apoptosis; increased cleaved caspase-3 protein expression and cleaved caspase-3/caspase-3 ratio; enhanced lactate dehydrogenase viability; increased tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and reactive oxygen species, and decreased superoxide dismutase activity in SH-SY5Y cells were inhibited by SOX2-OT-siRNA, and these inhibitions were reversed by miR-942-5p inhibitor. Moreover, the protective role of miR-942-5p mimic in MPP+-induced SH-SY5Y cells was eliminated by the NAIF1 plasmid. Overall, lncRNA SOX2-OT-mediated regulation of oxidative stress, inflammation, and neuronal apoptosis were directly controlled by the miR-942-5p/NAIF1 signal axis in MPP+-induced SH-SY5Y cells.
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Affiliation(s)
- Yabi Guo
- Rehabilitation Medicine Center, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Yanyang Liu
- Rehabilitation Medicine Center, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Hong Wang
- Rehabilitation Medicine Center, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Peijun Liu
- Rehabilitation Medicine Center, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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19
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Wang S, Wen Q, Xiong B, Zhang L, Yu X, Ouyang X. Long Noncoding RNA NEAT1 Knockdown Ameliorates 1-Methyl-4-Phenylpyridine-Induced Cell Injury Through MicroRNA-519a-3p/SP1 Axis in Parkinson Disease. World Neurosurg 2021; 156:e93-e103. [PMID: 34508910 DOI: 10.1016/j.wneu.2021.08.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Parkinson disease is a neurodegenerative disease and is characterized by resting tremor, dementia, and gait disorder. Previous studies have indicated that long noncoding RNA participates in the regulation of the pathogenesis of Parkinson disease. The study aimed to reveal the effects of long noncoding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) on 1-methyl-4-phenylpyridine (MPP+)-induced human neuroblastoma cell injury and the underlying mechanism. METHODS The expressions of NEAT1, microRNA (miR)-519a-3p, and transcription factor specific protein 1 (SP1) were detected by quantitative real-time polymerase chain reaction. The protein expressions of SP1 and inflammation-related factors were determined by Western blot. Cell viability was determined by 3-(4,5-dimethylthazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Cell apoptosis was investigated by flow cytometry analysis. The targeting relationship between miR-519a-3p and NEAT1 or SP1 was predicted by starBase online database and verified by a dual-luciferase reporter assay. RESULTS NEAT1 and SP1 expressions were significantly upregulated, whereas miR-519a-3p was downregulated in MPP+-treated neuroblastoma cells in a dose- and time-dependent manner when compared with control groups. NEAT1 knockdown restrained MPP+-induced repression of cell viability and promotion of cell apoptosis and inflammation. Additionally, NEAT1 served as a sponge of miR-519a-3p and regulated MPP+-caused cell injury by interacting with miR-519a-3p. Also, SP1, a target gene of miR-519a-3p, rescued miR-519a-3p-mediated actions under MPP+ treatment. Importantly, NEAT1 stimulated SP1 expression through interaction with miR-519a-3p. CONCLUSIONS NEAT1 silencing protected against MPP+-induced neuroblastoma cell injury by regulating the miR-519a-3p/SP1 pathway. This finding provides a novel direction for the development of therapeutic strategies for Parkinson disease.
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Affiliation(s)
- Shuihua Wang
- Department of Neurology, 908 Hospital of PLA Joint Logistics Support Force, Nanchang, China
| | - Qinli Wen
- Department of Pharmacy, Jiangxi Cancer Hospital, Nanchang, China
| | - Bohai Xiong
- Department of Neurology, 908 Hospital of PLA Joint Logistics Support Force, Nanchang, China
| | - Li Zhang
- Department of Neurology, 908 Hospital of PLA Joint Logistics Support Force, Nanchang, China
| | - Xiaoli Yu
- Department of Neurology, 908 Hospital of PLA Joint Logistics Support Force, Nanchang, China.
| | - Xiaochun Ouyang
- Department of Neurology, 908 Hospital of PLA Joint Logistics Support Force, Nanchang, China
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20
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Shi WZ, Li W, Cheng Y, Zhang M, Niu XC, Gao QW, Lu Y, Tian T, Du S, Mi Y, Chang MZ, Tian Y. The cytoprotective role of omentin against oxidative stress-induced PC12 apoptosis. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2021; 49:483-492. [PMID: 34151664 DOI: 10.1080/21691401.2021.1892707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/15/2021] [Indexed: 10/21/2022]
Abstract
Oxidative stress has been proven to play a critical role in the pathogenesis of neuronal injury. As a novel adipocytokine, omentin is produced by visceral adipose with insulin sensitizing effects and has been revealed to possess anti-inflammatory effects. However, the possible effect of omentin on oxidative stress remains unknown. The present study aimed to detect the potential protective effect of omentin against hydrogen peroxide (H2O2)-induced cytotoxicity of PC12 cells. The results showed that no cytotoxic effect was shown in PC12 cells co-cultured with omentin alone at a concentration of 50-1000 ng/mL. The CCK8 and TUNEL assays suggested that omentin could remarkably attenuate apoptosis induced by 100 μM H2O2. The PCR and western blotting showed that the expression levels of Bax was significantly inhibited by omentin via the upregulation of miR-128-3p at its 3'-UTR. Taken together, these results indicated that omentin protects PC12 cells against H2O2-induced apoptosis, and further studies need to be conducted before utilization in the clinic for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Wen-Zhen Shi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Wu Li
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Ye Cheng
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Meng Zhang
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Xiao-Chen Niu
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Qi-Wei Gao
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
| | - Ying Lu
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Tian Tian
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Shan Du
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Yan Mi
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
| | - Ming-Ze Chang
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
| | - Ye Tian
- Medical Research Center, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi'an, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences, Northwest University, Xi'an, China
- Medical Research and Experimental Center, School of Medicine, Yan'an University, Yan'an, Shaanxi, China
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21
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Disruption of Alternative Splicing in the Amygdala of Pigs Exposed to Maternal Immune Activation. IMMUNO 2021. [DOI: 10.3390/immuno1040035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The inflammatory response of gestating females to infection or stress can disrupt gene expression in the offspring’s amygdala, resulting in lasting neurodevelopmental, physiological, and behavioral disorders. The effects of maternal immune activation (MIA) can be impacted by the offspring’s sex and exposure to additional stressors later in life. The objectives of this study were to investigate the disruption of alternative splicing patterns associated with MIA in the offspring’s amygdala and characterize this disruption in the context of the second stress of weaning and sex. Differential alternative splicing was tested on the RNA-seq profiles of a pig model of viral-induced MIA. Compared to controls, MIA was associated with the differential alternative splicing (FDR-adjusted p-value < 0.1) of 292 and 240 genes in weaned females and males, respectively, whereas 132 and 176 genes were differentially spliced in control nursed female and male, respectively. The majority of the differentially spliced (FDR-adjusted p-value < 0.001) genes (e.g., SHANK1, ZNF672, KCNA6) and many associated enriched pathways (e.g., Fc gamma R-mediated phagocytosis, non-alcoholic fatty liver disease, and cGMP-PKG signaling) have been reported in MIA-related disorders including autism and schizophrenia in humans. Differential alternative splicing associated with MIA was detected in the gene MAG across all sex-stress groups except for unstressed males and SLC2A11 across all groups except unstressed females. Precise understanding of the effect of MIA across second stressors and sexes necessitates the consideration of splicing isoform profiles.
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22
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Kuo MC, Liu SCH, Hsu YF, Wu RM. The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways. J Biomed Sci 2021; 28:78. [PMID: 34794432 PMCID: PMC8603508 DOI: 10.1186/s12929-021-00775-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023] Open
Abstract
The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson's disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson's disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.
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Affiliation(s)
- Ming-Che Kuo
- Department of Medicine, Section of Neurology, Cancer Center, National Taiwan University Hospital, Taipei, Taiwan
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sam Chi-Hao Liu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fang Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
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23
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Zhu Z, Huang P, Sun R, Li X, Li W, Gong W. A Novel Long-Noncoding RNA LncZFAS1 Prevents MPP +-Induced Neuroinflammation Through MIB1 Activation. Mol Neurobiol 2021; 59:778-799. [PMID: 34775541 PMCID: PMC8857135 DOI: 10.1007/s12035-021-02619-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Parkinson's disease remains one of the leading neurodegenerative diseases in developed countries. Despite well-defined symptomology and pathology, the complexity of Parkinson's disease prevents a full understanding of its etiological mechanism. Mechanistically, α-synuclein misfolding and aggregation appear to be central for disease progression, but mitochondrial dysfunction, dysfunctional protein clearance and ubiquitin/proteasome systems, and neuroinflammation have also been associated with Parkinson's disease. Particularly, neuroinflammation, which was initially thought to be a side effect of Parkinson's disease pathogenesis, has now been recognized as driver of Parkinson's disease exacerbation. Next-generation sequencing has been used to identify a plethora of long noncoding RNAs (lncRNA) with important transcriptional regulatory functions. Moreover, a myriad of lncRNAs are known to be regulators of inflammatory signaling and neurodegenerative diseases, including IL-1β secretion and Parkinson's disease. Here, LncZFAS1 was identified as a regulator of inflammasome activation, and pyroptosis in human neuroblast SH-SY5Y cells following MPP+ treatment, a common in vitro Parkinson's disease cell model. Mechanistically, TXNIP ubiquitination through MIB1 E3 ubiquitin ligase regulates NLRP3 inflammasome activation in neuroblasts. In contrast, MPP+ activates the NLPR3 inflammasome through miR590-3p upregulation and direct interference with MIB1-dependent TXNIP ubiquitination. LncZFAS overexpression inhibits this entire pathway through direct interference with miR590-3p, exposing a novel research idea regarding the mechanism of Parkinson's disease.
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Affiliation(s)
- Ziman Zhu
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, 100144, China
| | - Peiling Huang
- Department of Neurological Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, 100144, China
| | - Ruifeng Sun
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, 100144, China
| | - Xiaoling Li
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, 100144, China
| | - Wenshan Li
- Beijing Rehabilitation Medicine Academy, Capital Medical University, Beijing, 100144, China
| | - Weijun Gong
- Department of Neurological Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, 100144, China.
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24
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Stat3-Induced lncRNA Kcnq1ot1 Regulates the Apoptosis of Neuronal Cells in Spinal Cord Injury. J Mol Neurosci 2021; 72:610-617. [PMID: 34731364 DOI: 10.1007/s12031-021-01932-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023]
Abstract
Emerging evidence validates the vital roles of long noncoding RNAs (lncRNAs) in spinal cord injury (SCI), which attracts great attention. In the present study, our study investigated the function and in-depth mechanism of lncRNA Kcnq1 overlapping transcript 1 (Kcnq1ot1) in SCI. Results indicated that lncRNA Kcnq1ot1 expression upregulated in the hypoxia-administered neuronal cells (PC12 cells) and SCI rat models. Moreover, transcription factor signal transducer and activator of transcription 3 (Stat3) accelerated the transcriptional enrichment of Kcnq1ot1 in SCI cellular model. Functional experiments demonstrated that Kcnq1ot1 knockdown repressed the apoptosis of neuronal cells. Mechanistically, Kcnq1ot1 recruited EZH2 to the promoter region of p27 to repress its transcription. Taken together, our results indicate that Stat3-induced lncRNA Kcnq1ot1 regulates the apoptosis in SCI through epigenetically silencing p27, contributing to novel therapeutic target for SCI.
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25
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Irwin AB, Bahabry R, Lubin FD. A putative role for lncRNAs in epigenetic regulation of memory. Neurochem Int 2021; 150:105184. [PMID: 34530054 PMCID: PMC8552959 DOI: 10.1016/j.neuint.2021.105184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
The central dogma of molecular genetics is defined as encoded genetic information within DNA, transcribed into messenger RNA, which contain the instructions for protein synthesis, thus imparting cellular functionality and ultimately life. This molecular genetic theory has given birth to the field of neuroepigenetics, and it is now well established that epigenetic regulation of gene transcription is critical to the learning and memory process. In this review, we address a potential role for a relatively new player in the field of epigenetic crosstalk - long non-coding RNAs (lncRNAs). First, we briefly summarize epigenetic mechanisms in memory formation and examine what little is known about the emerging role of lncRNAs during this process. We then focus discussions on how lncRNAs interact with epigenetic mechanisms to control transcriptional programs under various conditions in the brain, and how this may be applied to regulation of gene expression necessary for memory formation. Next, we explore how epigenetic crosstalk in turn serves to regulate expression of various individual lncRNAs themselves. To highlight the importance of further exploring the role of lncRNA in epigenetic regulation of gene expression, we consider the significant relationship between lncRNA dysregulation and declining memory reserve with aging, Alzheimer's disease, and epilepsy, as well as the promise of novel therapeutic interventions. Finally, we conclude with a discussion of the critical questions that remain to be answered regarding a role for lncRNA in memory.
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Affiliation(s)
- Ashleigh B Irwin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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26
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Chen X, Cao W, Zhuang Y, Chen S, Li X. Integrative analysis of potential biomarkers and immune cell infiltration in Parkinson's disease. Brain Res Bull 2021; 177:53-63. [PMID: 34536521 DOI: 10.1016/j.brainresbull.2021.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Parkinson's disease (PD) is a common neurodegenerative disease in the elderly population. However, there are no reliable diagnostic biomarkers for PD, and the pathogenesis of PD still needs further study. The aim of the current study was to identify potential biomarkers and explore the pathogenesis of PD. METHODS We conducted an integrative analysis of messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) expression profiles of PD using data from the Gene Expression Omnibus (GEO). The GSE110720, GSE110719 and GSE133347 data sets were selected and analysed. Gene ontology (GO) enrichment and gene set variation analysis (GSVA) were performed for annotation, visualization, and integrated discovery. Protein-protein interaction (PPI) and competing endogenous RNA (ceRNA) networks were constructed, and hub genes were identified. Meanwhile, the immune infiltration analysis of hub genes was analysed. Moreover, receiver operating characteristic (ROC) curves were generated to verify the diagnostic value of the differentially expressed genes (DEGs). Finally, the genes with high area under the curve (AUC) values were verified by human samples. RESULTS We identified 464 DEGs closely related to PD, including 154 mRNAs, 134 miRNAs, and 176 lncRNAs. The GO analyses indicated that changes in PD were mainly enriched in receptor ligand activity and cytokine receptor binding. The KEGG enrichment analysis showed that these DEGs were significantly involved in cytokine-cytokine receptor interactions, signalling pathways regulating the pluripotency of stem cells and Th17 cell differentiation. GSVA suggested that growth factor binding, IL2-stat5 signalling, and IL6-jak-stat3 signalling were crucial in the development of PD. A total of five hub genes (NPBWR2, CXCL10, CXCL5, S1PR5, and GALR1) were selected via the PPI network. A ceRNA network of the CXCL5, CXCL10 and S1PR5 genes was constructed, and target genes of the three genes were screened. The immune infiltration analysis showed that there were significant differences in a variety of immune cells between the hub genes. The expression of DEGs was validated in clinical human samples by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The expression levels of hsa-miR6895-5p, hsa-miR6791-5p, hsa-miR518f-5p, hsa-miR455-3p and TEKT4P2 were decreased, while the levels of TPTE2P6 were increased in human samples. These findings are consistent with the bioinformatics analysis results. CONCLUSION We found that the immune inflammatory response and immune cell regulation were involved in the pathogenesis of PD. Five hub genes involved in the immune infiltration biological processes of PD based on bioinformatics. We verified the DEGs with significant differences by qRT-PCR. These findings might provide new insight into the pathogenesis of PD and the development of diagnostic and therapeutic strategies for PD.
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Affiliation(s)
- Xiaopeng Chen
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Wei Cao
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Yuansu Zhuang
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Siyuan Chen
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China
| | - Xuezhong Li
- Department of Neurology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 221000, Jiangsu, China.
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27
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Zhang M, He P, Bian Z. Long Noncoding RNAs in Neurodegenerative Diseases: Pathogenesis and Potential Implications as Clinical Biomarkers. Front Mol Neurosci 2021; 14:685143. [PMID: 34421536 PMCID: PMC8371338 DOI: 10.3389/fnmol.2021.685143] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022] Open
Abstract
Neurodegenerative diseases (NDDs), including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), and amyotrophic lateral sclerosis (ALS), are progressive and ultimately fatal. NDD onset is influenced by several factors including heredity and environmental cues. Long noncoding RNAs (lncRNAs) are a class of noncoding RNA molecules with: (i) lengths greater than 200 nucleotides, (ii) diverse biological functions, and (iii) highly conserved structures. They directly interact with molecules such as proteins and microRNAs and subsequently regulate the expression of their targets at the genetic, transcriptional, and post-transcriptional levels. Emerging studies indicate the important roles of lncRNAs in the progression of neurological diseases including NDDs. Additionally, improvements in detection technologies have enabled quantitative lncRNA detection and application to circulating fluids in clinical settings. Here, we review current research on lncRNAs in animal models and patients with NDDs. We also discuss the potential applicability of circulating lncRNAs as biomarkers in NDD diagnostics and prognostics. In the future, a better understanding of the roles of lncRNAs in NDDs will be essential to exploit these new therapeutic targets and improve noninvasive diagnostic methods for diseases.
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Affiliation(s)
- Meng Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ping He
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhigang Bian
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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28
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Qi Z, Li J, Li M, Du X, Zhang L, Wang S, Xu B, Liu W, Xu Z, Deng Y. The Essential Role of Epigenetic Modifications in Neurodegenerative Diseases with Dyskinesia. Cell Mol Neurobiol 2021; 42:2459-2472. [PMID: 34383231 DOI: 10.1007/s10571-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022]
Abstract
Epigenetics play an essential role in the occurrence and improvement of many diseases. Evidence shows that epigenetic modifications are crucial to the regulation of gene expression. DNA methylation is closely linked to embryonic development in mammalian. In recent years, epigenetic drugs have shown unexpected therapeutic effects on neurological diseases, leading to the study of the epigenetic mechanism in neurodegenerative diseases. Unlike genetics, epigenetics modify the genome without changing the DNA sequence. Research shows that epigenetics is involved in all aspects of neurodegenerative diseases. The study of epigenetic will provide valuable insights into the molecular mechanism of neurodegenerative diseases, which may lead to new treatments and diagnoses. This article reviews the role of epigenetic modifications neurodegenerative diseases with dyskinesia, and discusses the therapeutic potential of epigenetic drugs in neurodegenerative diseases.
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Affiliation(s)
- Zhipeng Qi
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Jiashuo Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Minghui Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Xianchao Du
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Lei Zhang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Shuang Wang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Zhaofa Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China.
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29
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Craig DW, Hutchins E, Violich I, Alsop E, Gibbs JR, Levy S, Robison M, Prasad N, Foroud T, Crawford KL, Toga AW, Whitsett TG, Kim S, Casey B, Reimer A, Hutten SJ, Frasier M, Kern F, Fehlman T, Keller A, Cookson MR, Van Keuren-Jensen K. RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson's disease. NATURE AGING 2021; 1:734-747. [PMID: 37117765 DOI: 10.1038/s43587-021-00088-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/21/2021] [Indexed: 04/30/2023]
Abstract
Changes in the blood-based RNA transcriptome have the potential to inform biomarkers of Parkinson's disease (PD) progression. Here we sequenced a discovery set of whole-blood RNA species in 4,871 longitudinally collected samples from 1,570 clinically phenotyped individuals from the Parkinson's Progression Marker Initiative (PPMI) cohort. Samples were sequenced to an average of 100 million read pairs to create a high-quality transcriptome. Participants with PD in the PPMI had significantly altered RNA expression (>2,000 differentially expressed genes), including an early and persistent increase in neutrophil gene expression, with a concomitant decrease in lymphocyte cell counts. This was validated in a cohort from the Parkinson's Disease Biomarkers Program (PDBP) consisting of 1,599 participants and by alterations in immune cell subtypes. This publicly available transcriptomic dataset, coupled with available detailed clinical data, provides new insights into PD biological processes impacting whole blood and new paths for developing diagnostic and prognostic PD biomarkers.
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Affiliation(s)
- David W Craig
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Elizabeth Hutchins
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Ivo Violich
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Eric Alsop
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Madison Robison
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Karen L Crawford
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Timothy G Whitsett
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Seungchan Kim
- Center for Computational Systems Biology, Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Bradford Casey
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Alyssa Reimer
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Samantha J Hutten
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Mark Frasier
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlman
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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30
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He S, Huang L, Shao C, Nie T, Xia L, Cui B, Lu F, Zhu L, Chen B, Yang Q. Several miRNAs derived from serum extracellular vesicles are potential biomarkers for early diagnosis and progression of Parkinson's disease. Transl Neurodegener 2021; 10:25. [PMID: 34315539 PMCID: PMC8317324 DOI: 10.1186/s40035-021-00249-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/08/2021] [Indexed: 12/21/2022] Open
Abstract
Background Blood-based test for predicting disease progression and early diagnosis of Parkinson’s disease (PD) is an unmet need in the clinic. The profiles of microRNAs (miRNAs) are regarded as potential diagnostic biomarkers for human diseases, whereas miRNAs in the periphery are susceptible to the influence of various components. MiRNAs enriched in serum extracellular vesicles (EVs) have demonstrated disease-specific advantages in diagnosis due to their high abundance, stability and resistance to degradation. This study was aimed to screen differentially expressed EV-derived miRNAs between healthy controls and PD patients to aid in diagnosis of PD. Methods A total of 31 healthy controls and 72 patients with a diagnosis of PD at different Hoehn and Yahr stages in Tangdu Hospital were included. In total, 185 differentially expressed miRNAs were obtained through RNA sequencing of serum EVs as well as edgeR and t-test analyses. Subsequently, the weighted gene co-expression network analysis (WGCNA) was utilized to identify the commonly expressed miRNAs in all stages of PD by constructing connections between modules, and specifically expressed miRNAs in each stage of PD by functional enrichment analysis. After aligning these miRNAs with PD-related miRNAs in Human miRNA Disease Database, the screened miRNAs were further validated by receiver operating characteristic (ROC) curves and quantitative real-time polymerase chain reaction (qRT-PCR) using peripheral blood EVs from 40 more participants. Results WGCNA showed that 4 miRNAs were commonly associated with all stages of PD and 13 miRNAs were specifically associated with different stages of PD. Of the 17 obtained miRNAs, 7 were validated by ROC curve analysis and 7 were verified in 40 more participants by qRT-PCR. Six miRNAs were verified by both methods, which included 2 miRNAs that were commonly expressed in all stages of PD and 4 miRNAs that were specifically expressed in different stages of PD. Conclusions The 6 serum EV-derived miRNAs, hsa-miR-374a-5p, hsa-miR-374b-5p, hsa-miR-199a-3p, hsa-miR-28-5p, hsa-miR-22-5p and hsa-miR-151a-5p, may potentially be used as biomarkers for PD progression and for early diagnosis of PD in populations. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-021-00249-y.
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Affiliation(s)
- Shulei He
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Lu Huang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China.,Department of Neurosurgery and Institute for Functional Brain Disorders, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Ci Shao
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Li Xia
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China.,Department of Neurosurgery and Institute for Functional Brain Disorders, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Bozhou Cui
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Lin Zhu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China
| | - Bolin Chen
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, China.
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31
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Advances with Long Non-Coding RNAs in Alzheimer's Disease as Peripheral Biomarker. Genes (Basel) 2021; 12:genes12081124. [PMID: 34440298 PMCID: PMC8391483 DOI: 10.3390/genes12081124] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
One of the most compelling needs in the study of Alzheimer’s disease (AD) is the characterization of cognitive decline peripheral biomarkers. In this context, the theme of altered RNA processing has emerged as a contributing factor to AD. In particular, the significant role of long non-coding RNAs (lncRNAs) associated to AD is opening new perspectives in AD research. This class of RNAs may offer numerous starting points for new investigations about pathogenic mechanisms and, in particular, about peripheral biomarkers. Indeed, altered lncRNA signatures are emerging as potential diagnostic biomarkers. In this review, we have collected and fully explored all the presented data about lncRNAs and AD in the peripheral system to offer an overview about this class of non-coding RNAs and their possible role in AD.
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32
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Yang H. LncRNA MALAT1 potentiates inflammation disorder in Parkinson's disease. Int J Immunogenet 2021; 48:419-428. [PMID: 34291564 DOI: 10.1111/iji.12549] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
With this investigation, we investigated on the contribution of lncRNA MALAT1 to inflammation disorder in Parkinson's Disease (PD). Serum samples were gathered from sporadic PD patients and healthy controls, and single nucleotide polymorphisms (SNPs) of MALAT1, including rs11227209, rs3200401, rs4102217, rs591291, rs619586 and rs664589, were identified. Serum level of MALAT1 was quantified using RT-PCR, and IL-1β, IL-6, TNF-α and IFN-γ levels in serum were measured with ELISA kits. Inflammation cell models were established by treating PC12 cells with LPS, and cytokine production of pcDNA3.1-MALAT1/si-MALAT1-transfected PC12 cells was evaluated. The results showed that PD patients with high serum level of MALAT1 were associated with lower MMSE score and higher serum levels of IL-1β, IL-6, TNF-α and IFN-γ than patients carrying low serum level of MALAT1 (p < .05). Mutant alleles of SNPs in MALAT1, including rs3200401 (C>T) and rs4102217 (G>C), tended to elevate PD susceptibility and facilitate cytokine production, as compared with their wild alleles (p < .05). And LPS-exposed PC12 cells secreted larger amounts of inflammation cytokines in the pcDNA3.1-MALAT1 group than in the Mock group (p < .05). In conclusion, MALAT1 participated in modifying inflammation disorder underlying PD aetiology, suggesting that it might be a promising therapeutic target for PD.
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Affiliation(s)
- Huimin Yang
- Department of Neurology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Taghizadeh E, Gheibihayat SM, Taheri F, Afshani SM, Farahani N, Saberi A. LncRNAs as putative biomarkers and therapeutic targets for Parkinson's disease. Neurol Sci 2021; 42:4007-4015. [PMID: 34254198 DOI: 10.1007/s10072-021-05408-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/13/2021] [Indexed: 11/29/2022]
Abstract
Parkinson's disease (PD) is known as one of the most common degenerative disorders related to the damage of the central nervous system (CNS). This brain disorder is also characterized by the formation of Lewy bodies in the cytoplasm of the dopaminergic neurons in the substantia nigra pars compacta (SNc), which consequently leads to motor and non-motor symptoms. With regard to the growing trend in the number of cases with PD and its effects on individuals, families, and communities, immediate treatments together with diagnostic methods are required. In this respect, long non-coding ribonucleic acids (lncRNAs) represent a large class of ncRNAs with more than 200 nucleotides in length, playing key roles in some important processes including gene expression, cell differentiation, genomic imprinting, apoptosis, and cell cycle. They are highly expressed in the CNS and previous studies have further reported that the expression profile of lncRNAs is disrupted in human diseases such as neurodegenerative disorders. Since the levels of some lncRNAs change over time in the brains of patients with PD, a number of previous studies have examined their potentials as biomarkers for this brain disorder. Therefore, the main purpose of this study was to review the advances in the related literature on lncRNAs as diagnostic, therapeutic, and prognostic biomarkers for PD.
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Affiliation(s)
- Eskandar Taghizadeh
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.
| | - Seyed Mohammad Gheibihayat
- Department of Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Forough Taheri
- Islamic Azad University (Shahrekord Branch), Shahrekord, Iran
| | - Seyed Mohammadreza Afshani
- Department of Cardiology, Imam Khomeini Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmeh Farahani
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Alihossein Saberi
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Lilach S, Hagai B, Zvi I, Hermona S, Wael M. MicroRNA expression changes in Parkinson's disease (PD) patients' leukocytes prior to and following deep brain stimulation (DBS). AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2021; 10:28-33. [PMID: 34327050 PMCID: PMC8310831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/09/2021] [Indexed: 06/13/2023]
Abstract
The second most prevalent neurodegenerative disorder worldwide in the elderly is Parkinson's disease (PD). It is a major risk factor for aging. Objectives: Currently the involvement of miRNAs in the disease is mainly unclear. Additionally, the disease aetiology is complex and there are no available disease-modifying medications. Therefore, more evidence is required concerning its pathogenesis and developing new treatment modalities. Methods: Here, we studied the expression profiles of about 900 miRNAs in PD patients prior to and following deep brain stimulation (DBS) both on and following 1 hour off electrical stimulation and as compared with age and gender matched healthy control (HC) donor samples, using Affymetrix miRNA microarrays. We analysed statistically the data using Affymetrix expression console software. Results: We detected significantly altered miRNAs pre and post DBS treatment. Conclusions: Our findings indicate the involvement of miRNAs in PD. Future studies can enlarge the number of samples and use RNA sequencing platform to quantify further miRNAs in PD samples. We may also use the expression levels of miRNAs as biomarkers for PD in the blood.
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Affiliation(s)
| | | | - Israel Zvi
- The Hebrew University of JerusalemIsrael
| | | | - Mohamed Wael
- BMS Department, KOM, IIUMMalaysia
- Department of Clinical Pharmacology, Menoufia Medical School, Menoufia UniversityEgypt
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Annesley SJ, Fisher PR. Lymphoblastoid Cell Lines as Models to Study Mitochondrial Function in Neurological Disorders. Int J Mol Sci 2021; 22:4536. [PMID: 33926115 PMCID: PMC8123577 DOI: 10.3390/ijms22094536] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022] Open
Abstract
Neurological disorders, including neurodegenerative diseases, are collectively a major cause of death and disability worldwide. Whilst the underlying disease mechanisms remain elusive, altered mitochondrial function has been clearly implicated and is a key area of study in these disorders. Studying mitochondrial function in these disorders is difficult due to the inaccessibility of brain tissue, which is the key tissue affected in these diseases. To overcome this issue, numerous cell models have been used, each providing unique benefits and limitations. Here, we focussed on the use of lymphoblastoid cell lines (LCLs) to study mitochondrial function in neurological disorders. LCLs have long been used as tools for genomic analyses, but here we described their use in functional studies specifically in regard to mitochondrial function. These models have enabled characterisation of the underlying mitochondrial defect, identification of altered signalling pathways and proteins, differences in mitochondrial function between subsets of particular disorders and identification of biomarkers of the disease. The examples provided here suggest that these cells will be useful for development of diagnostic tests (which in most cases do not exist), identification of drug targets and testing of pharmacological agents, and are a worthwhile model for studying mitochondrial function in neurological disorders.
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Affiliation(s)
- Sarah Jane Annesley
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia;
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Kay MK, Zhang J, Choudhury M. Screening for alternative splicing of lncRNA Dleu2 in the mouse liver cell line AML-12. Biomed Rep 2021; 14:50. [PMID: 33859821 DOI: 10.3892/br.2021.1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/19/2021] [Indexed: 11/05/2022] Open
Abstract
The long non coding RNA deleted in leukemia 2 gene (Dleu2) has recently been demonstrated to be an active player in the progression of several types of cancer, including hepatocellular carcinoma. Dleu2 may serve a role in modulating the downstream effects-mediated by alternative splicing of its multiple exons. However, the proportional expression of these alternative splicing populations of the Dleu2 exons is currently unknown. To determine how Dleu2 could be affected by alternative splicing, a series of alternative splicing primer sets were designed to investigate which transcripts were preferentially activated when Dleu2 was targeted for downregulation or upregulation. A specific Dleu2 small interfering RNA that targeted an exon upstream of the tumor suppressor microRNA site significantly knocked down Dleu2 expression across all the primer sets used, which targeted 13 different alternative splicing transcripts over 5 different promoter sites in the mouse liver cell line, AML-12. Similarly, 50 µM Resveratrol led to significant upregulation of Dleu2 in 11 alternative splicing transcripts. These results show that Dleu2 is capable of successful modulation across alternative splicing transcripts that can be screened, and also that Resveratrol can be a potential nutraceutical, which may potentially lead to novel approaches in the use of lncRNA Dleu2 for diagnostics and regulation.
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Affiliation(s)
- Matthew Krivacka Kay
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| | - Jian Zhang
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| | - Mahua Choudhury
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
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Yang J, Feng E, Ren Y, Qiu S, Zhao L, Li X. Long non-coding (lnc)RNA profiling and the role of a key regulator lnc-PNRC2-1 in the transforming growth factor- β1-induced epithelial-mesenchymal transition of CNE1 nasopharyngeal carcinoma cells. J Int Med Res 2021; 49:300060521996515. [PMID: 33752469 PMCID: PMC7995461 DOI: 10.1177/0300060521996515] [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] [Indexed: 11/30/2022] Open
Abstract
Objectives To identify key long non-coding (lnc)RNAs responsible for the epithelial–mesenchymal transition (EMT) of CNE1 nasopharyngeal carcinoma cells and to investigate possible regulatory mechanisms in EMT. Methods CNE1 cells were divided into transforming growth factor (TGF)-β1-induced EMT and control groups. The mRNA and protein expression of EMT markers was determined by real-time quantitative PCR and western blotting. Differentially expressed genes (DEGs) between the two groups were identified by RNA sequencing analysis, and DEG functions were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses. EMT marker expression was re-evaluated by western blotting after knockdown of a selected lncRNA. Results TGF-β1-induced EMT was characterized by decreased E-cadherin and increased vimentin, N-cadherin, and Twist expression at both mRNA and protein levels. Sixty lncRNA genes were clustered in a heatmap, and mRNA expression of 14 dysregulated lncRNAs was consistent with RNA sequencing. Knockdown of lnc-PNRC2-1 increased expression of its antisense gene MYOM3 and reduced expression of EMT markers, resembling treatment with the TGF-β1 receptor inhibitor LY2109761. Conclusion Various lncRNAs participated indirectly in the TGF-β1-induced EMT of CNE1 cells. Lnc-PNRC2-1 may be a key regulator of this and is a potential target to alleviate CNE1 cell EMT.
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Affiliation(s)
- Jie Yang
- Head and Neck Tumor Research Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province & Yunnan Cancer Center), Kunming, Yunnan, China
| | - Enzi Feng
- Head and Neck Tumor Research Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province & Yunnan Cancer Center), Kunming, Yunnan, China
| | - Yanxin Ren
- Head and Neck Tumor Research Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province & Yunnan Cancer Center), Kunming, Yunnan, China
| | - Shun Qiu
- Head and Neck Tumor Research Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province & Yunnan Cancer Center), Kunming, Yunnan, China
| | - Liufang Zhao
- Head and Neck Tumor Research Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province & Yunnan Cancer Center), Kunming, Yunnan, China
| | - Xiaojiang Li
- Head and Neck Tumor Research Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province & Yunnan Cancer Center), Kunming, Yunnan, China
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38
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Xin C, Liu J. Long Non-coding RNAs in Parkinson's Disease. Neurochem Res 2021; 46:1031-1042. [PMID: 33544326 DOI: 10.1007/s11064-021-03230-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/07/2020] [Accepted: 01/02/2021] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder and is associated with a range of motor and non-motor clinical symptoms. The underlying molecular pathogenesis of PD involves a variety of pathways and mechanisms, including α-synuclein proteostasis, mitochondrial dysfunction, oxidative stress, autophagy and apoptosis, neuroinflammation, and epigenetic regulation. Long non-coding RNAs (lncRNAs) are involved in the regulation of multiple pathological processes of PD. In this review, we provide an overview of large-scale studies on lncRNA expression profiling in PD patients and models, as well as highlight the impacts of lncRNAs on the pathogenesis of PD, which could provide basic information regarding the putative lncRNA-based biomarkers and therapeutic targets for the early diagnosis and treatment strategies for PD.
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Affiliation(s)
- Chengqi Xin
- Stem Cell Clinical Research Center, National Joint Engineering Laboratory, Regenerative Medicine Center, The First Affiliated Hospital of Dalian Medical University, No. 193, Lianhe Road, Shahekou District, Dalian City, Liaoning Province, 116011, People's Republic of China.,Dalian Innovation Institute of Stem Cell and Precision Medicine, No. 57, Xinda Street, Dalian High-Tech Park, Dalian City, Liaoning Province, 116023, People's Republic of China
| | - Jing Liu
- Stem Cell Clinical Research Center, National Joint Engineering Laboratory, Regenerative Medicine Center, The First Affiliated Hospital of Dalian Medical University, No. 193, Lianhe Road, Shahekou District, Dalian City, Liaoning Province, 116011, People's Republic of China. .,Dalian Innovation Institute of Stem Cell and Precision Medicine, No. 57, Xinda Street, Dalian High-Tech Park, Dalian City, Liaoning Province, 116023, People's Republic of China.
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Zhu Y, Lin Y, He Y, Wang H, Chen S, Li Z, Song N, Sun F. Deletion of lncRNA5512 has no effect on spermatogenesis and reproduction in mice. Reprod Fertil Dev 2021; 32:706-713. [PMID: 32317095 DOI: 10.1071/rd19246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/21/2019] [Indexed: 01/13/2023] Open
Abstract
Long non-coding (lnc) RNAs are a series of RNAs longer than 200 nucleotides that do not code for protein products. Whole-genome expression profiles of lncRNAs suggest that they play important roles in spermatogenesis because they are particularly abundant in testes. However, most of their characteristics and functions remain unclear. The aim of this study was to define the function of lncRNA5512, which is abundant in spermatocytes and round spermatids, in mouse fertility invivo. To investigate this we generated lncRNA5512-knockout mice by clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) 9 technology. Knockout mice showed normal spermatogenesis and fertility, and had no detectable abnormalities. This indicates that lncRNA5512 does not affect mouse fertility despite its high expression in the testes. Its specific localisation in spermatocytes and round spermatids suggests that it could be a useful marker for the identification of spermatocytes and round spermatids in mouse testes.
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Affiliation(s)
- Yu Zhu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Yu Lin
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Yue He
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Hanshu Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Shitao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Zhenhua Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China
| | - Ning Song
- Shanghai Key Laboratory of Reproductive Medicine, School of Medicine, Shanghai Jiao Tong University, 280 South Chongqing Road, Huangpu District, Shanghai 200025, China; and Corresponding authors. ;
| | - Fei Sun
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, 910 Hengshan Road, Xuhui District, Shanghai 200030, China; and Corresponding authors. ;
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Rezaei O, Nateghinia S, Estiar MA, Taheri M, Ghafouri-Fard S. Assessment of the role of non-coding RNAs in the pathophysiology of Parkinson's disease. Eur J Pharmacol 2021; 896:173914. [PMID: 33508286 DOI: 10.1016/j.ejphar.2021.173914] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/14/2021] [Accepted: 01/21/2021] [Indexed: 02/08/2023]
Abstract
Parkinson's disease (PD) is the second main neurodegenerative disease causing motor abnormalities in the middle-aged and old individuals. In some cases, cognitive dysfunction also occurs. The clinical signs of PD are bradykinesia, rigidity and resting tremor. As these signs might be detected in other neurological conditions such as multiple systems atrophy and corticobasal degeneration, it is necessary to find specific and sensitive markers for this disorder. Non-coding RNAs are implicated in the different PD-associated features such as α-synuclein expression and Lewy body construction, mitochondrial dysfunction, apoptosis, neuroinflammation and defects in glial cell-derived neurotrophic factor. Several researches have confirmed dysregulation of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in brain tissues, plasma exosomes and leukocytes of affected individuals or animal models of PD. A number of these transcripts directly regulate the neurodegenerative process in PD. In the current study, we review the current data about dysregulation of ncRNAs and the role of their genomic variants in the pathogenesis of PD.
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Affiliation(s)
- Omidvar Rezaei
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeedeh Nateghinia
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Zhang Y, Shao W, Wu J, Huang S, Yang H, Luo Z, Zheng F, Wang YL, Cai P, Guo Z, Wu S, Li H. Inflammatory lncRNA AK039862 regulates paraquat-inhibited proliferation and migration of microglial and neuronal cells through the Pafah1b1/Foxa1 pathway in co-culture environments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111424. [PMID: 33120262 DOI: 10.1016/j.ecoenv.2020.111424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Emerging evidences having suggested that particular lncRNAs have a potential effect on PD progression through provoking damage and inflammatory responses of microglia/ dopaminergic cells. In addition, paraquat can be accumulated in human body through various approaches and have an increased risk for Parkinson's disease. However, the specific role and mechanism of lncRNA related to neurotoxic in the progression of PD is unclear. In our study, a mouse PD model was established induced by the intraperitoneal injection of paraquat (5 mg/kg and 10 mg/kg) every three days (10 times). We determined differential expression of lncRNA AK039862 and its potential targeted genes Pafah1b1/Foxa1 in PD mouse model, then we used fluorescence in situ hybridization (FISH) to visualize the cellular distribution of AK039862. Short interfering RNAs (siRNAs) and overexpression plasmids were designed for knockdown or overexpression of AK039862. To simulate the coexisting dopaminergic cells and microglia cells in vitro, we applied several non-contact co-culture models, including conditioned medium and Transwell co-culture systems. Cytotoxicity of PQ was evaluated using bv2 cells with the concentrations: 30, 60 μM, and mn9d cells with the concentrations: 50, 100 μM. As a result, we depicted multiple interesting individual and interactive features of inflammatory lncRNA AK039862 involved in PQ-induced cellular functional effects. First, we detected that AK039862 contributed to the neuronal injury process in PQ-treated mice and co-localization of AK039862 with dopaminergic cells in vivo. And interestingly, we demonstrated that PQ significantly inhibited microglia and dopaminergic cells proliferation and microglia migration in vitro. Further research indicated that the PQ-induced low expression of AK039862 rescued microglia proliferation and migration inhibition via the AK039862/Pafah1b1/Foxa1 pathway. Meanwhile, AK039862 also participated in the interaction between microglia and dopaminergic cells with PQ treatment in non-contact co-culture models. In summary, we found that PQ inhibited the proliferation and migration of microglial cells, and elucidated AK039862 played a key role in PQ-induced neuroinflammatory damage through Pafah1b1/Foxa1. Finally, inflammatory AK039862 is involved in the complex communication between microglia and dopaminergic cells in the environment of PQ damage.
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Affiliation(s)
- Yinyin Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Nutrition and Food Hygiene, Faculty of Naval Medicine, The Second Military Medical University, Shanghai 200433, China.
| | - Wenya Shao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Jingwen Wu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Shouxiong Huang
- Department of Environmental Health, College of Medicine, University of Cincinnati, Ohio 45267, United States.
| | - Hongyu Yang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Zhousong Luo
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Yuan-Liang Wang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Ping Cai
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Zhenkun Guo
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Siying Wu
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China; Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350122, China.
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Liau WS, Samaddar S, Banerjee S, Bredy TW. On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biol 2021; 18:1025-1036. [PMID: 33397182 DOI: 10.1080/15476286.2020.1868165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | | | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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Garofalo M, Pandini C, Bordoni M, Pansarasa O, Rey F, Costa A, Minafra B, Diamanti L, Zucca S, Carelli S, Cereda C, Gagliardi S. Alzheimer's, Parkinson's Disease and Amyotrophic Lateral Sclerosis Gene Expression Patterns Divergence Reveals Different Grade of RNA Metabolism Involvement. Int J Mol Sci 2020; 21:ijms21249500. [PMID: 33327559 PMCID: PMC7765024 DOI: 10.3390/ijms21249500] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/27/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by a progressive degeneration of the central or peripheral nervous systems. A central role of the RNA metabolism has emerged in these diseases, concerning mRNAs processing and non-coding RNAs biogenesis. We aimed to identify possible common grounds or differences in the dysregulated pathways of AD, PD, and ALS. To do so, we performed RNA-seq analysis to investigate the deregulation of both coding and long non-coding RNAs (lncRNAs) in ALS, AD, and PD patients and controls (CTRL) in peripheral blood mononuclear cells (PBMCs). A total of 293 differentially expressed (DE) lncRNAs and 87 mRNAs were found in ALS patients. In AD patients a total of 23 DE genes emerged, 19 protein coding genes and four lncRNAs. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, we found common affected pathways and biological processes in ALS and AD. In PD patients only five genes were found to be DE. Our data brought to light the importance of lncRNAs and mRNAs regulation in three principal neurodegenerative disorders, offering starting points for new investigations on deregulated pathogenic mechanisms.
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Affiliation(s)
- Maria Garofalo
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Cecilia Pandini
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
| | - Matteo Bordoni
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy;
| | - Orietta Pansarasa
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
| | - Federica Rey
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, University of Milan, Via G.B Grassi 74, 20157 Milan, Italy; (F.R.); (S.C.)
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, Via G.B. Grassi 74, 20157 Milano, Italy
| | - Alfredo Costa
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Brigida Minafra
- Parkinson Unit and Movement disorders Mondino Foundation IRCCS, 27100 Pavia, Italy;
| | - Luca Diamanti
- Neuro-Oncology Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Susanna Zucca
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- enGenomesrl, 27100 Pavia, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, University of Milan, Via G.B Grassi 74, 20157 Milan, Italy; (F.R.); (S.C.)
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, Via G.B. Grassi 74, 20157 Milano, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- Correspondence:
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
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Bordone MC, Barbosa-Morais NL. Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer's and Parkinson's Brains With Digital Cytometry. Front Neurosci 2020; 14:607215. [PMID: 33362460 PMCID: PMC7756021 DOI: 10.3389/fnins.2020.607215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative disorders worldwide, with age being their major risk factor. The increasing worldwide life expectancy, together with the scarcity of available treatment choices, makes it thus pressing to find the molecular basis of AD and PD so that the causing mechanisms can be targeted. To study these mechanisms, gene expression profiles have been compared between diseased and control brain tissues. However, this approach is limited by mRNA expression profiles derived for brain tissues highly reflecting their degeneration in cellular composition but not necessarily disease-related molecular states. We therefore propose to account for cell type composition when comparing transcriptomes of healthy and diseased brain samples, so that the loss of neurons can be decoupled from pathology-associated molecular effects. This approach allowed us to identify genes and pathways putatively altered systemically and in a cell-type-dependent manner in AD and PD brains. Moreover, using chemical perturbagen data, we computationally identified candidate small molecules for specifically targeting the profiled AD/PD-associated molecular alterations. Our approach therefore not only brings new insights into the disease-specific and common molecular etiologies of AD and PD but also, in these realms, foster the discovery of more specific targets for functional and therapeutic exploration.
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Affiliation(s)
- Marie C Bordone
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Fazeli S, Motovali-Bashi M, Peymani M, Hashemi MS, Etemadifar M, Nasr-Esfahani MH, Ghaedi K. A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PLoS One 2020; 15:e0240855. [PMID: 33171483 PMCID: PMC7654768 DOI: 10.1371/journal.pone.0240855] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023] Open
Abstract
Parkinson’s disease (PD) is diagnosed when motor symptoms emerges, which almost 70% of dopamine neurons are lost. Therefore, early diagnosis of PD is crucial to prevent the progress of disease. Blood-based biomarkers, which are minimally invasive, potentially used for diagnosis of PD, including miRNAs. The aim of this study was to assess whether SRRM2 and miR-27a/b-3p could act as early diagnostic biomarkers for PD. Total RNAs from PBMCs of 30 PD’s patients and 14 healthy age and gender matched subjects was extracted. The expression levels of respective genes were assessed. Data were presented applying a two-tailed unpaired t-test and one-way ANOVA. We observed significant down-regulation of SRRM2 (p = 0.0002) and miR-27a-3p (p = 0.0001), and up-regulation of miR-27b-3p (p = 0.02) in PBMCs of Parkinson's patients. Down-regulation of miR-27a-3p is associated with increasing disease severity, whereas the up-regulation of miR-27b-3p was observed mostly at HY-1 and disease duration between 3–5 years. There was a negative correlation between SRRM2 and miR-27b-3p expressions, and miR-27a-3p positively was correlated with miR-27b-3p. Based on functional enrichment analysis, SRRM2 and miR-27a/b-3p acted on common functional pathways. miR-27a/b-3p could potentially predict the progression and severity of PD. Although both miRs had no similarity on expression, a positive correlation between both miRs was identified, supporting their potential role as biomarkers in clinical PD stages. Of note that SRRM2 and miR-27a-3p were able to distinguish PD patients from healthy individuals. Functional analysis of the similarity between genes associated with SRRM2 and miR-27a/b-3p indicates common functional pathways and their dysfunction correlates with molecular etiopathology mechanisms of PD onset.
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Affiliation(s)
- Soudabeh Fazeli
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Motovali-Bashi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Islamic Azad University, Shahrekord, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
| | - Motahare-Sadat Hashemi
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- * E-mail: (MMB); , (KG); (MP)
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Dykstra-Aiello C, Sharp FR, Jickling GC, Hull H, Hamade F, Shroff N, Durocher M, Cheng X, Zhan X, Liu D, Ander BP, Stamova BS. Alternative Splicing of Putative Stroke/Vascular Risk Factor Genes Expressed in Blood Following Ischemic Stroke Is Sexually Dimorphic and Cause-Specific. Front Neurol 2020; 11:584695. [PMID: 33193047 PMCID: PMC7642687 DOI: 10.3389/fneur.2020.584695] [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: 07/17/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies have identified putative ischemic stroke risk genes, yet, their expression after stroke is unexplored in spite of growing interest in elucidating their specific role and identifying candidate genes for stroke treatment. Thus, we took an exploratory approach to investigate sexual dimorphism, alternative splicing, and etiology in putative risk gene expression in blood following cardioembolic, atherosclerotic large vessel disease and small vessel disease/lacunar causes of ischemic stroke in each sex compared to controls. Whole transcriptome arrays assessed 71 putative stroke/vascular risk factor genes for blood RNA expression at gene-, exon-, and alternative splicing-levels. Male (n = 122) and female (n = 123) stroke and control volunteers from three university medical centers were matched for race, age, vascular risk factors, and blood draw time since stroke onset. Exclusion criteria included: previous stroke, drug abuse, subarachnoid or intracerebral hemorrhage, hemorrhagic transformation, infection, dialysis, cancer, hematological abnormalities, thrombolytics, anticoagulants or immunosuppressants. Significant differential gene expression (fold change > |1.2|, p < 0.05, partial correlation > |0.4|) and alternative splicing (false discovery rate p < 0.3) were assessed. At gene level, few were differentially expressed: ALDH2, ALOX5AP, F13A1, and IMPA2 (males, all stroke); ITGB3 (females, cardioembolic); ADD1 (males, atherosclerotic); F13A1, IMPA2 (males, lacunar); and WNK1 (females, lacunar). GP1BA and ITGA2B were alternatively spliced in both sexes (all patients vs. controls). Six genes in males, five in females, were alternatively spliced in all stroke compared to controls. Alternative splicing and exon-level analyses associated many genes with specific etiology in either sex. Of 71 genes, 70 had differential exon-level expression in stroke patients compared to control subjects. Among stroke patients, 24 genes represented by differentially expressed exons were male-specific, six were common between sexes, and two were female-specific. In lacunar stroke, expression of 19 differentially expressed exons representing six genes (ADD1, NINJ2, PCSK9, PEMT, SMARCA4, WNK1) decreased in males and increased in females. Results demonstrate alternative splicing and sexually dimorphic expression of most putative risk genes in stroke patients' blood. Since expression was also often cause-specific, sex, and etiology are factors to consider in stroke treatment trials and genetic association studies as society trends toward more personalized medicine.
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Affiliation(s)
- Cheryl Dykstra-Aiello
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Frank R Sharp
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Glen C Jickling
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Heather Hull
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Farah Hamade
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Natasha Shroff
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Marc Durocher
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Xiyuan Cheng
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Xinhua Zhan
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - DaZhi Liu
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Bradley P Ander
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
| | - Boryana S Stamova
- Department of Neurology, Medical Investigation of Neurodevelopmental Disorders (MIND) Institute Biosciences Building, University of California, Davis, Sacramento, CA, United States
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47
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Meydan C, Madrer N, Soreq H. The Neat Dance of COVID-19: NEAT1, DANCR, and Co-Modulated Cholinergic RNAs Link to Inflammation. Front Immunol 2020; 11:590870. [PMID: 33163005 PMCID: PMC7581732 DOI: 10.3389/fimmu.2020.590870] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 pandemic exerts inflammation-related parasympathetic complications and post-infection manifestations with major inter-individual variability. To seek the corresponding transcriptomic origins for the impact of COVID-19 infection and its aftermath consequences, we sought the relevance of long and short non-coding RNAs (ncRNAs) for susceptibility to COVID-19 infection. We selected inflammation-prone men and women of diverse ages among the cohort of Genome Tissue expression (GTEx) by mining RNA-seq datasets from their lung, and blood tissues, followed by quantitative qRT-PCR, bioinformatics-based network analyses and thorough statistics compared to brain cell culture and infection tests with COVID-19 and H1N1 viruses. In lung tissues from 57 inflammation-prone, but not other GTEx donors, we discovered sharp declines of the lung pathology-associated ncRNA DANCR and the nuclear paraspeckles forming neuroprotective ncRNA NEAT1. Accompanying increases in the acetylcholine-regulating transcripts capable of controlling inflammation co-appeared in SARS-CoV-2 infected but not H1N1 influenza infected lung cells. The lung cells-characteristic DANCR and NEAT1 association with inflammation-controlling transcripts could not be observed in blood cells, weakened with age and presented sex-dependent links in GTEx lung RNA-seq dataset. Supporting active involvement in the inflammatory risks accompanying COVID-19, DANCR’s decline associated with decrease of the COVID-19-related cellular transcript ACE2 and with sex-related increases in coding transcripts potentiating acetylcholine signaling. Furthermore, transcription factors (TFs) in lung, brain and cultured infected cells created networks with the candidate transcripts, indicating tissue-specific expression patterns. Supporting links of post-infection inflammatory and cognitive damages with cholinergic mal-functioning, man and woman-originated cultured cholinergic neurons presented differentiation-related increases of DANCR and NEAT1 targeting microRNAs. Briefly, changes in ncRNAs and TFs from inflammation-prone human lung tissues, SARS-CoV-2-infected lung cells and man and woman-derived differentiated cholinergic neurons reflected the inflammatory pathobiology related to COVID-19. By shifting ncRNA differences into comparative diagnostic and therapeutic profiles, our RNA-sequencing based Resource can identify ncRNA regulating candidates for COVID-19 and its associated immediate and predicted long-term inflammation and neurological complications, and sex-related therapeutics thereof. Our findings encourage diagnostics of involved tissue, and further investigation of NEAT1-inducing statins and anti-cholinergic medications in the COVID-19 context.
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Affiliation(s)
- Chanan Meydan
- Department of Internal Medicine, Mayanei Hayeshua Medical Center, Bnei Brak, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Central District, Leumit Health Services, Tel Aviv, Israel
| | - Nimrod Madrer
- The Department of Biological Chemistry and The Edmond and Lilly Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Department of Biological Chemistry and The Edmond and Lilly Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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48
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Wang D, Gao H, Li Y, Jiang S, Yong Y, Yang X. Genome-Scale Expression Pattern of Long Non-Coding RNAs in Chinese Uyghur Patients with Parkinson's Disease. Med Sci Monit 2020; 26:e925888. [PMID: 33031356 PMCID: PMC7552881 DOI: 10.12659/msm.925888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/23/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts thought to regulate gene expression at the post-transcriptional level. Some lncRNAs are associated with Parkinson's disease (PD) and participate in pathological processes of PD. The incidence of PD is relatively high in members of the Uyghur minority living in Xingjiang province of China. This study measured the expression of lncRNAs in the peripheral blood cells of Chinese Uyghur individuals with and without PD and analyzed the possible function of these lncRNAs in the development of PD. MATERIAL AND METHODS Peripheral blood samples were collected from 55 Uyghur patients with PD and 55 healthy volunteers. Total RNA was extracted, and the levels of expression of whole-genome lncRNAs and mRNAs in 10 samples (5 PD and 5 controls) were determined by microarray method. The expression levels of lncRNAs in all 100 subjects were determined by qRT-PCR. The lncRNA expression profiles of PD patients were determined based on lncRNA microarray chip analysis, and differentially expressed lncRNAs were identified. The results of chip analysis were confirmed in a large clinical cohort. RESULTS Comparison of subjects with and without PD identified 32 significantly up-regulated and 18 significantly down-regulated lncRNAs in the PD group. GO analysis showed that mRNAs encoding proteins involved in the regulation of biological processes were differentially expressed, with the inflammatory immune response being the most significantly related pathway. CONCLUSIONS The expression of lncRNAs in peripheral blood differed significantly in PD patients and controls. These differentially expressed lncRNAs may play a role in the development of PD.
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Affiliation(s)
- Dan Wang
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, P.R. China
| | - Hua Gao
- Department of Neurology, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, P.R. China
| | - Yanxia Li
- Department of Rehabilitation, Second Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, P.R. China
| | - Sen Jiang
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, P.R. China
| | - Yuxuan Yong
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, P.R. China
| | - Xinling Yang
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, P.R. China
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Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen‐Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. EMBO Mol Med 2020; 12:e11942. [PMID: 32715657 PMCID: PMC7507321 DOI: 10.15252/emmm.201911942] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are brain-abundant RNAs of mostly unknown functions. To seek their roles in Parkinson's disease (PD), we generated an RNA sequencing resource of several brain region tissues from dozens of PD and control donors. In the healthy substantia nigra (SN), circRNAs accumulate in an age-dependent manner, but in the PD SN this correlation is lost and the total number of circRNAs reduced. In contrast, the levels of circRNAs are increased in the other studied brain regions of PD patients. We also found circSLC8A1 to increase in the SN of PD individuals. CircSLC8A1 carries 7 binding sites for miR-128 and is strongly bound to the microRNA effector protein Ago2. Indeed, RNA targets of miR-128 are also increased in PD individuals, suggesting that circSLC8A1 regulates miR-128 function and/or activity. CircSLC8A1 levels also increased in cultured cells exposed to the oxidative stress-inducing agent paraquat but were decreased in cells treated with the neuroprotective antioxidant regulator drug Simvastatin. Together, our work links circSLC8A1 to oxidative stress-related Parkinsonism and suggests further exploration of its molecular function in PD.
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Affiliation(s)
- Mor Hanan
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Alon Simchovitz
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Nadav Yayon
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Shani Vaknine
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Roni Cohen‐Fultheim
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Miriam Karmon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Nimrod Madrer
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Talia Miriam Rohrlich
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Moria Maman
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Estelle R Bennett
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - David S Greenberg
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Eran Meshorer
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Department of GeneticsThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat GanIsrael
| | - Hermona Soreq
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Sebastian Kadener
- Department of Biological ChemistryThe Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
- Biology DepartmentBrandeis UniversityWalthamMAUSA
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50
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Acharya S, Salgado-Somoza A, Stefanizzi FM, Lumley AI, Zhang L, Glaab E, May P, Devaux Y. Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson's Disease. Int J Mol Sci 2020; 21:E6513. [PMID: 32899928 PMCID: PMC7555192 DOI: 10.3390/ijms21186513] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023] Open
Abstract
Parkinson's disease (PD) is a complex and heterogeneous disorder involving multiple genetic and environmental influences. Although a wide range of PD risk factors and clinical markers for the symptomatic motor stage of the disease have been identified, there are still no reliable biomarkers available for the early pre-motor phase of PD and for predicting disease progression. High-throughput RNA-based biomarker profiling and modeling may provide a means to exploit the joint information content from a multitude of markers to derive diagnostic and prognostic signatures. In the field of PD biomarker research, currently, no clinically validated RNA-based biomarker models are available, but previous studies reported several significantly disease-associated changes in RNA abundances and activities in multiple human tissues and body fluids. Here, we review the current knowledge of the regulation and function of non-coding RNAs in PD, focusing on microRNAs, long non-coding RNAs, and circular RNAs. Since there is growing evidence for functional interactions between the heart and the brain, we discuss the benefits of studying the role of non-coding RNAs in organ interactions when deciphering the complex regulatory networks involved in PD progression. We finally review important concepts of harmonization and curation of high throughput datasets, and we discuss the potential of systems biomedicine to derive and evaluate RNA biomarker signatures from high-throughput expression data.
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Affiliation(s)
- Shubhra Acharya
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Andrew I. Lumley
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Lu Zhang
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
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