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Quan W, Qin Y, Li J, Wang L, Song J, Xu J, Chen J. Causal role of myeloid cells in Parkinson's disease: Mendelian randomization study. Inflamm Res 2024; 73:809-818. [PMID: 38538756 DOI: 10.1007/s00011-024-01867-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 04/30/2024] Open
Abstract
BACKGROUND Previous studies have observed elevated myeloid cells in the peripheral blood of patients with Parkinson's disease (PD), but the causal relationship between them remains to be elucidated. We investigated whether there is a causal relationship between different subtypes of peripheral blood myeloid cells and PD using Mendelian randomization (MR) combined with bioinformatics analysis. Exploring the etiology of PD from the perspective of genetics can remove confounding factors and provide a more reliable theoretical basis for elucidating the pathogenesis of PD. METHODS Comprehensive two-sample MR analysis and sensitivity analyses were conducted to explore the causal associations between 64 myeloid cell signatures and PD risk. The Venn diagram and protein-protein interaction network analysis of instrumental variables (IV) corresponding genes were used to further investigate the potential mechanism of myeloid cells influencing the pathogenesis of PD. RESULTS We investigated the impact of four immunophenotypes on the risk of PD, including Im MDSC% CD33dim HLA DR- CD66b- (relative count), CD33dim HLA DR+ CD11b+% CD33dim HLA DR+ (relative count), and CD11b on Mo MDSC (MFI) and CD11b on CD33br HLA DR+ CD14dim (MFI), while an immunophenotype's protective effect on PD was observed CD45 on Im MDSC (MFI). The results of bioinformatics analysis showed that CD33, NTRK2, PLD2, GRIK2 and RELN had protein interactions with the risk genes of PD. CONCLUSIONS Our study has demonstrated a close genetic correlation between different subtypes of myeloid cells and PD, providing guidance for early identification and immunotherapeutic development in patients with PD.
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Affiliation(s)
- Wei Quan
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China
| | - Yidan Qin
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China
| | - Jia Li
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China
| | - Lin Wang
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China
| | - Jia Song
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China
| | - Jing Xu
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China
| | - Jiajun Chen
- Department of Neurology, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Road, Changchun, 130021, Jilin, China.
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Doskas T, Vadikolias K, Ntoskas K, Vavougios GD, Tsiptsios D, Stamati P, Liampas I, Siokas V, Messinis L, Nasios G, Dardiotis E. Neurocognitive Impairment and Social Cognition in Parkinson's Disease Patients. Neurol Int 2024; 16:432-449. [PMID: 38668129 PMCID: PMC11054167 DOI: 10.3390/neurolint16020032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
In addition to motor symptoms, neurocognitive impairment (NCI) affects patients with prodromal Parkinson's disease (PD). NCI in PD ranges from subjective cognitive complaints to dementia. The purpose of this review is to present the available evidence of NCI in PD and highlight the heterogeneity of NCI phenotypes as well as the range of factors that contribute to NCI onset and progression. A review of publications related to NCI in PD up to March 2023 was performed using PubMed/Medline. There is an interconnection between the neurocognitive and motor symptoms of the disease, suggesting a common underlying pathophysiology as well as an interconnection between NCI and non-motor symptoms, such as mood disorders, which may contribute to confounding NCI. Motor and non-motor symptom evaluation could be used prognostically for NCI onset and progression in combination with imaging, laboratory, and genetic data. Additionally, the implications of NCI on the social cognition of afflicted patients warrant its prompt management. The etiology of NCI onset and its progression in PD is multifactorial and its effects are equally grave as the motor effects. This review highlights the importance of the prompt identification of subjective cognitive complaints in PD patients and NCI management.
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Affiliation(s)
- Triantafyllos Doskas
- Department of Neurology, Athens Naval Hospital, 11521 Athens, Greece;
- Department of Neurology, General University Hospital of Alexandroupoli, 68100 Alexandroupoli, Greece; (K.V.); (D.T.)
| | - Konstantinos Vadikolias
- Department of Neurology, General University Hospital of Alexandroupoli, 68100 Alexandroupoli, Greece; (K.V.); (D.T.)
| | | | - George D. Vavougios
- Department of Neurology, Athens Naval Hospital, 11521 Athens, Greece;
- Department of Neurology, Faculty of Medicine, University of Cyprus, 1678 Lefkosia, Cyprus
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Dimitrios Tsiptsios
- Department of Neurology, General University Hospital of Alexandroupoli, 68100 Alexandroupoli, Greece; (K.V.); (D.T.)
| | - Polyxeni Stamati
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.S.); (I.L.); (V.S.); (E.D.)
| | - Ioannis Liampas
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.S.); (I.L.); (V.S.); (E.D.)
| | - Vasileios Siokas
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.S.); (I.L.); (V.S.); (E.D.)
| | - Lambros Messinis
- School of Psychology, Laboratory of Neuropsychology and Behavioural Neuroscience, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Grigorios Nasios
- Department of Speech and Language Therapy, School of Health Sciences, University of Ioannina, 45500 Ioannina, Greece;
| | - Efthimios Dardiotis
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.S.); (I.L.); (V.S.); (E.D.)
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Tian Q, Sun X, Li C, Yang Y, Hou B, Xie A. CD33 polymorphisms and Parkinson's disease Parkinson's disease in northern Chinese Han population: A case-control study. Neurosci Lett 2023; 812:137400. [PMID: 37479176 DOI: 10.1016/j.neulet.2023.137400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
OBJECTIVE Parkinson's disease (PD) represents the multisystem illness involving immunological and neuroinflammatory dysfunction. The present work focused on evaluating link of CD33 single nucleotide polymorphisms (SNPs) with PD vulnerability of the northern Chinese Han people, considering CD33's role as a critical immunoregulatory receptor in neuroinflammatory responses. METHODS The present case-control study included 475 PD cases together with 475 normal controls. A further division of PD patients into two categories was made: 74 patients with early-onset PD (EOPD; onset age ≤ 50 years) and 401 patients with late-onset PD (LOPD; onset age > 50 years). DNA extraction was conducted, followed by genotyping for 2SNPs of CD33 polymorphisms with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). RESULTS Alleles (G vs. A, P = 0.028) and AA genotypes (P = 0.042) of rs12985029 were significantly different between the groups. Distinctions were observed between the two groups in the recessive, co-dominant, and additive models (nominal P = 0.030, nominal P = 0.045, and P = 0.032). AA genotype frequency among male PD was higher compared to corresponding male controls (P = 0.034), and in the male group allele A was a factor causing the disease (P = 0.026). The rs12985029 genotypes and allele frequency were different in EOPD compared with LOPD (P = 0.002, P = 0.002, respectively), and in LOPD group relative to healthy control group (P = 0.020 and P = 0.004, separately). Regarding the rs3826656 polymorphism, the frequency of GA genotype was higher in the control group than in the case group (nominal P = 0.036). Overdominance and co-dominant models were different between these groups (P = 0.026, nominal P = 0.030). Subgroup analysis revealed genotype frequency differences between rs3826656 LOPD group and control group (P = 0.018). Furthermore, relationship between rs3826656 and rs12985029 (D' = 0.162, r2 = 0.021) did not reach a complete level of linkage disequilibrium (LD) of northern Chinese Han people. CONCLUSION This study establishes an association between CD33 rs12985029 and rs3826656 polymorphisms and PD risk among the selected northern Chinese Han people. The GA genotype, rs3826656, may act as a protective factor against PD, while the A allele, rs12985029,could be genetic risk factor related to PD. Future research should include larger sample sizes and other human populations to further investigate how CD33 polymorphisms contribute to PD.
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Affiliation(s)
- Qing Tian
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China; Cerebral Vascular Disease Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaohui Sun
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chengqian Li
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yong Yang
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Binghui Hou
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Anmu Xie
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China; Cerebral Vascular Disease Institute, Affiliated Hospital of Qingdao University, Qingdao, China.
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Kim SH, Lim KH, Yang S, Joo JY. Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer's disease. FASEB J 2023; 37:e22702. [PMID: 36520044 DOI: 10.1096/fj.202201197r] [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: 07/28/2022] [Revised: 11/09/2022] [Accepted: 11/28/2022] [Indexed: 12/16/2022]
Abstract
Neurodegenerative diseases result from the interplay of abnormal gene expression and various pathological factors. Therefore, a disease-specific integrative genetic approach is required to understand the complexities and causes of target diseases. Recent studies have identified the correlation between genes encoding several transmembrane proteins, such as the cluster of differentiation (CD) and Alzheimer's disease (AD) pathogenesis. In this study, CD48 and CD40 gene expression in AD, a neurodegenerative disease, was analyzed to infer this link. Total RNA sequencing was performed using an Alzheimer's disease mouse model brain and blood, and gene expression was determined using a genome-wide association study (GWAS). We observed a marked elevation of CD48 and CD40 genes in Alzheimer's disease. Indeed, the upregulation of both CD48 and CD40 genes was significantly increased in the severe Alzheimer's disease group. With the elevation of CD48 and CD40 genes in Alzheimer's disease, associations of protein levels were also markedly increased in tissues. In addition, overexpression of CD48 and CD40 genes triggered tau aggregation, and co-expression of these genes accelerated aggregation. The nuclear factor kappa B (NF-ĸB) signaling pathway was enriched by CD48 and CD40 gene expression: it was also associated with tau pathology. Our data suggested that the CD48 and CD40 genes are novel AD-related genes, and this approach may be useful as a diagnostic or therapeutic target for the disease.
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Affiliation(s)
- Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
| | - Key-Hwan Lim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, Republic of Korea.,Department of Pharmacy, College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
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The Role of Bromodomain and Extraterminal (BET) Proteins in Controlling the Phagocytic Activity of Microglia In Vitro: Relevance to Alzheimer's Disease. Int J Mol Sci 2022; 24:ijms24010013. [PMID: 36613460 PMCID: PMC9820364 DOI: 10.3390/ijms24010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The correct phagocytic activity of microglia is a prerequisite for maintaining homeostasis in the brain. In the analysis of mechanisms regulating microglial phagocytosis, we focused on the bromodomain and extraterminal domain (BET) proteins: Brd2, Brd3, and Brd4, the acetylation code readers that control gene expression in cooperation with transcription factors. We used pharmacological (JQ1) and genetic (siRNA) inhibition of BET proteins in murine microglial cell line BV2. Inhibition of BET proteins reduced the phagocytic activity of BV2, as determined by using a fluorescent microspheres-based assay and fluorescently labelled amyloid-beta peptides. Gene silencing experiments demonstrated that all brain-existing BET isoforms control phagocytosis in microglia. From a set of 84 phagocytosis-related genes, we have found the attenuation of the expression of 14: Siglec1, Sirpb1a, Cd36, Clec7a, Itgam, Tlr3, Fcgr1, Cd14, Marco, Pld1, Fcgr2b, Anxa1, Tnf, Nod1, upon BET inhibition. Further analysis of the mRNA level of other phagocytosis-related genes which were involved in the pathomechanism of Alzheimer's disease demonstrated that JQ1 significantly reduced the expression of Cd33, Trem2, and Zyx. Our results indicate the important role of BET proteins in controlling microglial phagocytosis; therefore, targeting BET may be the efficient method of modulating microglial activity.
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Siokas V, Aloizou A, Liampas I, Bakirtzis C, Tsouris Z, Sgantzos M, Liakos P, Bogdanos DP, Hadjigeorgiou GM, Dardiotis E. Myelin-associated oligodendrocyte basic protein rs616147 polymorphism as a risk factor for Parkinson's disease. Acta Neurol Scand 2022; 145:223-228. [PMID: 34694630 DOI: 10.1111/ane.13538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/25/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND The rs616147 polymorphism of the myelin-associated oligodendrocyte basic protein (MOBP) gene locus has been associated with amyotrophic lateral sclerosis (ALS). ALS and Parkinson's disease (PD) are two common neurodegenerative disorders that share features regarding their etiology, pathophysiology, and genetic backgrounds. While the MOBP rs616147 polymorphism has been associated with ALS, little is known about its role in PD. OBJECTIVE To assess the role of MOBP rs616147 on PD risk. METHODS This case-control comparison study consists of 358 PD-affected cases and 358 controls from the Neurology Clinic of the University Hospital of Larissa, University of Thessaly, Faculty of Medicine, in Greece. The diagnosis of PD was made by a specialist neurologist according to the UK Parkinson's Disease Society Brain Bank's clinical criteria. All the participants were genotyped for the MOBP rs616147. Furthermore, in order to validate our results, we genotyped 327 patients with Alzheimer's disease (AD) for MOBP rs616147 and compared them with the control group. RESULTS According to the univariate analysis, there was a significant association between rs616147 and PD in the dominant (OR [95% C.I.] = 0.70 [0.52-0.94], p = .018), the overdominant (OR [95% C.I.] = 0.68 [0.50-0.92], p = .011), and in the codominant (G/A VS G/G; OR [95% C.I.] = 0.66 [0.48-0.91], p = .035) modes of inheritance. In contrast, there was no association between the MOBP rs616147 polymorphism and AD. CONCLUSIONS We provide preliminary results associating MOBP rs616147 genetic variant with PD.
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Affiliation(s)
- Vasileios Siokas
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
| | - Athina‐Maria Aloizou
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
| | - Ioannis Liampas
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
| | - Christos Bakirtzis
- B' Department of Neurology Multiple Sclerosis Center AHEPA University Hospital Aristotle University of Thessaloniki Thessaloniki Greece
| | - Zisis Tsouris
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
| | - Markos Sgantzos
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
| | - Panagiotis Liakos
- Laboratory of Biochemistry Faculty of Medicine University of Thessaly Larissa Greece
| | - Dimitrios P. Bogdanos
- Faculty of Medicine Department of Rheumatology and Clinical Immunology University General Hospital of Larissa School of Health Sciences University of Thessaly Larissa Greece
| | - Georgios M. Hadjigeorgiou
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
- Department of Neurology Medical School University of Cyprus Nicosia Cyprus
| | - Efthimios Dardiotis
- Laboratory of Neurogenetics Department of Neurology University Hospital of Larissa Faculty of Medicine School of Health Sciences Larissa Greece
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Pateraki G, Anargyros K, Aloizou AM, Siokas V, Bakirtzis C, Liampas I, Tsouris Z, Ziogka P, Sgantzos M, Folia V, Peristeri E, Dardiotis E. Therapeutic application of rTMS in neurodegenerative and movement disorders: A review. J Electromyogr Kinesiol 2021; 62:102622. [PMID: 34890834 DOI: 10.1016/j.jelekin.2021.102622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 12/11/2022] Open
Abstract
Transcranial magnetic stimulation (TMS) is a non-invasive form of brain stimulation that makes use of the magnetic field generated when an electric current passes through a magnetic coil placed over the scalp. It can be applied as a single stimulus at a time, in pairs of stimuli, or repetitively in trains of stimuli (repetitive TMS, rTMS). RTMS can induce changes in brain activity, whose after-effects reflect the processes of long-term potentiation and long-term depression, as certain protocols, namely those using low frequencies (≤1 Hz) seem to suppress cortical excitability, while those using high frequencies (>1 Hz) seem to enhance it. It is a technique with very few and mostly mild side-effects, whose effects can persist for long time periods, and as such, it has been studied as a potential treatment option in a multitude of neurodegenerative diseases, including those affecting movement. Although rTMS has received approval as a treatment strategy of only a few aspects in movement disorders in the latest guidelines, its further use seems to also be promising in their context. In this review, we gathered the available literature on the therapeutic application of rTMS in movement disorders, namely Parkinson's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Dystonia, Tic disorders and Essential Tremor.
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Affiliation(s)
- Georgia Pateraki
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Konstantinos Anargyros
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Athina-Maria Aloizou
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Vasileios Siokas
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Christos Bakirtzis
- B' Department of Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Liampas
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Zisis Tsouris
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Pinelopi Ziogka
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Markos Sgantzos
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Vasiliki Folia
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Eleni Peristeri
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece
| | - Efthimios Dardiotis
- Department of Neurology, University Hospital of Larissa, School of Medicine, University of Thessaly, Larissa, Greece.
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Najafi S, Tan SC, Raee P, Rahmati Y, Asemani Y, Lee EHC, Hushmandi K, Zarrabi A, Aref AR, Ashrafizadeh M, Kumar AP, Ertas YN, Ghani S, Aghamiri S. Gene regulation by antisense transcription: A focus on neurological and cancer diseases. Biomed Pharmacother 2021; 145:112265. [PMID: 34749054 DOI: 10.1016/j.biopha.2021.112265] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in high-throughput sequencing over the past decades have led to the identification of thousands of non-coding RNAs (ncRNAs), which play a major role in regulating gene expression. One emerging class of ncRNAs is the natural antisense transcripts (NATs), the RNA molecules transcribed from the opposite strand of a protein-coding gene locus. NATs are known to concordantly and discordantly regulate gene expression in both cis and trans manners at the transcriptional, post-transcriptional, translational, and epigenetic levels. Aberrant expression of NATs can therefore cause dysregulation in many biological pathways and has been observed in many genetic diseases. This review outlines the involvements and mechanisms of NATs in the pathogenesis of various diseases, with a special emphasis on neurodegenerative diseases and cancer. We also summarize recent findings on NAT knockdown and/or overexpression experiments and discuss the potential of NATs as promising targets for future gene therapies.
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Affiliation(s)
- Sajad Najafi
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yazdan Rahmati
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Yahya Asemani
- Department of Immunology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - E Hui Clarissa Lee
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey; Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul, Sariyer 34396, Turkey
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Vice President at Translational Sciences, Xsphera Biosciences Inc, 6 Tide Street, Boston, MA 02210, USA
| | - Milad Ashrafizadeh
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey; Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey; ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri 38039, Turkey
| | - Sepideh Ghani
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Aghamiri
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Rikos D, Siokas V, Burykina TI, Drakoulis N, Dardiotis E, Zintzaras E. Replication of chromosomal loci involved in Parkinson's disease: A quantitative synthesis of GWAS. Toxicol Rep 2021; 8:1762-1768. [PMID: 34712594 PMCID: PMC8528647 DOI: 10.1016/j.toxrep.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/15/2021] [Accepted: 10/09/2021] [Indexed: 11/16/2022] Open
Abstract
The first quantitative synthesis of GWAS regarding Parkinson’s Disease. Fifteen Parkinson’s Disease GWASs with 191.397 available SNPs pooled. User friendly software (METRADISC-XL) implemented. Seven chromosomal regions (bins) were replicated as associated with the Parkinson’s Disease trait.
Introduction Parkinson’s disease is a neurodegenerative disorder with a complex etiology coming from interactions between genetic and environmental factors. Research on Parkinson’s disease genetics has been an effortful struggle, while new technologies and novel study designs served as indispensable boosters. Until now, 90 loci and 20 disease-causing gene mutations have been identified. In this study we describe a novel non-parametric approach to GWAS meta-analysis and its application in PD genetics. Methods A literature search was conducted to identify Genome-Wide Association Studies (GWAS) regarding Parkinson’s disease. We applied predefined inclusion criteria and extracted the reported SNPs and their respective position and statistical significance. We divided all chromosomes in approximately equal genetic distance segments called bins and recorded the most significant SNP from each bin and each study and ranked them in terms of their p-value. Ranks from each bin were summed, averaged and added in a heterogeneity-based analysis using the METRADISC-XL software. Weighted and unweighted analysis was performed. Results Five-hundred and forty-three SNPs and their respective p-values from 15 studies were matched in their corresponding bins. The METRADISC-XL analysis resulted in 7 bins with a significant p-value. A bin on chromosome 4 where the SNCA gene is located found with genome-wide significant association with Parkinson’s Disease. Conclusion This is the first time a non-parametric method is applied in GWAS meta-analysis. The results add some insight on the overall understanding of Parkinson’s disease genetics and serve as a first step of further convergent analysis with Genome-wide linkage studies.
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Affiliation(s)
- Dimitrios Rikos
- Department of Neurology, University Hospital of Larissa, Faculty of Medicine, University of Thessaly, Larissa, Greece.,Department of Biomathematics, Faculty of Medicine, University of Thessaly Larissa, Greece
| | - Vasileios Siokas
- Department of Neurology, University Hospital of Larissa, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Tatyana I Burykina
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 119048 Moscow, Russian Federation
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 17551 Athens, Greece
| | - Efthimios Dardiotis
- Department of Neurology, University Hospital of Larissa, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Elias Zintzaras
- Department of Biomathematics, Faculty of Medicine, University of Thessaly Larissa, Greece.,The Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, United States
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