1
|
Wu YS, Zheng WH, Liu TH, Sun Y, Xu YT, Shao LZ, Cai QY, Tang YQ. Joint-tissue integrative analysis identifies high-risk genes for Parkinson's disease. Front Neurosci 2024; 18:1309684. [PMID: 38576865 PMCID: PMC10991821 DOI: 10.3389/fnins.2024.1309684] [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: 10/08/2023] [Accepted: 02/22/2024] [Indexed: 04/06/2024] Open
Abstract
The loss of dopaminergic neurons in the substantia nigra and the abnormal accumulation of synuclein proteins and neurotransmitters in Lewy bodies constitute the primary symptoms of Parkinson's disease (PD). Besides environmental factors, scholars are in the early stages of comprehending the genetic factors involved in the pathogenic mechanism of PD. Although genome-wide association studies (GWAS) have unveiled numerous genetic variants associated with PD, precisely pinpointing the causal variants remains challenging due to strong linkage disequilibrium (LD) among them. Addressing this issue, expression quantitative trait locus (eQTL) cohorts were employed in a transcriptome-wide association study (TWAS) to infer the genetic correlation between gene expression and a particular trait. Utilizing the TWAS theory alongside the enhanced Joint-Tissue Imputation (JTI) technique and Mendelian Randomization (MR) framework (MR-JTI), we identified a total of 159 PD-associated genes by amalgamating LD score, GTEx eQTL data, and GWAS summary statistic data from a substantial cohort. Subsequently, Fisher's exact test was conducted on these PD-associated genes using 5,152 differentially expressed genes sourced from 12 PD-related datasets. Ultimately, 29 highly credible PD-associated genes, including CTX1B, SCNA, and ARSA, were uncovered. Furthermore, GO and KEGG enrichment analyses indicated that these genes primarily function in tissue synthesis, regulation of neuron projection development, vesicle organization and transportation, and lysosomal impact. The potential PD-associated genes identified in this study not only offer fresh insights into the disease's pathophysiology but also suggest potential biomarkers for early disease detection.
Collapse
Affiliation(s)
- Ya-Shi Wu
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Wen-Han Zheng
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yan Sun
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yu-Ting Xu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Li-Zhen Shao
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Qin-Yu Cai
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Ya Qin Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| |
Collapse
|
2
|
Besin V, Humardani FM, Yulianti T, Justyn M. Genomic profile of Parkinson's disease in Asians. Clin Chim Acta 2024; 552:117682. [PMID: 38016627 DOI: 10.1016/j.cca.2023.117682] [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: 09/28/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023]
Abstract
Parkinson's Disease (PD) has witnessed an alarming rise in prevalence, highlighting the suboptimal nature of early diagnostic and therapeutic strategies. To address this issue, genetic testing has emerged as a potential avenue. In this comprehensive review, we have meticulously summarized the variants associated with PD in Asian populations. Our review reveals that these variants exert their influence on diverse biological pathways, encompassing the autophagy-lysosome pathway, cholesterol metabolism, circadian rhythm regulation, immune system response, and synaptic function. Conventionally, PD has been linked to other diseases; however, our findings shed light on a shared genetic susceptibility among these conditions, implying an underlying pathophysiological mechanism that unifies them. Moreover, it is noteworthy that these PD-associated variants can significantly impact drug responses during therapeutic interventions. This review not only provides a consolidated overview of the genetic variants associated with PD in Asian populations but also contributes novel insights into the intricate relationships between PD and other diseases by elucidating shared genetic components. These findings underscore the importance of personalized approaches in diagnosing and treating PD based on individual genetic profiles to optimize patient outcomes.
Collapse
Affiliation(s)
- Valentinus Besin
- Faculty of Medicine, University of Surabaya, Surabaya 60292, Indonesia
| | - Farizky Martriano Humardani
- Faculty of Medicine, University of Surabaya, Surabaya 60292, Indonesia; Magister in Biomedical Science Program, Faculty of Medicine Universitas Brawijaya, Malang 65112, Indonesia.
| | - Trilis Yulianti
- Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Matthew Justyn
- Faculty of Pharmacy, Padjajaran University, Sumedang 45363, Indonesia
| |
Collapse
|
3
|
Tian Y, Ma G, Li H, Zeng Y, Zhou S, Wang X, Shan S, Xu Y, Xiong J, Cheng G. Shared Genetics and Comorbid Genes of Amyotrophic Lateral Sclerosis and Parkinson's Disease. Mov Disord 2023; 38:1813-1821. [PMID: 37534731 DOI: 10.1002/mds.29572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Comorbidity exists between amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD), but the role of genetic factors is unclear. OBJECTIVE We aim to investigate genetic correlation, causal relationship, and comorbid genes between ALS and PD. METHODS Leveraging the largest genome-wide association study data (ALS: 27,205 cases, 110,881 controls; PDG: 33,674 cases, 449,056 controls), we used linkage disequilibrium score regression and Mendelian randomization analysis for genetic correlation and causal inference. We performed genome-wide cross-trait analysis via Multi-Trait Analysis of Genome-Wide Association Studies and Cross-Phenotype Association to identify specific single-nucleotide polymorphisms, followed by functional mapping and annotation. Integrating expression quantitative trait loci data from 13 brain regions, we conducted a transcriptome-wide association study via functional summary-based imputation and joint-tissue imputation to explore comorbid genes, followed by pathway enrichment analysis. RESULTS We found that PD positively correlates with ALS (rg = 0.144, P = 0.026) and confers a causal effect (odds ratio = 1.09, 95% confidence interval: 1.03-1.15, P = 3.00 × 10-3 ). We identified nine single-nucleotide polymorphisms (eight new), associating with three risk loci (chromosomes 4, 10, and 17) and seven genes (TMEM175, MAPT, NSF, LRRC37A2, ARHGAP27, GAK, and FGFRL1). In transcriptome-wide association study analysis, we showed six previously unreported pleiotropic genes (KANSL1, ARL17B, EFNA1, WNT3, ERCC8, and ADAM15), and we found these candidate genes are mainly enriched in negative regulation of neuron projection development (GO:0010977). CONCLUSIONS Our work demonstrates shared genetic architecture between ALS and PD, reports new pleiotropic genes, and sheds light on the comorbid mechanism. © 2023 International Parkinson and Movement Disorder Society.
Collapse
Affiliation(s)
- Ye Tian
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Guochen Ma
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Haoqi Li
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yaxian Zeng
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Siquan Zhou
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xiaoyu Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Shufang Shan
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yujie Xu
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jingyuan Xiong
- Healthy Food Evaluation Research Center, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Guo Cheng
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
4
|
Miyazaki M, Hiramoto M, Takano N, Kokuba H, Takemura J, Tokuhisa M, Hino H, Kazama H, Miyazawa K. Targeted disruption of GAK stagnates autophagic flux by disturbing lysosomal dynamics. Int J Mol Med 2021; 48:195. [PMID: 34468012 PMCID: PMC8416139 DOI: 10.3892/ijmm.2021.5028] [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: 04/27/2021] [Accepted: 08/05/2021] [Indexed: 01/13/2023] Open
Abstract
The autophagy-lysosome system allows cells to adapt to environmental changes by regulating the degradation and recycling of cellular components, and to maintain homeostasis by removing aggregated proteins and defective organelles. Cyclin G-associated kinase (GAK) is involved in the regulation of clathrin-dependent endocytosis and cell cycle progression. In addition, a single nucleotide polymorphism at the GAK locus has been reported as a risk factor for Parkinson's disease. However, the roles of GAK in the autophagy-lysosome system are not completely understood, thus the present study aimed to clarify this. In the present study, under genetic disruption or chemical inhibition of GAK, analyzing autophagic flux and observing morphological changes of autophagosomes and autolysosomes revealed that GAK controlled lysosomal dynamics via actomyosin regulation, resulting in a steady progression of autophagy. GAK knockout (KO) in A549 cells impaired autophagosome-lysosome fusion and autophagic lysosome reformation, which resulted in the accumulation of enlarged autophagosomes and autolysosomes during prolonged starvation. The stagnation of autophagic flux accompanied by these phenomena was also observed with the addition of a GAK inhibitor. Furthermore, the addition of Rho-associated protein kinase (ROCK) inhibitor or ROCK1 knockdown mitigated GAK KO-mediated effects. The results suggested a vital role of GAK in controlling lysosomal dynamics via maintaining lysosomal homeostasis during autophagy.
Collapse
Affiliation(s)
- Masaya Miyazaki
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Masaki Hiramoto
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Naoharu Takano
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Hiroko Kokuba
- Laboratory of Electron Microscopy, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Jun Takemura
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Mayumi Tokuhisa
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Hirotsugu Hino
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Hiromi Kazama
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| | - Keisuke Miyazawa
- Department of Biochemistry, Tokyo Medical University, Tokyo 160‑8402, Japan
| |
Collapse
|
5
|
Joseph C, Mangani AS, Gupta V, Chitranshi N, Shen T, Dheer Y, Kb D, Mirzaei M, You Y, Graham SL, Gupta V. Cell Cycle Deficits in Neurodegenerative Disorders: Uncovering Molecular Mechanisms to Drive Innovative Therapeutic Development. Aging Dis 2020; 11:946-966. [PMID: 32765956 PMCID: PMC7390532 DOI: 10.14336/ad.2019.0923] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022] Open
Abstract
Cell cycle dysregulation has been implicated in the pathogenesis of neurodegenerative disorders. Specialised function obligates neuronal cells to subsist in a quiescent state of cell cycle once differentiated and therefore the circumstances and mechanisms underlying aberrant cell cycle activation in post-mitotic neurons in physiological and disease conditions remains an intriguing area of research. There is a strict requirement of concurrence to cell cycle regulation for neurons to ensure intracellular biochemical conformity as well as interrelationship with other cells within neural tissues. This review deliberates on various mechanisms underlying cell cycle regulation in neuronal cells and underscores potential implications of their non-compliance in neural pathology. Recent research suggests that successful duplication of genetic material without subsequent induction of mitosis induces inherent molecular flaws that eventually assert as apoptotic changes. The consequences of anomalous cell cycle activation and subsequent apoptosis are demonstrated by the increased presence of molecular stress response and apoptotic markers. This review delineates cell cycle events under normal physiological conditions and deficits amalgamated by alterations in protein levels and signalling pathways associated with cell-division are analysed. Cell cycle regulators essentially, cyclins, CDKs, cip/kip family of inhibitors, caspases, bax and p53 have been identified to be involved in impaired cell cycle regulation and associated with neural pathology. The pharmacological modulators of cell cycle that are shown to impart protection in various animal models of neurological deficits are summarised. Greater understanding of the molecular mechanisms that are indispensable to cell cycle regulation in neurons in health and disease conditions will facilitate targeted drug development for neuroprotection.
Collapse
Affiliation(s)
- Chitra Joseph
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Veer Gupta
- 2School of Medicine, Deakin University, Melbourne, VIC, Australia
| | - Nitin Chitranshi
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ting Shen
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Yogita Dheer
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Devaraj Kb
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Mehdi Mirzaei
- 3Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Yuyi You
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.,4Save Sight Institute, Sydney University, Sydney, NSW 2109, Australia
| | - Stuart L Graham
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.,4Save Sight Institute, Sydney University, Sydney, NSW 2109, Australia
| | - Vivek Gupta
- 1Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
6
|
Qu Y, Chen X, Xu MM, Sun Q. Relationship between high dietary fat intake and Parkinson's disease risk: a meta-analysis. Neural Regen Res 2019; 14:2156-2163. [PMID: 31397355 PMCID: PMC6788237 DOI: 10.4103/1673-5374.262599] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE: To assess whether dietary fat intake influences Parkinson’s disease risk. DATA SOURCES: We systematically surveyed the Embase and PubMed databases, reviewing manuscripts published prior to October 2018. The following terms were used: (“Paralysis agitans” OR “Parkinson disease” OR “Parkinson” OR “Parkinson’s” OR “Parkinson’s disease”) AND (“fat” OR “dietary fat” OR “dietary fat intake”). DATA SELECTION: Included studies were those with both dietary fat intake and Parkinson’s disease risk as exposure factors. The Newcastle-Ottawa Scale was adapted to investigate the quality of included studies. Stata V12.0 software was used for statistical analysis. OUTCOME MEASURES: The primary outcomes included the relationship between high total energy intake, high total fat intake, and Parkinson’s disease risk. The secondary outcomes included the relationship between different kinds of fatty acids and Parkinson’s disease risk. RESULTS: Nine articles met the inclusion criteria and were incorporated into this meta-analysis. Four studies scored 7 and the other five studies scored 9 on the Newcastle-Ottawa Scale, meaning that all studies were of high quality. Meta-analysis results showed that high total energy intake was associated with an increased risk of Parkinson’s disease (P = 0.000, odds ratio (OR) = 1.49, 95% confidence interval (CI): 1.26–1.75); in contrast, high total fat intake was not associated with Parkinson’s disease risk (P = 0.123, OR = 1.07, 95% CI: 0.91–1.25). Subgroup analysis revealed that polyunsaturated fatty acid intake (P = 0.010, OR = 1.03, 95% CI: 0.88–1.20) reduced the risk of Parkinson’s disease, while arachidonic acid (P = 0.026, OR = 1.15, 95% CI: 0.97–1.37) and cholesterol (P = 0.002, OR = 1.09, 95% CI: 0.92–1.29) both increased the risk of Parkinson’s disease. Subgroup analysis also demonstrated that, although the results were not significant, consumption of n-3 polyunsaturated fatty acids (P = 0.071, OR = 0.88, 95% CI: 0.73–1.05), α-linolenic acid (P = 0.06, OR = 0.86, 95% CI: 0.72–1.02), and the n-3 to n-6 ratio (P = 0.458, OR = 0.89, 95% CI: 0.75–1.06) were all linked with a trend toward reduced Parkinson’s disease risk. Monounsaturated fatty acid (P = 0.450, OR = 1.06, 95% CI: 0.91–1.23), n-6 polyunsaturated fatty acids (P = 0.100, OR = 1.15, 95% CI: 0.96–1.36) and linoleic acid (P = 0.053, OR = 1.11, 95% CI: 0.94–1.32) intakes were associated with a non-significant trend toward higher PD risk. Saturated fatty acid (P = 0.619, OR = 1.01, 95% CI: 0.87–1.18) intake was not associated with Parkinson’s disease. CONCLUSION: Dietary fat intake affects Parkinson’s disease risk, although this depends on the fatty acid subtype. Higher intake of polyunsaturated fatty acids may reduce the risk of Parkinson’s disease, while higher cholesterol and arachidonic acid intakes may elevate Parkinson’s disease risk. However, further studies and evidence are needed to validate any link between dietary fat intake and Parkinson’s disease.
Collapse
Affiliation(s)
- Yan Qu
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
| | - Xi Chen
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
| | - Man-Man Xu
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao, Shandong Province, China
| | - Qiang Sun
- Intensive Care Unit, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| |
Collapse
|
7
|
Jiménez-Jiménez FJ, Alonso-Navarro H, García-Martín E, Agúndez JAG. Advances in understanding genomic markers and pharmacogenetics of Parkinson's disease. Expert Opin Drug Metab Toxicol 2016; 12:433-48. [PMID: 26910127 DOI: 10.1517/17425255.2016.1158250] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The inheritance pattern of Parkinson's disease (PD) is likely multifactorial (owing to the interplay of genetic predisposition and environmental factors). Many pharmacogenetic studies have tried to establish a possible role of candidate genes in PD risk. Several studies have focused on the influence of genes in the response to antiparkinsonian drugs and in the risk of developing side-effects of these drugs. AREAS COVERED This review presents an overview of current knowledge, with particular emphasis on the most recent advances, both in case-control association studies on the role of candidate genes in the risk for PD as well as pharmacogenetic studies on the role of genes in the development of side effects of antiparkinsonian drugs. The most reliable results should be derived from meta-analyses of case-control association studies on candidate genes involving large series of PD patients and controls, and from genome-wide association studies (GWAS). EXPERT OPINION Prospective studies of large samples involving several genes with a detailed history of exposure to environmental factors in the same cohort of subjects, should be useful to clarify the role of genes in the risk for PD. The results of studies on the role of genes in the development of side-effects of antiparkinsonian drugs should, at this stage, only be considered preliminary.
Collapse
Affiliation(s)
| | | | | | - José A G Agúndez
- b Department of Pharmacology , University of Extremadura , Cáceres , Spain
| |
Collapse
|