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Feng T, Zheng H, Zhang Z, Fan P, Yang X. Mechanism and therapeutic targets of the involvement of a novel lysosomal proton channel TMEM175 in Parkinson's disease. Ageing Res Rev 2024:102373. [PMID: 38960046 DOI: 10.1016/j.arr.2024.102373] [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: 02/11/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
Parkinson's disease (PD), recognized as the second most prevalent neurodegenerative disease in the aging population, presents a significant challenge due to the current lack of effective treatment methods to mitigate its progression. Many pathogenesis of PD are related to lysosomal dysfunction. Moreover, extensive genetic studies have shown a significant correlation between the lysosomal membrane protein TMEM175 and the risk of developing PD. Building on this discovery, TMEM175 has been identified as a novel potassium ion channel. Intriguingly, further investigations have found that potassium ion channels gradually close and transform into hydrion "excretion" channels in the microenvironment of lysosomes. This finding was further substantiated by studies on TMEM175 knockout mice, which exhibited pronounced motor dysfunction in pole climbing and suspension tests, alongside a notable reduction in dopamine neurons within the substantia nigra compacta. Despite these advancements, the current research landscape is not without its controversies. In light of this, the present review endeavors to methodically examine and consolidate a vast array of recent literature on TMEM175. This comprehensive analysis spans from the foundational research on the structure and function of TMEM175 to expansive population genetics studies and mechanism research utilizing cellular and animal models.A thorough understanding of the structure and function of TMEM175, coupled with insights into the intricate mechanisms underpinning lysosomal dysfunction in PD dopaminergic neurons, is imperative. Such knowledge is crucial for pinpointing precise intervention targets, thereby paving the way for novel therapeutic strategies that could potentially alter the neurodegenerative trajectory of PD.
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Affiliation(s)
- Tingting Feng
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063,China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063,China
| | | | - Zhan Zhang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063,China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063,China
| | - Peidong Fan
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063,China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063,China
| | - Xinling Yang
- Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063,China; Xinjiang Medical University, Urumqi 830017,China.
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Çelik MH, Gagneur J, Lim RG, Wu J, Thompson LM, Xie X. Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers. HGG ADVANCES 2024; 5:100318. [PMID: 38872308 DOI: 10.1016/j.xhgg.2024.100318] [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: 11/17/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
The high heritability of amyotrophic lateral sclerosis (ALS) contrasts with its low molecular diagnosis rate post-genetic testing, pointing to potential undiscovered genetic factors. To aid the exploration of these factors, we introduced EpiOut, an algorithm to identify chromatin accessibility outliers that are regions exhibiting divergent accessibility from the population baseline in a single or few samples. Annotation of accessible regions with histone chromatin immunoprecipitation sequencing and Hi-C indicates that outliers are concentrated in functional loci, especially among promoters interacting with active enhancers. Across different omics levels, outliers are robustly replicated, and chromatin accessibility outliers are reliable predictors of gene expression outliers and aberrant protein levels. When promoter accessibility does not align with gene expression, our results indicate that molecular aberrations are more likely to be linked to post-transcriptional regulation rather than transcriptional regulation. Our findings demonstrate that the outlier detection paradigm can uncover dysregulated regions in rare diseases. EpiOut is available at github.com/uci-cbcl/EpiOut.
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Affiliation(s)
- Muhammed Hasan Çelik
- Department of Computer Science, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany; Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Ryan G Lim
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Leslie M Thompson
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA; UCI MIND, University of California Irvine, Irvine, CA, USA; Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California Irvine, Irvine, CA, USA; Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Xiaohui Xie
- Department of Computer Science, University of California Irvine, Irvine, CA, USA.
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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.
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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
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Song Z, Li W, Han Y, Xu Y, Wang Y. Investigating the shared genetic architecture between frailty and insomnia. Front Aging Neurosci 2024; 16:1358996. [PMID: 38425786 PMCID: PMC10903740 DOI: 10.3389/fnagi.2024.1358996] [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: 12/21/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Background The epidemiological association between frailty and insomnia is well established, yet the presence of a common genetic etiology is still uncertain. Further exploration is needed to ascertain the causal relationship between frailty and insomnia. Methods Utilizing data obtained from genome-wide association studies (GWAS) summaries, we utilized the linkage disequilibrium score regression (LDSC) to determine the genetic correlation existing between frailty and insomnia. The determination of causality was achieved through the application of two-sample Mendelian randomization. We investigated the enrichment of single nucleotide polymorphism (SNP) at various tissue types utilizing stratified LD score regression (S-LDSC) and multimarker analysis of genome annotation (MAGMA). Common risk SNPs were identified using Multi-Trait Analysis of GWAS (MTAG) and Cross-Phenotype Association (CPASSOC). We further investigated the expression profiles of risk genes in tissues using Summary-data-based Mendelian randomization(SMR) based on pooled data, to explore potential functional genes. Results Our findings indicated a significant genetic correlation between frailty and insomnia, highlighting SNPs sharing risk (rs34290943, rs10865954), with a pronounced correlation in the localized genomic region 3p21.31. Partitioned genetic analysis revealed 24 functional elements significantly associated with both frailty and insomnia. Furthermore, mendelian randomization revealed a causal connection between frailty and insomnia. The genetic correlation between frailty and insomnia showed enrichment in 11 brain regions (S-LDSC) and 9 brain regions (MAGMA), where four functional genes (RMB6, MST1R, RF123, and FAM212A) were identified. Conclusion This study suggests the existence of a genetic correlation and common risk genes between frailty and insomnia, contributing to a deeper comprehension of their pathogenesis and assists in identifying potential therapeutic targets.
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Affiliation(s)
- Zhiwei Song
- Department of Neurology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Wangyu Li
- Department of Pain Management, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Yupeng Han
- Department of Anesthesiology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Yiya Xu
- Department of Neurology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Yinzhou Wang
- Department of Neurology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Medical Analysis, Fujian Academy of Medical Sciences, Fuzhou, Fujian, China
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Ouyang J, Peng S, Wu G, Liu R. Association Between Neurodegenerative Diseases and an Increased Risk of Epilepsy Based on Single Nucleotide Polymorphisms: A Mendelian Randomization Study. Mol Neurobiol 2024:10.1007/s12035-024-03955-6. [PMID: 38261256 DOI: 10.1007/s12035-024-03955-6] [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: 05/21/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
Epilepsy is a common neurological disorder characterized by transient brain dysfunction, attributed to a multitude of factors. The purpose of this study is to explore whether neurodegenerative diseases, specifically Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS), have a causal effect on epilepsy. Mendelian randomization (MR) methods were used to analyze the causal association between neurodegenerative diseases (AD, PD, ALS, and MS) and epilepsy based on single nucleotide polymorphisms from genome-wide association studies, including inverse-variance weighted, weighted median, MR-Egger, and weighted mode methods. The reliability and stability of the MR analysis results were assessed by the MR-Egger intercept, MR-PRESSO, and heterogeneity tests. Forty-three SNPs were selected for the MR analysis of MS and epilepsy. The inverse-variance weighted method showed a significant causal association between MS and increased risk of epilepsy (odds ratio 1.046; 95% confidence interval 1.001-1.093; P = 0.043). However, AD (P = 0.986), PD (P = 0.894), and ALS (P = 0.533) were not causally associated with epilepsy. Sensitivity analysis showed that the results were robust. The MR study confirmed the causal relationship between genetically predicted MS and epilepsy but did not support the causal relationship between genetically predicted AD, PD, and ALS on epilepsy.
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Affiliation(s)
- Jia Ouyang
- Department of Neurosurgery, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Shijun Peng
- Department of Neurosurgery, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Guangyong Wu
- Department of Neurosurgery, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Ruen Liu
- Department of Neurosurgery, Peking University People's Hospital, Beijing, 100044, People's Republic of China.
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