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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; 100:102373. [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] [MESH Headings] [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; Xinjiang Medical University, Urumqi 830017, 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
- 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; Xinjiang Medical University, Urumqi 830017, China.
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Tripathi S, Bhawana. Epigenetic Orchestration of Neurodegenerative Disorders: A Possible Target for Curcumin as a Therapeutic. Neurochem Res 2024; 49:2319-2335. [PMID: 38856890 DOI: 10.1007/s11064-024-04167-z] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024]
Abstract
Epigenetic modulations play a major role in gene expression and thus are responsible for various physiological changes including age-associated neurological disorders. Neurodegenerative diseases such as Alzheimer's (AD), Parkinson's (PD), Huntington's disease (HD), although symptomatically different, may share common underlying mechanisms. Most neurodegenerative diseases are associated with increased oxidative stress, aggregation of certain proteins, mitochondrial dysfunction, inactivation/dysregulation of protein degradation machinery, DNA damage and cell excitotoxicity. Epigenetic modulations has been reported to play a significant role in onset and progression of neurodegenerative diseases by regulating these processes. Previous studies have highlighted the marked antioxidant and neuroprotective abilities of polyphenols such as curcumin, by increased activity of detoxification systems like superoxide dismutase (SOD), catalase or glutathione peroxidase. The role of curcumin as an epigenetic modulator in neurological disorders and neuroinflammation apart from other chronic diseases have also been reported by a few groups. Nonetheless, the evidences for the role of curcumin mediated epigenetic modulation in its neuroprotective ability are still limited. This review summarizes the current knowledge of the role of mitochondrial dysfunction, epigenetic modulations and mitoepigenetics in age-associated neurological disorders such as PD, AD, HD, Amyotrophic Lateral Sclerosis (ALS), and Multiple Sclerosis (MS), and describes the neuroprotective effects of curcumin in the treatment and/or prevention of these neurodegenerative diseases by regulation of the epigenetic machinery.
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Affiliation(s)
- Shweta Tripathi
- Department of Paramedical Sciences, Faculty of Allied Health Sciences, SGT University, Gurugram, 122505, Haryana, India.
| | - Bhawana
- Department of Paramedical Sciences, Faculty of Allied Health Sciences, SGT University, Gurugram, 122505, Haryana, India
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Chen YC, Liaw YC, Nfor ON, Hsiao CH, Zhong JH, Wu SL, Liaw YP. Epigenetic associations of GPNMB rs199347 variant with alcohol consumption in Parkinson's disease. Front Psychiatry 2024; 15:1377403. [PMID: 39091454 PMCID: PMC11293056 DOI: 10.3389/fpsyt.2024.1377403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Alcohol consumption can induce a neuroinflammatory response and contribute to the progression of neurodegeneration. However, its association with Parkinson's disease (PD), the second most common neurodegenerative disorder, remains undetermined. Recent studies suggest that the glycoprotein non-metastatic melanoma protein B (GPNMB) is a potential biomarker for PD. We evaluated the association of rs199347, a variant of the GPNMB gene, with alcohol consumption and methylation upstream of GPNMB. Methods We retrieved genetic and DNA methylation data obtained from participants enrolled in the Taiwan Biobank (TWB) between 2008 and 2016. After excluding individuals with incomplete or missing information about potential PD risk factors, we included 1,357 participants in our final analyses. We used multiple linear regression to assess the association of GPNMB rs199347 and chronic alcohol consumption (and other potential risk factors) with GPNMB cg17274742 methylation. Results There was no difference between the distribution of GPNMB rs199347 genotypes between chronic alcohol consumers and the other study participants. A significant interaction was observed between the GPNMB rs199347 variant and alcohol consumption (p = 0.0102) concerning cg17274742 methylation. Compared to non-chronic alcohol consumers with the AA genotype, alcohol drinkers with the rs199347 GG genotype had significantly lower levels (hypomethylation) of cg17274742 (p = 0.0187). Conclusion Alcohol consumption among individuals with the rs199347 GG genotype was associated with lower levels of cg17274742 methylation, which could increase expression of the GPNMB gene, an important neuroinflammatory-related risk gene for PD.
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Affiliation(s)
- Yen-Chung Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chia Liaw
- Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, National Changhua University of Education, Changhua, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
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Xu H, Gupta S, Dinsmore I, Kollu A, Cawley AM, Anwar MY, Chen HH, Petty LE, Seshadri S, Graff M, Below P, Brody JA, Chittoor G, Fisher-Hoch SP, Heard-Costa NL, Levy D, Lin H, Loos RJF, Mccormick JB, Rotter JI, Mirshahi T, Still CD, Destefano A, Cupples LA, Mohlke KL, North KE, Justice AE, Liu CT. Integrating Genetic and Transcriptomic Data to Identify Genes Underlying Obesity Risk Loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.11.24308730. [PMID: 38903089 PMCID: PMC11188121 DOI: 10.1101/2024.06.11.24308730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Genome-wide association studies (GWAS) have identified numerous body mass index (BMI) loci. However, most underlying mechanisms from risk locus to BMI remain unknown. Leveraging omics data through integrative analyses could provide more comprehensive views of biological pathways on BMI. We analyzed genotype and blood gene expression data in up to 5,619 samples from the Framingham Heart Study (FHS). Using 3,992 single nucleotide polymorphisms (SNPs) at 97 BMI loci and 20,692 transcripts within 1 Mb, we performed separate association analyses of transcript with BMI and SNP with transcript (PBMI and PSNP, respectively) and then a correlated meta-analysis between the full summary data sets (PMETA). We identified transcripts that met Bonferroni-corrected significance for each omic, were more significant in the correlated meta-analysis than each omic, and were at least nominally associated with BMI in FHS data. Among 308 significant SNP-transcript-BMI associations, we identified seven genes (NT5C2, GSTM3, SNAPC3, SPNS1, TMEM245, YPEL3, and ZNF646) in five association regions. Using an independent sample of blood gene expression data, we validated results for SNAPC3 and YPEL3. We tested for generalization of these associations in hypothalamus, nucleus accumbens, and liver and observed significant (PMETA<0.05 & PMETA
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Affiliation(s)
- Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, 801 Massachusettes Ave, Boston, MA, 02118, USA
| | - Shreyash Gupta
- Department of Population Health Sciences, Geisinger, 100 N. Academy Ave., Danville, PA, 17822, USA
| | - Ian Dinsmore
- Department of Genomic Health, Geisinger, 100 N. Academy Ave., Danville, PA, 17822, USA
| | - Abbey Kollu
- Department of Psychology and Neuroscience, University of North Carolina, 235 E. Cameron Avenue, Chapel Hill, NC, 27599, USA
| | - Anne Marie Cawley
- Marsico Lung Institute, University of North Carolina, 125 Mason Farm Rd, Chapel Hill, NC, 27599, USA
| | - Mohammad Y. Anwar
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Hung-Hsin Chen
- Institute of Biomedical Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Taipei, Nangang District, 115201, Taiwan
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN, 37232, USA
| | - Lauren E. Petty
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN, 37232, USA
| | - Sudha Seshadri
- Department of Biostatistics, School of Public Health, Boston University, 801 Massachusettes Ave, Boston, MA, 02118, USA
- Department of Neurology, School of Medicine, Boston University, 85 East Concord Street, Boston, MA, 02118, USA
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, UT Health San Antonio, 8300 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Piper Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN, 37232, USA
| | - Jennifer A. Brody
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, 1730 Minor Ave, Seattle, WA, 98101, USA
| | - Geetha Chittoor
- Department of Population Health Sciences, Geisinger, 100 N. Academy Ave., Danville, PA, 17822, USA
| | - Susan P. Fisher-Hoch
- Department of Epidemiology, School of Public Health, UT Health Houston, Regional Academic Health Center, One West University Blvd, Brownsville, TX, 78520, USA
| | - Nancy L. Heard-Costa
- Framingham Heart Study, 73 Mt Wayte Ave, Framingham, MA, 01702, USA
- Department of Neurology, Chobanian & Avedisian School of Medicine, Boston University, 72 E Concord St, Boston, MA, 02118, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute of the National Institutes of Health, 6701 Rockledge Drive, Bethesda, MD, 20892, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, 55 N Lake Ave, Worcester, MA, 01655, USA
| | - Ruth JF. Loos
- Charles Bronfman Institute for Personalized Medicine at Mount Sinai, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Joseph B. Mccormick
- Department of Epidemiology, School of Public Health, UT Health Houston, Regional Academic Health Center, One West University Blvd, Brownsville, TX, 78520, USA
| | - Jerome I. Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, 1124 West Carson Street, Torrance, CA, 90502, USA
| | - Tooraj Mirshahi
- Department of Genomic Health, Geisinger, 100 N. Academy Ave., Danville, PA, 17822, USA
| | - Christopher D. Still
- Center for Obesity and Metabolic Health, Geisinger, 100 N. Academy Ave., Danville, PA, 17822, USA
| | - Anita Destefano
- Department of Biostatistics, School of Public Health, Boston University, 801 Massachusettes Ave, Boston, MA, 02118, USA
- Department of Neurology, School of Medicine, Boston University, 85 East Concord Street, Boston, MA, 02118, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, 801 Massachusettes Ave, Boston, MA, 02118, USA
| | - Karen L Mohlke
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, 135 Dauer Drive, Chapel Hill, NC, 27599, USA
| | - Anne E. Justice
- Department of Population Health Sciences, Geisinger, 100 N. Academy Ave., Danville, PA, 17822, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, 801 Massachusettes Ave, Boston, MA, 02118, USA
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Chen YC, Liaw YC, Nfor ON, Hsiao CH, Zhong JH, Wu SL, Liaw YP. Epigenetic regulation of Parkinson's disease risk variant GPNMB cg17274742 methylation by sex and exercise from Taiwan Biobank. Front Aging Neurosci 2023; 15:1235840. [PMID: 37744396 PMCID: PMC10513104 DOI: 10.3389/fnagi.2023.1235840] [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: 06/06/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Parkinson's disease (PD) is a complex neurodegenerative disease with an elusive etiology that involves the interaction between genetic, behavioral, and environmental factors. Recently, epigenetic modifications, particularly DNA methylation, have been recognized to play an important role in the onset of PD. Glycoprotein non-metastatic melanoma protein B (GPNMB), a type I transmembrane protein crucial for immune cell activation and maturation, has emerged as a potential biomarker for the risk of PD. This research aims to investigate the influence of exercise and gender on the regulation of methylation levels of GPNMB cg17274742 in individuals. Methods We analyze data from 2,474 participants in the Taiwan Biobank, collected from 2008 and 2016. Methylation levels at the GPNMB cg17274742 CpG site were measured using Illumina Infinium MethylationEPIC beads. After excluding individuals with incomplete data or missing information on possible risk factors, our final analysis included 1,442 participants. We used multiple linear regression models to assess the association between sex and exercise with adjusted levels of GPNMB cg17274742 for age, BMI, smoking, drinking, coffee consumption, serum uric acid levels, and hypertension. Results Our results demonstrated that exercise significantly influenced the methylation levels of GPNMB cg17274742 in males (β = -0.00242; p = 0.0026), but not in females (β = -0.00002362; p = 0.9785). Furthermore, male participants who exercised showed significantly lower levels of methylation compared to the reference groups of the female and non-exercising reference groups (β = -0.00357; p = 0.0079). The effect of the interaction between gender and exercise on the methylation of GPNMB cg17274742 was statistically significant (p = 0.0078). Conclusion This study suggests that gender and exercise can modulate GPNMB cg17274742, with hypomethylation observed in exercise men. More research is needed to understand the underlying mechanisms and implications of these epigenetic changes in the context of risk and prevention strategies.
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Affiliation(s)
- Yen-Chung Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chia Liaw
- Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, Changhua National University of Education, Changhua, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
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Wu L, Lin Y, Song J, Li L, Rao X, Wan W, Wei G, Hua F, Ying J. TMEM175: A lysosomal ion channel associated with neurological diseases. Neurobiol Dis 2023; 185:106244. [PMID: 37524211 DOI: 10.1016/j.nbd.2023.106244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/09/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
Lysosomes are acidic intracellular organelles with autophagic functions that are critical for protein degradation and mitochondrial homeostasis, while abnormalities in lysosomal physiological functions are closely associated with neurological disorders. Transmembrane protein 175 (TMEM175), an ion channel in the lysosomal membrane that is essential for maintaining lysosomal acidity, has been proven to coordinate with V-ATPase to modulate the luminal pH of the lysosome to assist the digestion of abnormal proteins and organelles. However, there is considerable controversy about the characteristics of TMEM175. In this review, we introduce the research progress on the structural, modulatory, and functional properties of TMEM175, followed by evidence of its relevance for neurological disorders. Finally, we discuss the potential value of TMEM175 as a therapeutic target in the hope of providing new directions for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Luojia Wu
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Yue Lin
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Jiali Song
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Longshan Li
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Xiuqin Rao
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Wei Wan
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Gen Wei
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China
| | - Fuzhou Hua
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China.
| | - Jun Ying
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, 330006, Nanchang, Jiangxi, China; Key Laboratory of Anesthesiology of Jiangxi Province, 1# Minde Road, 330006 Nanchang City, Jiangxi Privince, China.
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Tang T, Jian B, Liu Z. Transmembrane Protein 175, a Lysosomal Ion Channel Related to Parkinson's Disease. Biomolecules 2023; 13:biom13050802. [PMID: 37238672 DOI: 10.3390/biom13050802] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Lysosomes are membrane-bound organelles with an acidic lumen and are traditionally characterized as a recycling center in cells. Lysosomal ion channels are integral membrane proteins that form pores in lysosomal membranes and allow the influx and efflux of essential ions. Transmembrane protein 175 (TMEM175) is a unique lysosomal potassium channel that shares little sequence similarity with other potassium channels. It is found in bacteria, archaea, and animals. The prokaryotic TMEM175 consists of one six-transmembrane domain that adopts a tetrameric architecture, while the mammalian TMEM175 is comprised of two six-transmembrane domains that function as a dimer in lysosomal membranes. Previous studies have demonstrated that the lysosomal K+ conductance mediated by TMEM175 is critical for setting membrane potential, maintaining pH stability, and regulating lysosome-autophagosome fusion. AKT and B-cell lymphoma 2 regulate TMEM175's channel activity through direct binding. Two recent studies reported that the human TMEM175 is also a proton-selective channel under normal lysosomal pH (4.5-5.5) as the K+ permeation dramatically decreased at low pH while the H+ current through TMEM175 greatly increased. Genome-wide association studies and functional studies in mouse models have established that TMEM175 is implicated in the pathogenesis of Parkinson's disease, which sparks more research interests in this lysosomal channel.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Boshuo Jian
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zhenjiang Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
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Riederer P, Nagatsu T, Youdim MBH, Wulf M, Dijkstra JM, Sian-Huelsmann J. Lewy bodies, iron, inflammation and neuromelanin: pathological aspects underlying Parkinson's disease. J Neural Transm (Vienna) 2023; 130:627-646. [PMID: 37062012 PMCID: PMC10121516 DOI: 10.1007/s00702-023-02630-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/29/2023] [Indexed: 04/17/2023]
Abstract
Since the description of some peculiar symptoms by James Parkinson in 1817, attempts have been made to define its cause or at least to enlighten the pathology of "Parkinson's disease (PD)." The vast majority of PD subtypes and most cases of sporadic PD share Lewy bodies (LBs) as a characteristic pathological hallmark. However, the processes underlying LBs generation and its causal triggers are still unknown. ɑ-Synuclein (ɑ-syn, encoded by the SNCA gene) is a major component of LBs, and SNCA missense mutations or duplications/triplications are causal for rare hereditary forms of PD. Thus, it is imperative to study ɑ-syn protein and its pathology, including oligomerization, fibril formation, aggregation, and spreading mechanisms. Furthermore, there are synergistic effects in the underlying pathogenic mechanisms of PD, and multiple factors-contributing with different ratios-appear to be causal pathological triggers and progression factors. For example, oxidative stress, reduced antioxidative capacity, mitochondrial dysfunction, and proteasomal disturbances have each been suggested to be causal for ɑ-syn fibril formation and aggregation and to contribute to neuroinflammation and neural cell death. Aging is also a major risk factor for PD. Iron, as well as neuromelanin (NM), show age-dependent increases, and iron is significantly increased in the Parkinsonian substantia nigra (SN). Iron-induced pathological mechanisms include changes of the molecular structure of ɑ-syn. However, more recent PD research demonstrates that (i) LBs are detected not only in dopaminergic neurons and glia but in various neurotransmitter systems, (ii) sympathetic nerve fibres degenerate first, and (iii) at least in "brain-first" cases dopaminergic deficiency is evident before pathology induced by iron and NM. These recent findings support that the ɑ-syn/LBs pathology as well as iron- and NM-induced pathology in "brain-first" cases are important facts of PD pathology and via their interaction potentiate the disease process in the SN. As such, multifactorial toxic processes posted on a personal genetic risk are assumed to be causal for the neurodegenerative processes underlying PD. Differences in ratios of multiple factors and their spatiotemporal development, and the fact that common triggers of PD are hard to identify, imply the existence of several phenotypical subtypes, which is supported by arguments from both the "bottom-up/dual-hit" and "brain-first" models. Therapeutic strategies are necessary to avoid single initiation triggers leading to PD.
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Affiliation(s)
- Peter Riederer
- Clinic and Policlinic for Psychiatry, Psychosomatics and Psychotherapy, University Hospital Wuerzburg, Margarete-Höppel-Platz 1, 97080, Würzburg, Germany.
- Department of Psychiatry, University of Southern Denmark Odense, J.B. Winslows Vey 18, 5000, Odense, Denmark.
| | - Toshiharu Nagatsu
- Center for Research Promotion and Support, School of Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | | | - Max Wulf
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, 44801, Bochum, Germany
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Allele-specific expression analysis for complex genetic phenotypes applied to a unique dilated cardiomyopathy cohort. Sci Rep 2023; 13:564. [PMID: 36631531 PMCID: PMC9834222 DOI: 10.1038/s41598-023-27591-7] [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: 09/12/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Allele-specific expression (ASE) analysis detects the relative abundance of alleles at heterozygous loci as a proxy for cis-regulatory variation, which affects the personal transcriptome and proteome. This study describes the development and application of an ASE analysis pipeline on a unique cohort of 87 well phenotyped and RNA sequenced patients from the Maastricht Cardiomyopathy Registry with dilated cardiomyopathy (DCM), a complex genetic disorder with a remaining gap in explained heritability. Regulatory processes for which ASE is a proxy might explain this gap. We found an overrepresentation of known DCM-associated genes among the significant results across the cohort. In addition, we were able to find genes of interest that have not been associated with DCM through conventional methods such as genome-wide association or differential gene expression studies. The pipeline offers RNA sequencing data processing, individual and population level ASE analyses as well as group comparisons and several intuitive visualizations such as Manhattan plots and protein-protein interaction networks. With this pipeline, we found evidence supporting the case that cis-regulatory variation contributes to the phenotypic heterogeneity of DCM. Additionally, our results highlight that ASE analysis offers an additional layer to conventional genomic and transcriptomic analyses for candidate gene identification and biological insight.
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Chen SY, Li C, Luo Z, Li X, Jia X, Lai SJ. Favoring Expression of Yak Alleles in Interspecies F1 Hybrids of Cattle and Yak Under High-Altitude Environments. Front Vet Sci 2022; 9:892663. [PMID: 35847643 PMCID: PMC9280030 DOI: 10.3389/fvets.2022.892663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022] Open
Abstract
Both cis- and trans-regulation could cause differential expression between the parental alleles in diploid species that might have broad biological implications. Due to the relatively distant genetic divergence between cattle and yak, as well as their differential adaptation to high-altitude environments, we investigated genome-wide allelic differential expression (ADE) in their F1 hybrids using Nanopore long-read RNA-seq technology. From adult F1 hybrids raised in high-altitude, ten lung and liver tissues were individually sequenced for producing 31.6 M full-length transcript sequences. Mapping against autosomal homologous regions between cattle and yak, we detected 17,744 and 14,542 protein-encoding genes expressed in lung and liver tissues, respectively. According to the parental assignments of transcript sequences, a total of 3,381 genes were detected to show ADE in at least one sample. There were 186 genes showing ubiquitous ADE in all the studied animals, and among them 135 and 37 genes had consistent higher expression of yak and cattle alleles, respectively. Functional analyses revealed that the genes with favoring expression of yak alleles have been involved in the biological progresses related with hypoxia adaptation and immune response. In contrast, the genes with favoring expression of cattle alleles have been enriched into different biological progresses, such as secretion of endocrine hormones and lipid metabolism. Our results would support unequal contribution of parental genes to environmental adaptation in the F1 hybrids of cattle and yak.
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Affiliation(s)
- Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Shi-Yi Chen
| | - Cao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhihao Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Longri Breeding Farm of Sichuan Province, Hongyuan, China
| | - Xiaowei Li
- Longri Breeding Farm of Sichuan Province, Hongyuan, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Harwood MP, Alves I, Edgington H, Agbessi M, Bruat V, Soave D, Lamaze FC, Favé MJ, Awadalla P. Recombination affects allele-specific expression of deleterious variants in human populations. SCIENCE ADVANCES 2022; 8:eabl3819. [PMID: 35559670 PMCID: PMC9106294 DOI: 10.1126/sciadv.abl3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
How the genetic composition of a population changes through stochastic processes, such as genetic drift, in combination with deterministic processes, such as selection, is critical to understanding how phenotypes vary in space and time. Here, we show how evolutionary forces affecting selection, including recombination and effective population size, drive genomic patterns of allele-specific expression (ASE). Integrating tissue-specific genotypic and transcriptomic data from 1500 individuals from two different cohorts, we demonstrate that ASE is less often observed in regions of low recombination, and loci in high or normal recombination regions are more efficient at using ASE to underexpress harmful mutations. By tracking genetic ancestry, we discriminate between ASE variability due to past demographic effects, including subsequent bottlenecks, versus local environment. We observe that ASE is not randomly distributed along the genome and that population parameters influencing the efficacy of natural selection alter ASE levels genome wide.
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Affiliation(s)
- Michelle P. Harwood
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Isabel Alves
- Université de Nantes, CHU Nantes, CNRS, INSERM, L’Institut du thorax, F-44000 Nantes, France
| | | | | | - Vanessa Bruat
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Mathematics, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Fabien C. Lamaze
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, QC, Canada
| | | | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022; 74:101554. [PMID: 34973458 DOI: 10.1016/j.arr.2021.101554] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is a common motor disorder that has become increasingly prevalent in the ageing population. Recent works have suggested that circadian rhythms disruption is a common event in PD patients. Clock genes regulate the circadian rhythm of biological processes in eukaryotic organisms, but their roles in PD remain unclear. Despite this, several lines of evidence point to the possibility that clock genes may have a significant impact on the development and progression of the disease. This review aims to consolidate recent understanding of the roles of clock genes in PD. We first summarized the findings of clock gene expression and epigenetic analyses in PD patients and animal models. We also discussed the potential contributory role of clock gene variants in the development of PD and/or its symptoms. We further reviewed the mechanisms by which clock genes affect mitochondrial dynamics as well as the rhythmic synthesis and secretion of endocrine hormones, the impairment of which may contribute to the development of PD. Finally, we discussed the limitations of the currently available studies, and suggested future potential studies to deepen our understanding of the roles of clock genes in PD pathogenesis.
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Affiliation(s)
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Mai Abdelgawad
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef 62511, Egypt
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
| | - Muhammad Bilal
- College of Pharmacy, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | | | | | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Peterlee Place NSW2700, Australia; AFNP Med, Haidingergasse 29, 1030 Wien, Austria
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022; 74:101554. [DOI: https:/doi.org/10.1016/j.arr.2021.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022. [DOI: https://doi.org/10.1016/j.arr.2021.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sarchione A, Marchand A, Taymans JM, Chartier-Harlin MC. Alpha-Synuclein and Lipids: The Elephant in the Room? Cells 2021; 10:2452. [PMID: 34572099 PMCID: PMC8467310 DOI: 10.3390/cells10092452] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/17/2022] Open
Abstract
Since the initial identification of alpha-synuclein (α-syn) at the synapse, numerous studies demonstrated that α-syn is a key player in the etiology of Parkinson's disease (PD) and other synucleinopathies. Recent advances underline interactions between α-syn and lipids that also participate in α-syn misfolding and aggregation. In addition, increasing evidence demonstrates that α-syn plays a major role in different steps of synaptic exocytosis. Thus, we reviewed literature showing (1) the interplay among α-syn, lipids, and lipid membranes; (2) advances of α-syn synaptic functions in exocytosis. These data underscore a fundamental role of α-syn/lipid interplay that also contributes to synaptic defects in PD. The importance of lipids in PD is further highlighted by data showing the impact of α-syn on lipid metabolism, modulation of α-syn levels by lipids, as well as the identification of genetic determinants involved in lipid homeostasis associated with α-syn pathologies. While questions still remain, these recent developments open the way to new therapeutic strategies for PD and related disorders including some based on modulating synaptic functions.
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Affiliation(s)
| | | | | | - Marie-Christine Chartier-Harlin
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172—LilNCog—Lille Neuroscience and Cognition, F-59000 Lille, France; (A.S.); (A.M.); (J.-M.T.)
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Markopoulou K, Chase BA, Premkumar AP, Schoneburg B, Kartha N, Wei J, Yu H, Epshteyn A, Garduno L, Pham A, Vazquez R, Frigerio R, Maraganore D. Variable Effects of PD-Risk Associated SNPs and Variants in Parkinsonism-Associated Genes on Disease Phenotype in a Community-Based Cohort. Front Neurol 2021; 12:662278. [PMID: 33935957 PMCID: PMC8079937 DOI: 10.3389/fneur.2021.662278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic risk factors for Parkinson's disease (PD) risk and progression have been identified from genome-wide association studies (GWAS), as well as studies of familial forms of PD, implicating common variants at more than 90 loci and pathogenic or likely pathogenic variants at 16 loci. With the goal of understanding whether genetic variants at these PD-risk loci/genes differentially contribute to individual clinical phenotypic characteristics of PD, we used structured clinical documentation tools within the electronic medical record in an effort to provide a standardized and detailed clinical phenotypic characterization at the point of care in a cohort of 856 PD patients. We analyzed common SNPs identified in previous GWAS studies, as well as low-frequency and rare variants at parkinsonism-associated genes in the MDSgene database for their association with individual clinical characteristics and test scores at baseline assessment in our community-based PD patient cohort: age at onset, disease duration, Unified Parkinson's Disease Rating Scale I-VI, cognitive status, initial and baseline motor and non-motor symptoms, complications of levodopa therapy, comorbidities and family history of neurological disease with one or more than one affected family members. We find that in most cases an individual common PD-risk SNP identified in GWAS is associated with only a single clinical feature or test score, while gene-level tests assessing low-frequency and rare variants reveal genes associated in either a unique or partially overlapping manner with the different clinical features and test scores. Protein-protein interaction network analysis of the identified genes reveals that while some of these genes are members of already identified protein networks others are not. These findings indicate that genetic risk factors for PD differentially affect the phenotypic presentation and that genes associated with PD risk are also differentially associated with individual disease phenotypic characteristics at baseline. These findings raise the intriguing possibility that different SNPs/gene effects impact discrete phenotypic characteristics. Furthermore, they support the hypothesis that different gene and protein-protein interaction networks that underlie PD risk, the PD phenotype, and the neurodegenerative process leading to the disease phenotype, and point to the significance of the genetic background on disease phenotype.
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Affiliation(s)
- Katerina Markopoulou
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Bruce A. Chase
- Health Information Technology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Ashvini P. Premkumar
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Bernadette Schoneburg
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Ninith Kartha
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, United States
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, United States
| | - Alexander Epshteyn
- Health Information Technology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Lisette Garduno
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Anna Pham
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Rosa Vazquez
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Roberta Frigerio
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL, United States
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