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Lei B, Li Y, Fu W, Yang P, Chen S, Wang T, Xiao X, Niu T, Fu Y, Wang S, Han H, Qin J. Alzheimer's disease diagnosis from multi-modal data via feature inductive learning and dual multilevel graph neural network. Med Image Anal 2024; 97:103213. [PMID: 38850625 DOI: 10.1016/j.media.2024.103213] [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: 09/12/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/10/2024]
Abstract
Multi-modal data can provide complementary information of Alzheimer's disease (AD) and its development from different perspectives. Such information is closely related to the diagnosis, prevention, and treatment of AD, and hence it is necessary and critical to study AD through multi-modal data. Existing learning methods, however, usually ignore the influence of feature heterogeneity and directly fuse features in the last stages. Furthermore, most of these methods only focus on local fusion features or global fusion features, neglecting the complementariness of features at different levels and thus not sufficiently leveraging information embedded in multi-modal data. To overcome these shortcomings, we propose a novel framework for AD diagnosis that fuses gene, imaging, protein, and clinical data. Our framework learns feature representations under the same feature space for different modalities through a feature induction learning (FIL) module, thereby alleviating the impact of feature heterogeneity. Furthermore, in our framework, local and global salient multi-modal feature interaction information at different levels is extracted through a novel dual multilevel graph neural network (DMGNN). We extensively validate the proposed method on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and experimental results demonstrate our method consistently outperforms other state-of-the-art multi-modal fusion methods. The code is publicly available on the GitHub website. (https://github.com/xiankantingqianxue/MIA-code.git).
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Affiliation(s)
- Baiying Lei
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Yafeng Li
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Wanyi Fu
- Department of Electronic Engineering, Tsinghua University, Beijing Key Laboratory of Magnetic Resonance Imaging Devices and Technology, China
| | - Peng Yang
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Shaobin Chen
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Tianfu Wang
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Xiaohua Xiao
- The First Affiliated Hospital of Shenzhen University, Shenzhen University Medical School, Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 530031, China
| | - Tianye Niu
- Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Yu Fu
- Department of Neurology, Peking University Third Hospital, No. 49, North Garden Rd., Haidian District, Beijing, 100191, China.
| | - Shuqiang Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongbin Han
- Institute of Medical Technology, Peking University Health Science Center, Department of Radiology, Peking University Third Hospital, Beijing Key Laboratory of Magnetic Resonance Imaging Devices and Technology, Beijing, 100191, China; The second hospital of Dalian Medical University,Research and developing center of medical technology, Dalian, 116027, China.
| | - Jing Qin
- Center for Smart Health, School of Nursing, The Hong Kong Polytechnic University, Hong Kong, China
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Hou T, Liu K, Fa W, Liu C, Zhu M, Liang X, Ren Y, Xu S, Wang X, Tang S, Wang Y, Cong L, Tan Q, Du Y, Qiu C. Association of polygenic risk scores with Alzheimer's disease and plasma biomarkers among Chinese older adults: A community-based study. Alzheimers Dement 2024. [PMID: 39171679 DOI: 10.1002/alz.13924] [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: 12/29/2023] [Revised: 03/07/2024] [Accepted: 03/25/2024] [Indexed: 08/23/2024]
Abstract
INTRODUCTION We examined the associations of polygenic risk score (PRS) with Alzheimer's disease (AD) and plasma biomarkers in the Chinese population. METHODS This population-based study used baseline data from MIND-China (2018; n = 4873) and follow-up data from dementia-free individuals (2014-2018; n = 2117). We measured AD-related plasma biomarkers in a subsample (n = 1256). Data were analyzed using logistic and Cox regression models. RESULTS We developed PRS with (PRSAPOE) and without (PRSnon- APOE) apolipoprotein E (APOE) gene. In the longitudinal analysis, PRSAPOE was associated with a multivariable-adjusted hazards ratio of 1.91 (95% CI = 1.13-3.23) for AD. PRSAPOE in combination with demographics yielded discriminative (area under the curve [AUC]) and predictive(C-statistic) accuracy of 0.80 (95% confidence interval [CI] = 0.77-0.84) and 0.80 (0.77-0.82), respectively. PRSnon- APOE showed an association with AD risk similar to PRSAPOE. PRSAPOE, but not PRSnon- APOE, was associated with reduced plasma Aβ42/Aβ40 ratio and increased Neurofilament light chain (NfL) (p < 0.05). DISCUSSION The PRS with and without APOE gene, in combination with demographics, shows good discriminative and predictive ability for AD. The AD-related pathologies underlie AD risk associated with PRSAPOE. HIGHLIGHTS The PRSAPOE and PRSnon- APOE were associated with AD risk in the Chinese population. The PRSAPOE and PRSnon- APOE, in combination with demographics, showed good discriminative and predictive ability for AD. The AD-related pathologies underlie the AD risk associated with PRSAPOE but not PRSnon- APOE.
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Affiliation(s)
- Tingting Hou
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Keke Liu
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Wenxin Fa
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Cuicui Liu
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Min Zhu
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Xiaoyan Liang
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
| | - Yifei Ren
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
| | - Shan Xu
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
| | - Xiang Wang
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
| | - Shi Tang
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Yongxiang Wang
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Institute of Brain Science and Brain-Inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Department of Neurobiology, Care Sciences and Society, Aging Research Center and Center for Alzheimer Research, Karolinska Institute-Stockholm University, Solna, Sweden
| | - Lin Cong
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
| | - Qihuan Tan
- Department of Public Health, Epidemiology and Biostatistics, University of Southern Denmark, Odense, Denmark
| | - Yifeng Du
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, P.R. China
- Shandong Provincial Clinical Research Centre for Neurological Diseases, Jinan, Shandong, P.R. China
- Department of Neurology, Key Laboratory of Endocrine Glucose & Lipids Metabolism and Brain Aging, Ministry of Education, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Institute of Brain Science and Brain-Inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Chengxuan Qiu
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, P.R. China
- Institute of Brain Science and Brain-Inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Department of Neurobiology, Care Sciences and Society, Aging Research Center and Center for Alzheimer Research, Karolinska Institute-Stockholm University, Solna, Sweden
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Jonson C, Levine KS, Lake J, Hertslet L, Jones L, Patel D, Kim J, Bandres‐Ciga S, Terry N, Mata IF, Blauwendraat C, Singleton AB, Nalls MA, Yokoyama JS, Leonard HL. Assessing the lack of diversity in genetics research across neurodegenerative diseases: A systematic review of the GWAS Catalog and literature. Alzheimers Dement 2024; 20:5740-5756. [PMID: 39030740 PMCID: PMC11350004 DOI: 10.1002/alz.13873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 07/22/2024]
Abstract
The under-representation of non-European cohorts in neurodegenerative disease genome-wide association studies (GWAS) hampers precision medicine efforts. Despite the inherent genetic and phenotypic diversity in these diseases, GWAS research consistently exhibits a disproportionate emphasis on participants of European ancestry. This study reviews GWAS up to 2022, focusing on non-European or multi-ancestry neurodegeneration studies. We conducted a systematic review of GWAS results and publications up to 2022, focusing on non-European or multi-ancestry neurodegeneration studies. Rigorous article inclusion and quality assessment methods were employed. Of 123 neurodegenerative disease (NDD) GWAS reviewed, 82% predominantly featured European ancestry participants. A single European study identified over 90 risk loci, compared to a total of 50 novel loci in identified in all non-European or multi-ancestry studies. Notably, only six of the loci have been replicated. The significant under-representation of non-European ancestries in NDD GWAS hinders comprehensive genetic understanding. Prioritizing genomic diversity in future research is crucial for advancing NDD therapies and understanding. HIGHLIGHTS: Eighty-two percent of neurodegenerative genome-wide association studies (GWAS) focus on Europeans. Only 6 of 50 novel neurodegenerative disease (NDD) genetic loci have been replicated. Lack of diversity significantly hampers understanding of NDDs. Increasing diversity in NDD genetic research is urgently required. New initiatives are aiming to enhance diversity in NDD research.
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Affiliation(s)
- Caroline Jonson
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Kristin S. Levine
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
| | - Julie Lake
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Linnea Hertslet
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Lietsel Jones
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
| | - Dhairya Patel
- Integrative Neurogenomics UnitLaboratory of NeurogeneticsNational Institute on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Jeff Kim
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Sara Bandres‐Ciga
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Nancy Terry
- Division of Library ServicesOffice of Research ServicesNational Institutes of HealthBethesdaMarylandUSA
| | - Ignacio F. Mata
- Genomic Medicine Institute, Lerner Research Institute, Genomic MedicineCleveland Clinic FoundationClevelandOhioUSA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Integrative Neurogenomics UnitLaboratory of NeurogeneticsNational Institute on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Andrew B. Singleton
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Mike A. Nalls
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Jennifer S. Yokoyama
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Hampton L. Leonard
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
- Laboratory of NeurogeneticsNational Institutes on AgingNational Institutes of HealthBethesdaMarylandUSA
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
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Lee S, Hecker J, Hahn G, Mullin K, Lutz SM, Tanzi RE, Lange C, Prokopenko D. On the effect heterogeneity of established disease susceptibility loci for Alzheimer's disease across different genetic ancestries. Alzheimers Dement 2024; 20:3397-3405. [PMID: 38563508 PMCID: PMC11095441 DOI: 10.1002/alz.13796] [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: 11/17/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Genome-wide association studies have identified numerous disease susceptibility loci (DSLs) for Alzheimer's disease (AD). However, only a limited number of studies have investigated the dependence of the genetic effect size of established DSLs on genetic ancestry. METHODS We utilized the whole genome sequencing data from the Alzheimer's Disease Sequencing Project (ADSP) including 35,569 participants. A total of 25,459 subjects in four distinct populations (African ancestry, non-Hispanic White, admixed Hispanic, and Asian) were analyzed. RESULTS We found that nine DSLs showed significant heterogeneity across populations. Single nucleotide polymorphism (SNP) rs2075650 in translocase of outer mitochondrial membrane 40 (TOMM40) showed the largest heterogeneity (Cochran's Q = 0.00, I2 = 90.08), followed by other SNPs in apolipoprotein C1 (APOC1) and apolipoprotein E (APOE). Two additional loci, signal-induced proliferation-associated 1 like 2 (SIPA1L2) and solute carrier 24 member 4 (SLC24A4), showed significant heterogeneity across populations. DISCUSSION We observed substantial heterogeneity for the APOE-harboring 19q13.32 region with TOMM40/APOE/APOC1 genes. The largest risk effect was seen among African Americans, while Asians showed a surprisingly small risk effect.
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Affiliation(s)
- Sanghun Lee
- Department of Medical Consilience, Division of Medicine, Graduate school, Dankook University, Yongin-si, Gyeonggi-do, South Korea
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Georg Hahn
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kristina Mullin
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Sharon M Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
| | - Rudolph E Tanzi
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
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Gao S, Wang T, Han Z, Hu Y, Zhu P, Xue Y, Huang C, Chen Y, Liu G. Interpretation of 10 years of Alzheimer's disease genetic findings in the perspective of statistical heterogeneity. Brief Bioinform 2024; 25:bbae140. [PMID: 38711368 PMCID: PMC11074593 DOI: 10.1093/bib/bbae140] [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: 08/21/2023] [Revised: 02/22/2024] [Accepted: 03/14/2024] [Indexed: 05/08/2024] Open
Abstract
Common genetic variants and susceptibility loci associated with Alzheimer's disease (AD) have been discovered through large-scale genome-wide association studies (GWAS), GWAS by proxy (GWAX) and meta-analysis of GWAS and GWAX (GWAS+GWAX). However, due to the very low repeatability of AD susceptibility loci and the low heritability of AD, these AD genetic findings have been questioned. We summarize AD genetic findings from the past 10 years and provide a new interpretation of these findings in the context of statistical heterogeneity. We discovered that only 17% of AD risk loci demonstrated reproducibility with a genome-wide significance of P < 5.00E-08 across all AD GWAS and GWAS+GWAX datasets. We highlighted that the AD GWAS+GWAX with the largest sample size failed to identify the most significant signals, the maximum number of genome-wide significant genetic variants or maximum heritability. Additionally, we identified widespread statistical heterogeneity in AD GWAS+GWAX datasets, but not in AD GWAS datasets. We consider that statistical heterogeneity may have attenuated the statistical power in AD GWAS+GWAX and may contribute to explaining the low repeatability (17%) of genome-wide significant AD susceptibility loci and the decreased AD heritability (40-2%) as the sample size increased. Importantly, evidence supports the idea that a decrease in statistical heterogeneity facilitates the identification of genome-wide significant genetic loci and contributes to an increase in AD heritability. Collectively, current AD GWAX and GWAS+GWAX findings should be meticulously assessed and warrant additional investigation, and AD GWAS+GWAX should employ multiple meta-analysis methods, such as random-effects inverse variance-weighted meta-analysis, which is designed specifically for statistical heterogeneity.
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Affiliation(s)
- Shan Gao
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No. 10, Xitoutiao, You’an Men Wai, Fengtai District, Beijing 100069, China
| | - Tao Wang
- Chinese Institute for Brain Research, No. 26, Kexueyuan Road, Changping District, Beijing 102206, China
| | - Zhifa Han
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, No. 5, Dongdan Santichao, Dongcheng District, Beijing 100193, China
| | - Yang Hu
- School of Computer Science and Technology, Harbin Institute of Technology, No. 92, Xidazhi Street, Nangang District, Harbin 150006, China
| | - Ping Zhu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No. 10, Xitoutiao, You’an Men Wai, Fengtai District, Beijing 100069, China
| | - Yanli Xue
- School of Biomedical Engineering, Capital Medical University, No. 10 Xitoutiao, You'an Men Wai, Fengtai District, Beijing 100069, China
| | - Chen Huang
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida WaiLong, Taipa 999078, Macao SAR, China
| | - Yan Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wannan Medical College, No. 22, Wenchang Road, Wuhu 241002, Anhui, China
- Institute of Chronic Disease Prevention and Control, Wannan Medical College, No. 22, Wenchang Road, Wuhu 241002, Anhui, China
| | - Guiyou Liu
- Chinese Institute for Brain Research, No. 26, Kexueyuan Road, Changping District, Beijing 102206, China
- Department of Epidemiology and Biostatistics, School of Public Health, Wannan Medical College, No. 22, Wenchang Road, Wuhu 241002, Anhui, China
- Institute of Chronic Disease Prevention and Control, Wannan Medical College, No. 22, Wenchang Road, Wuhu 241002, Anhui, China
- Key Laboratory of Cerebral Microcirculation in Universities of Shandong, Department of Neurology, Second Affiliated Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271000, Shandong, China
- Beijing Key Laboratory of Hypoxia Translational Medicine, National Engineering Laboratory of Internet Medical Diagnosis and Treatment Technology, Xuanwu Hospital, Capital Medical University, No. 45, Changchun Road, Xicheng District, Beijing 100053, China
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Zarrella JA, Tsurumi A. Genome-wide transcriptome profiling and development of age prediction models in the human brain. Aging (Albany NY) 2024; 16:4075-4094. [PMID: 38428408 PMCID: PMC10968712 DOI: 10.18632/aging.205609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/28/2023] [Indexed: 03/03/2024]
Abstract
Aging-related transcriptome changes in various regions of the healthy human brain have been explored in previous works, however, a study to develop prediction models for age based on the expression levels of specific panels of transcripts is lacking. Moreover, studies that have assessed sexually dimorphic gene activities in the aging brain have reported discrepant results, suggesting that additional studies would be advantageous. The prefrontal cortex (PFC) region was previously shown to have a particularly large number of significant transcriptome alterations during healthy aging in a study that compared different regions in the human brain. We harmonized neuropathologically normal PFC transcriptome datasets obtained from the Gene Expression Omnibus (GEO) repository, ranging in age from 21 to 105 years, and found a large number of differentially regulated transcripts in the old and elderly, compared to young samples overall, and compared female and male-specific expression alterations. We assessed the genes that were associated with age by employing ontology, pathway, and network analyses. Furthermore, we applied various established (least absolute shrinkage and selection operator (Lasso) and Elastic Net (EN)) and recent (eXtreme Gradient Boosting (XGBoost) and Light Gradient Boosting Machine (LightGBM)) machine learning algorithms to develop accurate prediction models for chronological age and validated them. Studies to further validate these models in other large populations and molecular studies to elucidate the potential mechanisms by which the transcripts identified may be related to aging phenotypes would be advantageous.
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Affiliation(s)
- Joseph A. Zarrella
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Shriner's Hospitals for Children-Boston, Boston, MA 02114, USA
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7
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Jonson C, Levine KS, Lake J, Hertslet L, Jones L, Patel D, Kim J, Bandres-Ciga S, Terry N, Mata IF, Blauwendraat C, Singleton AB, Nalls MA, Yokoyama JS, Leonard HL. Assessing the lack of diversity in genetics research across neurodegenerative diseases: a systematic review of the GWAS Catalog and literature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.08.24301007. [PMID: 38260595 PMCID: PMC10802650 DOI: 10.1101/2024.01.08.24301007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Importance The under-representation of participants with non-European ancestry in genome-wide association studies (GWAS) is a critical issue that has significant implications, including hindering the progress of precision medicine initiatives. This issue is particularly significant in the context of neurodegenerative diseases (NDDs), where current therapeutic approaches have shown limited success. Addressing this under-representation is crucial to harnessing the full potential of genomic medicine in underserved communities and improving outcomes for NDD patients. Objective Our primary objective was to assess the representation of non-European ancestry participants in genetic discovery efforts related to NDDs. We aimed to quantify the extent of inclusion of diverse ancestry groups in NDD studies and determine the number of associated loci identified in more inclusive studies. Specifically, we sought to highlight the disparities in research efforts and outcomes between studies predominantly involving European ancestry participants and those deliberately targeting non-European or multi-ancestry populations across NDDs. Evidence Review We conducted a systematic review utilizing existing GWAS results and publications to assess the inclusion of diverse ancestry groups in neurodegeneration and neurogenetics studies. Our search encompassed studies published up to the end of 2022, with a focus on identifying research that deliberately included non-European or multi-ancestry cohorts. We employed rigorous methods for the inclusion of identified articles and quality assessment. Findings Our review identified a total of 123 NDD GWAS. Strikingly, 82% of these studies predominantly featured participants of European ancestry. Endeavors specifically targeting non-European or multi-ancestry populations across NDDs identified only 52 risk loci. This contrasts with predominantly European studies, which reported over 90 risk loci for a single disease. Encouragingly, over 65% of these discoveries occurred in 2020 or later, indicating a recent increase in studies deliberately including non-European cohorts. Conclusions and relevance Our findings underscore the pressing need for increased diversity in neurodegenerative research. The significant under-representation of non-European ancestry participants in NDD GWAS limits our understanding of the genetic underpinnings of these diseases. To advance the field of neurodegenerative research and develop more effective therapies, it is imperative that future investigations prioritize and harness the genomic diversity present within and across global populations.
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Affiliation(s)
- Caroline Jonson
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
- Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, CA, USA
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Kristin S. Levine
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
| | - Julie Lake
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Linnea Hertslet
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
| | - Lietsel Jones
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
| | - Dhairya Patel
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jeff Kim
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
| | - Nancy Terry
- Division of Library Services, Office of Research Services, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Ignacio F. Mata
- Genomic Medicine Institute, Lerner Research Institute, Genomic Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Mike A. Nalls
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
| | - Jennifer S. Yokoyama
- Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, CA, USA
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD USA 20892
- DataTecnica LLC, Washington, DC USA 20037
- Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD USA 20892
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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Li J, Yang M, Wei R, Cao Y, Fan X, Zhang S. The Predictive Ability of Blood Neurofilament Light Chain in Predicting Cognitive Decline in the Alzheimer's Disease Continuum: A Systematic Review and Meta-Analysis. J Alzheimers Dis 2024; 97:1589-1620. [PMID: 38306045 DOI: 10.3233/jad-231080] [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] [Indexed: 02/03/2024]
Abstract
Background Alzheimer's disease (AD) is a neurodegenerative disease with insidious onset. Identifying candidate predictors to forecast AD dementia risk before disease onset is crucial for early diagnosis and treatment. Objective We aimed to assess the predictive ability of blood neurofilament light (NfL) chain in anticipating cognitive decline in the AD continuum. Methods We systematically searched PubMed, Web of Science, and Embase from inception until April 7, 2023. Longitudinal observational studies examining the association between baseline blood NfL and cognitive decline or clinical disease conversion were included based on inclusion/exclusion criteria. The final effect size was represented by adjusted hazard ratios (HR) or standardized beta (s.β) coefficients with a 95% confidence interval (CI). Results A total of 2,862 articles were identified, and 26 studies were included in this meta-analysis. The results indicated that baseline blood NfL could predict cognitive decline, with MMSE [s.β= -0.17, 95% CI (-0.26, -0.07)]; PACC [s.β= -0.09, 95% CI (-0.16, -0.03)]; ADAS-cog [s.β= 0.21, 95% CI (0.13, 0.29)]; CDR-SOB [s.β= 0.27, 95% CI (0.03, 0.50)]; Global cognitive composite [s.β= -0.05, 95% CI (-0.08, -0.01)]; Memory subdomain [s.β= -0.06, 95% CI (-0.09, -0.03)]; Language subdomain [s.β= -0.07, 95% CI (-0.10, -0.05)]; Executive function subdomain [s.β= -0.02, 95% CI (-0.03, -0.01)]; Visuospatial subdomain [s.β= -0.06, 95% CI (-0.08, -0.04)]. Additionally, baseline blood NfL could predict disease progression (conversion from CU/SCD/MCI to MCI/AD) in the AD continuum [Adjust HR = 1.32, 95% CI (1.12, 1.56)]. Conclusions Baseline blood NfL demonstrated predictive capabilities for global cognition and its memory, language, executive function, visuospatial subdomains decline in the AD continuum. Moreover, it exhibited the potential to predict disease progression in non-AD dementia participants.
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Affiliation(s)
- Jianhong Li
- Fujian Key Laboratory of Aptamers Technology, 900TH hospital of Joint Logistics Support Force, People's Liberation Army (PLA), Fuzhou, Fujian, China
| | - Minguang Yang
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Renli Wei
- The Institute of Rehabilitation Industry, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Yue Cao
- Fujian Key Laboratory of Aptamers Technology, 900TH hospital of Joint Logistics Support Force, People's Liberation Army (PLA), Fuzhou, Fujian, China
| | - Xu Fan
- The Institute of Rehabilitation Industry, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Shenghang Zhang
- Fujian Key Laboratory of Aptamers Technology, 900TH hospital of Joint Logistics Support Force, People's Liberation Army (PLA), Fuzhou, Fujian, China
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9
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Sun Y, Zhu J, Yang Y, Zhang Z, Zhong H, Zeng G, Zhou D, Nowakowski RS, Long J, Wu C, Wu L. Identification of candidate DNA methylation biomarkers related to Alzheimer's disease risk by integrating genome and blood methylome data. Transl Psychiatry 2023; 13:387. [PMID: 38092781 PMCID: PMC10719322 DOI: 10.1038/s41398-023-02695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/16/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Alzheimer disease (AD) is a common neurodegenerative disease with a late onset. It is critical to identify novel blood-based DNA methylation biomarkers to better understand the extent of the molecular pathways affected in AD. Two sets of blood DNA methylation genetic prediction models developed using different reference panels and modelling strategies were leveraged to evaluate associations of genetically predicted DNA methylation levels with AD risk in 111,326 (46,828 proxy) cases and 677,663 controls. A total of 1,168 cytosine-phosphate-guanine (CpG) sites showed a significant association with AD risk at a false discovery rate (FDR) < 0.05. Methylation levels of 196 CpG sites were correlated with expression levels of 130 adjacent genes in blood. Overall, 52 CpG sites of 32 genes showed consistent association directions for the methylation-gene expression-AD risk, including nine genes (CNIH4, THUMPD3, SERPINB9, MTUS1, CISD1, FRAT2, CCDC88B, FES, and SSH2) firstly reported as AD risk genes. Nine of 32 genes were enriched in dementia and AD disease categories (P values ranged from 1.85 × 10-4 to 7.46 × 10-6), and 19 genes in a neurological disease network (score = 54) were also observed. Our findings improve the understanding of genetics and etiology for AD.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P. R. China
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Yaohua Yang
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, 22093, USA
| | - Zichen Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Guanghua Zeng
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P. R. China
| | - Dan Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P.R. China
| | - Richard S Nowakowski
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, 32304, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
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10
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Bae J, Logan PE, Acri DJ, Bharthur A, Nho K, Saykin AJ, Risacher SL, Nudelman K, Polsinelli AJ, Pentchev V, Kim J, Hammers DB, Apostolova LG. A simulative deep learning model of SNP interactions on chromosome 19 for predicting Alzheimer's disease risk and rates of disease progression. Alzheimers Dement 2023; 19:5690-5699. [PMID: 37409680 PMCID: PMC10770299 DOI: 10.1002/alz.13319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/25/2023] [Accepted: 05/12/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Identifying genetic patterns that contribute to Alzheimer's disease (AD) is important not only for pre-symptomatic risk assessment but also for building personalized therapeutic strategies. METHODS We implemented a novel simulative deep learning model to chromosome 19 genetic data from the Alzheimer's Disease Neuroimaging Initiative and the Imaging and Genetic Biomarkers of Alzheimer's Disease datasets. The model quantified the contribution of each single nucleotide polymorphism (SNP) and their epistatic impact on the likelihood of AD using the occlusion method. The top 35 AD-risk SNPs in chromosome 19 were identified, and their ability to predict the rate of AD progression was analyzed. RESULTS Rs561311966 (APOC1) and rs2229918 (ERCC1/CD3EAP) were recognized as the most powerful factors influencing AD risk. The top 35 chromosome 19 AD-risk SNPs were significant predictors of AD progression. DISCUSSION The model successfully estimated the contribution of AD-risk SNPs that account for AD progression at the individual level. This can help in building preventive precision medicine.
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Affiliation(s)
- Jinhyeong Bae
- Department of Neurology, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Paige E. Logan
- Department of Neurology, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Dominic J. Acri
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Apoorva Bharthur
- Department of Neurology, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Shannon L. Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Kelly Nudelman
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Angelina J. Polsinelli
- Department of Neurology, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Valentin Pentchev
- Department of Information Technology, Indiana University Network Science Institute, Bloomington, IN, 47408, United States
| | - Jungsu Kim
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Dustin B. Hammers
- Department of Neurology, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Liana G. Apostolova
- Department of Neurology, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
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11
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Li Y, Xu M, Xiang BL, Li X, Zhang DF, Zhao H, Bi R, Yao YG. Functional genomics identify causal variant underlying the protective CTSH locus for Alzheimer's disease. Neuropsychopharmacology 2023; 48:1555-1566. [PMID: 36739351 PMCID: PMC10516988 DOI: 10.1038/s41386-023-01542-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/30/2022] [Accepted: 01/25/2023] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent age-related neurodegenerative disease, which has a high heritability of up to 79%. Exploring the genetic basis is essential for understanding the pathogenic mechanisms underlying AD development. Recent genome-wide association studies (GWASs) reported an AD-associated signal in the Cathepsin H (CTSH) gene in European populations. However, the exact functional/causal variant(s), and the genetic regulating mechanism of CTSH in AD remain to be determined. In this study, we carried out a comprehensive study to characterize the role of CTSH variants in the pathogenesis of AD. We identified rs2289702 in CTSH as the most significant functional variant that is associated with a protective effect against AD. The genetic association between rs2289702 and AD was validated in independent cohorts of the Han Chinese population. The CTSH mRNA expression level was significantly increased in AD patients and AD animal models, and the protective allele T of rs2289702 was associated with a decreased expression level of CTSH through the disruption of the binding affinity of transcription factors. Human microglia cells with CTSH knockout showed a significantly increased phagocytosis of Aβ peptides. Our study identified CTSH as being involved in AD genetic susceptibility and uncovered the genetic regulating mechanism of CTSH in pathogenesis of AD.
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Affiliation(s)
- Yu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Bo-Lin Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Xiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Hui Zhao
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, 650204, Kunming, China
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China.
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, 650204, Kunming, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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12
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Lambert JC, Ramirez A, Grenier-Boley B, Bellenguez C. Step by step: towards a better understanding of the genetic architecture of Alzheimer's disease. Mol Psychiatry 2023; 28:2716-2727. [PMID: 37131074 PMCID: PMC10615767 DOI: 10.1038/s41380-023-02076-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023]
Abstract
Alzheimer's disease (AD) is considered to have a large genetic component. Our knowledge of this component has progressed over the last 10 years, thanks notably to the advent of genome-wide association studies and the establishment of large consortia that make it possible to analyze hundreds of thousands of cases and controls. The characterization of dozens of chromosomal regions associated with the risk of developing AD and (in some loci) the causal genes responsible for the observed disease signal has confirmed the involvement of major pathophysiological pathways (such as amyloid precursor protein metabolism) and opened up new perspectives (such as the central role of microglia and inflammation). Furthermore, large-scale sequencing projects are starting to reveal the major impact of rare variants - even in genes like APOE - on the AD risk. This increasingly comprehensive knowledge is now being disseminated through translational research; in particular, the development of genetic risk/polygenic risk scores is helping to identify the subpopulations more at risk or less at risk of developing AD. Although it is difficult to assess the efforts still needed to comprehensively characterize the genetic component of AD, several lines of research can be improved or initiated. Ultimately, genetics (in combination with other biomarkers) might help to redefine the boundaries and relationships between various neurodegenerative diseases.
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Affiliation(s)
- Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Neurodegenerative diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- Department of Psychiatry & Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Benjamin Grenier-Boley
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Céline Bellenguez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
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13
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Shigemizu D, Akiyama S, Suganuma M, Furutani M, Yamakawa A, Nakano Y, Ozaki K, Niida S. Classification and deep-learning-based prediction of Alzheimer disease subtypes by using genomic data. Transl Psychiatry 2023; 13:232. [PMID: 37386009 DOI: 10.1038/s41398-023-02531-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common multifactorial neurodegenerative disease among elderly people. LOAD is heterogeneous, and the symptoms vary among patients. Genome-wide association studies (GWAS) have identified genetic risk factors for LOAD but not for LOAD subtypes. Here, we examined the genetic architecture of LOAD based on Japanese GWAS data from 1947 patients and 2192 cognitively normal controls in a discovery cohort and 847 patients and 2298 controls in an independent validation cohort. Two distinct groups of LOAD patients were identified. One was characterized by major risk genes for developing LOAD (APOC1 and APOC1P1) and immune-related genes (RELB and CBLC). The other was characterized by genes associated with kidney disorders (AXDND1, FBP1, and MIR2278). Subsequent analysis of albumin and hemoglobin values from routine blood test results suggested that impaired kidney function could lead to LOAD pathogenesis. We developed a prediction model for LOAD subtypes using a deep neural network, which achieved an accuracy of 0.694 (2870/4137) in the discovery cohort and 0.687 (2162/3145) in the validation cohort. These findings provide new insights into the pathogenic mechanisms of LOAD.
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Affiliation(s)
- Daichi Shigemizu
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan.
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Shintaro Akiyama
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Mutsumi Suganuma
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Motoki Furutani
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, 734-8553, Japan
| | - Akiko Yamakawa
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Yukiko Nakano
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, 734-8553, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, 734-8553, Japan
| | - Shumpei Niida
- Core Facility Administration, Research Institute, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
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14
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Sun Y, Bae YE, Zhu J, Zhang Z, Zhong H, Yu J, Wu C, Wu L. A splicing transcriptome-wide association study identifies novel altered splicing for Alzheimer's disease susceptibility. Neurobiol Dis 2023:106209. [PMID: 37354922 DOI: 10.1016/j.nbd.2023.106209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/26/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023] Open
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease in aging individuals. Alternative splicing is reported to be relevant to AD development while their roles in etiology of AD remain largely elusive. We performed a comprehensive splicing transcriptome-wide association study (spTWAS) using intronic excision expression genetic prediction models of 12 brain tissues developed through three modelling strategies, to identify candidate susceptibility splicing introns for AD risk. A total of 111,326 (46,828 proxy) cases and 677,663 controls of European ancestry were studied. We identified 343 associations of 233 splicing introns (143 genes) with AD risk after Bonferroni correction (0.05/136,884 = 3.65 × 10-7). Fine-mapping analyses supported 155 likely causal associations corresponding to 83 splicing introns of 55 genes. Eighteen causal splicing introns of 15 novel genes (EIF2D, WDR33, SAP130, BYSL, EPHB6, MRPL43, VEGFB, PPP1R13B, TLN2, CLUHP3, LRRC37A4P, CRHR1, LINC02210, ZNF45-AS1, and XPNPEP3) were identified for the first time to be related to AD susceptibility. Our study identified novel genes and splicing introns associated with AD risk, which can improve our understanding of the etiology of AD.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian 364012, PR China; Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ye Eun Bae
- Department of Statistics, Florida State University, Tallahassee, FL 32304, USA
| | - Jingjing Zhu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Zichen Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32304, USA
| | - Hua Zhong
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Jie Yu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian 364012, PR China
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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15
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Reitz C, Pericak-Vance MA, Foroud T, Mayeux R. A global view of the genetic basis of Alzheimer disease. Nat Rev Neurol 2023; 19:261-277. [PMID: 37024647 PMCID: PMC10686263 DOI: 10.1038/s41582-023-00789-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
The risk of Alzheimer disease (AD) increases with age, family history and informative genetic variants. Sadly, there is still no cure or means of prevention. As in other complex diseases, uncovering genetic causes of AD could identify underlying pathological mechanisms and lead to potential treatments. Rare, autosomal dominant forms of AD occur in middle age as a result of highly penetrant genetic mutations, but the most common form of AD occurs later in life. Large-scale, genome-wide analyses indicate that 70 or more genes or loci contribute to AD. One of the major factors limiting progress is that most genetic data have been obtained from non-Hispanic white individuals in Europe and North America, preventing the development of personalized approaches to AD in individuals of other ethnicities. Fortunately, emerging genetic data from other regions - including Africa, Asia, India and South America - are now providing information on the disease from a broader range of ethnicities. Here, we summarize the current knowledge on AD genetics in populations across the world. We predominantly focus on replicated genetic discoveries but also include studies in ethnic groups where replication might not be feasible. We attempt to identify gaps that need to be addressed to achieve a complete picture of the genetic and molecular factors that drive AD in individuals across the globe.
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Affiliation(s)
- Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
- Department of Neurology, Columbia University, New York, NY, USA.
- Department of Epidemiology, Columbia University, New York, NY, USA.
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16
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Zhou X, Chen Y, Ip FCF, Jiang Y, Cao H, Lv G, Zhong H, Chen J, Ye T, Chen Y, Zhang Y, Ma S, Lo RMN, Tong EPS, Mok VCT, Kwok TCY, Guo Q, Mok KY, Shoai M, Hardy J, Chen L, Fu AKY, Ip NY. Deep learning-based polygenic risk analysis for Alzheimer's disease prediction. COMMUNICATIONS MEDICINE 2023; 3:49. [PMID: 37024668 PMCID: PMC10079691 DOI: 10.1038/s43856-023-00269-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND The polygenic nature of Alzheimer's disease (AD) suggests that multiple variants jointly contribute to disease susceptibility. As an individual's genetic variants are constant throughout life, evaluating the combined effects of multiple disease-associated genetic risks enables reliable AD risk prediction. Because of the complexity of genomic data, current statistical analyses cannot comprehensively capture the polygenic risk of AD, resulting in unsatisfactory disease risk prediction. However, deep learning methods, which capture nonlinearity within high-dimensional genomic data, may enable more accurate disease risk prediction and improve our understanding of AD etiology. Accordingly, we developed deep learning neural network models for modeling AD polygenic risk. METHODS We constructed neural network models to model AD polygenic risk and compared them with the widely used weighted polygenic risk score and lasso models. We conducted robust linear regression analysis to investigate the relationship between the AD polygenic risk derived from deep learning methods and AD endophenotypes (i.e., plasma biomarkers and individual cognitive performance). We stratified individuals by applying unsupervised clustering to the outputs from the hidden layers of the neural network model. RESULTS The deep learning models outperform other statistical models for modeling AD risk. Moreover, the polygenic risk derived from the deep learning models enables the identification of disease-associated biological pathways and the stratification of individuals according to distinct pathological mechanisms. CONCLUSION Our results suggest that deep learning methods are effective for modeling the genetic risks of AD and other diseases, classifying disease risks, and uncovering disease mechanisms.
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Affiliation(s)
- Xiaopu Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Yu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Fanny C F Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Yuanbing Jiang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Han Cao
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ge Lv
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Huan Zhong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
| | - Jiahang Chen
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tao Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Yuewen Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
- Chinese Academy of Sciences Key Laboratory of Brain Connectome and Manipulation, Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Yulin Zhang
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Shuangshuang Ma
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Ronnie M N Lo
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Estella P S Tong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Vincent C T Mok
- Gerald Choa Neuroscience Centre, Lui Che Woo Institute of Innovative Medicine, Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Timothy C Y Kwok
- Therese Pei Fong Chow Research Centre for Prevention of Dementia, Division of Geriatrics, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qihao Guo
- Department of Gerontology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Kin Y Mok
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Maryam Shoai
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - John Hardy
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- HKUST Jockey Club Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Lei Chen
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Amy K Y Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China
| | - Nancy Y Ip
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, China.
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong, 518057, China.
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17
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Li X, Xu M, Bi R, Tan LW, Yao YG, Zhang DF. Common and rare variants of EGF increase the genetic risk of Alzheimer's disease as revealed by targeted sequencing of growth factors in Han Chinese. Neurobiol Aging 2023; 123:170-181. [PMID: 36437134 DOI: 10.1016/j.neurobiolaging.2022.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/21/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease with high heritability. Growth factors (GFs) might contribute to the development of AD due to their broad effects on neuronal system. We herein aimed to investigate the role of rare and common variants of GFs in genetic susceptibility of AD. We screened 23 GFs in 6324 individuals using targeted sequencing. A rare-variant-based burden test and common-variant-based single-site association analyses were performed to identify AD-associated GF genes and variants. The burden test showed an enrichment of rare missense variants (p = 6.08 × 10-4) in GF gene-set in AD patients. Among the GFs, EGF showed the strongest signal of enrichment, especially for loss-of-function variants (p = 0.0019). A common variant rs4698800 of EGF showed significant associations with AD risk (p = 3.24 × 10-5, OR = 1.26). The risk allele of rs4698800 was associated with an increased EGF expression, whereas EGF was indeed upregulated in AD brain. These findings suggested EGF as a novel risk gene for AD.
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Affiliation(s)
- Xiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Wen Tan
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Disease, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
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18
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Miyashita A, Kikuchi M, Hara N, Ikeuchi T. Genetics of Alzheimer's disease: an East Asian perspective. J Hum Genet 2023; 68:115-124. [PMID: 35641666 PMCID: PMC9968656 DOI: 10.1038/s10038-022-01050-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is an age-related multifactorial neurodegenerative disorder. Advances in genome technology, including next generation sequencing have uncovered complex genetic effects in AD by analyzing both common and rare functional variants. Multiple lines of evidence suggest that the pathogenesis of AD is influenced by multiple genetic components rather than single genetic factor. Previous genetic studies on AD have predominantly included European ancestry cohorts; hence, the non-European population may be underrepresented, potentially leading to reduced diversity in AD genetic research. Additionally, ethnic diversity may result in dissimilar effects of genetic determinants in AD. APOE genotypes are a well-established genetic risk factor in AD, with the East Asian population having a higher risk of AD associated with the APOE ε4 allele. To date, seven genome-wide association studies (GWAS) have been conducted in East Asians, which report a total of 26 AD-associated loci. Several rare variants, including the p.H157Y variant in TREM2, and the p.G186R and p.R274W variants in SHARPIN are associated with risk of AD in East Asians. Extending genetic studies to diverse populations, including East Asians is necessary, which could yield more comprehensive insights into AD, and here we review the recent findings regarding the genetic determinants of AD from an East Asian perspective.
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Affiliation(s)
- Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Norikazu Hara
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan.
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19
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TOMM40 Genetic Variants Cause Neuroinflammation in Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24044085. [PMID: 36835494 PMCID: PMC9962462 DOI: 10.3390/ijms24044085] [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: 11/30/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Translocase of outer mitochondrial membrane 40 (TOMM40) is located in the outer membrane of mitochondria. TOMM40 is essential for protein import into mitochondria. TOMM40 genetic variants are believed to increase the risk of Alzheimer's disease (AD) in different populations. In this study, three exonic variants (rs772262361, rs157581, and rs11556505) and three intronic variants (rs157582, rs184017, and rs2075650) of the TOMM40 gene were identified from Taiwanese AD patients using next-generation sequencing. Associations between the three TOMM40 exonic variants and AD susceptibility were further evaluated in another AD cohort. Our results showed that rs157581 (c.339T > C, p.Phe113Leu, F113L) and rs11556505 (c.393C > T, p.Phe131Leu, F131L) were associated with an increased risk of AD. We further utilized cell models to examine the role of TOMM40 variation in mitochondrial dysfunction that causes microglial activation and neuroinflammation. When expressed in BV2 microglial cells, the AD-associated mutant (F113L) or (F131L) TOMM40 induced mitochondrial dysfunction and oxidative stress-induced activation of microglia and NLRP3 inflammasome. Pro-inflammatory TNF-α, IL-1β, and IL-6 released by mutant (F113L) or (F131L) TOMM40-activated BV2 microglial cells caused cell death of hippocampal neurons. Taiwanese AD patients carrying TOMM40 missense (F113L) or (F131L) variants displayed an increased plasma level of inflammatory cytokines IL-6, IL-18, IL-33, and COX-2. Our results provide evidence that TOMM40 exonic variants, including rs157581 (F113L) and rs11556505 (F131L), increase the AD risk of the Taiwanese population. Further studies suggest that AD-associated mutant (F113L) or (F131L) TOMM40 cause the neurotoxicity of hippocampal neurons by inducing the activation of microglia and NLRP3 inflammasome and the release of pro-inflammatory cytokines.
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20
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Andrade-Guerrero J, Santiago-Balmaseda A, Jeronimo-Aguilar P, Vargas-Rodríguez I, Cadena-Suárez AR, Sánchez-Garibay C, Pozo-Molina G, Méndez-Catalá CF, Cardenas-Aguayo MDC, Diaz-Cintra S, Pacheco-Herrero M, Luna-Muñoz J, Soto-Rojas LO. Alzheimer's Disease: An Updated Overview of Its Genetics. Int J Mol Sci 2023; 24:ijms24043754. [PMID: 36835161 PMCID: PMC9966419 DOI: 10.3390/ijms24043754] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease in the world. It is classified as familial and sporadic. The dominant familial or autosomal presentation represents 1-5% of the total number of cases. It is categorized as early onset (EOAD; <65 years of age) and presents genetic mutations in presenilin 1 (PSEN1), presenilin 2 (PSEN2), or the Amyloid precursor protein (APP). Sporadic AD represents 95% of the cases and is categorized as late-onset (LOAD), occurring in patients older than 65 years of age. Several risk factors have been identified in sporadic AD; aging is the main one. Nonetheless, multiple genes have been associated with the different neuropathological events involved in LOAD, such as the pathological processing of Amyloid beta (Aβ) peptide and Tau protein, as well as synaptic and mitochondrial dysfunctions, neurovascular alterations, oxidative stress, and neuroinflammation, among others. Interestingly, using genome-wide association study (GWAS) technology, many polymorphisms associated with LOAD have been identified. This review aims to analyze the new genetic findings that are closely related to the pathophysiology of AD. Likewise, it analyzes the multiple mutations identified to date through GWAS that are associated with a high or low risk of developing this neurodegeneration. Understanding genetic variability will allow for the identification of early biomarkers and opportune therapeutic targets for AD.
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Affiliation(s)
- Jesús Andrade-Guerrero
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Querétaro, Mexico
| | - Alberto Santiago-Balmaseda
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
| | - Paola Jeronimo-Aguilar
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Isaac Vargas-Rodríguez
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Querétaro, Mexico
| | - Ana Ruth Cadena-Suárez
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores Cuautitlán, Universidad-Nacional Autónoma de México, Cuatitlan 53150, Edomex, Mexico
| | - Carlos Sánchez-Garibay
- Departamento de Neuropatología, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México 14269, Mexico
| | - Glustein Pozo-Molina
- Laboratorio de Genética y Oncología Molecular, Laboratorio 5, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
| | - Claudia Fabiola Méndez-Catalá
- Laboratorio de Genética y Oncología Molecular, Laboratorio 5, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- División de Investigación y Posgrado, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de Mexico, Tlalnepantla 54090, Edomex, Mexico
| | - Maria-del-Carmen Cardenas-Aguayo
- Laboratory of Cellular Reprogramming, Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Sofía Diaz-Cintra
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Querétaro, Mexico
| | - Mar Pacheco-Herrero
- Neuroscience Research Laboratory, Faculty of Health Sciences, Pontificia Universidad Católica Madre y Maestra, Santiago de los Caballeros 51000, Dominican Republic
| | - José Luna-Muñoz
- National Dementia BioBank, Ciencias Biológicas, Facultad de Estudios Superiores Cuautitlán, Universidad-Nacional Autónoma de México, Cuatitlan 53150, Edomex, Mexico
- National Brain Bank-UNPHU, Universidad Nacional Pedro Henríquez Ureña, Santo Domingo 1423, Dominican Republic
- Correspondence: (J.L.-M.); (L.O.S.-R.); Tel.: +52-55-45-23-41-20 (J.L.-M.); +52-55-39-37-94-30 (L.O.S.-R.)
| | - Luis O. Soto-Rojas
- Laboratorio de Patogénesis Molecular, Laboratorio 4, Edificio A4, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Red MEDICI, Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Edomex, Mexico
- Correspondence: (J.L.-M.); (L.O.S.-R.); Tel.: +52-55-45-23-41-20 (J.L.-M.); +52-55-39-37-94-30 (L.O.S.-R.)
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21
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Li X, Zhang DF, Bi R, Tan LW, Chen X, Xu M, Yao YG. Convergent transcriptomic and genomic evidence supporting a dysregulation of CXCL16 and CCL5 in Alzheimer's disease. Alzheimers Res Ther 2023; 15:17. [PMID: 36670424 PMCID: PMC9863145 DOI: 10.1186/s13195-022-01159-5] [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: 10/20/2022] [Accepted: 12/29/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND Neuroinflammatory factors, especially chemokines, have been widely reported to be involved in the pathogenesis of Alzheimer's disease (AD). It is unclear how chemokines are altered in AD, and whether dysregulation of chemokines is the cause, or the consequence, of the disease. METHODS We initially screened the transcriptomic profiles of chemokines from publicly available datasets of brain tissues of AD patients and mouse models. Expression alteration of chemokines in the blood from AD patients was also measured to explore whether any chemokine might be used as a potential biomarker for AD. We further analyzed the association between the coding variants of chemokine genes and genetic susceptibility of AD by targeted sequencing of a Han Chinese case-control cohort. Mendelian randomization (MR) was performed to infer the causal association of chemokine dysregulation with AD development. RESULTS Three chemokine genes (CCL5, CXCL1, and CXCL16) were consistently upregulated in brain tissues from AD patients and the mouse models and were positively correlated with Aβ and tau pathology in AD mice. Peripheral blood mRNA expression of CXCL16 was upregulated in mild cognitive impairment (MCI) and AD patients, indicating the potential of CXCL16 as a biomarker for AD development. None of the coding variants within any chemokine gene conferred a genetic risk to AD. MR analysis confirmed a causal role of CCL5 dysregulation in AD mediated by trans-regulatory variants. CONCLUSIONS In summary, we have provided transcriptomic and genomic evidence supporting an active role of dysregulated CXCL16 and CCL5 during AD development.
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Affiliation(s)
- Xiao Li
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204 Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 China
| | - Deng-Feng Zhang
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204 Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 China
| | - Rui Bi
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204 Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 China ,grid.9227.e0000000119573309CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Li-Wen Tan
- grid.216417.70000 0001 0379 7164Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Xiaogang Chen
- grid.216417.70000 0001 0379 7164Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, 410011 China
| | - Min Xu
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204 Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 China
| | - Yong-Gang Yao
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204 Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 China ,grid.9227.e0000000119573309CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031 China
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22
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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23
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Adewale BA, Coker MM, Ogunniyi A, Kalaria RN, Akinyemi RO. Biomarkers and Risk Assessment of Alzheimer's Disease in Low- and Middle-Income Countries. J Alzheimers Dis 2023; 95:1339-1349. [PMID: 37694361 DOI: 10.3233/jad-221030] [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] [Indexed: 09/12/2023]
Abstract
Dementia is a chronic syndrome which is common among the elderly and is associated with significant morbidity and mortality for patients and their caregivers. Alzheimer's disease (AD), the most common form of clinical dementia, is biologically characterized by the deposition of amyloid-β plaques and neurofibrillary tangles in the brain. The onset of AD begins decades before manifestation of symptoms and clinical diagnosis, underlining the need to shift from clinical diagnosis of AD to a more objective diagnosis using biomarkers. Having performed a literature search of original articles and reviews on PubMed and Google Scholar, we present this review detailing the existing biomarkers and risk assessment tools for AD. The prevalence of dementia in low- and middle-income countries (LMICs) is predicted to increase over the next couple of years. Thus, we aimed to identify potential biomarkers that may be appropriate for use in LMICs, considering the following factors: sensitivity, specificity, invasiveness, and affordability of the biomarkers. We also explored risk assessment tools and the potential use of artificial intelligence/machine learning solutions for diagnosing, assessing risks, and monitoring the progression of AD in low-resource settings. Routine use of AD biomarkers has yet to gain sufficient ground in clinical settings. Therefore, clinical diagnosis of AD will remain the mainstay in LMICs for the foreseeable future. Efforts should be made towards the development of low-cost, easily administered risk assessment tools to identify individuals who are at risk of AD in the population. We recommend that stakeholders invest in education, research and development targeted towards effective risk assessment and management.
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Affiliation(s)
- Boluwatife Adeleye Adewale
- Faculty of Clinical Sciences, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Motunrayo Mojoyin Coker
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adesola Ogunniyi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Neurology, University College Hospital, Ibadan, Nigeria
| | - Rajesh N Kalaria
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
- Translational and Clinical Research Institute, Newcastle University, United Kingdom
| | - Rufus Olusola Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Neurology, University College Hospital, Ibadan, Nigeria
- Centre for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Translational and Clinical Research Institute, Newcastle University, United Kingdom
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24
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Liu Z, Guan R, Bu F, Pan L. Treatment of Alzheimer's disease by combination of acupuncture and Chinese medicine based on pathophysiological mechanism: A review. Medicine (Baltimore) 2022; 101:e32218. [PMID: 36626477 PMCID: PMC9750551 DOI: 10.1097/md.0000000000032218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by neurodegeneration, nerve loss, neurofibrillary tangles, and Aβ plaques. In modern medical science, there has been a serious obstacle to the effective treatment of AD. At present, there is no clinically proven and effective western medicine treatment for AD. The reason is that the etiology of AD is not yet fully understood. In 2018, the international community put forward a purely biological definition of AD, but soon this view of biomarkers was widely questioned, because the so-called AD biomarkers are shared with other neurological diseases, the diagnostic accuracy is low, and they face various challenges in the process of clinical diagnosis and treatment. Nowadays, scholars increasingly regard AD as the result of multimechanism and multicenter interaction. Because there is no exact Western medicine treatment for AD, the times call for the comprehensive treatment of AD in traditional Chinese medicine (TCM). AD belongs to the category of "dull disease" in TCM. For thousands of years, TCM has accumulated a lot of relevant treatment experience in the process of diagnosis and treatment. TCM, acupuncture, and the combination of acupuncture and medicine all play an important role in the treatment of AD. Based on the research progress of modern medicine on the pathophysiology of AD, this paper discusses the treatment of this disease with the combination of acupuncture and medicine.
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Affiliation(s)
- Zhao Liu
- Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang Province, China
- * Correspondence: Zhao Liu, Heilongjiang University of Traditional Chinese Medicine, 24 Heping Road, Harbin, Heilongjiang Province 150006, China (e-mail: )
| | - Ruiqian Guan
- Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang Province, China
- Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Fan Bu
- Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Limin Pan
- Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang Province, China
- Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang Province, China
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25
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Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
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Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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26
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Harerimana NV, Goate AM, Bowles KR. The influence of 17q21.31 and APOE genetic ancestry on neurodegenerative disease risk. Front Aging Neurosci 2022; 14:1021918. [DOI: 10.3389/fnagi.2022.1021918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genomic research over the last two decades have greatly enhanced our knowledge concerning the genetic landscape and pathophysiological processes involved in multiple neurodegenerative diseases. However, current insights arise almost exclusively from studies on individuals of European ancestry. Despite this, studies have revealed that genetic variation differentially impacts risk for, and clinical presentation of neurodegenerative disease in non-European populations, conveying the importance of ancestry in predicting disease risk and understanding the biological mechanisms contributing to neurodegeneration. We review the genetic influence of two important disease-associated loci, 17q21.31 (the “MAPT locus”) and APOE, to neurodegenerative disease risk in non-European populations, touching on global population differences and evolutionary genetics by ancestry that may underlie some of these differences. We conclude there is a need to increase representation of non-European ancestry individuals in genome-wide association studies (GWAS) and biomarker analyses in order to help resolve existing disparities in understanding risk for, diagnosis of, and treatment for neurodegenerative diseases in diverse populations.
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27
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Santana DA, Bedrat A, Puga RD, Turecki G, Mechawar N, Faria TC, Gigek CO, Payão SL, Smith MA, Lemos B, Chen ES. The role of H3K9 acetylation and gene expression in different brain regions of Alzheimer's disease patients. Epigenomics 2022; 14:651-670. [PMID: 35588246 DOI: 10.2217/epi-2022-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To evaluate H3K9 acetylation and gene expression profiles in three brain regions of Alzheimer's disease (AD) patients and elderly controls, and to identify AD region-specific abnormalities. Methods: Brain samples of auditory cortex, hippocampus and cerebellum from AD patients and controls underwent chromatin immunoprecipitation sequencing, RNA sequencing and network analyses. Results: We found a hyperacetylation of AD cerebellum and a slight hypoacetylation of AD hippocampus. The transcriptome revealed differentially expressed genes in the hippocampus and auditory cortex. Network analysis revealed Rho GTPase-mediated mechanisms. Conclusions: These findings suggest that some crucial mechanisms, such as Rho GTPase activity and cytoskeletal organization, are differentially dysregulated in brain regions of AD patients at the epigenetic and transcriptomic levels, and might contribute toward future research on AD pathogenesis.
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Affiliation(s)
- Daliléia A Santana
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Amina Bedrat
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Renato D Puga
- Hermes Pardini Institute, São Paulo, SP, 04038-030, Brazil
| | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Tathyane C Faria
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Carolina O Gigek
- Department of Pathology, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, 04023-062, Brazil
| | - Spencer Lm Payão
- Department of Genetics, Blood Center, Faculdade de Medicina de Marília (FAMEMA), Marília, SP, 17519-050, Brazil
| | - Marília Ac Smith
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Bernardo Lemos
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Elizabeth S Chen
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil.,Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
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28
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Jiao B, Xiao X, Yuan Z, Guo L, Liao X, Zhou Y, Zhou L, Wang X, Liu X, Liu H, Jiang Y, Lin Z, Zhu Y, Yang Q, Zhang W, Li J, Shen L. Associations of risk genes with onset age and plasma biomarkers of Alzheimer's disease: a large case-control study in mainland China. Neuropsychopharmacology 2022; 47:1121-1127. [PMID: 35001095 PMCID: PMC8938514 DOI: 10.1038/s41386-021-01258-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/28/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022]
Abstract
Most genetic studies concerning risk genes in Alzheimer's disease (AD) are from Caucasian populations, whereas the data remain limited in the Chinese population. In this study, we systematically explored the relationship between AD and risk genes in mainland China. We sequenced 33 risk genes previously reported to be associated with AD in a total of 3604 individuals in the mainland Chinese population. Common variant (MAF ≥ 0.01) based association analysis and gene-based (MAF < 0.01) association test were performed by PLINK 1.9 and Sequence Kernel Association Test-Optimal, respectively. Polygenic risk score (PRS) was calculated, and receiver operating characteristic curve (AUC) was computed. Plasma Aβ42, Aβ40, total tau (T-tau), and neurofilament light chain (NFL) were tested in a subgroup, and their associations with PRS were conducted using the Spearman correlation test. Six common variants varied significantly between AD patients and cognitively normal controls after the adjustment of age, gender, and APOE ε4 status, including variants in ABCA7 (n = 5) and APOE (n = 1). Among them, four variants were novel and two were reported previously. The AUC of PRS was 0.71. The high PRS was significantly associated with an earlier age at onset (P = 4.30 × 10-4). PRS was correlated with plasma Aβ42, Aβ42/Aβ40 ratio, T-tau, and NFL levels. Gene-based association test revealed that ABCA7 and UNC5C reached statistical significance. The common variants in APOE and ABCA7, as well as rare variants in ABCA7 and UNC5C, may contribute to the etiology of AD. Moreover, the PRS, to some extent, could predict the risk, onset age, and biological changes of AD.
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Affiliation(s)
- Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lina Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Liao
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yafang Zhou
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yaling Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhuojie Lin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qijie Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Weiwei Zhang
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.
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29
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Association and interaction of TOMM40 and PVRL2 with plasma amyloid-β and Alzheimer's disease among Chinese older adults: a population-based study. Neurobiol Aging 2022; 113:143-151. [DOI: 10.1016/j.neurobiolaging.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/12/2021] [Accepted: 12/31/2021] [Indexed: 12/11/2022]
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30
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Xiao X, Guo L, Liao X, Zhou Y, Zhang W, Zhou L, Wang X, Liu X, Liu H, Xu T, Zhu Y, Yang Q, Hao X, Liu Y, Wang J, Li J, Jiao B, Shen L. The role of vascular dementia associated genes in patients with Alzheimer's disease: A large case-control study in the Chinese population. CNS Neurosci Ther 2021; 27:1531-1539. [PMID: 34551193 PMCID: PMC8611771 DOI: 10.1111/cns.13730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/01/2021] [Accepted: 09/05/2021] [Indexed: 12/16/2022] Open
Abstract
Aim The role of vascular dementia (VaD)‐associated genes in Alzheimer's disease (AD) remains elusive despite similar clinical and pathological features. We aimed to explore the relationship between these genes and AD in the Chinese population. Methods Eight VaD‐associated genes were screened by a targeted sequencing panel in a sample of 3604 individuals comprising 1192 AD patients and 2412 cognitively normal controls. Variants were categorized into common variants and rare variants according to minor allele frequency (MAF). Common variant (MAF ≥ 0.01)‐based association analysis was conducted by PLINK 1.9. Rare variant (MAF < 0.01) association study and gene‐based aggregation testing of rare variants were performed by PLINK 1.9 and Sequence Kernel Association Test‐Optimal (SKAT‐O test), respectively. Age at onset (AAO) and Mini‐Mental State Examination (MMSE) association studies were performed with PLINK 1.9. Analyses were adjusted for age, gender, and APOE ε4 status. Results Four common COL4A1 variants, including rs874203, rs874204, rs16975492, and rs1373744, exhibited suggestive associations with AD. Five rare variants, NOTCH3 rs201436750, COL4A1 rs747972545, COL4A1 rs201481886, CST3 rs765692764, and CST3 rs140837441, showed nominal association with AD risk. Gene‐based aggregation testing revealed that HTRA1 was nominally associated with AD. In the AAO and MMSE association studies, variants in GSN, ITM2B, and COL4A1 reached suggestive significance. Conclusion Common variants in COL4A1 and rare variants in HTRA1, NOTCH3, COL4A1, and CST3 may be implicated in AD pathogenesis. Besides, GSN, ITM2B, and COL4A1 are probably involved in the development of AD endophenotypes.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lina Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Liao
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Yafang Zhou
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Weiwei Zhang
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tianyan Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qijie Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoli Hao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yingzi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
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31
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Kang S, Gim J, Lee J, Gunasekaran TI, Choi KY, Lee JJ, Seo EH, Ko PW, Chung JY, Choi SM, Lee YM, Jeong JH, Park KW, Song MK, Lee HW, Kim KW, Choi SH, Lee DY, Kim SY, Kim H, Kim BC, Ikeuchi T, Lee KH. Potential Novel Genes for Late-Onset Alzheimer's Disease in East-Asian Descent Identified by APOE-Stratified Genome-Wide Association Study. J Alzheimers Dis 2021; 82:1451-1460. [PMID: 34151794 PMCID: PMC8461686 DOI: 10.3233/jad-210145] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The present study reports two novel genome-wide significant loci for late-onset Alzheimer’s disease (LOAD) identified from APOE ε4 non-carrier subjects of East Asian origin. A genome-wide association study of Alzheimer’s disease was performed in 2,291 Korean seniors in the discovery phase, from the Gwangju Alzheimer’ and Related Dementias (GARD) cohort study. The study was replicated in a Japanese cohort of 1,956 subjects that suggested two novel susceptible SNPs in two genes: LRIG1 and CACNA1A. This study demonstrates that the discovery of AD-associated variants is feasible in non-European ethnic groups using samples comprising fewer subjects from the more homogeneous genetic background.
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Affiliation(s)
- Sarang Kang
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea
| | - Jungsoo Gim
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea.,Neurozen Inc., Seoul, Republic of Korea.,Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Jiwoon Lee
- Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Tamil Iniyan Gunasekaran
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Kyu Yeong Choi
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea
| | - Jang Jae Lee
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea
| | - Eun Hyun Seo
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Premedical Science, Chosun University College of Medicine, Gwangju, Republic of Korea
| | - Pan-Woo Ko
- Department of Neurology, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Ji Yeon Chung
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Neurology, Chosun University Hospital, Gwangju, Republic of Korea
| | - Seong-Min Choi
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Neurology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Young Min Lee
- Department of Psychiatry, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Jee Hyang Jeong
- Department of Neurology, Ewha Womans University Mokdong Hospital, Ewha WomansUniversity School of Medicine, Seoul, Republic of Korea
| | - Kyung Won Park
- Department of Neurology, Donga University College of Medicine, Busan, Republic of Korea
| | - Min Kyung Song
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Chonnam National University Gwangju 2nd Geriatric Hospital, Gwangju, Republic of Korea
| | - Ho-Won Lee
- Department of Neurology, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Ki Woong Kim
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Seong Hye Choi
- Department of Neurology, Inha University School of Medicine, Incheon, Republic of Korea
| | - Dong Young Lee
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sang Yun Kim
- Department of Neurology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hoowon Kim
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Neurology, Chosun University Hospital, Gwangju, Republic of Korea
| | - Byeong C Kim
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Neurology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kun Ho Lee
- Gwangju Alzheimer's & Related Dementias Cohort Research Center, Chosun University, Gwangju, Republic of Korea.,Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea.,Neurozen Inc., Seoul, Republic of Korea.,Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea.,Korea Brain Research Institute, Daegu, Republic of Korea
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32
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Li W, Wang S, Zhang H, Li B, Xu L, Li Y, Kong C, Jiao H, Wang Y, Pang Y, Qin W, Jia L, Jia J. Honokiol Restores Microglial Phagocytosis by Reversing Metabolic Reprogramming. J Alzheimers Dis 2021; 82:1475-1485. [PMID: 34151796 DOI: 10.3233/jad-210177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Dysfunction of microglia has been increasingly recognized as a causative factor in Alzheimer's disease (AD); thus, developing medicines capable of restoring microglial functions is critically important and constitutes a promising therapeutic strategy. Honokiol is a natural neuroprotective compound extracted from Magnolia officinalis, which may play roles in AD therapy. OBJECTIVE This study aimed to evaluate the role and the underlying mechanisms of honokiol in microglial phagocytosis. METHODS MTT and flow cytometry were used to assess the cell viability and apoptosis, respectively. Phagocytic capacity, mitochondrial reactive oxygen species production, and membrane potential were evaluated using fluorescence microscopy. Seahorse XF24 extracellular flux analyzer was for cell glycolysis and oxidative phosphorylation detection. Mass spectrometry was applied for metabolites measurement. Quantitative real-time polymerase chain reaction and western blotting were performed to detect the mRNA and protein level of PPARγ and PGC1α, respectively. RESULTS Honokiol alleviated Aβ42-induced BV2 neurotoxicity. Honokiol promoted phagocytic efficiency of BV2 cells through reversing a metabolic switch from oxidative phosphorylation to anaerobic glycolysis and enhancing ATP production. Meanwhile, honokiol reduced mitochondrial reactive oxygen species production and elevated mitochondrial membrane potential. Moreover, honokiol increased the expression of PPARγ and PGC1α, which might play positive roles in energy metabolism and microglial phagocytosis. CONCLUSION In this study, honokiol was identified as an effect natural product capable of enhancing mitochondrial function thus promoting microglial phagocytic function.
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Affiliation(s)
- Wenwen Li
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Shiyuan Wang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Heng Zhang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Bingqiu Li
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Lingzhi Xu
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Yan Li
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Chaojun Kong
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Haishan Jiao
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Yan Wang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Yana Pang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Wei Qin
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Longfei Jia
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Jianping Jia
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China.,Beijing Key Laboratory of Geriatric Cognitive Disorders, Beijing, China.,Clinical Center for Neurodegenerative Disease and Memory Impairment, Capital Medical University, Beijing, China.,Center of Alzheimer's Disease, Beijing Institute of Brain Disorders, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
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33
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Paraoxonase Role in Human Neurodegenerative Diseases. Antioxidants (Basel) 2020; 10:antiox10010011. [PMID: 33374313 PMCID: PMC7824310 DOI: 10.3390/antiox10010011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
The human body has biological redox systems capable of preventing or mitigating the damage caused by increased oxidative stress throughout life. One of them are the paraoxonase (PON) enzymes. The PONs genetic cluster is made up of three members (PON1, PON2, PON3) that share a structural homology, located adjacent to chromosome seven. The most studied enzyme is PON1, which is associated with high density lipoprotein (HDL), having paraoxonase, arylesterase and lactonase activities. Due to these characteristics, the enzyme PON1 has been associated with the development of neurodegenerative diseases. Here we update the knowledge about the association of PON enzymes and their polymorphisms and the development of multiple sclerosis (MS), amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD) and Parkinson's disease (PD).
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