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Park YJ, Shin HY, Kim JI. Exploring the role of apolipoprotein E gene promoter polymorphisms in susceptibility to normal-tension glaucoma in a Korean population. Sci Rep 2024; 14:8972. [PMID: 38637538 PMCID: PMC11026505 DOI: 10.1038/s41598-024-58442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/29/2024] [Indexed: 04/20/2024] Open
Abstract
Glaucoma, particularly primary open-angle glaucoma (POAG), poses a significant global health concern. Distinguished by intraocular pressure (IOP), POAG encompasses high-tension glaucoma (HTG) and normal-tension glaucoma (NTG). Apolipoprotein E (APOE) is a multifaceted protein with roles in lipid metabolism, neurobiology, and neurodegenerative diseases. However, controversies persist regarding the impact of APOE single-nucleotide polymorphisms (SNPs) on open-angle glaucoma and NTG. This study aimed to identify APOE-specific SNPs influencing NTG risk. A cohort of 178 patients with NTG recruited from Uijeongbu St. Mary's Hospital and 32,858 individuals from the Korean Genome and Epidemiology Study (KoGES) cohort were included in the analysis. Genotype and haplotype analyses were performed on three promoter SNPs (rs449647, rs769446, and rs405509) and two exonic SNPs (rs429358 and rs7412) located on chromosome 19. Among the five SNPs, rs769446 genotypes exhibited significant differences between cases and controls. The minor allele C of rs769446 emerged as a protective factor against NTG. Furthermore, haplotype analysis of the five SNPs revealed that the A-T-G-T-T haplotype was a statistically significant risk factor for NTG. This study indicated an association between APOE promoter SNPs and NTG in the Korean population. Further studies are required to understand how APOE promoter SNPs contribute to NTG pathogenesis.
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Affiliation(s)
- Young Jun Park
- Medical Research Center, Genomic Medicine Institute, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Hye-Young Shin
- Department of Ophthalmology, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 271, Cheonbo-ro, Uijeongbu-si, Gyeonggi-do, Republic of Korea.
- Department of Ophthalmology, Uijeongbu St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Jong-Il Kim
- Medical Research Center, Genomic Medicine Institute, Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, Republic of Korea.
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Wang Y, Ma X, Guo J, Li Y, Xiong Y. Correlation between ESR1 and APOE gene polymorphisms and risk of osteonecrosis of the femoral head: a case-control study. J Orthop Surg Res 2023; 18:968. [PMID: 38102657 PMCID: PMC10722694 DOI: 10.1186/s13018-023-04447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Osteonecrosis of the femoral head (ONFH) is a disease with a high disability rate, and genetic factors are closely related to its pathogenesis. This study aimed to investigate the possible correlation between ESR1 and APOE gene polymorphisms and the risk of ONFH. METHODS In this case-control study, the potential association between three genetic variants (rs2982573 C < T, rs10872678 C < T, and rs9322332 A < C) of the ESR1 gene and two genetic variants (rs7259620 A < G and rs769446 C < T) of the APOE gene with the risk of ONFH was investigated. Correlations between gene polymorphisms and ONFH risk were assessed using logistic regression analysis, with calculation of odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS The overall analysis demonstrated that rs9322332 in the ESR1 gene exhibited a correlation with a decreased risk of ONFH under the homozygous (AA vs.CC: OR = 0.69, 95% CI [0.53-0.90], p = 0.006), dominant (CA + AA vs. CC: OR = 0.70, 95% CI [0.54-0.90], p = 0.006), and additive (OR = 0.79, 95% CI [0.66-0.95], p = 0.013) models. The stratification analysis revealed that rs9322332 was linked to a lower risk of ONFH in subgroups characterized by individuals aged over 51 years and non-smokers. Nevertheless, there were no notable correlations found between ESR1 rs2982573 and rs10872678, as well as APOE rs7259620 and rs769446, with the risk of ONFH. CONCLUSION ESR1-rs9322332 is closely linked to a decreased risk of ONFH, thereby enhancing our understanding of the relationship between gene polymorphisms and ONFH.
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Affiliation(s)
- Yuan Wang
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, 710069, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, Weifang, 261031, Shandong, China
| | - Xiaoya Ma
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, 710069, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Jinping Guo
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, 710069, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yujie Li
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, 710069, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yuyan Xiong
- College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi'an, 710069, Shaanxi, China.
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
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Kong W, Xu F, Wang S, Wei K, Wen G, Yu Y. Application of orthogonal sparse joint non-negative matrix factorization based on connectivity in Alzheimer's disease research. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9923-9947. [PMID: 37322917 DOI: 10.3934/mbe.2023435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Based on the mining of micro- and macro-relationships of genetic variation and brain imaging data, imaging genetics has been widely applied in the early diagnosis of Alzheimer's disease (AD). However, effective integration of prior knowledge remains a barrier to determining the biological mechanism of AD. This paper proposes a new connectivity-based orthogonal sparse joint non-negative matrix factorization (OSJNMF-C) method based on integrating the structural magnetic resonance image, single nucleotide polymorphism and gene expression data of AD patients; the correlation information, sparseness, orthogonal constraint and brain connectivity information between the brain image data and genetic data are designed as constraints in the proposed algorithm, which efficiently improved the accuracy and convergence through multiple iterative experiments. Compared with the competitive algorithm, OSJNMF-C has significantly smaller related errors and objective function values than the competitive algorithm, showing its good anti-noise performance. From the biological point of view, we have identified some biomarkers and statistically significant relationship pairs of AD/mild cognitive impairment (MCI), such as rs75277622 and BCL7A, which may affect the function and structure of multiple brain regions. These findings will promote the prediction of AD/MCI.
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Affiliation(s)
- Wei Kong
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Feifan Xu
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Shuaiqun Wang
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Kai Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gen Wen
- Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yaling Yu
- Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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Zhou X, Fu AK, Ip NY. APOE signaling in neurodegenerative diseases: an integrative approach targeting APOE coding and noncoding variants for disease intervention. Curr Opin Neurobiol 2021; 69:58-67. [PMID: 33647674 DOI: 10.1016/j.conb.2021.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
APOE (apolipoprotein E) is a key regulator of lipid metabolism and a leading genetic risk factor for Alzheimer's disease. While APOE participates in multiple biological pathways, its roles in diseases are largely due to the mutant protein encoded by APOE-ε4. However, emerging evidence suggests that some noncoding Alzheimer's disease risk variants residing in APOE and its nearby regions exert APOE-ε4-independent risks and modify APOE gene expression. Moreover, intervention strategies targeting APOE are being explored. In this review, we summarize the literature on the genetic risks and roles of APOE in biological systems. Moreover, we propose an integrative approach to evaluate disease risk and tailor interventions to aid research on APOE-associated diseases.
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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, 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, Hong Kong University of Science and Technology Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, 518057 Shenzhen, Guangdong, China
| | - Amy Ky Fu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, 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, Hong Kong University of Science and Technology Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, 518057 Shenzhen, Guangdong, 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, 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, Hong Kong University of Science and Technology Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, 518057 Shenzhen, Guangdong, China.
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Mezlini AM, Magdamo C, Merrill E, Chibnik LB, Blacker DL, Hyman BT, Das S. Characterizing Clinical and Neuropathological Traits of APOE Haplotypes in African Americans and Europeans. J Alzheimers Dis 2020; 78:467-477. [PMID: 33016904 PMCID: PMC7774865 DOI: 10.3233/jad-200228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The APOEɛ4 allele is the largest genetic risk factor for late-onset Alzheimer's disease (AD). Recent literature suggested that the contribution of APOEɛ4 to AD risk could be population-specific, with ɛ4 conferring a lower risk to Blacks or African Americans. OBJECTIVE To investigate the effect of APOE haplotypes on AD risk in individuals with European ancestry (EU) and Blacks or African Americans (AA). METHODS We selected data from 1) the National Alzheimer's Coordinating Center: a total of 3,486 AD cases and 4,511 controls (N = 7,997, 60% female) with genotypes from the Alzheimer's Disease Genetics Consortium (ADGC), and 2) the Rush University Religious Orders Study and Memory and Aging Project (ROSMAP) cohort with 578 AD and 670 controls (N = 1,248, 60% female). Using ɛ3 homozygotes as the reference, we compared the association of various APOE haplotypes with the clinical and neuropathological correlates of dementia in AA and EU. RESULTS In both cohorts, we find no difference in the odds or age of onset of AD among the ɛ4-linked haplotypes defined by rs769449 within either AA or EU. Additionally, while APOEɛ4 was associated with a faster rate of decline, no differences were found in rate of decline, clinical or neuropathological features among the ɛ4-linked haplotypes. Further analysis with other variants near the APOE locus failed to identify any effect modification. CONCLUSION Our study finds similar effects of the ɛ4-linked haplotypes defined by rs769449 on AD as compared to ɛ3 in both AA and EU. Future studies are required to understand the heterogeneity of APOE conferred risk of AD among various genotypes and populations.
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Affiliation(s)
- Aziz M. Mezlini
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Colin Magdamo
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - Emily Merrill
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
| | - Lori B. Chibnik
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Deborah L. Blacker
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bradley T. Hyman
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
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Bales KR, Paul SM. Targeting apolipoprotein E for treating Alzheimer's disease. Neurosci Lett 2019; 709:134366. [PMID: 31336138 DOI: 10.1016/j.neulet.2019.134366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023]
Abstract
The ε4 allele of the apolipoprotein E gene represents the most widely reproduced and robust susceptibility loci for the most common late onset and sporadic forms of Alzheimer's disease. While the discovery of this now widely replicated association was reported more than 25 years ago, few therapeutic interventions that specifically target the apolipoprotein pathway in brain have emerged. Here we discuss our current understanding of apolipoprotein E biology in brain, its relationship to the pathogenesis of Alzheimer's disease and present potential future avenues for exploration that may be amenable to drug development.
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Affiliation(s)
- Kelly R Bales
- Neuroscience Discovery, Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland.
| | - Steven M Paul
- Karuna Therapeutics, Inc., Boston, MA, United States
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Non-coding variability at the APOE locus contributes to the Alzheimer's risk. Nat Commun 2019; 10:3310. [PMID: 31346172 PMCID: PMC6658518 DOI: 10.1038/s41467-019-10945-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 06/10/2019] [Indexed: 12/30/2022] Open
Abstract
Alzheimer’s disease (AD) is a leading cause of mortality in the elderly. While the coding change of APOE-ε4 is a key risk factor for late-onset AD and has been believed to be the only risk factor in the APOE locus, it does not fully explain the risk effect conferred by the locus. Here, we report the identification of AD causal variants in PVRL2 and APOC1 regions in proximity to APOE and define common risk haplotypes independent of APOE-ε4 coding change. These risk haplotypes are associated with changes of AD-related endophenotypes including cognitive performance, and altered expression of APOE and its nearby genes in the human brain and blood. High-throughput genome-wide chromosome conformation capture analysis further supports the roles of these risk haplotypes in modulating chromatin states and gene expression in the brain. Our findings provide compelling evidence for additional risk factors in the APOE locus that contribute to AD pathogenesis. Several studies show that APOE-ε4 coding variants are associated with Alzheimer’s disease (AD) risk. Here, Zhou et al. perform fine-mapping of the APOE region and find AD risk haplotypes with non-coding variants in the PVRL2 and APOC1 regions that are associated with relevant endophenotypes.
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Abstract
PURPOSE OF REVIEW Over the last decade over 40 loci have been associated with risk of Alzheimer's disease (AD). However, most studies have either focused on identifying risk loci or performing unbiased screens without a focus on protective variation in AD. Here, we provide a review of known protective variants in AD and their putative mechanisms of action. Additionally, we recommend strategies for finding new protective variants. RECENT FINDINGS Recent Genome-Wide Association Studies have identified both common and rare protective variants associated with AD. These include variants in or near APP, APOE, PLCG2, MS4A, MAPT-KANSL1, RAB10, ABCA1, CCL11, SORL1, NOCT, SCL24A4-RIN3, CASS4, EPHA1, SPPL2A, and NFIC. SUMMARY There are very few protective variants with functional evidence and a derived allele with a frequency below 20%. Additional fine mapping and multi-omic studies are needed to further validate and characterize known variants as well as specialized genome-wide scans to identify novel variants.
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Affiliation(s)
- Shea J Andrews
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Equal first author
| | - Brian Fulton-Howard
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Equal first author
| | - Alison Goate
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
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