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Cheng PL, Wang H, Dombroski BA, Farrell JJ, Horng I, Chung T, Tosto G, Kunkle BW, Bush WS, Vardarajan B, Schellenberg GD, Lee WP. A Specialized Reference Panel with Structural Variants Integration for Improving Genotype Imputation in Alzheimer's Disease and Related Dementias (ADRD). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.22.24310827. [PMID: 39108532 PMCID: PMC11302603 DOI: 10.1101/2024.07.22.24310827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
We developed an imputation panel for Alzheimer's disease (AD) and related dementias (ADRD) using whole-genome sequencing (WGS) data from the Alzheimer's Disease Sequencing Project (ADSP). Recognizing the significant associations between structural variants (SVs) and AD, and their underrepresentation in existing public reference panels, our panel uniquely integrates single nucleotide variants (SNVs), short insertions and deletions (indels), and SVs. This panel enhances the imputation of disease susceptibility, including rare AD-associated SNVs, indels, and SVs, onto genotype array data, offering a cost-effective alternative to whole-genome sequencing while significantly augmenting statistical power. Notably, we discovered 10 rare indels nominal significant related to AD that are absent in the TOPMed-r2 panel and identified three suggestive significant (p-value < 1E-05) AD-associated SVs in the genes EXOC3L2 and DMPK , were identified. These findings provide new insights into AD genetics and underscore the critical role of imputation panels in advancing our understanding of complex diseases like ADRD.
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Besin V, Martriano Humardani F, Thalia Mulyanata L. Neurogenomics of Alzheimer's Disease (AD): An Asian Population Review. Clin Chim Acta 2023; 546:117389. [PMID: 37211175 DOI: 10.1016/j.cca.2023.117389] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
Alzheimer's disease (AD) is on the rise worldwide. Generally, AD is considered neurodegenerative when the production and clearance of amyloid-β (Aβ) are imbalanced. Recent research on genome-wide association studies (GWAS) has been explosive; GWAS indicates a relationship between single nucleotide polymorphism (SNP) and AD. GWAS also reveals ethnic differences between Caucasians and Asians. This indicates that pathogenesis between ethnic groups is distinct. According to current scientific knowledge, AD is a disease with a complex pathogenesis that includes impaired neuronal cholesterol regulation, immunity regulation, neurotransmitters regulation, Aβ clearance, Aβ production, and vascular regulation. Here, we demonstrate the pathogenesis of AD in an Asian population and the SNP risk of AD for future AD screening before onset. According to our knowledge, this is the first review of Alzheimer's disease to demonstrate the pathogenesis of AD based on SNP in an Asian population.
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Affiliation(s)
- Valentinus Besin
- Faculty of Medicine, University of Surabaya, Surabaya 60292, Indonesia.
| | - Farizky Martriano Humardani
- Faculty of Medicine, University of Surabaya, Surabaya 60292, Indonesia; Magister in Biomedical Science Program, Faculty of Medicine Universitas Brawijaya, Malang 65112, Indonesia
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Watanabe C, Shibuya H, Ichiyama Y, Okamura E, Tsukiyama-Fujii S, Tsukiyama T, Matsumoto S, Matsushita J, Azami T, Kubota Y, Ohji M, Sugiyama F, Takahashi S, Mizuno S, Tamura M, Mizutani KI, Ema M. Essential Roles of Exocyst Complex Component 3-like 2 on Cardiovascular Development in Mice. Life (Basel) 2022; 12:life12111730. [PMID: 36362885 PMCID: PMC9694714 DOI: 10.3390/life12111730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 12/01/2022] Open
Abstract
Angiogenesis is a process to generate new blood vessels from pre-existing vessels and to maintain vessels, and plays critical roles in normal development and disease. However, the molecular mechanisms underlying angiogenesis are not fully understood. This study examined the roles of exocyst complex component (Exoc) 3-like 2 (Exoc3l2) during development in mice. We found that Exoc3l1, Exoc3l2, Exoc3l3 and Exoc3l4 are expressed abundantly in endothelial cells at embryonic day 8.5. The generation of Exoc3l2 knock-out (KO) mice showed that disruption of Exoc3l2 resulted in lethal in utero. Substantial numbers of Exoc3l2 KO embryos exhibited hemorrhaging. Deletion of Exoc3l2 using Tie2-Cre transgenic mice demonstrated that Exoc3l2 in hematopoietic and endothelial lineages was responsible for the phenotype. Taken together, these findings reveal that Exoc3l2 is essential for cardiovascular and brain development in mice.
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Affiliation(s)
- Chisato Watanabe
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Hirotoshi Shibuya
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Yusuke Ichiyama
- Department of Ophthalmology, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Eiichi Okamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Setsuko Tsukiyama-Fujii
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Tomoyuki Tsukiyama
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Shoma Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Jun Matsushita
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Takuya Azami
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Yoshiaki Kubota
- Department of Anatomy, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masahito Ohji
- Department of Ophthalmology, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
- Correspondence: (M.T.); (K.-i.M.); (M.E.); Tel.: +81-29-836-9013 (M.T.); +81-78-974-4632 (ext. 73121) (K.-i.M.); +81-77-548-2334 (M.E.)
| | - Ken-ichi Mizutani
- Laboratory of Stem Cell Biology, Graduate School of Pharmaceutical Sciences, Kobe Gakuin University, Kobe 650-8586, Japan
- Correspondence: (M.T.); (K.-i.M.); (M.E.); Tel.: +81-29-836-9013 (M.T.); +81-78-974-4632 (ext. 73121) (K.-i.M.); +81-77-548-2334 (M.E.)
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu 520-2192, Japan
- Correspondence: (M.T.); (K.-i.M.); (M.E.); Tel.: +81-29-836-9013 (M.T.); +81-78-974-4632 (ext. 73121) (K.-i.M.); +81-77-548-2334 (M.E.)
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Differential gene expression by RNA-seq during Alzheimer’s disease-like progression in the Drosophila melanogaster model. Neurosci Res 2022; 180:1-12. [DOI: 10.1016/j.neures.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 01/10/2023]
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Coninx E, Chew YC, Yang X, Guo W, Coolkens A, Baatout S, Moons L, Verslegers M, Quintens R. Hippocampal and cortical tissue-specific epigenetic clocks indicate an increased epigenetic age in a mouse model for Alzheimer's disease. Aging (Albany NY) 2020; 12:20817-20834. [PMID: 33082299 PMCID: PMC7655172 DOI: 10.18632/aging.104056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 04/17/2023]
Abstract
Epigenetic clocks are based on age-associated changes in DNA methylation of CpG-sites, which can accurately measure chronological age in different species. Recently, several studies have indicated that the difference between chronological and epigenetic age, defined as the age acceleration, could reflect biological age indicating functional decline and age-associated diseases. In humans, an epigenetic clock associated Alzheimer's disease (AD) pathology with an acceleration of the epigenetic age. In this study, we developed and validated two mouse brain region-specific epigenetic clocks from the C57BL/6J hippocampus and cerebral cortex. Both clocks, which could successfully estimate chronological age, were further validated in a widely used mouse model for AD, the triple transgenic AD (3xTg-AD) mouse. We observed an epigenetic age acceleration indicating an increased biological age for the 3xTg-AD mice compared to non-pathological C57BL/6J mice, which was more pronounced in the cortex as compared to the hippocampus. Genomic region enrichment analysis revealed that age-dependent CpGs were enriched in genes related to developmental, aging-related, neuronal and neurodegenerative functions. Due to the limited access of human brain tissues, these epigenetic clocks specific for mouse cortex and hippocampus might be important in further unravelling the role of epigenetic mechanisms underlying AD pathology or brain aging in general.
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Affiliation(s)
- Emma Coninx
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Yap Ching Chew
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Xiaojing Yang
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Wei Guo
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Amelie Coolkens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Roel Quintens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
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Park S, Kang S. A minor allele of the haplotype located in the 19q13 loci is associated with a decreased risk of hyper-LDL-cholesterolemia, and a balanced diet and high protein intake can reduce the risk. Lipids Health Dis 2020; 19:178. [PMID: 32727492 PMCID: PMC7391697 DOI: 10.1186/s12944-020-01352-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Although the human chromosome 19q13 loci are reported to be associated with hyper-LDL-cholesterolemia, the haplotype of single nucleotide polymorphism (SNP) has not been studied. Therefore, the association of the haplotype in 19q13 loci with hyper-LDL-cholesterolemia was determined and their interactions with lifestyles and nutrient intakes were evaluated in 28,445 Koreans aged > 40 years. METHODS SNPs were selected from 19q13 loci that had an association with hyper-LDL-cholesterolemia with the adjustment of confounders (age, gender, area of residence, and body mass index). Haplotype was constructed from the selected SNPs. An adjusted odds ratio of the haplotype for hyper-LDL-cholesterolemia and the interaction between haplotype and lifestyles was analyzed after adjusting for covariates. RESULTS Hyper-LDL-cholesterolemia had an association with apolipoprotein E (APOE)_ rs7259620, translocase of outer mitochondrial membrane 40(TOMM40)_rs157581, poliovirus receptor-related 2(PVRL2)_rs403155, exocyst complex component 3-like 2(EXOC3L2)_ rs10406604 and CD3e molecule-associated protein (CD3EAP)_rs3212986 in 19q13. The haplotype of these SNPs had a negative association with hyper-total-cholesterolemia and hyper-LDL-cholesterolemia by 0.669 and 0.684 times, respectively, after adjusting for covariates. The incidence of cardiovascular diseases, especially myocardial infarction, had a negative association with the minor alleles. The balanced diet pattern (BD) and protein intake had a significant interaction with the haplotype: the major-allele of the haplotype exhibited a positive association with hyper-LDL-cholesterolemia, compared to the minor allele, only when combined with a high intake of BD. The participants with the minor allele exhibited a lower hyper-LDL-cholesterolemia risk compared to those with the major allele only with high protein intake. CONCLUSION The minor allele of haplotype located in 19q13 loci protected against hyper-LDL-cholesterolemia, especially with BD and high protein intake. The minor allele also had a negative association with myocardial infarction events.
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Affiliation(s)
- Sunmin Park
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, 165 Sechul-Ri, BaeBang-Yup, Asan-Si, ChungNam-Do, 31499, South Korea.
| | - Suna Kang
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, 165 Sechul-Ri, BaeBang-Yup, Asan-Si, ChungNam-Do, 31499, South Korea
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