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Wightman DP, Savage JE, de Leeuw CA, Jansen IE, Posthuma D. Rare variant aggregation in 148,508 exomes identifies genes associated with proxy dementia. Sci Rep 2023; 13:2179. [PMID: 36750708 PMCID: PMC9905079 DOI: 10.1038/s41598-023-29108-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Proxy phenotypes allow for the utilization of genetic data from large population cohorts to analyze late-onset diseases by using parental diagnoses as a proxy for genetic disease risk. Proxy phenotypes based on parental diagnosis status have been used in previous studies to identify common variants associated with Alzheimer's disease. As of yet, proxy phenotypes have not been used to identify genes associated with Alzheimer's disease through rare variants. Here we show that a proxy Alzheimer's disease/dementia phenotype can capture known Alzheimer's disease risk genes through rare variant aggregation. We generated a proxy Alzheimer's disease/dementia phenotype for 148,508 unrelated individuals of European ancestry in the UK biobank in order to perform exome-wide rare variant aggregation analyses to identify genes associated with proxy Alzheimer's disease/dementia. We identified four genes significantly associated with the proxy phenotype, three of which were significantly associated with proxy Alzheimer's disease/dementia in an independent replication cohort consisting of 197,506 unrelated individuals of European ancestry in the UK biobank. All three of the replicated genes have been previously associated with clinically diagnosed Alzheimer's disease (SORL1, TREM2, and TOMM40/APOE). We show that proxy Alzheimer's disease/dementia can be used to identify genes associated with Alzheimer's disease through rare variant aggregation.
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Affiliation(s)
- Douglas P Wightman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands.
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| | - Iris E Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, The Netherlands
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Yu X, Lophatananon A, Mekli K, Burns A, Muir KR, Guo H. A suggested shared aetiology of dementia - a colocalization study. Neurobiol Aging 2022; 117:71-82. [PMID: 35675752 DOI: 10.1016/j.neurobiolaging.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/11/2022]
Abstract
Identification of shared causal genes between dementia and its related clinical outcomes can help understand shared aetiology and multimorbidity surrounding dementia. We performed the HyPrColoc colocalization analysis to detect possible shared causal genes between dementia or Alzheimer's disease (AD) and 5 selected traits: stroke, diabetes, atherosclerosis, cholesterol level, and alcohol consumption within 601 dementia or AD associated genetic regions using summary results of the UK Biobank genome-wide association studies. Functional analysis was performed on the candidate causal genes to explore potential biological pathways. Rs150562240 in the LPIN3 gene was identified as a candidate shared causal variant across dementia, AD and atherosclerosis. Evidence for pairwise colocalization between dementia and stroke, dementia (or AD) and atherosclerosis, and dementia (or AD) and diabetes was found in 2, 6 and 2 genetic regions respectively. Colocalization signals between diabetes and the other 3 non-dementia/AD traits were detected in 5 regions. The colocalization evidence shown in our study suggested shared aetiology between dementia and related diseases such as stroke, atherosclerosis, and diabetes.
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Affiliation(s)
- Xinzhu Yu
- Centre for Biostatistics, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Artitaya Lophatananon
- Centre for Integrated Genomic Medicine, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Krisztina Mekli
- Centre for Integrated Genomic Medicine, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Alistair Burns
- Division of Neuroscience and Experimental Psychology, School of Social Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Kenneth R Muir
- Centre for Integrated Genomic Medicine, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK
| | - Hui Guo
- Centre for Biostatistics, Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester UK.
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Neuroinflammation in Alzheimer's Disease. Biomedicines 2021; 9:biomedicines9050524. [PMID: 34067173 PMCID: PMC8150909 DOI: 10.3390/biomedicines9050524] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease associated with human aging. Ten percent of individuals over 65 years have AD and its prevalence continues to rise with increasing age. There are currently no effective disease modifying treatments for AD, resulting in increasingly large socioeconomic and personal costs. Increasing age is associated with an increase in low-grade chronic inflammation (inflammaging) that may contribute to the neurodegenerative process in AD. Although the exact mechanisms remain unclear, aberrant elevation of reactive oxygen and nitrogen species (RONS) levels from several endogenous and exogenous processes in the brain may not only affect cell signaling, but also trigger cellular senescence, inflammation, and pyroptosis. Moreover, a compromised immune privilege of the brain that allows the infiltration of peripheral immune cells and infectious agents may play a role. Additionally, meta-inflammation as well as gut microbiota dysbiosis may drive the neuroinflammatory process. Considering that inflammatory/immune pathways are dysregulated in parallel with cognitive dysfunction in AD, elucidating the relationship between the central nervous system and the immune system may facilitate the development of a safe and effective therapy for AD. We discuss some current ideas on processes in inflammaging that appear to drive the neurodegenerative process in AD and summarize details on a few immunomodulatory strategies being developed to selectively target the detrimental aspects of neuroinflammation without affecting defense mechanisms against pathogens and tissue damage.
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Yee A, Tsui NBY, Kwan RYC, Leung AYM, Lai CKY, Chung T, Lau JYN, Fok M, Dai DLK, Lau LT. Apolipoprotein E Gene Revisited: Contribution of Rare Variants to Alzheimer's Disease Susceptibility in Southern Chinese. Curr Alzheimer Res 2021; 18:67-79. [PMID: 33761857 DOI: 10.2174/1567205018666210324111401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND APOE ε4 is the best-known risk factor for late-onset alzheimer's disease (AD). Population studies have demonstrated a relatively low prevalence of APOE ε4 among Chinese population, implying additional risk factors that are Chinese-specific may exist. Apart from - alleles, genetic variation profile along the full-length APOE has rarely been investigated. OBJECTIVE In this study, we filled this gap by comprehensively determining all genetic variations in APOE and investigated their potential associations with late-onset AD and mild cognitive impairment (MCI) in southern Chinese. METHODS Two hundred and fifty-seven southern Chinese participants were recruited, of whom 69 were AD patients, 83 had MCI, and 105 were normal controls. Full-length APOE from promoter to 3'UTR regions were sequenced. Genetic variants were identified and compared among the three groups. RESULTS While APOE ε4 was more significantly found in AD patients, the prevalence of APOE ε4 in southern Chinese AD patients was the lowest when compared to other areas of China and nearby regions, as well as other countries worldwide. We further identified 13 rare non-singleton variants in APOE. Significantly more AD patients carried any of the rare non-singleton variants than MCI and normal subjects. Such difference was observed in the non-carriers of ε4-allele only. Among the identified rare variants, the potential functional impact was predicted for rs532314089, rs553874843, rs533904656 and rs370594287. CONCLUSION Our study suggests an ethnic difference in genetic risk composition of AD in southern Chinese. Rare variants on APOE are a potential candidate for AD risk stratification biomarker in addition to APOE-ε4.
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Affiliation(s)
- Anita Yee
- Avalon Genomics (Hong Kong) Limited, Shatin,Hong Kong
| | | | - Rick Y C Kwan
- Centre for Gerontological Nursing, School of Nursing, The Hong Kong Polytechnic University, Hung Hom,Hong Kong
| | - Angela Y M Leung
- Centre for Gerontological Nursing, School of Nursing, The Hong Kong Polytechnic University, Hung Hom,Hong Kong
| | - Claudia K Y Lai
- Centre for Gerontological Nursing, School of Nursing, The Hong Kong Polytechnic University, Hung Hom,Hong Kong
| | - Teresa Chung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Hong Kong
| | | | - Manson Fok
- Faculty of Health Sciences, Macau University of Science and Technology, Taipa, Macau,Hong Kong
| | - David L K Dai
- Hong Kong Alzheimer's Disease Association, Wang Tau Hom,Hong Kong
| | - Lok-Ting Lau
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,Hong Kong
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Neuner SM, Tcw J, Goate AM. Genetic architecture of Alzheimer's disease. Neurobiol Dis 2020; 143:104976. [PMID: 32565066 PMCID: PMC7409822 DOI: 10.1016/j.nbd.2020.104976] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Advances in genetic and genomic technologies over the last thirty years have greatly enhanced our knowledge concerning the genetic architecture of Alzheimer's disease (AD). Several genes including APP, PSEN1, PSEN2, and APOE have been shown to exhibit large effects on disease susceptibility, with the remaining risk loci having much smaller effects on AD risk. Notably, common genetic variants impacting AD are not randomly distributed across the genome. Instead, these variants are enriched within regulatory elements active in human myeloid cells, and to a lesser extent liver cells, implicating these cell and tissue types as critical to disease etiology. Integrative approaches are emerging as highly effective for identifying the specific target genes through which AD risk variants act and will likely yield important insights related to potential therapeutic targets in the coming years. In the future, additional consideration of sex- and ethnicity-specific contributions to risk as well as the contribution of complex gene-gene and gene-environment interactions will likely be necessary to further improve our understanding of AD genetic architecture.
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Affiliation(s)
- Sarah M Neuner
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Julia Tcw
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
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Alzheimer’s Disease Genetics: Review of Novel Loci Associated with Disease. CURRENT GENETIC MEDICINE REPORTS 2020. [DOI: 10.1007/s40142-020-00182-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Giau VV, Senanarong V, Bagyinszky E, An SSA, Kim S. Analysis of 50 Neurodegenerative Genes in Clinically Diagnosed Early-Onset Alzheimer's Disease. Int J Mol Sci 2019; 20:E1514. [PMID: 30917570 PMCID: PMC6471359 DOI: 10.3390/ijms20061514] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 01/22/2023] Open
Abstract
Alzheimer's disease (AD), Parkinson's disease (PD), frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and prion diseases have a certain degree of clinical, pathological, and molecular overlapping. Previous studies revealed that many causative mutations in AD, PD, and FTD/ALS genes could be found in clinical familial and sporadic AD. To further elucidate the missing heritability in early-onset Alzheimer's disease (EOAD), we genetically characterized a Thai EOAD cohort by Next-Generation Sequencing (NGS) with a high depth of coverage, capturing variants in 50 previously recognized AD and other related disorders' genes. A novel mutation, APP p.V604M, and the known causative variant, PSEN1 p.E184G, were found in two of the familiar cases. Remarkably, among 61 missense variants were additionally discovered from 21 genes out of 50 genes, six potential mutations including MAPT P513A, LRRK2 p.R1628P, TREM2 p.L211P, and CSF1R (p.P54Q and pL536V) may be considered to be probably/possibly pathogenic and risk factors for other dementia leading to neuronal degeneration. All allele frequencies of the identified missense mutations were compared to 622 control individuals. Our study provides initial evidence that AD and other neurodegenerative diseases may represent shades of the same disease spectrum, and consideration should be given to offer exactly embracing genetic testing to patients diagnosed with EOAD. Our results need to be further confirmed with a larger cohort from this area.
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Affiliation(s)
- Vo Van Giau
- Department of Bionano Technology, Gachon University, Sungnam 13120, Korea.
| | | | - Eva Bagyinszky
- Department of Bionano Technology, Gachon University, Sungnam 13120, Korea.
| | - Seong Soo A An
- Department of Bionano Technology, Gachon University, Sungnam 13120, Korea.
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Sungnam 13620, Korea.
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Drange OK, Smeland OB, Shadrin AA, Finseth PI, Witoelar A, Frei O, Wang Y, Hassani S, Djurovic S, Dale AM, Andreassen OA. Genetic Overlap Between Alzheimer's Disease and Bipolar Disorder Implicates the MARK2 and VAC14 Genes. Front Neurosci 2019; 13:220. [PMID: 30930738 PMCID: PMC6425305 DOI: 10.3389/fnins.2019.00220] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Alzheimer's disease (AD) and bipolar disorder (BIP) are complex traits influenced by numerous common genetic variants, most of which remain to be detected. Clinical and epidemiological evidence suggest that AD and BIP are related. However, it is not established if this relation is of genetic origin. Here, we applied statistical methods based on the conditional false discovery rate (FDR) framework to detect genetic overlap between AD and BIP and utilized this overlap to increase the power to identify common genetic variants associated with either or both traits. Methods: We obtained genome wide association studies data from the International Genomics of Alzheimer's Project part 1 (17,008 AD cases and 37,154 controls) and the Psychiatric Genetic Consortium Bipolar Disorder Working Group (20,352 BIP cases and 31,358 controls). We used conditional QQ-plots to assess overlap in common genetic variants between AD and BIP. We exploited the genetic overlap to re-rank test-statistics for AD and BIP and improve detection of genetic variants using the conditional FDR framework. Results: Conditional QQ-plots demonstrated a polygenic overlap between AD and BIP. Using conditional FDR, we identified one novel genomic locus associated with AD, and nine novel loci associated with BIP. Further, we identified two novel loci jointly associated with AD and BIP implicating the MARK2 gene (lead SNP rs10792421, conjunctional FDR = 0.030, same direction of effect) and the VAC14 gene (lead SNP rs11649476, conjunctional FDR = 0.022, opposite direction of effect). Conclusion: We found polygenic overlap between AD and BIP and identified novel loci for each trait and two jointly associated loci. Further studies should examine if the shared loci implicating the MARK2 and VAC14 genes could explain parts of the shared and distinct features of AD and BIP.
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Affiliation(s)
- Ole Kristian Drange
- Department of Research and Development, Department of Mental Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Østmarka, Division of Mental Health Care, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Olav Bjerkehagen Smeland
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Alexey A. Shadrin
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Per Ivar Finseth
- Department of Brøset, Division of Mental Health Care, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Aree Witoelar
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Oleksandr Frei
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Yunpeng Wang
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Sahar Hassani
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anders M. Dale
- Center for Multimodal Imaging and Genetics, Department of Radiology, University of California, San Diego, La Jolla, CA, United States
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Ole A. Andreassen
- Norwegian Centre for Mental Disorders Research, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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Benefits and Challenges of Rare Genetic Variation in Alzheimer’s Disease. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-0161-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Centenarian controls increase variant effect sizes by an average twofold in an extreme case-extreme control analysis of Alzheimer's disease. Eur J Hum Genet 2018; 27:244-253. [PMID: 30258121 PMCID: PMC6336855 DOI: 10.1038/s41431-018-0273-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/13/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022] Open
Abstract
The detection of genetic loci associated with Alzheimer's disease (AD) requires large numbers of cases and controls because variant effect sizes are mostly small. We hypothesized that variant effect sizes should increase when individuals who represent the extreme ends of a disease spectrum are considered, as their genomes are assumed to be maximally enriched or depleted with disease-associated genetic variants. We used 1,073 extensively phenotyped AD cases with relatively young age at onset as extreme cases (66.3 ± 7.9 years), 1,664 age-matched controls (66.0 ± 6.5 years) and 255 cognitively healthy centenarians as extreme controls (101.4 ± 1.3 years). We estimated the effect size of 29 variants that were previously associated with AD in genome-wide association studies. Comparing extreme AD cases with centenarian controls increased the variant effect size relative to published effect sizes by on average 1.90-fold (SE = 0.29, p = 9.0 × 10-4). The effect size increase was largest for the rare high-impact TREM2 (R74H) variant (6.5-fold), and significant for variants in/near ECHDC3 (4.6-fold), SLC24A4-RIN3 (4.5-fold), NME8 (3.8-fold), PLCG2 (3.3-fold), APOE-ε2 (2.2-fold), and APOE-ε4 (twofold). Comparing extreme phenotypes enabled us to replicate the AD association for 10 variants (p < 0.05) in relatively small samples. The increase in effect sizes depended mainly on using centenarians as extreme controls: the average variant effect size was not increased in a comparison of extreme AD cases and age-matched controls (0.94-fold, p = 6.8 × 10-1), suggesting that on average the tested genetic variants did not explain the extremity of the AD cases. Concluding, using centenarians as extreme controls in AD case-control studies boosts the variant effect size by on average twofold, allowing the replication of disease-association in relatively small samples.
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Abstract
Alzheimer's disease (AD), the main form of dementia in the elderly, is the most common progressive neurodegenerative disease characterized by rapidly progressive cognitive dysfunction and behavior impairment. AD exhibits a considerable heritability and great advances have been made in approaches to searching the genetic etiology of AD. In AD genetic studies, methods have developed from classic linkage-based and candidate-gene-based association studies to genome-wide association studies (GWAS) and next generation sequencing (NGS). The identification of new susceptibility genes has provided deeper insights to understand the mechanisms underlying AD. In addition to searching novel genes associated with AD in large samples, the NGS technologies can also be used to shed light on the 'black matter' discovery even in smaller samples. The shift in AD genetics between traditional studies and individual sequencing will allow biomaterials of each patient as the central unit of genetic studies. This review will cover genetic findings in AD and consequences of AD genetic findings. Firstly, we will discuss the discovery of mutations in APP, PSEN1, PSEN2, APOE, and ADAM10. Then we will summarize and evaluate the information obtained from GWAS of AD. Finally, we will outline the efforts to identify rare variants associated with AD using NGS.
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Verma SS, Ritchie MD. Another Round of "Clue" to Uncover the Mystery of Complex Traits. Genes (Basel) 2018; 9:E61. [PMID: 29370075 PMCID: PMC5852557 DOI: 10.3390/genes9020061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
A plethora of genetic association analyses have identified several genetic risk loci. Technological and statistical advancements have now led to the identification of not only common genetic variants, but also low-frequency variants, structural variants, and environmental factors, as well as multi-omics variations that affect the phenotypic variance of complex traits in a population, thus referred to as complex trait architecture. The concept of heritability, or the proportion of phenotypic variance due to genetic inheritance, has been studied for several decades, but its application is mainly in addressing the narrow sense heritability (or additive genetic component) from Genome-Wide Association Studies (GWAS). In this commentary, we reflect on our perspective on the complexity of understanding heritability for human traits in comparison to model organisms, highlighting another round of clues beyond GWAS and an alternative approach, investigating these clues comprehensively to help in elucidating the genetic architecture of complex traits.
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Affiliation(s)
- Shefali Setia Verma
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marylyn D Ritchie
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Stem Cell Technology for (Epi)genetic Brain Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:443-475. [PMID: 28523560 DOI: 10.1007/978-3-319-53889-1_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the enormous efforts of the scientific community over the years, effective therapeutics for many (epi)genetic brain disorders remain unidentified. The common and persistent failures to translate preclinical findings into clinical success are partially attributed to the limited efficiency of current disease models. Although animal and cellular models have substantially improved our knowledge of the pathological processes involved in these disorders, human brain research has generally been hampered by a lack of satisfactory humanized model systems. This, together with our incomplete knowledge of the multifactorial causes in the majority of these disorders, as well as a thorough understanding of associated (epi)genetic alterations, has been impeding progress in gaining more mechanistic insights from translational studies. Over the last years, however, stem cell technology has been offering an alternative approach to study and treat human brain disorders. Owing to this technology, we are now able to obtain a theoretically inexhaustible source of human neural cells and precursors in vitro that offer a platform for disease modeling and the establishment of therapeutic interventions. In addition to the potential to increase our general understanding of how (epi)genetic alterations contribute to the pathology of brain disorders, stem cells and derivatives allow for high-throughput drugs and toxicity testing, and provide a cell source for transplant therapies in regenerative medicine. In the current chapter, we will demonstrate the validity of human stem cell-based models and address the utility of other stem cell-based applications for several human brain disorders with multifactorial and (epi)genetic bases, including Parkinson's disease (PD), Alzheimer's disease (AD), fragile X syndrome (FXS), Angelman syndrome (AS), Prader-Willi syndrome (PWS), and Rett syndrome (RTT).
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Simino J, Wang Z, Bressler J, Chouraki V, Yang Q, Younkin SG, Seshadri S, Fornage M, Boerwinkle E, Mosley TH. Whole exome sequence-based association analyses of plasma amyloid-β in African and European Americans; the Atherosclerosis Risk in Communities-Neurocognitive Study. PLoS One 2017; 12:e0180046. [PMID: 28704393 PMCID: PMC5509141 DOI: 10.1371/journal.pone.0180046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022] Open
Abstract
Objective We performed single-variant and gene-based association analyses of plasma amyloid-β (aβ) concentrations using whole exome sequence from 1,414 African and European Americans. Our goal was to identify genes that influence plasma aβ42 concentrations and aβ42:aβ40 ratios in late middle age (mean = 59 years), old age (mean = 77 years), or change over time (mean = 18 years). Methods Plasma aβ measures were linearly regressed onto age, gender, APOE ε4 carrier status, and time elapsed between visits (fold-changes only) separately by race. Following inverse normal transformation of the residuals, seqMeta was used to conduct race-specific single-variant and gene-based association tests while adjusting for population structure. Linear regression models were fit on autosomal variants with minor allele frequencies (MAF)≥1%. T5 burden and Sequence Kernel Association (SKAT) gene-based tests assessed functional variants with MAF≤5%. Cross-race fixed effects meta-analyses were Bonferroni-corrected for the number of variants or genes tested. Results Seven genes were associated with aβ in late middle age or change over time; no associations were identified in old age. Single variants in KLKB1 (rs3733402; p = 4.33x10-10) and F12 (rs1801020; p = 3.89x10-8) were significantly associated with midlife aβ42 levels through cross-race meta-analysis; the KLKB1 variant replicated internally using 1,014 additional participants with exome chip. ITPRIP, PLIN2, and TSPAN18 were associated with the midlife aβ42:aβ40 ratio via the T5 test; TSPAN18 was significant via the cross-race meta-analysis, whereas ITPRIP and PLIN2 were European American-specific. NCOA1 and NT5C3B were associated with the midlife aβ42:aβ40 ratio and the fold-change in aβ42, respectively, via SKAT in African Americans. No associations replicated externally (N = 725). Conclusion We discovered age-dependent genetic effects, established associations between vascular-related genes (KLKB1, F12, PLIN2) and midlife plasma aβ levels, and identified a plausible Alzheimer’s Disease candidate gene (ITPRIP) influencing cell death. Plasma aβ concentrations may have dynamic biological determinants across the lifespan; plasma aβ study designs or analyses must consider age.
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Affiliation(s)
- Jeannette Simino
- Gertrude C. Ford MIND Center, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Department of Data Science, John D. Bower School of Population Health, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- * E-mail:
| | - Zhiying Wang
- Human Genetics Center, Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Jan Bressler
- Human Genetics Center, Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Vincent Chouraki
- Lille University, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk factors and molecular determinants of aging-related diseases; Lille, France
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Steven G. Younkin
- Department of Neuroscience, Mayo Clinic College of Medicine, Mayo Clinic Jacksonville, Jacksonville, Florida, United States of America
| | - Sudha Seshadri
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, United States of America
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
- The Brown Foundation Institute of Molecular Medicine, Research Center for Human Genetics, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
- The Brown Foundation Institute of Molecular Medicine, Research Center for Human Genetics, The University of Texas Health Science Center, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Thomas H. Mosley
- Gertrude C. Ford MIND Center, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Department of Medicine, University of Mississippi Medical Center, Jackson, Massachusetts, United States of America
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15
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Abdala BB, Dos Santos JM, Gonçalves AP, da Motta LB, Laks J, de Borges MB, Gonçalves Pimentel MM, Santos-Rebouças CB. Influence of low frequency PSEN1 variants on familial Alzheimer's disease risk in Brazil. Neurosci Lett 2017; 653:341-345. [PMID: 28554858 DOI: 10.1016/j.neulet.2017.05.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/11/2017] [Accepted: 05/24/2017] [Indexed: 11/29/2022]
Abstract
About 30-70% of familial Alzheimer's disease (AD) cases are related to mutations in presenilin-1 gene (PSEN1). Although the role of mutations and common variants in AD had been extensively investigated, the contribution of rare or low frequency PSEN1 variants on AD risk remains unclear. In the current study, we performed a mutational screening of PSEN1 coding exons and flanking intronic sequences among 53 index cases with familial history of AD from Rio de Janeiro (Brazil). Two missense variants (rs63750592; rs17125721), one rare and a low frequency variant, and two intronic variants (rs3025786; rs165932) were identified. In silico tools were used to predict the functional impact of the variants, revealing no changes in protein functionality by exonic variants. Otherwise, all variants were predicted to alter splicing signals. Prediction results, together with previous reports, suggest a correlation between rs17125721 and AD. So, a subsequent case-control study to evaluate the role of rs1712572 on AD risk was performed in an additional sample of 120 AD sporadic cases and in 149 elderly healthy controls by TaqMan Genotyping Assay. Our data indicates a risk association for rs17125721 in familial AD cases (OR=6.0; IC95%=1.06-33.79; p=0.042). In addition, we tested the multiplicative interaction between allele ε4 of the apolipoprotein E (APOE) and rs17125721 and no statistical association was found. Taken together, our findings provide new insight about the genetic relevance of low frequency PSEN1 variants for familial AD development.
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Affiliation(s)
- Bianca Barbosa Abdala
- Departamento de Genética, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Luciana Branco da Motta
- Núcleo de Atenção ao Idoso, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jerson Laks
- Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Programa de Pós Graduação em Biomedicina Translacional, Universidade do Grande Rio, Rio de Janeiro, Brazil
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16
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Hinz FI, Geschwind DH. Molecular Genetics of Neurodegenerative Dementias. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023705. [PMID: 27940516 DOI: 10.1101/cshperspect.a023705] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neurodegenerative dementias are clinically heterogeneous, progressive diseases with frequently overlapping symptoms, such as cognitive impairments and behavior and movement deficits. Although a majority of cases appear to be sporadic, there is a large genetic component that has yet to be fully explained. Here, we review the recent genetic and genomic findings pertaining to Alzheimer's disease, frontotemporal dementia, Lewy body dementia, and prion dementia. In this review, we describe causal and susceptibility genes identified for these dementias and discuss recent research pertaining to the molecular function of these genes. Of particular interest, there is a large overlap in clinical phenotypes, genes, and/or aggregating protein products involved in these diseases, as well as frequent comorbid presentation, indicating that these dementias may represent a continuum of syndromes rather than individual diseases.
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Affiliation(s)
- Flora I Hinz
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095.,Center for Autism Research and Treatment and Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California 90024
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17
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Santos CY, Snyder PJ, Wu WC, Zhang M, Echeverria A, Alber J. Pathophysiologic relationship between Alzheimer's disease, cerebrovascular disease, and cardiovascular risk: A review and synthesis. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2017; 7:69-87. [PMID: 28275702 PMCID: PMC5328683 DOI: 10.1016/j.dadm.2017.01.005] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As the population ages due to demographic trends and gains in life expectancy, the incidence and prevalence of dementia increases, and the need to understand the etiology and pathogenesis of dementia becomes ever more urgent. Alzheimer's disease (AD), the most common form of dementia, is a complex disease, the mechanisms of which are poorly understood. The more we learn about AD, the more questions are raised about our current conceptual models of disease. In the absence of a cure or the means by which to slow disease progress, it may be prudent to apply our current knowledge of the intersection between AD, cardiovascular disease, and cerebrovascular disease to foster efforts to delay or slow the onset of AD. This review discusses our current understanding of the epidemiology, genetics, and pathophysiology of AD, the intersection between AD and vascular causes of dementia, and proposes future directions for research and prevention.
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Affiliation(s)
- Cláudia Y. Santos
- Lifespan Clinical Research Center, Rhode Island Hospital, Providence, RI, USA
- Interdisciplinary Neuroscience Program, University of Rhode Island, Kingston, RI, USA
| | - Peter J. Snyder
- Lifespan Clinical Research Center, Rhode Island Hospital, Providence, RI, USA
- Interdisciplinary Neuroscience Program, University of Rhode Island, Kingston, RI, USA
- Department of Neurology, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Wen-Chih Wu
- Division of Cardiology, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Mia Zhang
- Griffith University School of Medicine, Gold Coast, Queensland, Australia
| | - Ana Echeverria
- University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Jessica Alber
- Lifespan Clinical Research Center, Rhode Island Hospital, Providence, RI, USA
- Department of Neurology, Warren Alpert Medical School of Brown University, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
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18
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Shi Y, Inoue H, Wu JC, Yamanaka S. Induced pluripotent stem cell technology: a decade of progress. Nat Rev Drug Discov 2017; 16:115-130. [PMID: 27980341 PMCID: PMC6416143 DOI: 10.1038/nrd.2016.245] [Citation(s) in RCA: 886] [Impact Index Per Article: 126.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the advent of induced pluripotent stem cell (iPSC) technology a decade ago, enormous progress has been made in stem cell biology and regenerative medicine. Human iPSCs have been widely used for disease modelling, drug discovery and cell therapy development. Novel pathological mechanisms have been elucidated, new drugs originating from iPSC screens are in the pipeline and the first clinical trial using human iPSC-derived products has been initiated. In particular, the combination of human iPSC technology with recent developments in gene editing and 3D organoids makes iPSC-based platforms even more powerful in each area of their application, including precision medicine. In this Review, we discuss the progress in applications of iPSC technology that are particularly relevant to drug discovery and regenerative medicine, and consider the remaining challenges and the emerging opportunities in the field.
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Affiliation(s)
- Yanhong Shi
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010, USA
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Joseph C Wu
- Stanford Cardiovascular Institute, 265 Campus Drive, Room G1120B, Stanford, California 94305-5454, USA
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158, USA
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19
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20
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Hisama FM, Oshima J, Martin GM. How Research on Human Progeroid and Antigeroid Syndromes Can Contribute to the Longevity Dividend Initiative. Cold Spring Harb Perspect Med 2016; 6:a025882. [PMID: 26931459 DOI: 10.1101/cshperspect.a025882] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Although translational applications derived from research on basic mechanisms of aging are likely to enhance health spans and life spans for most of us (the longevity dividend), there will remain subsets of individuals with special vulnerabilities. Medical genetics is a discipline that describes such "private" patterns of aging and can reveal underlying mechanisms, many of which support genomic instability as a major mechanism of aging. We review examples of three classes of informative disorders: "segmental progeroid syndromes" (those that appear to accelerate multiple features of aging), "unimodal progeroid syndromes" (those that impact on a single disorder of aging), and "unimodal antigeroid syndromes," variants that provide enhanced protection against specific disorders of aging; we urge our colleagues to expand our meager research efforts on the latter, including ancillary somatic cell genetic approaches.
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Affiliation(s)
- Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195
| | - Junko Oshima
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195 Department of Medicine, Chiba University, Chiba 260-8670, Japan
| | - George M Martin
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195 International Registry of Werner Syndrome, University of Washington School of Medicine, Seattle, Washington 98195
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21
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Squitti R, Siotto M, Arciello M, Rossi L. Non-ceruloplasmin bound copper and ATP7B gene variants in Alzheimer's disease. Metallomics 2016; 8:863-73. [DOI: 10.1039/c6mt00101g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ATP7B, a protein mainly expressed in the hepatocytes, is a copper chaperone that loads the metal into the serum copper–protein ceruloplasmin during its synthesis and also escorts superfluous copper into the bile, by a sophisticated trafficking mechanism.
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Affiliation(s)
- R. Squitti
- Molecular Markers Laboratory
- IRCCS Istituto Centro San Giovanni di Dio-Fatebenefratelli
- 25125 Brescia, Italy
| | - M. Siotto
- Don Carlo Gnocchi ONLUS Foundation
- Milan, Italy
| | - M. Arciello
- Department of Biology
- University of Rome Tor Vergata
- Rome, Italy
| | - L. Rossi
- Department of Biology
- University of Rome Tor Vergata
- Rome, Italy
- Consorzio Interuniversitario “Istituto Nazionale Biostrutture e Biosistemi” (I.N.B.B.)
- Rome, Italy
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22
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Saad M, Brkanac Z, Wijsman EM. Family-based genome scan for age at onset of late-onset Alzheimer's disease in whole exome sequencing data. GENES, BRAIN, AND BEHAVIOR 2015; 14:607-17. [PMID: 26394601 PMCID: PMC4715764 DOI: 10.1111/gbb.12250] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/08/2015] [Accepted: 08/24/2015] [Indexed: 01/31/2023]
Abstract
Alzheimer's disease (AD) is a common and complex neurodegenerative disease. Age at onset (AAO) of AD is an important component phenotype with a genetic basis, and identification of genes in which variation affects AAO would contribute to identification of factors that affect timing of onset. Increase in AAO through prevention or therapeutic measures would have enormous benefits by delaying AD and its associated morbidities. In this paper, we performed a family-based genome-wide association study for AAO of late-onset AD in whole exome sequence data generated in multigenerational families with multiple AD cases. We conducted single marker and gene-based burden tests for common and rare variants, respectively. We combined association analyses with variance component linkage analysis, and with reference to prior studies, in order to enhance evidence of the identified genes. For variants and genes implicated by the association study, we performed a gene-set enrichment analysis to identify potential novel pathways associated with AAO of AD. We found statistically significant association with AAO for three genes (WRN, NTN4 and LAMC3) with common associated variants, and for four genes (SLC8A3, SLC19A3, MADD and LRRK2) with multiple rare-associated variants that have a plausible biological function related to AD. The genes we have identified are in pathways that are strong candidates for involvement in the development of AD pathology and may lead to a better understanding of AD pathogenesis.
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Affiliation(s)
- Mohamad Saad
- Department of Biostatistics, University of Washington, Seattle, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, USA
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, USA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, USA
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23
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Talwar P, Sinha J, Grover S, Rawat C, Kushwaha S, Agarwal R, Taneja V, Kukreti R. Dissecting Complex and Multifactorial Nature of Alzheimer's Disease Pathogenesis: a Clinical, Genomic, and Systems Biology Perspective. Mol Neurobiol 2015; 53:4833-64. [PMID: 26351077 DOI: 10.1007/s12035-015-9390-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/11/2015] [Indexed: 01/14/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by loss of memory and other cognitive functions. AD can be classified into familial AD (FAD) and sporadic AD (SAD) based on heritability and into early onset AD (EOAD) and late onset AD (LOAD) based on age of onset. LOAD cases are more prevalent with genetically complex architecture. In spite of significant research focused on understanding the etiological mechanisms, search for diagnostic biomarker(s) and disease-modifying therapy is still on. In this article, we aim to comprehensively review AD literature on established etiological mechanisms including role of beta-amyloid and apolipoprotein E (APOE) along with promising newer etiological factors such as epigenetic modifications that have been associated with AD suggesting its multifactorial nature. As genomic studies have recently played a significant role in elucidating AD pathophysiology, a systematic review of findings from genome-wide linkage (GWL), genome-wide association (GWA), genome-wide expression (GWE), and epigenome-wide association studies (EWAS) was conducted. The availability of multi-dimensional genomic data has further coincided with the advent of computational and network biology approaches in recent years. Our review highlights the importance of integrative approaches involving genomics and systems biology perspective in elucidating AD pathophysiology. The promising newer approaches may provide reliable means of early and more specific diagnosis and help identify therapeutic interventions for LOAD.
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Affiliation(s)
- Puneet Talwar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India.,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Juhi Sinha
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Sandeep Grover
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India.,Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Chitra Rawat
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India.,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Suman Kushwaha
- Institute of Human Behaviour and Allied Sciences (IHBAS), Delhi, India
| | - Rachna Agarwal
- Institute of Human Behaviour and Allied Sciences (IHBAS), Delhi, India
| | - Vibha Taneja
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Ritushree Kukreti
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India. .,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India.
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24
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Calero M, Gómez-Ramos A, Calero O, Soriano E, Avila J, Medina M. Additional mechanisms conferring genetic susceptibility to Alzheimer's disease. Front Cell Neurosci 2015; 9:138. [PMID: 25914626 PMCID: PMC4391239 DOI: 10.3389/fncel.2015.00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/23/2015] [Indexed: 01/18/2023] Open
Abstract
Familial Alzheimer’s disease (AD), mostly associated with early onset, is caused by mutations in three genes (APP, PSEN1, and PSEN2) involved in the production of the amyloid β peptide. In contrast, the molecular mechanisms that trigger the most common late onset sporadic AD remain largely unknown. With the implementation of an increasing number of case-control studies and the upcoming of large-scale genome-wide association studies there is a mounting list of genetic risk factors associated with common genetic variants that have been associated with sporadic AD. Besides apolipoprotein E, that presents a strong association with the disease (OR∼4), the rest of these genes have moderate or low degrees of association, with OR ranging from 0.88 to 1.23. Taking together, these genes may account only for a fraction of the attributable AD risk and therefore, rare variants and epistastic gene interactions should be taken into account in order to get the full picture of the genetic risks associated with AD. Here, we review recent whole-exome studies looking for rare variants, somatic brain mutations with a strong association to the disease, and several studies dealing with epistasis as additional mechanisms conferring genetic susceptibility to AD. Altogether, recent evidence underlines the importance of defining molecular and genetic pathways, and networks rather than the contribution of specific genes.
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Affiliation(s)
- Miguel Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Chronic Disease Programme, Instituto de Salud Carlos III Madrid, Spain ; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
| | - Alberto Gómez-Ramos
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Centro de Biología Molecular Severo Ochoa CSIC-UAM Madrid, Spain
| | - Olga Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Chronic Disease Programme, Instituto de Salud Carlos III Madrid, Spain
| | - Eduardo Soriano
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; University of Barcelona Barcelona, Spain
| | - Jesús Avila
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Centro de Biología Molecular Severo Ochoa CSIC-UAM Madrid, Spain
| | - Miguel Medina
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas Madrid, Spain ; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
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25
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Zhang Q. Associating rare genetic variants with human diseases. Front Genet 2015; 6:133. [PMID: 25904936 PMCID: PMC4389536 DOI: 10.3389/fgene.2015.00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/19/2015] [Indexed: 11/20/2022] Open
Affiliation(s)
- Qunyuan Zhang
- Division of Statistical Genomics, Washington University School of Medicine St. Louis, MO, USA
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