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G N S HS, Marise VLP, Satish KS, Yergolkar AV, Krishnamurthy M, Ganesan Rajalekshmi S, Radhika K, Burri RR. Untangling huge literature to disinter genetic underpinnings of Alzheimer's Disease: A systematic review and meta-analysis. Ageing Res Rev 2021; 71:101421. [PMID: 34371203 DOI: 10.1016/j.arr.2021.101421] [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: 03/21/2021] [Revised: 06/25/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Drug discovery for Alzheimer's Disease (AD) is channeled towards unravelling key disease specific drug targets/genes to predict promising therapeutic candidates. Though enormous literature on AD genetics is available, there exists dearth in data pertinent to drug targets and crucial pathological pathways intertwined in disease progression. Further, the research findings revealing genetic associations failed to demonstrate consistency across different studies. This scenario prompted us to initiate a systematic review and meta-analysis with an aim of unearthing significant genetic hallmarks of AD. Initially, a Boolean search strategy was developed to retrieve case-control studies from PubMed, Cochrane, ProQuest, Europe PMC, grey literature and HuGE navigator. Subsequently, certain inclusion and exclusion criteria were framed to shortlist the relevant studies. These studies were later critically appraised using New Castle Ottawa Scale and Q-Genie followed by data extraction. Later, meta-analysis was performed only for those Single Nucleotide Polymorphisms (SNPs) which were evaluated in at least two different ethnicities from two different reports. Among, 204,351 studies retrieved, 820 met our eligibility criteria and 117 were processed for systematic review after critical appraisal. Ultimately, meta-analysis was performed for 23 SNPs associated with 15 genes which revealed significant associations of rs3865444 (CD33), rs7561528 (BIN1) and rs1801133 (MTHFR) with AD risk.
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Li J, Zhou HD, Deng J, Zhu J, Li L, Zhang M, Zeng F, Wang YJ. The association of single nucleotide polymorphism of the Fyn gene with sporadic Alzheimer's disease in the Chinese Han population. Neurosci Lett 2014; 575:80-4. [PMID: 24852829 DOI: 10.1016/j.neulet.2014.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/19/2014] [Accepted: 05/07/2014] [Indexed: 10/25/2022]
Abstract
Recent studies suggested genetic factors contribute to the pathogenesis of sporadic Alzheimer's disease (sAD). Fibroblast Yes related novel (Fyn), a tau kinase, has been reported to be associated with aberrant phosphorylated tau and neurofibrillary tangles formation. Fyn gene may be a potential candidate gene for AD. To investigate the association of the polymorphisms in Fyn gene with the susceptibility to sAD, we conducted a case-control study in a Chinese Han cohort including 200 sAD patients and 243 control participants. Four single nucleotide polymorphisms (SNPs) (rs111787668, rs1057979, rs6916861 and rs12910) within the promoter region of Fyn gene and one (rs7768046) in intron were selected and genotyped with a polymerase chain reaction-ligase detection reaction (PCR-LDR) method. Logistic regression under four genetic models was used to analyze the association between target SNPs and the risk of sAD. After adjusting for age, sex and APOE ɛ4 status, no association was revealed between these SNPs or the haplotypes containing four SNPs and the risk of sAD (P>0.05). The SNPs in the selected regions of the Fyn gene are unlikely to confer the susceptibility of sAD in the Chinese Han population. Further studies with a larger sample size and different ethnic populations are needed to reveal the role of Fyn gene in the pathogenesis of sAD.
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Affiliation(s)
- Jing Li
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Hua-Dong Zhou
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Juan Deng
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Jie Zhu
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Lin Li
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Meng Zhang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Fan Zeng
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China.
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, China.
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Bekris LM, Millard S, Lutz F, Li G, Galasko DR, Farlow MR, Quinn JF, Kaye JA, Leverenz JB, Tsuang DW, Yu CE, Peskind ER. Tau phosphorylation pathway genes and cerebrospinal fluid tau levels in Alzheimer's disease. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:874-83. [PMID: 22927204 PMCID: PMC3626266 DOI: 10.1002/ajmg.b.32094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 08/03/2012] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is characterized by the presence in the brain of amyloid plaques, consisting predominately of the amyloid β peptide (Aβ), and neurofibrillary tangles, consisting primarily of tau. Hyper-phosphorylated-tau (p-tau) contributes to neuronal damage, and both p-tau and total-tau (t-tau) levels are elevated in AD cerebrospinal fluid (CSF) compared to cognitively normal controls. Our hypothesis was that increased ratios of CSF phosphorylated-tau levels relative to total-tau levels correlate with regulatory region genetic variation of kinase or phosphatase genes biologically associated with the phosphorylation status of tau. Eighteen SNPs located within 5' and 3' regions of 5 kinase and 4 phosphatase genes, as well as two SNPs within regulatory regions of the MAPT gene were chosen for this analysis. The study sample consisted of 101 AD patients and 169 cognitively normal controls. Rs7768046 in the FYN kinase gene and rs913275 in the PPP2R4 phosphatase gene were both associated with CSF p-tau and t-tau levels in AD. These SNPs were also differentially associated with either CSF t-tau (rs7768046) or CSF p-tau (rs913275) relative to t-tau levels in AD compared to controls. These results suggest that rs7768046 and rs913275 both influence CSF tau levels in an AD-associated manner.
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Affiliation(s)
- Lynn M. Bekris
- Geriatric Research, Education, and Clinical Center (GRECC), VA Puget Sound Health Care System, Seattle, Washington,Department of Medicine, University of Washington, Seattle, Washington,Correspondence to: Lynn M. Bekris, Ph.D., Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, VAPSHCS GRECC S182B, 1660 South Columbian Way, Seattle, WA 98108.
| | - Steve Millard
- Northwest Network VISN-20 Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Health Care System, Seattle, Washington
| | - Franziska Lutz
- Geriatric Research, Education, and Clinical Center (GRECC), VA Puget Sound Health Care System, Seattle, Washington,Department of Medicine, University of Washington, Seattle, Washington
| | - Gail Li
- Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Doug R. Galasko
- Department of Neurosciences, University of California at San Diego and VA Medical Center San Diego, San Diego, California
| | - Martin R. Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Joseph F. Quinn
- Department of Neurology, Oregon Health and Science University, Portland, Oregon,Portland VA Medical Center, Portland, Oregon
| | - Jeffrey A. Kaye
- Department of Neurology, Oregon Health and Science University, Portland, Oregon,Portland VA Medical Center, Portland, Oregon
| | - James B. Leverenz
- Northwest Network VISN-20 Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Health Care System, Seattle, Washington,Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington,Department of Neurology, University of Washington School of Medicine, Seattle, Washington,Northwest Network VISN-20 Parkinson’s Disease Research, Education and Clinical Center (PADRECC), Roseburg, Oregon
| | - Debby W. Tsuang
- Northwest Network VISN-20 Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Health Care System, Seattle, Washington,Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center (GRECC), VA Puget Sound Health Care System, Seattle, Washington,Department of Medicine, University of Washington, Seattle, Washington
| | - Elaine R. Peskind
- Northwest Network VISN-20 Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Health Care System, Seattle, Washington,Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
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Wang X, Fredericksen ZS, Vierkant RA, Kosel ML, Pankratz VS, Cerhan JR, Justenhoven C, Brauch H, Olson JE, Couch FJ. Association of genetic variation in mitotic kinases with breast cancer risk. Breast Cancer Res Treat 2009; 119:453-62. [PMID: 19404734 DOI: 10.1007/s10549-009-0404-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 04/09/2009] [Indexed: 11/26/2022]
Abstract
An RNAi-based functional screening of mitotic kinases in Drosophila recently identified a number of members of the kinome that are required for normal cell division. Depletion of these kinases resulted in a number of different mitotic abnormalities including spindle malformation, chromosome mis-segregation, centrosome amplification and failure of cytokinesis (Bettencourt-Dias et al. in Nature 432:980-987, 2004). Since mitotic defects are commonly observed in cancer cells, these kinases may contribute to tumor development and/or progression. To investigate whether common genetic variation in the mitotic kinases are associated with breast cancer risk, we genotyped 386 single nucleotide polymorphisms (SNPs) from 44 mitotic kinase genes, in 798 breast cancer cases and 843 unaffected controls from a clinic-based study. A total of 22 SNPs from 13 kinase genes displayed significant associations with breast cancer risk (P(trend) < or = 0.05), including two SNPs from FYN (rs6914091 and rs1465061) that remained of interest after accounting for multiple testing (q = 0.06). These associations were stronger when evaluating cases with estrogen and progesterone receptor positive tumors. In addition, haplotype-based tests identified significant associations with risk for common haplotypes of the MAST2 (P = 0.04) and MAP2K4 (P = 0.006) genes. Although requiring replication, these findings suggest that genetic polymorphisms in mitotic kinases that have been implicated in chromosome instability and aneuploidy may contribute to the development of breast cancer.
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Affiliation(s)
- Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.
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Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A. Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res 2008; 18:1150-62. [PMID: 18417725 DOI: 10.1101/gr.075622.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Common hereditary neurodevelopmental disorders such as autism, bipolar disorder, and schizophrenia are most likely both genetically multifactorial and heterogeneous. Because of these characteristics traditional methods for genetic analysis fail when applied to such diseases. To address the problem we propose a novel probabilistic framework that combines the standard genetic linkage formalism with whole-genome molecular-interaction data to predict pathways or networks of interacting genes that contribute to common heritable disorders. We apply the model to three large genotype-phenotype data sets, identify a small number of significant candidate genes for autism (24), bipolar disorder (21), and schizophrenia (25), and predict a number of gene targets likely to be shared among the disorders.
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Affiliation(s)
- Ivan Iossifov
- Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA
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