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  1. Article ; Online: Genetics of Alzheimer’s Disease

    Nilüfer Ertekin Taner

    Türk Nöroloji Dergisi, Vol 16, Iss 1, Pp 1-

    Lessons Learned in Two Decades

    2010  Volume 11

    Abstract: Alzheimer’s disease (AD) is the most common type of dementia. It is estimated that more than 35 million people worldwide will suffer from dementia in 2010. Without effective therapies, this epidemic is expected to affect more than 115 million patients ... ...

    Abstract Alzheimer’s disease (AD) is the most common type of dementia. It is estimated that more than 35 million people worldwide will suffer from dementia in 2010. Without effective therapies, this epidemic is expected to affect more than 115 million patients worldwide by 2050. Genetic studies can help us understand the disease pathophysiology, thereby providing potential therapeutic, presymptomatic predictive and preventative avenues. Since 1990, there has been evidence for a substantial genetic component underlying the risk for AD. Three genes with autosomal dominant mutations lead to early-onset familial AD, which explains less than 1% of all AD. Apolipoprotein ε4, the only widely accepted genetic risk factor for late-onset AD, accounts for only a portion of this risk. Genetic linkage and association studies have identified multiple candidate gene regions, although many resulting candidate genes suffer from lack of replication, at least partially due to underpowered studies in the setting of genetic heterogeneity and small-tomoderate effect size. Genome-wide association studies that assess hundreds of thousands of single-nucleotide polymorphisms (SNPs) in thousands of subjects have been viewed as a potentially powerful approach in uncovering common risk variations for genetically complex diseases such as AD. To date, 11 independent genome-wide association studies have been completed in late-onset AD (LOAD) that led to candidate regions and genes for follow-up. These studies provide evidence for novel, plausible genetic risk factors for AD, but still fail to account for all of the estimated risk. Additional genetic risk factors of even smaller effect size, rare variants and/or structural DNA polymorphisms may exist, which may escape detection by conventional methods. Alternative approaches such as nextgeneration sequencing, use of quantitative endophenotypes, copy number variation analyses, and meta-analyses may be required. This review summarizes the current knowledge on the genetics of AD and suggests a framework ...
    Keywords Alzheimer disease ; genetics ; linkage (genetics) ; association ; Medicine ; R ; Neurology. Diseases of the nervous system ; RC346-429
    Subject code 610
    Language English
    Publishing date 2010-03-01T00:00:00Z
    Publisher Galenos Yayinevi
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Genetics of Alzheimer’s Disease

    Nilüfer Ertekin Taner

    Türk Nöroloji Dergisi, Vol 16, Iss 1, Pp 1-

    Lessons Learned in Two Decades

    2010  Volume 11

    Abstract: Alzheimer’s disease (AD) is the most common type of dementia. It is estimated that more than 35 million people worldwide will suffer from dementia in 2010. Without effective therapies, this epidemic is expected to affect more than 115 million patients ... ...

    Abstract Alzheimer’s disease (AD) is the most common type of dementia. It is estimated that more than 35 million people worldwide will suffer from dementia in 2010. Without effective therapies, this epidemic is expected to affect more than 115 million patients worldwide by 2050. Genetic studies can help us understand the disease pathophysiology, thereby providing potential therapeutic, presymptomatic predictive and preventative avenues. Since 1990, there has been evidence for a substantial genetic component underlying the risk for AD. Three genes with autosomal dominant mutations lead to early-onset familial AD, which explains less than 1% of all AD. Apolipoprotein ε4, the only widely accepted genetic risk factor for late-onset AD, accounts for only a portion of this risk. Genetic linkage and association studies have identified multiple candidate gene regions, although many resulting candidate genes suffer from lack of replication, at least partially due to underpowered studies in the setting of genetic heterogeneity and small-tomoderate effect size. Genome-wide association studies that assess hundreds of thousands of single-nucleotide polymorphisms (SNPs) in thousands of subjects have been viewed as a potentially powerful approach in uncovering common risk variations for genetically complex diseases such as AD. To date, 11 independent genome-wide association studies have been completed in late-onset AD (LOAD) that led to candidate regions and genes for follow-up. These studies provide evidence for novel, plausible genetic risk factors for AD, but still fail to account for all of the estimated risk. Additional genetic risk factors of even smaller effect size, rare variants and/or structural DNA polymorphisms may exist, which may escape detection by conventional methods. Alternative approaches such as nextgeneration sequencing, use of quantitative endophenotypes, copy number variation analyses, and meta-analyses may be required. This review summarizes the current knowledge on the genetics of AD and suggests a framework ...
    Keywords Alzheimer disease ; genetics ; linkage (genetics) ; association ; Medicine ; R ; Neurology. Diseases of the nervous system ; RC346-429
    Subject code 610
    Language English
    Publishing date 2010-03-01T00:00:00Z
    Publisher Galenos Yayinevi
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Risk factors for severe COVID-19 differ by age for hospitalized adults

    Sevda Molani / Patricia V. Hernandez / Ryan T. Roper / Venkata R. Duvvuri / Andrew M. Baumgartner / Jason D. Goldman / Nilüfer Ertekin-Taner / Cory C. Funk / Nathan D. Price / Noa Rappaport / Jennifer J. Hadlock

    Scientific Reports, Vol 12, Iss 1, Pp 1-

    2022  Volume 9

    Abstract: Abstract Risk stratification for hospitalized adults with COVID-19 is essential to inform decisions about individual patients and allocation of resources. So far, risk models for severe COVID outcomes have included age but have not been optimized to best ...

    Abstract Abstract Risk stratification for hospitalized adults with COVID-19 is essential to inform decisions about individual patients and allocation of resources. So far, risk models for severe COVID outcomes have included age but have not been optimized to best serve the needs of either older or younger adults. Models also need to be updated to reflect improvements in COVID-19 treatments. This retrospective study analyzed data from 6906 hospitalized adults with COVID-19 from a community health system across five states in the western United States. Risk models were developed to predict mechanical ventilation illness or death across one to 56 days of hospitalization, using clinical data available within the first hour after either admission with COVID-19 or a first positive SARS-CoV-2 test. For the seven-day interval, models for age ≥ 18 and < 50 years reached AUROC 0.81 (95% CI 0.71–0.91) and models for age ≥ 50 years reached AUROC 0.82 (95% CI 0.77–0.86). Models revealed differences in the statistical significance and relative predictive value of risk factors between older and younger patients including age, BMI, vital signs, and laboratory results. In addition, for hospitalized patients, sex and chronic comorbidities had lower predictive value than vital signs and laboratory results.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Nerve growth factor receptor (Ngfr) induces neurogenic plasticity by suppressing reactive astroglial Lcn2/Slc22a17 signaling in Alzheimer’s disease

    Tohid Siddiqui / Mehmet Ilyas Cosacak / Stanislava Popova / Prabesh Bhattarai / Elanur Yilmaz / Annie J. Lee / Yuhao Min / Xue Wang / Mariet Allen / Özkan İş / Zeynep Tansu Atasavum / Natalia Rodriguez-Muela / Badri N. Vardarajan / Delaney Flaherty / Andrew F. Teich / Ismael Santa-Maria / Uwe Freudenberg / Carsten Werner / Giuseppe Tosto /
    Richard Mayeux / Nilüfer Ertekin-Taner / Caghan Kizil

    npj Regenerative Medicine, Vol 8, Iss 1, Pp 1-

    2023  Volume 18

    Abstract: Abstract Neurogenesis, crucial for brain resilience, is reduced in Alzheimer’s disease (AD) that induces astroglial reactivity at the expense of the pro-neurogenic potential, and restoring neurogenesis could counteract neurodegenerative pathology. ... ...

    Abstract Abstract Neurogenesis, crucial for brain resilience, is reduced in Alzheimer’s disease (AD) that induces astroglial reactivity at the expense of the pro-neurogenic potential, and restoring neurogenesis could counteract neurodegenerative pathology. However, the molecular mechanisms promoting pro-neurogenic astroglial fate despite AD pathology are unknown. In this study, we used APP/PS1dE9 mouse model and induced Nerve growth factor receptor (Ngfr) expression in the hippocampus. Ngfr, which promotes neurogenic fate of astroglia during the amyloid pathology-induced neuroregeneration in zebrafish brain, stimulated proliferative and neurogenic outcomes. Histological analyses of the changes in proliferation and neurogenesis, single-cell transcriptomics, spatial proteomics, and functional knockdown studies showed that the induced expression of Ngfr reduced the reactive astrocyte marker Lipocalin-2 (Lcn2), which we found was sufficient to reduce neurogenesis in astroglia. Anti-neurogenic effects of Lcn2 was mediated by Slc22a17, blockage of which recapitulated the pro-neurogenicity by Ngfr. Long-term Ngfr expression reduced amyloid plaques and Tau phosphorylation. Postmortem human AD hippocampi and 3D human astroglial cultures showed elevated LCN2 levels correlate with reactive gliosis and reduced neurogenesis. Comparing transcriptional changes in mouse, zebrafish, and human AD brains for cell intrinsic differential gene expression and weighted gene co-expression networks revealed common altered downstream effectors of NGFR signaling, such as PFKP, which can enhance proliferation and neurogenesis in vitro when blocked. Our study suggests that the reactive non-neurogenic astroglia in AD can be coaxed to a pro-neurogenic fate and AD pathology can be alleviated with Ngfr. We suggest that enhancing pro-neurogenic astroglial fate may have therapeutic ramifications in AD.
    Keywords Medicine ; R
    Subject code 572
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Cross species systems biology discovers glial DDR2, STOM, and KANK2 as therapeutic targets in progressive supranuclear palsy

    Yuhao Min / Xue Wang / Özkan İş / Tulsi A. Patel / Junli Gao / Joseph S. Reddy / Zachary S. Quicksall / Thuy Nguyen / Shu Lin / Frederick Q. Tutor-New / Jessica L. Chalk / Adriana O. Mitchell / Julia E. Crook / Peter T. Nelson / Linda J. Van Eldik / Todd E. Golde / Minerva M. Carrasquillo / Dennis W. Dickson / Ke Zhang /
    Mariet Allen / Nilüfer Ertekin-Taner

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 15

    Abstract: Abstract Progressive supranuclear palsy (PSP) is a neurodegenerative parkinsonian disorder characterized by cell-type-specific tau lesions in neurons and glia. Prior work uncovered transcriptome changes in human PSP brains, although their cell- ... ...

    Abstract Abstract Progressive supranuclear palsy (PSP) is a neurodegenerative parkinsonian disorder characterized by cell-type-specific tau lesions in neurons and glia. Prior work uncovered transcriptome changes in human PSP brains, although their cell-specificity is unknown. Further, systematic data integration and experimental validation platforms to prioritize brain transcriptional perturbations as therapeutic targets in PSP are currently lacking. In this study, we combine bulk tissue (n = 408) and single nucleus RNAseq (n = 34) data from PSP and control brains with transcriptome data from a mouse tauopathy and experimental validations in Drosophila tau models for systematic discovery of high-confidence expression changes in PSP with therapeutic potential. We discover, replicate, and annotate thousands of differentially expressed genes in PSP, many of which reside in glia-enriched co-expression modules and cells. We prioritize DDR2, STOM, and KANK2 as promising therapeutic targets in PSP with striking cross-species validations. We share our findings and data via our interactive application tool PSP RNAseq Atlas ( https://rtools.mayo.edu/PSP_RNAseq_Atlas/ ). Our findings reveal robust glial transcriptome changes in PSP, provide a cross-species systems biology approach, and a tool for therapeutic target discoveries in PSP with potential application in other neurodegenerative diseases.
    Keywords Science ; Q
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Molecular estimation of neurodegeneration pseudotime in older brains

    Sumit Mukherjee / Laura Heath / Christoph Preuss / Suman Jayadev / Gwenn A. Garden / Anna K. Greenwood / Solveig K. Sieberts / Philip L. De Jager / Nilüfer Ertekin-Taner / Gregory W. Carter / Lara M. Mangravite / Benjamin A. Logsdon

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: The limited understanding of the temporal molecular changes in late-onset Alzheimer’s disease hinder the development of therapeutic treatment. The authors use manifold learning to develop a molecular model for disease progression from RNASeq data from ... ...

    Abstract The limited understanding of the temporal molecular changes in late-onset Alzheimer’s disease hinder the development of therapeutic treatment. The authors use manifold learning to develop a molecular model for disease progression from RNASeq data from human postmortem brain samples.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Author Correction

    Sumit Mukherjee / Laura Heath / Christoph Preuss / Suman Jayadev / Gwenn A. Garden / Anna K. Greenwood / Solveig K. Sieberts / Philip L. De Jager / Nilüfer Ertekin-Taner / Gregory W. Carter / Lara M. Mangravite / Benjamin A. Logsdon

    Nature Communications, Vol 11, Iss 1, Pp 1-

    Molecular estimation of neurodegeneration pseudotime in older brains

    2020  Volume 1

    Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20261- ... ...

    Abstract A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20261-6
    Keywords Science ; Q
    Language English
    Publishing date 2020-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Molecular estimation of neurodegeneration pseudotime in older brains

    Sumit Mukherjee / Laura Heath / Christoph Preuss / Suman Jayadev / Gwenn A. Garden / Anna K. Greenwood / Solveig K. Sieberts / Philip L. De Jager / Nilüfer Ertekin-Taner / Gregory W. Carter / Lara M. Mangravite / Benjamin A. Logsdon

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: The limited understanding of the temporal molecular changes in late-onset Alzheimer’s disease hinder the development of therapeutic treatment. The authors use manifold learning to develop a molecular model for disease progression from RNASeq data from ... ...

    Abstract The limited understanding of the temporal molecular changes in late-onset Alzheimer’s disease hinder the development of therapeutic treatment. The authors use manifold learning to develop a molecular model for disease progression from RNASeq data from human postmortem brain samples.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Identification of missing variants by combining multiple analytic pipelines

    Yingxue Ren / Joseph S. Reddy / Cyril Pottier / Vivekananda Sarangi / Shulan Tian / Jason P. Sinnwell / Shannon K. McDonnell / Joanna M. Biernacka / Minerva M. Carrasquillo / Owen A. Ross / Nilüfer Ertekin-Taner / Rosa Rademakers / Matthew Hudson / Liudmila Sergeevna Mainzer / Yan W. Asmann

    BMC Bioinformatics, Vol 19, Iss 1, Pp 1-

    2018  Volume 12

    Abstract: Abstract Background After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires large sample sizes for ... ...

    Abstract Abstract Background After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires large sample sizes for statistical power and has brought up questions about whether the current variant calling practices are adequate for large cohorts. It is well-known that there are discrepancies between variants called by different pipelines, and that using a single pipeline always misses true variants exclusively identifiable by other pipelines. Nonetheless, it is common practice today to call variants by one pipeline due to computational cost and assume that false negative calls are a small percent of total. Results We analyzed 10,000 exomes from the Alzheimer’s Disease Sequencing Project (ADSP) using multiple analytic pipelines consisting of different read aligners and variant calling strategies. We compared variants identified by using two aligners in 50,100, 200, 500, 1000, and 1952 samples; and compared variants identified by adding single-sample genotyping to the default multi-sample joint genotyping in 50,100, 500, 2000, 5000 and 10,000 samples. We found that using a single pipeline missed increasing numbers of high-quality variants correlated with sample sizes. By combining two read aligners and two variant calling strategies, we rescued 30% of pass-QC variants at sample size of 2000, and 56% at 10,000 samples. The rescued variants had higher proportions of low frequency (minor allele frequency [MAF] 1–5%) and rare (MAF < 1%) variants, which are the very type of variants of interest. In 660 Alzheimer’s disease cases with earlier onset ages of ≤65, 4 out of 13 (31%) previously-published rare pathogenic and protective mutations in APP, PSEN1, and PSEN2 genes were undetected by the default one-pipeline approach but recovered by the multi-pipeline approach. Conclusions Identification of the complete variant set from sequencing data is the prerequisite of genetic association ...
    Keywords Missing variants ; Combining multiple bioinformatics pipelines ; Rare variants ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 670
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Atlas of RNA editing events affecting protein expression in aged and Alzheimer’s disease human brain tissue

    Yiyi Ma / Eric B. Dammer / Daniel Felsky / Duc M. Duong / Hans-Ulrich Klein / Charles C. White / Maotian Zhou / Benjamin A. Logsdon / Cristin McCabe / Jishu Xu / Minghui Wang / Thomas S. Wingo / James J. Lah / Bin Zhang / Julie Schneider / Mariet Allen / Xue Wang / Nilüfer Ertekin-Taner / Nicholas T. Seyfried /
    Allan I. Levey / David A. Bennett / Philip L. De Jager

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 16

    Abstract: Resources reporting RNA editing sites from brain tissue have been published. Here, the authors provide an atlas of RNA editing events found in the aged and Alzheimer’s disease human brain tissue resulting in changes at protein level. ...

    Abstract Resources reporting RNA editing sites from brain tissue have been published. Here, the authors provide an atlas of RNA editing events found in the aged and Alzheimer’s disease human brain tissue resulting in changes at protein level.
    Keywords Science ; Q
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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