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Yuan Y, Li H, Sreeram K, Malankhanova T, Boddu R, Strader S, Chang A, Bryant N, Yacoubian TA, Standaert DG, Erb M, Moore DJ, Sanders LH, Lutz MW, Velmeshev D, West AB. Single molecule array measures of LRRK2 kinase activity in serum link Parkinson's disease severity to peripheral inflammation. bioRxiv 2024:2024.04.15.589570. [PMID: 38659797 PMCID: PMC11042295 DOI: 10.1101/2024.04.15.589570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Background LRRK2-targeting therapeutics that inhibit LRRK2 kinase activity have advanced to clinical trials in idiopathic Parkinson's disease (iPD). LRRK2 phosphorylates Rab10 on endolysosomes in phagocytic cells to promote some types of immunological responses. The identification of factors that regulate LRRK2-mediated Rab10 phosphorylation in iPD, and whether phosphorylated-Rab10 levels change in different disease states, or with disease progression, may provide insights into the role of Rab10 phosphorylation in iPD and help guide therapeutic strategies targeting this pathway. Methods Capitalizing on past work demonstrating LRRK2 and phosphorylated-Rab10 interact on vesicles that can shed into biofluids, we developed and validated a high-throughput single-molecule array assay to measure extracellular pT73-Rab10. Ratios of pT73-Rab10 to total Rab10 measured in biobanked serum samples were compared between informative groups of transgenic mice, rats, and a deeply phenotyped cohort of iPD cases and controls. Multivariable and weighted correlation network analyses were used to identify genetic, transcriptomic, clinical, and demographic variables that predict the extracellular pT73-Rab10 to total Rab10 ratio. Results pT73-Rab10 is absent in serum from Lrrk2 knockout mice but elevated by LRRK2 and VPS35 mutations, as well as SNCA expression. Bone-marrow transplantation experiments in mice show that serum pT73-Rab10 levels derive primarily from circulating immune cells. The extracellular ratio of pT73-Rab10 to total Rab10 is dynamic, increasing with inflammation and rapidly decreasing with LRRK2 kinase inhibition. The ratio of pT73-Rab10 to total Rab10 is elevated in iPD patients with greater motor dysfunction, irrespective of disease duration, age, sex, or the usage of PD-related or anti-inflammatory medications. pT73-Rab10 to total Rab10 ratios are associated with neutrophil activation, antigenic responses, and the suppression of platelet activation. Conclusions The extracellular ratio of pT73-Rab10 to total Rab10 in serum is a novel pharmacodynamic biomarker for LRRK2-linked innate immune activation associated with disease severity in iPD. We propose that those iPD patients with higher serum pT73-Rab10 levels may benefit from LRRK2-targeting therapeutics to mitigate associated deleterious immunological responses.
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Koltai DC, Chin PAE, Lutz MW, Bouvé VL, Taylor JW, Gualtieri AL, Morgenlander JC. Neuropsychological normative standards for late career physicians. Clin Neuropsychol 2024:1-17. [PMID: 38424449 DOI: 10.1080/13854046.2024.2319899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
Objective: In the context of an aging, vital physician workforce, there is clear value in establishing a specialized neuropsychological normative dataset for the evaluation of late career physicians practicing clinical medicine. Methods: Physicians aged 60 and over in active clinical practice at 3 major medical centers in North Carolina were recruited to complete a comprehensive neuropsychological test battery. Results: The sample (n = 100) was aged 60-78. Reflecting medical school distributions for this age group, the sample was mostly male (76%) and was fairly racially homogenous (96% White). To amplify utility of the dataset, data were obtained for several measures across neurocognitive domains. Results are presented in percentile bands stratified by age and sex where needed, and regression formulas are presented for predictive precision for measures where both age and sex predicted performance. Important distinctions between our sample, the general population, and current comparative demographic norms were also confirmed. Conclusions: Here we present a preliminary normative dataset on a comprehensive neuropsychological test battery for late career physicians, the HEATS norms for highly educated aging treaters. These standards facilitate accurate, objective cognitive measurement as a part of clinical diagnostic and capacity evaluations. Co-norming the battery in a single, specialized sample further augments its utility in characterizing cognition. Future work to enhance the dataset to be maximally applicable across demographic groups is anticipated, as is research to explore the relationship between these standards and professional performance outcomes.
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Affiliation(s)
- Deborah C Koltai
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Psychiatry & Behavioral Science, Duke University School of Medicine, Durham, NC, USA
| | - Paula-Ann E Chin
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Victoria L Bouvé
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - J Wynne Taylor
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Alex L Gualtieri
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Joel C Morgenlander
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
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Zeng Y, Chen H, Liu X, Song Z, Yao Y, Lei X, Lv X, Cheng L, Chen Z, Bai C, Yin Z, Lv Y, Lu J, Li J, Land KC, Yashin A, O'Rand AM, Sun L, Yang Z, Tao W, Gu J, Gottschalk W, Tan Q, Christensen K, Hesketh T, Tian XL, Yang H, Egidi V, Caselli G, Robine JM, Wang H, Shi X, Vaupel JW, Lutz MW, Nie C, Min J. Genetic associations with longevity are on average stronger in females than in males. Heliyon 2024; 10:e23691. [PMID: 38192771 PMCID: PMC10772631 DOI: 10.1016/j.heliyon.2023.e23691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 01/10/2024] Open
Abstract
It is long observed that females tend to live longer than males in nearly every country. However, the underlying mechanism remains elusive. In this study, we discovered that genetic associations with longevity are on average stronger in females than in males through bio-demographic analyses of genome-wide association studies (GWAS) dataset of 2178 centenarians and 2299 middle-age controls of Chinese Longitudinal Healthy Longevity Study (CLHLS). This discovery is replicated across North and South regions of China, and is further confirmed by North-South discovery/replication analyses of different and independent datasets of Chinese healthy aging candidate genes with CLHLS participants who are not in CLHLS GWAS, including 2972 centenarians and 1992 middle-age controls. Our polygenic risk score analyses of eight exclusive groups of sex-specific genes, analyses of sex-specific and not-sex-specific individual genes, and Genome-wide Complex Trait Analysis using all SNPs all reconfirm that genetic associations with longevity are on average stronger in females than in males. Our discovery/replication analyses are based on genetic datasets of in total 5150 centenarians and compatible middle-age controls, which comprises the worldwide largest sample of centenarians. The present study's findings may partially explain the well-known male-female health-survival paradox and suggest that genetic variants may be associated with different reactions between males and females to the same vaccine, drug treatment and/or nutritional intervention. Thus, our findings provide evidence to steer away from traditional view that "one-size-fits-all" for clinical interventions, and to consider sex differences for improving healthcare efficiency. We suggest future investigations focusing on effects of interactions between sex-specific genetic variants and environment on longevity as well as biological function.
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Affiliation(s)
- Yi Zeng
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, 100871, China
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Huashuai Chen
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, 100871, China
- Business School of Xiangtan University, Xiangtan, 411105, China
| | | | - Zijun Song
- The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yao Yao
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Xiaoyan Lei
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Xiaozhen Lv
- French National Institute of Health and Medical Research (INSERM) and Ecole Pratique des Hautes Etudes (EPHE) FR, Italy
| | - Lingguo Cheng
- School of Business, Nanjing University, Nanjing, 210093, China
| | | | - Chen Bai
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA, 27710
| | - Zhaoxue Yin
- Division of Non-Communicable Disease Control and Community Health, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuebin Lv
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Jiehua Lu
- Department of Sociology, Peking University, Beijing, 100871, China
| | - Jianxin Li
- Department of Sociology, Peking University, Beijing, 100871, China
| | - Kenneth C. Land
- Duke Population Research Institute's Center for Population Health and Aging, Duke University, Durham, NC, USA, 27710
| | - Anatoliy Yashin
- Duke Population Research Institute's Center for Population Health and Aging, Duke University, Durham, NC, USA, 27710
| | - Angela M. O'Rand
- Duke Population Research Institute's Center for Population Health and Aging, Duke University, Durham, NC, USA, 27710
| | - Liang Sun
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
| | - Ze Yang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC, USA, 27710
| | - Qihua Tan
- University of Southern Denmark, Odense, DK-5000, Denmark
| | | | - Therese Hesketh
- Institute for Global Health, University College London, London, UK
- Institute for Global Health, School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Li Tian
- Human Aging Research Institute and School of Life Science, Nanchang University, Jiangxi, 330031, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310008, China310058
| | - Viviana Egidi
- Department of Statistical Sciences, University of Rome La Sapienza, Roma, 00161, Italy
| | - Graziella Caselli
- Department of Statistical Sciences, University of Rome La Sapienza, Roma, 00161, Italy
| | - Jean-Marie Robine
- French National Institute of Health and Medical Research (INSERM) and Ecole Pratique des Hautes Etudes (EPHE) FR, Italy
| | - Huali Wang
- The Third Affiliated Hospital of Health Science Center, Peking University, Italy
| | - Xiaoming Shi
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | | | - Michael W. Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC, USA, 27710
| | - Chao Nie
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
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Teipel SJ, Temp AGM, Lutz MW. Bayesian meta-analysis of phase 3 results of aducanumab, lecanemab, donanemab, and high-dose gantenerumab in prodromal and mild Alzheimer's disease. Alzheimers Dement (N Y) 2024; 10:e12454. [PMID: 38389855 PMCID: PMC10883242 DOI: 10.1002/trc2.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024]
Abstract
INTRODUCTION Phase 3 trials using the anti-amyloid antibodies aducanumab, lecanemab, donanemab, and high-dose gantenerumab in prodromal and mild Alzheimer's disease dementia were heterogeneous in respect to statistical significance of effects. However, heterogeneity of results has not yet directly be quantified. METHODS We used Bayesian random effects meta-analysis to quantify evidence for or against a treatment effect, and assessed the size of the effect and its heterogeneity. Data were extracted from published studies where available and Web based data reports, assuming a Gaussian data generation process. RESULTS We found moderate evidence in favor of a treatment effect (Bayes factor = 13.2). The effect was moderate to small with -0.33 (95% credible interval -0.54 to -0.10) points on the Clinical Dementia Rating - Sum of Boxes (CDR-SB) scale. The heterogeneity parameter was low to moderate with 0.21 (0.04 to 0.45) CDR-SB points. DISCUSSION Heterogeneity across studies was moderate despite some trials reaching statistical significance, while others did not. This suggests that the negative aducanumab and gantenerumab trials are in full agreement with the expected effect sizes.
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Affiliation(s)
- Stefan J Teipel
- Working group on clincial dementia research Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock Germany
- Department of Psychosomatic Medicine University Medicine Rostock Rostock Germany
| | - Anna G M Temp
- Working group on clincial dementia research Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock Germany
- Department of Neurology Berufsgenossenschaftliches Klinikum Hamburg Hamburg Germany
| | - Michael W Lutz
- Department of Neurology Duke University School of Medicine Durham North Carolina USA
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Mahzarnia A, Lutz MW, Badea A. A Continuous Extension of Gene Set Enrichment Analysis Using the Likelihood Ratio Test Statistics Identifies Vascular Endothelial Growth Factor as a Candidate Pathway for Alzheimer's Disease via ITGA5. J Alzheimers Dis 2024; 97:635-648. [PMID: 38160360 PMCID: PMC10836573 DOI: 10.3233/jad-230934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Alzheimer's disease (AD) involves brain neuropathologies such as amyloid plaque and hyperphosphorylated tau tangles and is accompanied by cognitive decline. Identifying the biological mechanisms underlying disease onset and progression based on quantifiable phenotypes will help understand disease etiology and devise therapies. OBJECTIVE Our objective was to identify molecular pathways associated with hallmark AD biomarkers and cognitive status, accounting for variables such as age, sex, education, and APOE genotype. METHODS We introduce a pathway-based statistical approach, extending the gene set likelihood ratio test to continuous phenotypes. We first analyzed independently each of the three phenotypes (amyloid-β, tau, cognition) using continuous gene set likelihood ratio tests to account for covariates, including age, sex, education, and APOE genotype. The analysis involved 634 subjects with data available for all three phenotypes, allowing for the identification of common pathways. RESULTS We identified 14 pathways significantly associated with amyloid-β; 5 associated with tau; and 174 associated with cognition, which showed a larger number of pathways compared to biomarkers. A single pathway, vascular endothelial growth factor receptor binding (VEGF-RB), exhibited associations with all three phenotypes. Mediation analysis showed that among the VEGF-RB family genes, ITGA5 mediates the relationship between cognitive scores and pathological biomarkers. CONCLUSIONS We presented a new statistical approach linking continuous phenotypes, gene expression across pathways, and covariates like sex, age, and education. Our results reinforced VEGF RB2's role in AD cognition and demonstrated ITGA5's significant role in mediating the AD pathology-cognition connection.
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Affiliation(s)
- Ali Mahzarnia
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Michael W. Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Alexandra Badea
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
- Biomedical Engineering, Duke University, Durham, NC, USA
- Brain Imaging and Analysis Center, Duke University School of Medicine, Durham, NC, USA
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6
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Moon HS, Mahzarnia A, Stout J, Anderson RJ, Strain M, Tremblay JT, Han ZY, Niculescu A, MacFarlane A, King J, Ashley-Koch A, Clark D, Lutz MW, Badea A. Multivariate investigation of aging in mouse models expressing the Alzheimer's protective APOE2 allele: integrating cognitive metrics, brain imaging, and blood transcriptomics. Brain Struct Funct 2024; 229:231-249. [PMID: 38091051 DOI: 10.1007/s00429-023-02731-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/03/2023] [Indexed: 01/31/2024]
Abstract
APOE allelic variation is critical in brain aging and Alzheimer's disease (AD). The APOE2 allele associated with cognitive resilience and neuroprotection against AD remains understudied. We employed a multipronged approach to characterize the transition from middle to old age in mice with APOE2 allele, using behavioral assessments, image-derived morphometry and diffusion metrics, structural connectomics, and blood transcriptomics. We used sparse multiple canonical correlation analyses (SMCCA) for integrative modeling, and graph neural network predictions. Our results revealed brain sub-networks associated with biological traits, cognitive markers, and gene expression. The cingulate cortex emerged as a critical region, demonstrating age-associated atrophy and diffusion changes, with higher fractional anisotropy in males and middle-aged subjects. Somatosensory and olfactory regions were consistently highlighted, indicating age-related atrophy and sex differences. The hippocampus exhibited significant volumetric changes with age, with differences between males and females in CA3 and CA1 regions. SMCCA underscored changes in the cingulate cortex, somatosensory cortex, olfactory regions, and hippocampus in relation to cognition and blood-based gene expression. Our integrative modeling in aging APOE2 carriers revealed a central role for changes in gene pathways involved in localization and the negative regulation of cellular processes. Our results support an important role of the immune system and response to stress. This integrative approach offers novel insights into the complex interplay among brain connectivity, aging, and sex. Our study provides a foundation for understanding the impact of APOE2 allele on brain aging, the potential for detecting associated changes in blood markers, and revealing novel therapeutic intervention targets.
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Affiliation(s)
- Hae Sol Moon
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Ali Mahzarnia
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Jacques Stout
- Brain Imaging and Analysis Center, Duke University School of Medicine, Durham, NC, USA
| | - Robert J Anderson
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Madison Strain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jessica T Tremblay
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Zay Yar Han
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Andrei Niculescu
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Anna MacFarlane
- Department of Neuroscience, Duke University, Durham, NC, USA
| | - Jasmine King
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Darin Clark
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Alexandra Badea
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Quantitative Imaging and Analysis Laboratory, Department of Radiology, Duke University School of Medicine, Durham, NC, USA.
- Brain Imaging and Analysis Center, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
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7
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Lutz MW, Chiba-Falek O. Bioinformatics pipeline to guide post-GWAS studies in Alzheimer's: A new catalogue of disease candidate short structural variants. Alzheimers Dement 2023; 19:4094-4109. [PMID: 37253165 PMCID: PMC10524333 DOI: 10.1002/alz.13168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Short structural variants (SSVs), including insertions/deletions (indels), are common in the human genome and impact disease risk. The role of SSVs in late-onset Alzheimer's disease (LOAD) has been understudied. In this study, we developed a bioinformatics pipeline of SSVs within LOAD-genome-wide association study (GWAS) regions to prioritize regulatory SSVs based on the strength of their predicted effect on transcription factor (TF) binding sites. METHODS The pipeline utilized publicly available functional genomics data sources including candidate cis-regulatory elements (cCREs) from ENCODE and single-nucleus (sn)RNA-seq data from LOAD patient samples. RESULTS We catalogued 1581 SSVs in candidate cCREs in LOAD GWAS regions that disrupted 737 TF sites. That included SSVs that disrupted the binding of RUNX3, SPI1, and SMAD3, within the APOE-TOMM40, SPI1, and MS4A6A LOAD regions. CONCLUSIONS The pipeline developed here prioritized non-coding SSVs in cCREs and characterized their putative effects on TF binding. The approach integrates multiomics datasets for validation experiments using disease models.
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Affiliation(s)
- Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
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8
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Qi R, Sammler E, Gonzalez-Hunt CP, Barraza I, Pena N, Rouanet JP, Naaldijk Y, Goodson S, Fuzzati M, Blandini F, Erickson KI, Weinstein AM, Lutz MW, Kwok JB, Halliday GM, Dzamko N, Padmanabhan S, Alcalay RN, Waters C, Hogarth P, Simuni T, Smith D, Marras C, Tonelli F, Alessi DR, West AB, Shiva S, Hilfiker S, Sanders LH. A blood-based marker of mitochondrial DNA damage in Parkinson's disease. Sci Transl Med 2023; 15:eabo1557. [PMID: 37647388 DOI: 10.1126/scitranslmed.abo1557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/11/2023] [Indexed: 09/01/2023]
Abstract
Parkinson's disease (PD) is the most common neurodegenerative movement disorder, and neuroprotective or disease-modifying interventions remain elusive. High-throughput markers aimed at stratifying patients on the basis of shared etiology are required to ensure the success of disease-modifying therapies in clinical trials. Mitochondrial dysfunction plays a prominent role in the pathogenesis of PD. Previously, we found brain region-specific accumulation of mitochondrial DNA (mtDNA) damage in PD neuronal culture and animal models, as well as in human PD postmortem brain tissue. To investigate mtDNA damage as a potential blood-based marker for PD, we describe herein a PCR-based assay (Mito DNADX) that allows for the accurate real-time quantification of mtDNA damage in a scalable platform. We found that mtDNA damage was increased in peripheral blood mononuclear cells derived from patients with idiopathic PD and those harboring the PD-associated leucine-rich repeat kinase 2 (LRRK2) G2019S mutation in comparison with age-matched controls. In addition, mtDNA damage was elevated in non-disease-manifesting LRRK2 mutation carriers, demonstrating that mtDNA damage can occur irrespective of a PD diagnosis. We further established that Lrrk2 G2019S knock-in mice displayed increased mtDNA damage, whereas Lrrk2 knockout mice showed fewer mtDNA lesions in the ventral midbrain, compared with wild-type control mice. Furthermore, a small-molecule kinase inhibitor of LRRK2 mitigated mtDNA damage in a rotenone PD rat midbrain neuron model and in idiopathic PD patient-derived lymphoblastoid cell lines. Quantifying mtDNA damage using the Mito DNADX assay may have utility as a candidate marker of PD and for measuring the pharmacodynamic response to LRRK2 kinase inhibitors.
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Affiliation(s)
- Rui Qi
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
| | - Esther Sammler
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH UK
| | - Claudia P Gonzalez-Hunt
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
| | - Ivana Barraza
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
| | - Nicholas Pena
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
| | - Jeremy P Rouanet
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yahaira Naaldijk
- Department of Anesthesiology and Department of Physiology, Pharmacology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Steven Goodson
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
| | - Marie Fuzzati
- IRCCS Mondino Foundation, National Institute of Neurology, Pavia 27100, Italy
| | - Fabio Blandini
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Kirk I Erickson
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- AdventHealth Research Institute, Neuroscience, Orlando, FL 32804, USA
| | - Andrea M Weinstein
- Department of Psychiatry, School of Medicine, University of Pittsburgh, PA 15213, USA
| | - Michael W Lutz
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - John B Kwok
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Glenda M Halliday
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Nicolas Dzamko
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Shalini Padmanabhan
- Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
| | - Roy N Alcalay
- Columbia University Irving Medical Center, New York, NY 10032, USA
- Movement Disorders Unit, Neurological Institute, Tel Aviv Sourasky Medical Centre, Sackler School of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Cheryl Waters
- Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Penelope Hogarth
- Departments of Molecular and Medical Genetics and Neurology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Tanya Simuni
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Danielle Smith
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Connie Marras
- Edmond J. Safra Program in Parkinson's Disease, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Canada
| | - Francesca Tonelli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH UK
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH UK
| | - Andrew B West
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology and Medicine, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sabine Hilfiker
- Department of Anesthesiology and Department of Physiology, Pharmacology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Laurie H Sanders
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, USA
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9
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Mahzarnia A, Lutz MW, Badea A. A Continuous Extension of Gene Set Enrichment Analysis using the Likelihood Ratio Test Statistics Identifies VEGF as a Candidate Pathway for Alzheimer's disease. bioRxiv 2023:2023.08.22.554319. [PMID: 37662249 PMCID: PMC10473614 DOI: 10.1101/2023.08.22.554319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Alzheimer's disease involves brain pathologies such as amyloid plaque depositions and hyperphosphorylated tau tangles and is accompanied by cognitive decline. Identifying the biological mechanisms underlying disease onset and progression based on quantifiable phenotypes will help understand the disease etiology and devise therapies. Objective Our objective was to identify molecular pathways associated with AD biomarkers (Amyloid-β and tau) and cognitive status (MMSE) accounting for variables such as age, sex, education, and APOE genotype. Methods We introduce a novel pathway-based statistical approach, extending the gene set likelihood ratio test to continuous phenotypes. We first analyzed independently each of the three phenotypes (Amyloid-β, tau, cognition), using continuous gene set likelihood ratio tests to account for covariates, including age, sex, education, and APOE genotype. The analysis involved a large sample size with data available for all three phenotypes, allowing for the identification of common pathways. Results We identified 14 pathways significantly associated with Amyloid-β, 5 associated with tau, and 174 associated with MMSE. Surprisingly, the MMSE outcome showed a larger number of significant pathways compared to biomarkers. A single pathway, vascular endothelial growth factor receptor binding (VEGF-RB), exhibited significant associations with all three phenotypes. Conclusions The study's findings highlight the importance of the VEGF signaling pathway in aging in AD. The complex interactions within the VEGF signaling family offer valuable insights for future therapeutic interventions.
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10
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Shi C, Gottschalk WK, Colton CA, Mukherjee S, Lutz MW. Alzheimer's Disease Protein Relevance Analysis Using Human and Mouse Model Proteomics Data. Front Syst Biol 2023; 3:1085577. [PMID: 37650081 PMCID: PMC10467016 DOI: 10.3389/fsysb.2023.1085577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The principles governing genotype-phenotype relationships are still emerging(1-3), and detailed translational as well as transcriptomic information is required to understand complex phenotypes, such as the pathogenesis of Alzheimer's disease. For this reason, the proteomics of Alzheimer disease (AD) continues to be studied extensively. Although comparisons between data obtained from humans and mouse models have been reported, approaches that specifically address the between-species statistical comparisons are understudied. Our study investigated the performance of two statistical methods for identification of proteins and biological pathways associated with Alzheimer's disease for cross-species comparisons, taking specific data analysis challenges into account, including collinearity, dimensionality reduction and cross-species protein matching. We used a human dataset from a well-characterized cohort followed for over 22 years with proteomic data available. For the mouse model, we generated proteomic data from whole brains of CVN-AD and matching control mouse models. We used these analyses to determine the reliability of a mouse model to forecast significant proteomic-based pathological changes in the brain that may mimic pathology in human Alzheimer's disease. Compared with LASSO regression, partial least squares discriminant analysis provided better statistical performance for the proteomics analysis. The major biological finding of the study was that extracellular matrix proteins and integrin-related pathways were dysregulated in both the human and mouse data. This approach may help inform the development of mouse models that are more relevant to the study of human late-onset Alzheimer's disease.
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Affiliation(s)
- Cathy Shi
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - W. Kirby Gottschalk
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Carol A. Colton
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Departments of Mathematics, Computer Science, and Biostatistics & Bioinformatics Duke University, Durham, NC 27708, USA
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
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11
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Kamalian A, Ho SG, Patel M, Lewis A, Bakker A, Albert M, O’Brien RJ, Moghekar A, Lutz MW. Exploratory Assessment of Proteomic Network Changes in Cerebrospinal Fluid of Mild Cognitive Impairment Patients: A Pilot Study. Biomolecules 2023; 13:1094. [PMID: 37509130 PMCID: PMC10377001 DOI: 10.3390/biom13071094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
(1) Background: Despite the existence of well-established, CSF-based biomarkers such as amyloid-β and phosphorylated-tau, the pathways involved in the pathophysiology of Alzheimer's disease (AD) remain an active area of research. (2) Methods: We measured 3072 proteins in CSF samples of AD-biomarker positive mild cognitive impairment (MCI) participants (n = 38) and controls (n = 48), using the Explore panel of the Olink proximity extension assay (PEA). We performed group comparisons, association studies with diagnosis, age, and APOE ε4 status, overrepresentation analysis (ORA), and gene set enrichment analysis (GSEA) to determine differentially expressed proteins and dysregulated pathways. (3) Results: GSEA results demonstrated an enrichment of granulocyte-related and chemotactic pathways (core enrichment proteins: ITGB2, ITGAM, ICAM1, SELL, SELP, C5, IL1A). Moreover, some of the well-replicated, differentially expressed proteins in CSF included: ITGAM, ITGB2, C1QA, TREM2, GFAP, NEFL, MMP-10, and a novel tau-related marker, SCRN1. (4) Conclusion: Our results highlight the upregulation of neuroinflammatory pathways, especially chemotactic and granulocyte recruitment in CSF of early AD patients.
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Affiliation(s)
- Aida Kamalian
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA; (A.K.)
| | - Sara G. Ho
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA; (A.K.)
| | - Megha Patel
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA; (A.K.)
| | - Alexandria Lewis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA; (A.K.)
| | - Arnold Bakker
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA; (A.K.)
| | - Richard J. O’Brien
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA; (A.K.)
| | - Michael W. Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
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12
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Li X, Koeberl DD, Lutz MW, Bedlack R. Clenbuterol Treatment Is Safe and Associated With Slowed Disease Progression in a Small Open-Label Trial in Patients With Amyotrophic Lateral Sclerosis. J Clin Neuromuscul Dis 2023; 24:214-221. [PMID: 37219865 DOI: 10.1097/cnd.0000000000000438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
OBJECTIVE Clenbuterol, a beta-agonist, has plausible mechanisms for treating amyotrophic lateral sclerosis (ALS). In this highly inclusive open-label trial (NCT04245709), we aimed to study the safety and efficacy of clenbuterol in patients with ALS. METHODS All participants received clenbuterol starting at 40 μg daily and increased to 80 μg twice daily. Outcomes included safety, tolerability, ALS Functional Rating Score (ALSFRS-R) progression, forced vital capacity (FVC) progression, and myometry. ALSFRS-R and FVC slopes measured during treatment were compared with slopes before treatment (calculated by assuming ALSFRS-R was 48 and FVC was 100% at ALS onset). RESULTS The 25 participants had a mean age of 59, mean disease duration of 43 months, ALSFRS-R score at enrollment 34, and FVC at enrollment 77%. Forty-eight percent were female, 68% were taking riluzole, and none were taking edaravone. Two participants experienced severe adverse events, neither related to the study. Twenty-four participants experienced adverse events, most commonly tremors/jitters, cramps/spasms, insomnia, and stiffness/spasticity. Fourteen participants withdrew early from the trial, 13 due to adverse events. Patients who withdrew early were significantly older and more likely to be male. Per-protocol and intention-to-treat analyses showed meaningfully slower ALSFRS-R and FVC progression during treatment. Hand grip dynamometry and myometry changes were highly variable between participants; most declined slowly, but some showed improvements. CONCLUSIONS Clenbuterol was safe but less tolerable at the doses we selected compared with an earlier Italian case series. Consistent with that series, our study suggested benefits on ALS progression. However, the latter result should be interpreted with caution as our study is limited by small sample size, large drop out, lack of randomization, and blinding and placebo controls. A larger, more traditional trial now seems warranted.
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13
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Sanders DB, Lutz MW, Raja SM, Juel VC, Guptill JT, Hobson-Webb LD, Massey JM. The Duke Myasthenia Gravis Clinic Registry: II. Analysis of outcomes. Muscle Nerve 2023; 67:291-296. [PMID: 36734303 DOI: 10.1002/mus.27794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023]
Abstract
INTRODUCTION/AIMS The Duke Myasthenia Gravis (MG) Clinic Registry contains comprehensive physician-derived data on patients with MG seen in the Duke MG Clinic since 1980. The aim of this study was to report outcomes in patients seen in the clinic and treated according to the International Consensus Guidance statements. METHODS This is a retrospective cohort study of patients initially seen after 2000 and followed for at least 2 years in the clinic. Treatment goal (TG) was defined as achieving MGFA post-intervention status of "minimal manifestations" or better; PIS was determined by the treating neurologist. Time-to-event analysis, including Cox proportional hazards modeling, was performed to assess the effect of sex, acetylcholine receptor antibody (AChR-Ab) status, age at disease onset, distribution (ocular vs generalized), thymectomy, and thymoma on the time to achieve TG. RESULTS Among the 367 cohort patients, 72% achieved TG (median time less than 2 years). A greater proportion of patients with AChR-Abs and thymectomy achieved TG and they did so sooner than patients without these antibodies or thymectomy. Otherwise, there were no significant differences in these findings within the tested subgroups. The disease duration at the first Duke Clinic visit was shorter in patients who achieved TG than in those who did not. DISCUSSION These results demonstrate outcomes that can be achieved in patients with MG treated according to the current Consensus Guidance statements. Among other things, they can be used to determine the added value and potential role of new treatment modalities developed since 2018.
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Affiliation(s)
- Donald B Sanders
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Michael W Lutz
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Shruti M Raja
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Vern C Juel
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Jeffrey T Guptill
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Lisa D Hobson-Webb
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Janice M Massey
- Neuromuscular Division, Department of Neurology, Duke University Medical Center, Durham, North Carolina
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14
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Masha N, Kimbrough DJ, Eckstein CP, Hudak NM, Skeen MB, Hartsell FL, Lutz MW, Shah S. Neuromyelitis optica: Clinical course and potential prognostic indicators. Mult Scler Relat Disord 2023; 69:104414. [PMID: 36463620 DOI: 10.1016/j.msard.2022.104414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune neurological disorder associated with antibodies to aquaporin-4 (AQP4). NMOSD has been thought to follow a progressive disease course, with step-wise accumulation of disability over time, even in patients undergoing immunosuppressive/immunomodulatory therapy. The influence of factors such as AQP4 seropositivity, AQP4 serum titer levels, and administration of plasmapheresis on NMOSD prognosis is, as yet, unclear. METHODS We performed a retrospective chart review of 53 persons with NMOSD at Duke University Hospital-collecting data on longitudinal disease course, imaging, demographics, and serum AQP4 titers (measured using the ELISA or FACS method). Most patients in our cohort were treated with high-dose corticosteroids and, following diagnosis, received maintenance immunosuppressive/immunomodulatory therapies. Longitudinal data on EDSS scores were used to calculate the slope of disability over time for each participant. We additionally investigated the correlation between initial AQP4 seropositivity, initial AQP4 serum titer levels, and treatment with plasmapheresis on disability progression for each participant. RESULTS Contrary to current views on NMOSD disease course, the majority of our participants showed either no change (31.9%) or improvement (27.1%) in disability over time. Our results additionally revealed no significant association between clinical prognosis and initial AQP4 seropositivity (p = 0.830), initial AQP4 serum titer levels (p = 0.338), or administration of plasmapheresis (p = 0.1149). CONCLUSIONS Our study presents a contemporary view of the clinical course of NMOSD and shows a more favorable view of its disease course than prior studies (performed before high-efficacy disease modifying therapies became widely-used for this patient population). Most patients in this study received treatment with high-dose corticosteroids following NMOSD flares, as well as a variety of maintenance immunosuppressive therapies. The results of this study cannot shed light on the disease course of untreated NMOSD. Our findings additionally challenge the theory that AQP4 seropositivity or serum titer levels at time of diagnosis may be used to effectively predict NMOSD prognosis. While we were unable to find evidence supporting a favorable effect of plasmapheresis administration on disease outcomes, further research is needed to determine the role plasmapheresis ought to play in the treatment of NMOSD.
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Affiliation(s)
- Nidhila Masha
- Duke University School of Medicine, 8 Searle Center Dr, Durham, NC 27710, USA.
| | - Dorlan J Kimbrough
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
| | - Christopher P Eckstein
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
| | - Nicholas M Hudak
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
| | - Mark B Skeen
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
| | - F Lee Hartsell
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
| | - Suma Shah
- Department of Neurology, Duke University Medical Center, 40 Duke Medicine Cir Clinic 1L, Durham, NC 27710, USA
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15
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Gottschalk WK, Mahon S, Hodgson D, Barrera J, Hill D, Wei A, Kumar M, Dai K, Anderson L, Mihovilovic M, Lutz MW, Chiba-Falek O. The APOE-TOMM40 Humanized Mouse Model: Characterization of Age, Sex, and PolyT Variant Effects on Gene Expression. J Alzheimers Dis 2023; 94:1563-1576. [PMID: 37458041 PMCID: PMC10733864 DOI: 10.3233/jad-230451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
BACKGROUND The human chromosome 19q13.32 is a gene rich region and has been associated with multiple phenotypes, including late onset Alzheimer's disease (LOAD) and other age-related conditions. OBJECTIVE Here we developed the first humanized mouse model that contains the entire TOMM40 and APOE genes with all intronic and intergenic sequences including the upstream and downstream regions. Thus, the mouse model carries the human TOMM40 and APOE genes and their intact regulatory sequences. METHODS We generated the APOE-TOMM40 humanized mouse model in which the entire mouse region was replaced with the human (h)APOE-TOMM40 loci including their upstream and downstream flanking regulatory sequences using recombineering technologies. We then measured the expression of the human TOMM40 and APOE genes in the mice brain, liver, and spleen tissues using TaqMan based mRNA expression assays. RESULTS We investigated the effects of the '523' polyT genotype (S/S or VL/VL), sex, and age on the human TOMM40- and APOE-mRNAs expression levels using our new humanized mouse model. The analysis revealed tissue specific and shared effects of the '523' polyT genotype, sex, and age on the regulation of the human TOMM40 and APOE genes. Noteworthy, the regulatory effect of the '523' polyT genotype was observed for all studied organs. CONCLUSION The model offers new opportunities for basic science, translational, and preclinical drug discovery studies focused on the APOE genomic region in relation to LOAD and other conditions in adulthood.
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Affiliation(s)
- William K. Gottschalk
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Scott Mahon
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Dellila Hodgson
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Delaney Hill
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Angela Wei
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Manish Kumar
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Kathy Dai
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Lauren Anderson
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Mirta Mihovilovic
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
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16
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Zou H, Luo S, Liu H, Lutz MW, Bennett DA, Plassman BL, Welsh-Bohmer KA. Genotypic Effects of the TOMM40'523 Variant and APOE on Longitudinal Cognitive Change over 4 Years: The TOMMORROW Study. J Prev Alzheimers Dis 2023; 10:886-894. [PMID: 37874111 PMCID: PMC10734664 DOI: 10.14283/jpad.2023.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
BACKGROUND The 523 poly-T length polymorphism (rs10524523) in TOMM40 has been reported to influence longitudinal cognitive test performance within APOE ε3/3 carriers. The results from prior studies are inconsistent. It is also unclear whether specific APOE and TOMM40 genotypes contribute to heterogeneity in longitudinal cognitive performance during the preclinical stages of AD. OBJECTIVES To determine the effects of these genes on longitudinal cognitive change in early preclinical stages of AD, we used the clinical trial data from the recently concluded TOMMORROW study to examine the effects of APOE and TOMM40 genotypes on neuropsychological test performance. DESIGN A phase 3, double-blind, placebo-controlled, randomized clinical trial. SETTING Academic affiliated and private research clinics in Australia, Germany, Switzerland, the UK, and the USA. PARTICIPANTS Cognitively normal older adults aged 65 to 83. INTERVENTION Pioglitazone tablet. MEASUREMENTS Participants from the TOMMORROW trial were stratified based on APOE genotype (APOE ε3/3, APOE ε3/4, APOE ε4/4). APOE ε3/3 carriers were further stratified by TOMM40'523 genotype. The final analysis dataset consists of 1,330 APOE ε3/3 carriers and 7,001 visits. Linear mixed models were used to compare the rates of decline in cognition across APOE groups and the APOE ε3/3 carriers with different TOMM40'523 genotypes. RESULTS APOE ε3/4 and APOE ε4/4 genotypes compared with the APOE ε3/3 genotype were associated with worse performance on measures of global cognition, episodic memory, and expressive language. Further, over the four years of observation, the APOE ε3/3 carriers with the TOMM40'523-S/S genotype showed better global cognition and accelerated rates of cognitive decline on tests of global cognition, executive function, and attentional processing compared to APOE ε3/3 carriers with TOMM40'523-S/VL and VL/VL genotypes and compared to the APOE ε3/4 and APOE ε4/4 carriers. CONCLUSIONS We suggest that both APOE and TOMM40 genotypes may independently contribute to cognitive heterogeneity in the pre-MCI stages of AD. Controlling for this genetic variability will be important in clinical trials designed to slow the rate of cognitive decline and/or prevent symptom onset in preclinical AD.
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Affiliation(s)
- H Zou
- Sheng Luo, PhD, Dept of Biostatistics and Bioinformatics, 2424 Erwin Rd, Suite 11082, Durham, NC, USA, 27705, Tel: 919-668-8038, Fax: 919-668-7059,
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17
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Li H, Liu H, Lutz MW, Luo S. Novel Genetic Variants in TP37, PIK3R1, CALM1, and PLCG2 of the Neurotrophin Signaling Pathway Are Associated with the Progression from Mild Cognitive Impairment to Alzheimer's Disease. J Alzheimers Dis 2023; 91:977-987. [PMID: 36530083 PMCID: PMC9905310 DOI: 10.3233/jad-220680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is a common neurodegenerative disease and mild cognitive impairment (MCI) is considered as the prodromal stage of AD. Previous studies showed that changes in the neurotrophin signaling pathway could lead to cognitive decline in AD. However, the association of single nucleotide polymorphisms (SNPs) in genes that are involved in this pathway with AD progression from MCI remains unclear. OBJECTIVE We investigated the associations between SNPs involved in the neurotrophin signaling pathway with AD progression. METHODS We performed single-locus analysis to identify neurotrophin-signaling-related SNPs associated with the AD progression using 767 patients from the Alzheimer's Disease Neuroimaging Initiative study and 1,373 patients from the National Alzheimer's Coordinating Center study. We constructed polygenic risk scores (PRSs) using the identified independent non-APOE SNPs and evaluated its prediction performance on AD progression. RESULTS We identified 25 SNPs significantly associated with AD progression with Bayesian false-discovery probability ≤0.8. Based on the linkage disequilibrium clumping and expression quantitative trait loci analysis, we found 6 potentially functional SNPs that were associated with AD progression independently. The PRS analysis quantified the combined effects of these SNPs on longitudinal cognitive assessments and biomarkers from cerebrospinal fluid and neuroimaging. The addition of PRSs to the prediction model for 3-year progression to AD from MCI significantly increased the predictive accuracy. CONCLUSION Genetic variants in the specific genes of the neurotrophin signaling pathway are predictors of AD progression. eQTL analysis supports that these SNPs regulate expression of key genes involved in the neurotrophin signaling pathway.
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Affiliation(s)
- Huiyue Li
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
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18
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Sutton P, Lutz MW, Hartsell FL, Kimbrough D, Tagg NT, Skeen M, Hudak NM, Eckstein C, Shah S. Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease: Presentation and outcomes of adults at a single center. J Neuroimmunol 2022; 373:577987. [PMID: 36272183 DOI: 10.1016/j.jneuroim.2022.577987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/18/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND/INTRODUCTION Myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is a chronic demyelinating disorder that has been increasingly recognized since the serum antibody became commercially available in 2017. The most common clinical presentation is optic neuritis, and first line acute treatment is intravenous (IV) steroids. However, there are many questions that remain unanswered. For clinicians and patients, the primary question is whether relapses will occur and whether to treat with chronic therapy. METHODS This retrospective chart review examined characteristics of thirty-three known adult MOGAD cases at a single institute. Data was collected on patient demographics, clinical presentation, objective diagnosis with MRI and serum antibody levels, acute and chronic treatment and disease outcomes. RESULTS Our MOGAD cases revealed a slight female to male predominance of 1.5:1. No racial groups were affected disproportionately, and age of symptom onset spanned a large range with a median of 40 years. The most common clinical and radiologic presentation was optic neuritis followed by transverse myelitis and brainstem symptoms/lesions. IV methylprednisolone was used in the vast majority of cases for acute treatment. 83.3% of our patients were treated with chronic therapy at some point during their disease course. Therapies include rituximab, IVIG, ocrelizumab, mycophenolate mofetil and ofatumumab. The majority of our patients were treated with rituximab and we did not see a significant benefit of yearly relapse reduction for rituximab versus other therapies. Our cohort had a higher-than- expected percentage of cases with relapsing disease (56.3%) compared to monophasic (43.8%). DISCUSSION/CONCLUSION Our study confirms prior data regarding the demographics, clinical presentation and radiologic presentation of MOGAD. There is no consensus on whether maintenance therapy should be started for MOGAD cases with a single clinical event. Our cohort showed a higher relapse rate than has been reported previously and all known relapses occurred within one year of diagnosis. More data is necessary to confirm risk of relapse in the years following diagnosis. In addition, further data on biomarkers are needed to predict the disease course could help guide management.
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Affiliation(s)
- Paige Sutton
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - Michael W Lutz
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - F Lee Hartsell
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - Dorlan Kimbrough
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - N Troy Tagg
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - Mark Skeen
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - Nicholas M Hudak
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - Christopher Eckstein
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA
| | - Suma Shah
- Duke University, Department of Neurology, 40 Duke Medicine Circle, Clinic 1L, Durham, NC 27710, USA.
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19
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Berger M, Cooter M, Roesler AS, Chunga S, Park J, Modliszewski JL, VanDusen KW, Thompson JW, Moseley A, Devinney MJ, Smani S, Hall A, Cai V, Browndyke JN, Lutz MW, Corcoran DL. Erratum to: APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid. J Alzheimers Dis 2022; 90:1339-1340. [PMID: 36373324 PMCID: PMC9756142 DOI: 10.3233/jad-229018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Temp AGM, Ly A, van Doorn J, Wagenmakers EJ, Tang Y, Lutz MW, Teipel S. A Bayesian perspective on Biogen's aducanumab trial. Alzheimers Dement 2022; 18:2341-2351. [PMID: 35235700 DOI: 10.1002/alz.12615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/31/2023]
Abstract
This perspective is a companion to a recent editorial on the use of Bayesian analysis in clinical research. We aim to introduce and highlight the relevance and advantages that Bayesian inference offers to clinical trials using the data on the amyloid antibody aducanumab presented at a Food and Drug Administration hearing in November 2020 as an applied example. We apply Bayesian analysis of model plausibility and effect sizes based on simulated data of the two phase 3 trials of aducanumab in prodromal and mild dementia stages of Alzheimer's disease (AD). Bayesian analysis can quantify evidence in favor of, or against, the presence of an effect (i.e., provide evidence of absence), as well as assess the strength of the effect. This is in contrast to the binary conclusions provided by frequentist tests.
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Affiliation(s)
- Anna G M Temp
- German Center for Neurodegenerative Diseases (DZNE), Rostock, Germany.,Translational Neurodegeneration Section "Albrecht Kossel," Department of Neurology, University of Rostock, Rostock, Germany
| | - Alexander Ly
- Department of Psychological Methods, University of Amsterdam, Amsterdam, the Netherlands.,Machine Learning Group, Centrum Wiskunde & Informatica, Amsterdam, the Netherlands
| | - Johnny van Doorn
- Department of Psychological Methods, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric-Jan Wagenmakers
- Department of Psychological Methods, University of Amsterdam, Amsterdam, the Netherlands
| | - Yi Tang
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, China
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Stefan Teipel
- German Center for Neurodegenerative Diseases (DZNE), Rostock, Germany.,Department of Psychosomatic Medicine and Psychotherapy, University Medicine Rostock, Rostock, Germany
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21
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Boccardi M, Handels R, Gold M, Grazia A, Lutz MW, Martin M, Nosheny R, Robillard JM, Weidner W, Alexandersson J, Thyrian JR, Winblad B, Barbarino P, Khachaturian AS, Teipel S. Clinical research in dementia: A perspective on implementing innovation. Alzheimers Dement 2022; 18:2352-2367. [PMID: 35325508 DOI: 10.1002/alz.12622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 01/31/2023]
Abstract
The increasing global prevalence of dementia demands concrete actions that are aimed strategically at optimizing processes that drive clinical innovation. The first step in this direction requires outlining hurdles in the transition from research to practice. The different parties needed to support translational processes have communication mismatches; methodological gaps hamper evidence-based decision-making; and data are insufficient to provide reliable estimates of long-term health benefits and costs in decisional models. Pilot projects are tackling some of these gaps, but appropriate methods often still need to be devised or adapted to the dementia field. A consistent implementation perspective along the whole translational continuum, explicitly defined and shared among the relevant stakeholders, should overcome the "research-versus-adoption" dichotomy, and tackle the implementation cliff early on. Concrete next steps may consist of providing tools that support the effective participation of heterogeneous stakeholders and agreeing on a definition of clinical significance that facilitates the selection of proper outcome measures.
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Affiliation(s)
- Marina Boccardi
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Rostock-Greifswald Standort, Rostock, Germany
| | - Ron Handels
- Alzheimer Centre Limburg, School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.,Division of Neurogeriatrics, Dept for Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | | | - Alice Grazia
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Rostock-Greifswald Standort, Rostock, Germany.,Department of Psychosomatic Medicine, Rostock Universitätsmedizin, Rostock, Germany
| | - Michael W Lutz
- Department of Neurology Duke University School of Medicine, Durham, North Carolina, USA
| | - Mike Martin
- Gerontology Center, University of Zurich, Zürich, Switzerland
| | - Rachel Nosheny
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, California, USA.,San Francisco Veteran's Administration Medical Center, San Francisco, California, USA
| | - Julie M Robillard
- The University of British Columbia; BC Children's & Women's Hospitals, Vancouver, Canada
| | | | | | - Jochen René Thyrian
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Rostock-Greifswald Standort, Greifswald, Germany.,Institute for Community Medicine, Section Epidemiology of Healthcare, University Medicine of Greifswald, Greifswald, Germany
| | - Bengt Winblad
- Division of Neurogeriatrics, Dept for Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | | | - Ara S Khachaturian
- Alzheimer's & Dementia: The Journal of the Alzheimer's Association, Rockville, Maryland, USA.,Campaign to Prevent Alzheimer's Disease, Rockville, Maryland, USA
| | - Stefan Teipel
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Rostock-Greifswald Standort, Rostock, Germany.,Department of Psychosomatic Medicine, Rostock Universitätsmedizin, Rostock, Germany
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22
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Lutz MW, Khachaturian AS, Zetterberg H, Blennow K, Willette AA, Mielke MM, Hayden KM, Dodge HH, Tang Y, Greenberg BD, Kukull WA, Khachaturian ZS. Biomarkers of Alzheimer syndrome and related dementias: A&D author's guide. Alzheimers Dement 2022; 18:1595-1601. [PMID: 36005812 PMCID: PMC9514317 DOI: 10.1002/alz.12772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Indexed: 01/24/2023]
Affiliation(s)
- Michael W. Lutz
- Department of NeurologyDuke University School of MedicineDurhamNCUSA
| | - Ara S. Khachaturian
- Alzheimer's & Dementia: The Journal of the Alzheimer's AssociationRockvilleMDUSA
| | - Henrik Zetterberg
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at the University of GothenburgMölndalSweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University HospitalMölndalSweden
- Department of Neurodegenerative DiseaseUCL Institute of Neurology, Queen SquareLondonUK
- UK Dementia Research Institute at UCLLondonUK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water BayHong KongChina
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of GothenburgGothenburgSweden
| | - Auriel A. Willette
- Department of Food Science and Human NutritionIowa State UniversityAmesIAUSA
- IAC Tracker Inc.AmesIAUSA
| | - Michelle M. Mielke
- Department of Epidemiology and PreventionWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Kathleen M. Hayden
- Department of Social Sciences and Health PolicyDivision of Public Health SciencesWake Forest University School of Medicine, Winston‐SalemNCUSA
| | - Hiroko H. Dodge
- Department of NeurologyLayton Aging and Alzheimer's Disease CenterOregon Health & Science UniversityPortlandORUSA
| | - Yi Tang
- Department of Neurology, Innovation Center for Neurological DisordersXuanwu Hospital, Capital Medical UniversityNational Center for Neurological DisordersBeijingChina
| | - Barry D. Greenberg
- Department of Neurology, Director, Alzheimer's Disease Translational CenterJohns Hopkins University School of MedicineBaltimoreMDUSA
- Alzheimer's & Dementia: Translational Research and Clinical InterventionsBaltimoreMDUSA
| | - Walter A Kukull
- Department of EpidemiologyUniversity of WashingtonSeattleWAUSA
| | - Zaven S Khachaturian
- Alzheimer's & Dementia: The Journal of the Alzheimer's AssociationRockvilleMDUSA
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23
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Gable KL, Peric S, Lutz MW, Bozovic I, Petrovic M, Stojanov A, Basta I, Allen JA. A longitudinal evaluation of fatigue in chronic inflammatory demyelinating polyneuropathy. Brain Behav 2022; 12:e2712. [PMID: 35862228 PMCID: PMC9392529 DOI: 10.1002/brb3.2712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/24/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS Fatigue is a common but poorly understood complaint in patients with immune-mediated polyneuropathies. We sought to evaluate changes in fatigue over 1 year in a cohort of chronic inflammatory demyelinating polyneuropathy (CIDP) patients and to correlate changes in fatigue with changes in disability and quality of life. Investigation into other factors that may contribute to fatigue with a particular interest in the role other chronic disease states may play was also performed. METHODS Fifty patients with CIDP who satisfied the 2010 EFNS/PNS diagnostic criteria were followed over the period of 1 year at three tertiary care centers in Serbia. Assessments of disability, quality of life, and patient perception of change and fatigue were collected at two time points 12 months apart. Comorbidities, treatment regimens, and sedating medication use was collected. RESULTS Disability, quality of life, and patient perception of change showed statistically significant correlations with change in fatigue (p < .01). Increased levels of fatigue were noted in patients who used sedating medications (p = .05) and who had a comorbid chronic medical condition (p = .01). INTERPRETATION Worsening fatigue correlates over time with increased disability and worse quality of life. Fatigue is not specific to CIDP, but is common in many chronic medical conditions and with the use of sedating medications. Our findings support the importance of identifying and supportively managing fatigue in patients with CIDP, but cautions against considering fatigue as a CIDP diagnostic symptom or using fatigue to justify immunotherapy utilization.
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Affiliation(s)
- Karissa L Gable
- Duke Neurological Disorders Clinic, Duke University Medical Center, Durham, North Carolina, USA
| | - Stojan Peric
- Faculty of Medicine and University Clinical Center of Serbia, Neurology Clinic, University of Belgrade, Belgrade, Serbia
| | - Michael W Lutz
- Duke Neurological Disorders Clinic, Duke University Medical Center, Durham, North Carolina, USA
| | - Ivo Bozovic
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Milutin Petrovic
- Neurology Clinic, University Clinical Center of Kragujevac, Kragujevac, Serbia
| | | | - Ivana Basta
- Faculty of Medicine and University Clinical Center of Serbia, Neurology Clinic, University of Belgrade, Belgrade, Serbia
| | - Jeffrey A Allen
- Department of Neurology, University of Minnesota, Minneapolis, Minnesota, USA
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24
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Upadhya S, Liu H, Luo S, Lutz MW, Chiba-Falek O. Polygenic Risk Score Effectively Predicts Depression Onset in Alzheimer’s Disease Based on Major Depressive Disorder Risk Variants. Front Neurosci 2022; 16:827447. [PMID: 35350557 PMCID: PMC8957806 DOI: 10.3389/fnins.2022.827447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/31/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Depression is a common, though heterogenous, comorbidity in late-onset Alzheimer’s Disease (LOAD) patients. In addition, individuals with depression are at greater risk to develop LOAD. In previous work, we demonstrated shared genetic etiology between depression and LOAD. Collectively, these previous studies suggested interactions between depression and LOAD. However, the underpinning genetic heterogeneity of depression co-occurrence with LOAD, and the various genetic etiologies predisposing depression in LOAD, are largely unknown. Methods Major Depressive Disorder (MDD) genome-wide association study (GWAS) summary statistics were used to create polygenic risk scores (PRS). The Religious Orders Society and Rush Memory and Aging Project (ROSMAP, n = 1,708) and National Alzheimer’s Coordinating Center (NACC, n = 10,256) datasets served as discovery and validation cohorts, respectively, to assess the PRS performance in predicting depression onset in LOAD patients. Results The PRS showed marginal results in standalone models for predicting depression onset in both ROSMAP (AUC = 0.540) and NACC (AUC = 0.527). Full models, with baseline age, sex, education, and APOEε4 allele count, showed improved prediction of depression onset (ROSMAP AUC: 0.606, NACC AUC: 0.581). In time-to-event analysis, standalone PRS models showed significant effects in ROSMAP (P = 0.0051), but not in NACC cohort. Full models showed significant performance in predicting depression in LOAD for both datasets (P < 0.001 for all). Conclusion This study provided new insights into the genetic factors contributing to depression onset in LOAD and advanced our knowledge of the genetics underlying the heterogeneity of depression in LOAD. The developed PRS accurately predicted LOAD patients with depressive symptoms, thus, has clinical implications including, diagnosis of LOAD patients at high-risk to develop depression for early anti-depressant treatment.
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Affiliation(s)
- Suraj Upadhya
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
| | - Hongliang Liu
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
- *Correspondence: Ornit Chiba-Falek,
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25
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Lutz MW, Chiba‐Falek O. Bioinformatics pipeline to guide late‐onset Alzheimer's disease (LOAD) post‐GWAS studies: Prioritizing transcription regulatory variants within LOAD‐associated regions. A&D Transl Res & Clin Interv 2022; 8:e12244. [PMID: 35229021 PMCID: PMC8864953 DOI: 10.1002/trc2.12244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Introduction As new late‐onset Alzheimer's disease (LOAD) genetic risk loci are identified and brain cell–type specific omics data becomes available, there is an unmet need for a bioinformatics framework to prioritize genes and variants for testing in single‐cell molecular profiling experiments and validation using disease models and gene editing technologies. Prior work has characterized and prioritized active enhancers located in LOAD‐genome‐wide association study (GWAS) regions and their potential interactions with candidate genes. The current study extends this work by focusing on single nucleotide polymorphisms (SNPs) within these LOAD enhancers and their impact on altering transcription factor (TF) binding. The proposed bioinformatics pipeline progresses from SNPs located in LOAD‐GWAS regions to a filtered set of candidate regulatory SNPs that have a predicted strong effect on TF binding. Methods Active enhancers within LOAD‐associated regions were identified and SNPs located in the enhancers were catalogued. SNPs that disrupt TF binding sites were prioritized and the respective TFs were filtered to include only those that were expressed in brain tissues relevant to LOAD. The TFs binding to the corresponding sequence was further confirmed by ChIP‐seq signals. Finally, the high‐priority candidate SNPs were evaluated as expression quantitative trait loci (eQTLs) in disease‐relevant tissues. Results We catalogued 61 strong enhancers in LOAD‐GWAS regions encompassing 326 SNPs and 104 TF binding sites. Seventy‐seven and 78 of the TFs were expressed in brain and monocytes, respectively, out of which 19 TF‐binding sites showed ChIP‐seq signals. Eleven SNPs were found to interrupt with TF binding out of which three SNPs were also significant eQTL. Discussion This study provides a framework to catalogue noncoding variations in enhancers located in LOAD‐GWAS loci and characterize their likelihood to perturb TF binding. The approach integrates multiple data types to characterize and prioritize SNPs for putative regulatory function using single‐cell multi‐omics assays and gene editing.
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Affiliation(s)
- Michael W. Lutz
- Division of Translational Brain Sciences Department of Neurology Duke University Medical Center Durham North Carolina USA
| | - Ornit Chiba‐Falek
- Division of Translational Brain Sciences Department of Neurology Duke University Medical Center Durham North Carolina USA
- Center for Genomic and Computational Biology Duke University Medical Center Durham North Carolina USA
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26
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Lutz MW, Brown MM, Kucgibhatla M, Plassman BL, Saldana S, Snively BM, Chen J, Henderson V, Manson JE, Pal L, Shadyab AH, Rapp SR, Hayden KM. Analysis of pleiotropic genetic effects on cognitive decline and systemic inflammation in the Women’s Health Initiative Memory Study. Alzheimers Dement 2021. [DOI: 10.1002/alz.050784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Brenda L Plassman
- Department of Psychiatry Duke University Medical Center Durham NC USA
| | | | | | | | | | - JoAnn E. Manson
- Department of Preventive Medicine Brigham and Women's Hospital Harvard Medical School Boston MA USA
| | - Lubna Pal
- Yale School of Medicine New Haven CT USA
| | - Aladdin H. Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science University of California San Diego La Jolla CA USA
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27
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Chiba‐Falek O, Lutz MW. Bioinformatics pipeline to advance the identification of transcription regulatory variants in LOAD noncoding regions. Alzheimers Dement 2021. [DOI: 10.1002/alz.050665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Kang JH, James ML, Gibson A, Inamullah O, Sherrill GC, Lutz MW, Swisher CB. Anticoagulation after Spontaneous Intraparenchymal Hemorrhage in Patients with Mechanical Heart Valves and Concomitant Atrial Fibrillation. J Neuroanaesth Crit Care 2021. [DOI: 10.1055/s-0041-1735653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Abstract
Aim Patients with mechanical heart valves and coexisting atrial fibrillation (AFib-MHV) who suffer an intraparenchymal hemorrhage (IPH, defined as bleeding solely within the brain parenchyma and/or ventricle) are at a high risk of thromboembolism without anticoagulation. Data are lacking regarding the safety of early re-initiation of anticoagulation in these patients.
Patients and Methods We performed a descriptive, single-institution retrospective analysis of patients with AFib-MHV who suffered a non-traumatic, supratentorial IPH between July 2013 and June 2017. We analyzed the patients and IPH characteristics, anticoagulation and antiplatelet use, the occurrence of thrombotic and hemorrhage complications, and discharge disposition. We described the timing of initiation of anticoagulation and outcomes after IPH while in-patient.
Results Six patients with AFib-MHV suffered a spontaneous IPH. Four were initiated on anticoagulation prior to discharge, of whom two were initiated within 3 days post-hemorrhage. These patients suffered no bleeding complications and were discharged home with a modified Rankin Scale of 1.
Conclusion Patients with AFib-MHV who suffer a spontaneous IPH are a rare population to study. Further studies to guide the management of restarting anticoagulation in this select population are warranted.
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Affiliation(s)
- Jennifer H. Kang
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael L. James
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
- Department of Anesthesiology, Duke University, Durham, North Carolina, United States
| | - Allison Gibson
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Ovais Inamullah
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Gary Clay Sherrill
- The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States
| | - Michael W. Lutz
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
| | - Christa B. Swisher
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States
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29
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Zhang Y, Fu S, Ding D, Lutz MW, Zeng Y, Yao Y. Leisure Activities, APOE ε4, and Cognitive Decline: A Longitudinal Cohort Study. Front Aging Neurosci 2021; 13:736201. [PMID: 34616288 PMCID: PMC8488387 DOI: 10.3389/fnagi.2021.736201] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 08/20/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Both leisure activities and the ε4 allele of the apolipoprotein E (APOE ε4) have been shown to affect cognitive health. We aimed to determine whether engagement in leisure activities protects against APOE ε4-related cognitive decline. Methods: We used the cohort data from the Chinese Longitudinal Healthy Longevity Survey. A total of 3,017 participants (mean age of 77.0 years, SD = 9.0; 49.3% female) from 23 provinces of China were recruited in 2008 and were reinterviewed in 2014. We assessed cognitive function using the Mini-Mental State Examination (MMSE). We calculated cognitive decline using subtraction of the MMSE score of each participant in 2008 and 2014. We genotyped a number of APOE ε4 alleles for each participant at baseline and determined the Index of Leisure Activities (ILAs) by summing up the frequency of nine types of typical activities in productive, social, and physical domains. We used ordinal logistic regression models to estimate the effects of leisure activities, APOE ε4, and their interaction on cognitive decline, statistically adjusted for a range of potential confounders. Results: There were significant associations between APOE ε4 and faster cognitive decline, independent of potential confounders, and between leisure activities and mitigated cognitive decline. The odds ratios were 1.25 (95% CI: 1.03, 1.53) and 0.93 (95% CI: 0.89, 0.97), respectively. We found significant interactions of APOE ε4 with leisure activities with a P-value of 0.018. We also observed interactive effects of subtypes of leisure activities: participants who regularly engaged in productive activities were more likely to reduce the risk of APOE ε4-related cognitive decline. Conclusion: Our findings provide support for the indication that participating in leisure activities reduces the risk of APOE ε4-related cognitive decline.
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Affiliation(s)
- Yun Zhang
- School of Sociology and Anthropology, Sun Yat-sen University, Guangzhou, China
| | - Shihui Fu
- Department of Cardiology, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Ding Ding
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States
| | - Yi Zeng
- Center for Healthy Aging and Development Studies at National School of Development, Peking University, Beijing, China.,Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham, NC, United States
| | - Yao Yao
- Center for Healthy Aging and Development Studies at National School of Development, Peking University, Beijing, China.,Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham, NC, United States.,China Center for Health Development Studies, Peking University, Beijing, China
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30
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Burns DK, Alexander RC, Welsh-Bohmer KA, Culp M, Chiang C, O'Neil J, Evans RM, Harrigan P, Plassman BL, Burke JR, Wu J, Lutz MW, Haneline S, Schwarz AJ, Schneider LS, Yaffe K, Saunders AM, Ratti E. Safety and efficacy of pioglitazone for the delay of cognitive impairment in people at risk of Alzheimer's disease (TOMMORROW): a prognostic biomarker study and a phase 3, randomised, double-blind, placebo-controlled trial. Lancet Neurol 2021; 20:537-547. [PMID: 34146512 DOI: 10.1016/s1474-4422(21)00043-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND The identification of people at risk of cognitive impairment is essential for improving recruitment in secondary prevention trials of Alzheimer's disease. We aimed to test and qualify a biomarker risk assignment algorithm (BRAA) to identify participants at risk of developing mild cognitive impairment due to Alzheimer's disease within 5 years, and to evaluate the safety and efficacy of low-dose pioglitazone to delay onset of mild cognitive impairment in these at-risk participants. METHODS In this phase 3, multicentre, randomised, double-blind, placebo-controlled, parallel-group study, we enrolled cognitively healthy, community living participants aged 65-83 years from 57 academic affiliated and private research clinics in Australia, Germany, Switzerland, the UK, and the USA. By use of the BRAA, participants were grouped as high risk or low risk. Participants at high risk were randomly assigned 1:1 to receive oral pioglitazone (0·8 mg/day sustained release) or placebo, and all low-risk participants received placebo. Study investigators, site staff, sponsor personnel, and study participants were masked to genotype, risk assignment, and treatment assignment. The planned study duration was the time to accumulate 202 events of mild cognitive impairment due to Alzheimer's disease in White participants who were at high risk (the population on whom the genetic analyses that informed the BRAA development was done). Primary endpoints were time-to-event comparisons between participants at high risk and low risk given placebo (for the BRAA objective), and between participants at high risk given pioglitazone or placebo (for the efficacy objective). The primary analysis included all participants who were randomly assigned, received at least one dose of study drug, and had at least one valid post-baseline visit, with significance set at p=0·01. The safety analysis included all participants who were randomly assigned and received at least one dose of study medication. An efficacy futility analysis was planned for when approximately 33% of the anticipated events occurred in the high-risk, White, non-Hispanic or Latino group. This trial is registered with ClinicalTrials.gov, NCT01931566. FINDINGS Between Aug 28, 2013, and Dec 21, 2015, we enrolled 3494 participants (3061 at high risk and 433 at low risk). Of those participants, 1545 were randomly assigned to pioglitazone and 1516 to placebo. 1104 participants discontinued treatment (464 assigned to the pioglitazone group, 501 in the placebo high risk group, and 139 in the placebo low risk group). 3399 participants had at least one dose of study drug or placebo and at least one post-baseline follow-up visit, and were included in the efficacy analysis. 3465 participants were included in the safety analysis (1531 assigned to the pioglitazone group, 1507 in the placebo high risk group, and 427 in the placebo low risk group). In the full analysis set, 46 (3·3%) of 1406 participants at high risk given placebo had mild cognitive impairment due to Alzheimer's disease, versus four (1·0%) of 402 participants at low risk given placebo (hazard ratio 3·26, 99% CI 0·85-12·45; p=0·023). 39 (2·7%) of 1430 participants at high risk given pioglitazone had mild cognitive impairment, versus 46 (3·3%) of 1406 participants at high risk given placebo (hazard ratio 0·80, 99% CI 0·45-1·40; p=0·307). In the safety analysis set, seven (0·5%) of 1531 participants at high risk given pioglitazone died versus 21 (1·4%) of 1507 participants at high risk given placebo. There were no other notable differences in adverse events between groups. The study was terminated in January, 2018, after failing to meet the non-futility threshold. INTERPRETATION Pioglitazone did not delay the onset of mild cognitive impairment. The biomarker algorithm demonstrated a 3 times enrichment of events in the high risk placebo group compared with the low risk placebo group, but did not reach the pre-specified significance threshold. Because we did not complete the study as planned, findings can only be considered exploratory. The conduct of this study could prove useful to future clinical development strategies for Alzheimer's disease prevention studies. FUNDING Takeda and Zinfandel.
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Affiliation(s)
| | | | - Kathleen A Welsh-Bohmer
- Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - Meredith Culp
- Takeda Development Center Americas, Cambridge, MA, USA
| | | | - Janet O'Neil
- Takeda Development Center Americas, Deerfield, IL, USA
| | | | | | - Brenda L Plassman
- Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA
| | - James R Burke
- Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA; Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Jingtao Wu
- Takeda Development Center Americas, Cambridge, MA, USA
| | - Michael W Lutz
- Joseph and Kathleen Bryan Alzheimer's Disease Research Center, Duke University Medical Center, Durham, NC, USA; Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | | | | | - Lon S Schneider
- Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Kristine Yaffe
- University of California at San Francisco, San Francisco, CA, USA
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Temp AGM, Lutz MW, Trepel D, Tang Y, Wagenmakers EJ, Khachaturian AS, Teipel S. How Bayesian statistics may help answer some of the controversial questions in clinical research on Alzheimer's disease. Alzheimers Dement 2021; 17:917-919. [PMID: 34115436 DOI: 10.1002/alz.12374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Anna G M Temp
- Clinical Research Section, German Centre for Neurodegenerative Diseases (DZNE), Rostock, Germany.,Translational Neurodegeneration Section "Albrecht Kossel,", Department of Neurology, University of Rostock, Rostock, Germany
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dominic Trepel
- School of Medicine, Trinity College Dublin, Dublin, Ireland.,Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland.,University California San Francisco, San Francisco, USA
| | - Yi Tang
- Department of Neurology, Xuanwu Hospital, National Center for Neurological Disorders, Capital Medical University, Beijing, China
| | - Eric-Jan Wagenmakers
- Department of Psychological Methods, University of Amsterdam, Amsterdam, the Netherlands
| | - Ara S Khachaturian
- Alzheimer's & Dementia: The Journal of the Alzheimer's Association, Rockville, Maryland, USA
| | - Stefan Teipel
- Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
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Bryan J, Mandan A, Kamat G, Gottschalk WK, Badea A, Adams KJ, Thompson JW, Colton CA, Mukherjee S, Lutz MW. Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. Alzheimers Dement 2021; 17:561-573. [PMID: 33480182 PMCID: PMC8044005 DOI: 10.1002/alz.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such as age or sex. Evaluation of AD biological pathways in the context of interactions with these covariates is critical to the understanding of AD as well as the development of model systems used to study the disease. METHODS Gene set enrichment methods are powerful tools used to interpret gene-level statistics at the level of biological pathways. We introduce a method for quantifying gene set enrichment using likelihood ratio-derived test statistics (gsLRT), which accounts for sample covariates like age and sex. We then use our method to test for age and sex interactions with protein expression levels in AD and to compare the pathway results between human and mouse species. RESULTS Our method, based on nested logistic regressions is competitive with the existing standard for gene set testing in the context of linear models and complex experimental design. The gene sets we identify as having a significant association with AD-both with and without additional covariate interactions-are validated by previous studies. Differences between gsLRT results on mouse and human datasets are observed. DISCUSSION Characterizing biological pathways involved in AD builds on the important work involving single gene drivers. Our gene set enrichment method finds pathways that are significantly related to AD while accounting for covariates that may be relevant to disease development. The method highlights commonalities and differences between human AD and mouse models, which may inform the development of higher fidelity models for the study of AD.
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Affiliation(s)
- Jordan Bryan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Arpita Mandan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Gauri Kamat
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | | | - Alexandra Badea
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Kendra J. Adams
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | | | - Carol A. Colton
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Departments of Mathematics, Computer Science, and Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Michael W. Lutz
- Department of Neurology, Duke University, Durham, NC 27708, USA
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Zhang Y, Jin X, Lutz MW, Ju SY, Liu K, Guo G, Zeng Y, Yao Y. Interaction between APOE ε4 and dietary protein intake on cognitive decline: A longitudinal cohort study. Clin Nutr 2021; 40:2716-2725. [PMID: 33933737 PMCID: PMC10106247 DOI: 10.1016/j.clnu.2021.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE To exam the association of cognitive decline with APOE ε4 allele carriage and dietary protein intake and investigate whether there is a gene-diet (GxD) interaction of APOE ε4 allele carriage and dietary protein intake on cognitive decline in a nationwide cohort of older adults. METHODS A cohort study of participants from Chinese Longitudinal Healthy Longevity Survey was conducted from 2008 to 2014. A total of 3029 participants (mean age of 77.0 years, SD = 9.0; 49.3% were women) was enrolled. We genotyped APOE ε4 allele for each participant and calculated the diversity of dietary protein intake (DDPI) by summing up the frequency of intake of the 6 protein-rich foods (meats, fish, eggs, nuts, dairy products, and bean products). We assessed cognitive function using the Mini-Mental State Examination (MMSE). We used ordinal regression model to estimate the independent and joint effects of APOE ε4 carrier and dietary protein intake on cognitive decline, adjusting for potential confounders of age, sex, education, socio-economic status, lifestyles, BMI, and cardiometabolic conditions. RESULTS There was significant association between carrying APOE ε4 allele and faster cognitive decline (Odds ratio: 1.19, 95% CI = 1.00-1.42), independent of potential confounders. While the associations of DDPI and the intake of 6 protein-rich foods with cognitive decline did not reach any statistical significance. We observed significant interactions of APOE ε4 with DDPI and fish intake, at multiple correction-adjusted Ps < 0.05. In those who were APOE ε4 carriers rather than non-carriers, both high DDPI (OR = 0.54, 95% CI: 0.34-0.88) and daily fish intake (OR = 0.43, 95% CI: 0.22-0.78) were significantly associated with slower cognitive decline, respectively. We also found that frequent intake of fish benefits women more than men regarding the mitigating of cognitive decline among APOE ε4 allele carriers (P for interaction = 0.016). CONCLUSIONS The results of this study support the hypothesis that diversified protein food intake in addition to frequent fish intake may reduce the detrimental effect of APOE ε4 on cognitive health.
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Affiliation(s)
- Yun Zhang
- School of Sociology and Anthropology, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Xurui Jin
- Global Health Research Center, Duke Kunshan University, Kunshan, Jiangsu, 215374, China.
| | - Michael W Lutz
- Department of Neurology, Duke University of Medicine, Durham, NC, 27710, USA.
| | - Sang-Yhun Ju
- Department of Family Medicine, St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Gyeonggi-do, 11765, Republic of Korea.
| | - Keyang Liu
- Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
| | - Guang Guo
- Department of Sociology, Carolina Population Center, Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Yi Zeng
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, 100871, China; Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham, NC, 27710, USA.
| | - Yao Yao
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, 100871, China; Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham, NC, 27710, USA.
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Deters KD, Mormino EC, Yu L, Lutz MW, Bennett DA, Barnes LL. TOMM40-APOE haplotypes are associated with cognitive decline in non-demented Blacks. Alzheimers Dement 2021; 17:1287-1296. [PMID: 33580752 DOI: 10.1002/alz.12295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/16/2020] [Accepted: 12/18/2020] [Indexed: 11/08/2022]
Abstract
INTRODUCTION The goal was to investigate effects of APOE-TOMM40-'523 haplotypes on cognitive decline in non-demented non-Hispanic Blacks (NHB), and determine whether effects differ from non-Hispanic Whites (NHW). METHODS The impact of zero to two copies of the '523-Short variant (S; poly-T alleles < 20) within apolipoprotein E (APOE) genotype on a composite measure of global cognition and five domains was examined. RESULTS In NHB with ε3/ε3 (N = 294), '523-S/S was associated with faster decline in global cognition (β = -0.048, P = 0.017), episodic memory (β = -0.05, P = 0.031), and visuospatial ability (β = -0.037, P = 0.034) relative to those without '523-S. For NHB ε4+ (N = 182), '523-S/S had slower decline in global cognition (β = 0.047, P = 0.042) and visuospatial ability (β = 0.07, P = 0.0005) relative to '523-S non-carriers. NHB ε4+ with '523-S also had a slower rate of decline than NHWs ε4+ with '523-S. DISCUSSION '523-S/S has a different effect on cognitive decline among NHB dependent on APOE allele. Differences in the effect of ε4-'523-S in NHB may explain prior mixed findings on ε4 and decline in this population.
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Affiliation(s)
- Kacie D Deters
- Stanford University School of Medicine, Department of Neurology and Neurological Sciences, Stanford, California, USA
| | - Elizabeth C Mormino
- Stanford University School of Medicine, Department of Neurology and Neurological Sciences, Stanford, California, USA
| | - Lei Yu
- Rush University Medical Center, Department of Neurological Sciences, Rush Alzheimer's Disease Center, Chicago, Illinois, USA
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, North Carolina, USA
| | - David A Bennett
- Rush University Medical Center, Department of Neurological Sciences, Rush Alzheimer's Disease Center, Chicago, Illinois, USA
| | - Lisa L Barnes
- Rush University Medical Center, Department of Neurological Sciences, Rush Alzheimer's Disease Center, Chicago, Illinois, USA
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Inamullah O, Chiang YP, Bishawi M, Weiss M, Lutz MW, Blue LJ, Feng W, Milano CA, Luedke M, Husseini NE. Characteristics of strokes associated with centrifugal flow left ventricular assist devices. Sci Rep 2021; 11:1645. [PMID: 33462301 PMCID: PMC7814026 DOI: 10.1038/s41598-021-81445-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/06/2021] [Indexed: 01/06/2023] Open
Abstract
Stroke is a devastating complication of left ventricular assist device (LVAD) therapy. Understanding the characteristics, risk factors and outcomes of strokes associated with the centrifugal flow LVADs is important to devise better strategies for management and prevention. This is a retrospective cohort study at a single US academic medical center. The cohort includes patients who received a first time Heartmate 3 (HM3) or Heartware (HVAD) LVAD between September 2009 through February 2018 and had a stroke while the LVAD was in place. Descriptive statistics were used when appropriate. A logistic regression analysis was used to determine predictors of poor outcome. Out of a total of 247 patients, 12.1% (N = 30, 24 HVAD and 6 HM3) had a stroke (63% ischemic) and 3 of these patients had pump thrombosis. Events per patient year (EPPY) were similar for HVAD and HM3 patients (0.3 ± 0.1). INR was subtherapeutic in 47.4% of ischemic stroke patients and supratherapeutic in 18.2% of hemorrhagic stroke patients. Concurrent infections were more common in the setting of hemorrhagic stroke than ischemic stroke (45.4% vs 5.3%, p = 0.008). Strokes were severe in most cases, with initial NIH stroke scale (NIHSS) higher in HM3 patients compared to HVAD patients (mean 24.6 vs 16) and associated with high in-patient mortality (21.1% of ischemic stroke vs. 88.8% of hemorrhagic stroke). Predictors of death within 30 days and disability at 90 days included creatinine at stroke onset, concurrent infection, hemorrhaghic stroke, and initial stroke severity (NIHSS). A score derived from these variables predicted with 100% certainty mortality at 30 days and mRS ≥ 4 at 90 days. For patients with centrifugal flow LVADs, ischemic strokes were more common but hemorrhagic strokes were associated with higher in-patient mortality and more frequently seen in the setting of concurrent infections. Infections, sub or supratherapeutic INR range, and comorbid cardiovascular risk factors may all be contributing to the stroke burden. These findings may inform future strategies for stroke prevention in this population.
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Affiliation(s)
- Ovais Inamullah
- Department of Neurology, Duke University Medical Center, 2301 Erwin Road, Durham, NC, 27710, USA.
| | - Yuting P Chiang
- Division of Cardiothoracic Surgery, Department of Surgery, Duke University Medical Center, Durham, USA
| | - Muath Bishawi
- Division of Cardiothoracic Surgery, Department of Surgery, Duke University Medical Center, Durham, USA
| | - Martin Weiss
- Department of Neurology, Duke University Medical Center, 2301 Erwin Road, Durham, NC, 27710, USA
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, 2301 Erwin Road, Durham, NC, 27710, USA
| | - Laura J Blue
- Division of Cardiothoracic Surgery, Department of Surgery, Duke University Medical Center, Durham, USA
| | - Wayne Feng
- Department of Neurology, Duke University Medical Center, 2301 Erwin Road, Durham, NC, 27710, USA
| | - Carmelo A Milano
- Division of Cardiothoracic Surgery, Department of Surgery, Duke University Medical Center, Durham, USA
| | - Matthew Luedke
- Department of Neurology, Duke University Medical Center, 2301 Erwin Road, Durham, NC, 27710, USA
| | - Nada El Husseini
- Department of Neurology, Duke University Medical Center, 2301 Erwin Road, Durham, NC, 27710, USA
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Berger M, Cooter M, Roesler AS, Chung S, Park J, Modliszewski JL, VanDusen KW, Thompson JW, Moseley A, Devinney MJ, Smani S, Hall A, Cai V, Browndyke JN, Lutz MW, Corcoran DL. APOE4 Copy Number-Dependent Proteomic Changes in the Cerebrospinal Fluid. J Alzheimers Dis 2020; 79:511-530. [PMID: 33337362 PMCID: PMC7902966 DOI: 10.3233/jad-200747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background: APOE4 has been hypothesized to increase Alzheimer’s disease risk by increasing neuroinflammation, though the specific neuroinflammatory pathways involved are unclear. Objective: Characterize cerebrospinal fluid (CSF) proteomic changes related to APOE4 copy number. Methods: We analyzed targeted proteomic data from ADNI CSF samples using a linear regression model adjusting for age, sex, and APOE4 copy number, and additional linear models also adjusting for AD clinical status or for CSF Aβ, tau, or p-tau levels. False discovery rate was used to correct for multiple comparisons correction. Results: Increasing APOE4 copy number was associated with a significant decrease in a CRP peptide level across all five models (q < 0.05 for each), and with significant increases in ALDOA, CH3L1 (YKL-40), and FABPH peptide levels (q < 0.05 for each) except when controlling for AD clinical status or neurodegeneration biomarkers (i.e., CSF tau or p-tau). In all models except the one controlling for CSF Aβ levels, though not statistically significant, there was a consistent inverse direction of association between APOE4 copy number and the levels of all 24 peptides from all 8 different complement proteins measured. The odds of this happening by chance for 24 unrelated peptides would be less than 1 in 16 million. Conclusion: Increasing APOE4 copy number was associated with decreased CSF CRP levels across all models, and increased CSF ALDOA, CH3L1, and FABH levels when controlling for CSF Aβ levels. Increased APOE4 copy number may also be associated with decreased CSF complement pathway protein levels, a hypothesis for investigation in future studies.
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Affiliation(s)
- Miles Berger
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Durham, NC, USA.,Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA
| | - Mary Cooter
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Alexander S Roesler
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Stacey Chung
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - John Park
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | | | - Keith W VanDusen
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - J Will Thompson
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Arthur Moseley
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Michael J Devinney
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Shayan Smani
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Ashley Hall
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Victor Cai
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Jeffrey N Browndyke
- Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Durham, NC, USA.,Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA.,Department of Psychiatry & Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - David L Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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Deters KD, Mormino EC, Yu L, Lutz MW, Bennett DA, Barnes LL. TOMM40‐APOE haplotypes are associated with cognitive decline in non‐demented blacks. Alzheimers Dement 2020. [DOI: 10.1002/alz.044105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Lei Yu
- Rush Alzheimer's Disease Center Rush University Medical Center Chicago IL USA
| | | | - David A Bennett
- Rush Alzheimer's Disease Center Rush University Medical Center Chicago IL USA
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center Rush University Medical Center Chicago IL USA
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Chiba‐Falek O, Lutz MW, Sprague D, Barrera J. Shared genetic etiology underlying Alzheimer’s disease and major depressive disorder. Alzheimers Dement 2020. [DOI: 10.1002/alz.037697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Lutz MW, Burns DK, Alexander R, Culp M, Yarnall D, Haneline S, Chiang C, Lai E, Metz C, Sundseth S, Guennel T, Marshall S, Andruss BF, Latham GJ, Hall B, Statt SN, Swanson T, Ratti E, Saunders AM. A genetic enrichment strategy for delay of onset of Alzheimer’s disease clinical trials. Alzheimers Dement 2020. [DOI: 10.1002/alz.044920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | - Meredith Culp
- Takeda Development Center Americas, Inc. Cambridge MA USA
| | | | | | - Carl Chiang
- Zinfandel Pharmaceuticals, Inc. Chapel Hill NC USA
| | - Eric Lai
- Takeda Development Center Americas, Inc. Cambridge MA USA
| | - Craig Metz
- Zinfandel Pharmaceuticals, Inc. Chapel Hill NC USA
| | | | - Tobi Guennel
- QuartzBio, part of Precision for Medicine Frederick MD USA
| | - Scott Marshall
- QuartzBio, part of Precision for Medicine Frederick MD USA
| | | | | | | | | | - Tom Swanson
- Zinfandel Pharmaceuticals, Inc. Chapel Hill NC USA
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Lutz MW, Luo S, Williamson DE, Chiba‐Falek O. Shared genetic etiology underlying late‐onset Alzheimer’s disease and post traumatic stress syndrome. Alzheimers Dement 2020. [DOI: 10.1002/alz.041284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Sheng Luo
- Duke University School of Medicine Durham NC USA
| | - Douglas E. Williamson
- Duke University Medical Center Durham NC USA
- Research Service Durham VA Medical Center Durham NC USA
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Casanova R, Saldana S, Lutz MW, Plassman BL, Kuchibhatla M, Hayden KM. Investigating Predictors of Cognitive Decline Using Machine Learning. J Gerontol B Psychol Sci Soc Sci 2020; 75:733-742. [PMID: 29718387 DOI: 10.1093/geronb/gby054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Genetic risks for cognitive decline are not modifiable; however their relative importance compared to modifiable factors is unclear. We used machine learning to evaluate modifiable and genetic risk factors for Alzheimer's disease (AD), to predict cognitive decline. METHODS Health and Retirement Study participants, aged 65-90 years, with DNA and >2 cognitive evaluations, were included (n = 7,142). Predictors included age, body mass index, gender, education, APOE ε4, cardiovascular, hypertension, diabetes, stroke, neighborhood socioeconomic status (NSES), and AD risk genes. Latent class trajectory analyses of cognitive scores determined the form and number of classes. Random Forests (RF) classification investigated predictors of cognitive trajectories. Performance metrics (accuracy, sensitivity, and specificity) were reported. RESULTS Three classes were identified. Discriminating highest from lowest classes produced the best RF performance: accuracy = 78% (1.0%), sensitivity = 75% (1.0%), and specificity = 81% (1.0%). Top ranked predictors were education, age, gender, stroke, NSES, and diabetes, APOE ε4 carrier status, and body mass index (BMI). When discriminating high from medium classes, top predictors were education, age, gender, stroke, diabetes, NSES, and BMI. When discriminating medium from the low classes, education, NSES, age, diabetes, and stroke were top predictors. DISCUSSION The combination of latent trajectories and RF classification techniques suggested that nongenetic factors contribute more to cognitive decline than genetic factors. Education was the most relevant predictor for discrimination.
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Affiliation(s)
- Ramon Casanova
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Santiago Saldana
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, North Carolina
| | - Brenda L Plassman
- Department of Neurology, Duke University Medical Center, Durham, North Carolina.,Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina
| | - Maragatha Kuchibhatla
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina
| | - Kathleen M Hayden
- Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston Salem, North Carolina
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Han B, Chen H, Yao Y, Liu X, Nie C, Min J, Zeng Y, Lutz MW. Genetic and non-genetic factors associated with the phenotype of exceptional longevity & normal cognition. Sci Rep 2020; 10:19140. [PMID: 33154391 PMCID: PMC7645680 DOI: 10.1038/s41598-020-75446-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
In this study, we split 2156 individuals from the Chinese Longitudinal Healthy Longevity Survey (CLHLS) data into two groups, establishing a phenotype of exceptional longevity & normal cognition versus cognitive impairment. We conducted a genome-wide association study (GWAS) to identify significant genetic variants and biological pathways that are associated with cognitive impairment and used these results to construct polygenic risk scores. We elucidated the important and robust factors, both genetic and non-genetic, in predicting the phenotype, using several machine learning models. The GWAS identified 28 significant SNPs at p-value [Formula: see text] significance level and we pinpointed four genes, ESR1, PHB, RYR3, GRIK2, that are associated with the phenotype though immunological systems, brain function, metabolic pathways, inflammation and diet in the CLHLS cohort. Using both genetic and non-genetic factors, four machine learning models have close prediction results for the phenotype measured in Area Under the Curve: random forest (0.782), XGBoost (0.781), support vector machine with linear kernel (0.780), and [Formula: see text] penalized logistic regression (0.780). The top four important and congruent features in predicting the phenotype identified by these four models are: polygenic risk score, sex, age, and education.
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Affiliation(s)
- Bin Han
- Department of Statistical Science, Duke University, Durham, NC, USA
| | - Huashuai Chen
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA
- Business School of Xiangtan University, Xiangtan, China
| | - Yao Yao
- Center for Healthy Aging and Development Studies, National School of Development, Raissun Institute for Advanced Studies, Peking University, Beijing, China
| | - Xiaomin Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Chao Nie
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Zeng
- Center for the Study of Aging and Human Development, Medical School of Duke University, Durham, NC, USA.
- Center for Healthy Aging and Development Studies, National School of Development, Raissun Institute for Advanced Studies, Peking University, Beijing, China.
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
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Kuchibhatla M, Hunter JC, Plassman BL, Lutz MW, Casanova R, Saldana S, Hayden KM. The association between neighborhood socioeconomic status, cardiovascular and cerebrovascular risk factors, and cognitive decline in the Health and Retirement Study (HRS). Aging Ment Health 2020; 24:1479-1486. [PMID: 31018653 DOI: 10.1080/13607863.2019.1594169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: A small but growing body of evidence supports a relationship between neighborhood socioeconomic status (NSES) and cognitive decline. Additional work is needed to characterize this relationship controlling for risk factors such as cardiovascular, cerebrovascular, and genetic risk factors.Methods: Cognitive decline was assessed in association with NSES, and cardiovascular and cerebrovascular risk factors (heart disease, diabetes, hypertension, and stroke) in 8,198 individuals from the 1992-2010 waves of the Health and Retirement Study (HRS). Latent class trajectory analysis determined the number of cognitive trajectory classes that best fit the data, and a multinomial logistic regression model in the latent class framework assessed the risk for cognitive classes conferred by NSES index score and heart disease, diabetes, hypertension, and stroke across three trajectory classes of cognitive function. The analyses controlled for genetic risk for cognitive decline (including APOE genotype) and demographic variables, including education.Results: The HRS sample was 57.6% female and 85.5% White, with a mean age of 67.5(3.5) years at baseline. The three-quadratic-class model best fit the data, where higher classes represented better cognitive function. Those with better cognitive function were mainly younger white females. Those in the highest quartile of NSES had 57% higher odds of being in the high cognitive function class. Heart disease, diabetes, hypertension, and stroke each increased the odds having of lower cognitive function.Conclusions: In examining the relationship of cognitive status with various variables, neighborhood socioeconomic status, cardiovascular risk, and cerebrovascular risk persisted across the cognitive trajectory classes.
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Affiliation(s)
- Maragatha Kuchibhatla
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA.,Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA
| | - Jaimie C Hunter
- Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Brenda L Plassman
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA.,Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Ramon Casanova
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Santiago Saldana
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kathleen M Hayden
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, USA.,Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC, USA
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44
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Pytte J, Flynn LL, Anderton RS, Mastaglia FL, Theunissen F, James I, Pfaff A, Koks S, Saunders AM, Bedlack R, Burns DK, Lutz MW, Siddique N, Siddique T, Roses AD, Akkari PA. Disease-modifying effects of an SCAF4 structural variant in a predominantly SOD1 ALS cohort. Neurol Genet 2020; 6:e470. [PMID: 32754644 PMCID: PMC7357414 DOI: 10.1212/nxg.0000000000000470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To test the hypothesis that rs573116164 will have disease-modifying effects in patients with superoxide dismutase 1 (SOD1) familial amyotrophic lateral sclerosis (fALS), we characterized rs573116164 within a cohort of 190 patients with fALS and 560 healthy age-matched controls to assess the variant for association with various measures of disease. METHODS Using a previously described bioinformatics evaluation algorithm, a polymorphic short structural variant associated with SOD1 was identified according to its theoretical effect on gene expression. An 12-18 poly-T repeat (rs573116164) within the 3' untranslated region of serine and arginine rich proteins-related carboxy terminal domain associated factor 4 (SCAF4), a gene that is adjacent to SOD1, was assessed for disease association and influence on survival and age at onset in an fALS cohort using PCR, Sanger sequencing, and capillary separation techniques for allele detection. RESULTS In a North American cohort of predominantly SOD1 fALS patients (n =190) and age-matched healthy controls (n = 560), we showed that carriage of an 18T SCAF4 allele was associated with disease within this cohort (odds ratio [OR] 6.6; 95% confidence interval [CI] 3.9-11.2; p = 4.0e-11), but also within non-SOD1 cases (n = 27; OR 5.3; 95% CI 1.9-14.5; p = 0.0014). This finding suggests genetically SOD1-independent effects of SCAF4 on fALS susceptibility. Furthermore, carriage of an 18T allele was associated with a 26-month reduction in survival time (95% CI 6.6-40.8; p = 0.014), but did not affect age at onset of disease. CONCLUSIONS The findings in this fALS cohort suggest that rs573116164 could have SOD1-independent and broader relevance in ALS, warranting further investigation in other fALS and sporadic ALS cohorts, as well as studies of functional effects of the 18T variant on gene expression.
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Affiliation(s)
- Julia Pytte
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Loren L Flynn
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ryan S Anderton
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Frank L Mastaglia
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Frances Theunissen
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ian James
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Abigail Pfaff
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Sulev Koks
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Ann M Saunders
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Richard Bedlack
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Daniel K Burns
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Michael W Lutz
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Nailah Siddique
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Teepu Siddique
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - Allen D Roses
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
| | - P Anthony Akkari
- Centre for Neuromuscular and Neurological Disorders (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), University of Western Australia, Crawley; Perron Institute for Neurological and Translational Science (J.P., L.L.F., R.S.A., F.L.M., F.T., A.P., S.K., P.A.A.), Nedlands; Centre for Molecular Medicine and Innovative Therapeutics (L.L.F., A.P., S.K., P.A.A.), Murdoch University; School of Health Sciences (R.S.A.), and Institute for Health Research (R.S.A.), University of Notre Dame Australia, Fremantle; Institute for Immunology and Infectious Diseases (I.J.), Murdoch University, Australia; Department of Neurology (A.M.S., R.B., M.W.L., A.D.R.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals, Inc. (A.M.S., D.K.B., A.D.R.), Durham, NC; ALS Clinic (R.B.), Duke University, Durham, NC; Departments of Neurology, Pathology and Cell and Molecular Biology (N.S., T.S.), the Les Turner ALS Center, Northwestern University Feinberg School of Medicine; and the Northwestern University Interdepartmental Neuroscience Program (N.S., T.S.), Chicago, IL
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Lutz MW, Luo S, Williamson DE, Chiba-Falek O. Shared genetic etiology underlying late-onset Alzheimer's disease and posttraumatic stress syndrome. Alzheimers Dement 2020; 16:1280-1292. [PMID: 32588970 DOI: 10.1002/alz.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Late-onset Alzheimer's disease (LOAD) manifests comorbid neuropsychiatric symptoms and posttraumatic stress disorder (PTSD) is associated with an increased risk for dementia in late life, suggesting the two disorders may share genetic etiologies. METHODS We performed genetic pleiotropy analysis using LOAD and PTSD genome-wide association study (GWAS) datasets from white and African-American populations, followed by functional-genomic analyses. RESULTS We found an enrichment for LOAD across increasingly stringent levels of significance with the PTSD GWAS association (LOAD|PTSD) in the discovery and replication cohorts and a modest enrichment for the reverse conditional association (PTSD|LOAD). LOAD|PTSD association analysis identified and replicated the MS4A genes region. These genes showed similar expression pattern in brain regions affected in LOAD, and across-brain-tissue analysis identified a significant association for MS4A6A. The African-American samples showed moderate enrichment; however, no false discovery rate-significant associations. DISCUSSION We demonstrated common genetic signatures for LOAD and PTSD and suggested immune response as a common pathway for these diseases.
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Affiliation(s)
- Michael W Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Douglas E Williamson
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina, USA.,Research Service, Durham VA Medical Center, Durham, North Carolina, USA.,Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, USA
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Zhao X, Liu X, Zhang A, Chen H, Huo Q, Li W, Ye R, Chen Z, Liang L, Liu QA, Shen J, Jin X, Li W, Nygaard M, Liu X, Hou Y, Ni T, Bolund L, Gottschalk W, Tao W, Gu J, Tian XL, Yang H, Wang J, Xu X, Lutz MW, Min J, Zeng Y, Nie C. The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. Aging (Albany NY) 2019; 10:1206-1222. [PMID: 29883365 PMCID: PMC6046244 DOI: 10.18632/aging.101461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/30/2018] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that the numbers of CNVs, especially deletions, increase significantly in a direct correlation with longevity. We identify eleven CNVs that strongly associate with longevity; four of them locate in the chromosome bands, 7p11.2, 20q13.33, 19p12 and 8p23.3 and overlap partially with the CNVs identified in long-lived Danish or U.S. populations, while the other seven have not been reported previously. These CNV regions encode nineteen known genes, and some of which have been shown to affect aging-related phenotypes such as the shortening of telomere length (ZNF208), the risk of cancer (FOXA1, LAMA5, ZNF716), and vascular and immune-related diseases (ARHGEF10, TOR2A, SH2D3C). In addition, we found several pathways enriched in long-lived genomes, including FOXA1 and FOXA transcription factor networks involved in regulating aging or age-dependent diseases such as cancer. Thus, our study has identified longevity-associated CNV regions and their affected genes and pathways. Our results suggest that the human genome structures such as CNVs might play an important role in determining a long life in human.
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Affiliation(s)
- Xin Zhao
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xiaomin Liu
- BGI Shenzhen, Shenzhen 518083, China.,School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | | | - Huashuai Chen
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China.,Business School of Xiangtan University, Xiangtan 411105, China
| | - Qing Huo
- BGI Shenzhen, Shenzhen 518083, China
| | | | - Rui Ye
- BGI Shenzhen, Shenzhen 518083, China
| | | | | | | | - Juan Shen
- BGI Shenzhen, Shenzhen 518083, China
| | - Xin Jin
- BGI Shenzhen, Shenzhen 518083, China
| | - Wenwen Li
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Marianne Nygaard
- The Danish Aging Research Center, Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense C 5000, Denmark
| | - Xiao Liu
- BGI Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen 518083, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Lars Bolund
- BGI Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - William Gottschalk
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Wei Tao
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Jun Gu
- School of Life Sciences, Peking University, Beijing 100080, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Human Aging Research Institute and School of Life Science Nanchang University, Nanchang 330000, China
| | | | - Jian Wang
- BGI Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI Shenzhen, Shenzhen 518083, China
| | - Michael W Lutz
- Department of Neurology, Medical Center, Duke University, Durham, NC 27704, USA
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yi Zeng
- Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University, Durham NC 27710, USA.,Center for Healthy Aging and Development Studies, Raissun Institute for Advanced Studies, National School of Development, Peking University, Beijing 10080, China
| | - Chao Nie
- BGI Shenzhen, Shenzhen 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
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Lutz MW, Sprague D, Chiba-Falek O. Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. Alzheimers Dement 2019; 15:1048-1058. [PMID: 31262699 PMCID: PMC6699885 DOI: 10.1016/j.jalz.2019.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/20/2019] [Accepted: 04/17/2019] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Genome-wide association studies (GWAS) discovered multiple late-onset Alzheimer's disease (LOAD)-associated SNPs and inferred the genes based on proximity; however, the actual causal genes are yet to be identified. METHODS We defined LOAD-GWAS regions by the most significantly associated SNP ±0.5 Mb and developed a bioinformatics pipeline that uses and integrates chromatin state segmentation track to map active enhancers and virtual 4C software to visualize interactions between active enhancers and gene promoters. We augmented our pipeline with biomedical and functional information. RESULTS We applied the bioinformatics pipeline using three ∼1 Mb LOAD-GWAS loci: BIN1, PICALM, CELF1. These loci contain 10-24 genes, an average of 106 active enhancers and 80 CTCF sites. Our strategy identified all genes corresponding to the promoters that interact with the active enhancer that is closest to the LOAD-GWAS-SNP and generated a shorter list of prioritized candidate LOAD genes (5-14/loci), feasible for post-GWAS investigations of causality. DISCUSSION Interpretation of LOAD-GWAS discoveries requires the integration of brain-specific functional genomic data sets and information related to regulatory activity.
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Affiliation(s)
- Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Daniel Sprague
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA.
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Chiba-Falek O, Sprague D, Lutz MW. P2-123: BIOINFORMATICS STRATEGY TO ADVANCE THE INTERPRETATION OF ALZHEIMER'S DISEASE GWAS DISCOVERIES: THE ROADS FROM ASSOCIATION TO CAUSATION. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.2530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Alexander R, Burns DK, Welsh-Bohmer KA, Burke JR, Chiang C, Culp M, Plassman BL, Wu J, Lutz MW, Rubens R, Evans R, Saunders AM, Ratti E. DT-02-02: TOMMORROW: RESULTS FROM A PHASE 3 TRIAL TO DELAY THE ONSET OF MCI DUE TO AD AND QUALIFY A GENETIC BIOMARKER ALGORITHM. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | | | - James R. Burke
- Bryan Alzheimer's Disease Research Center; Duke University; Durham NC USA
- Duke University Medical Center; Durham NC USA
| | - Carl Chiang
- Zinfandel Pharmaceuticals, Inc.; Durham NC USA
| | - Meredith Culp
- Takeda Development Center Americas, Inc.; Deerfield IL USA
| | - Brenda L. Plassman
- Bryan Alzheimer's Disease Research Center; Duke University; Durham NC USA
| | - Jingtao Wu
- Takeda Development Center Americas, Inc.; Cambridge MA USA
| | | | - Robert Rubens
- Takeda Development Center Americas, Inc.; Cambridge MA USA
| | - Rebecca Evans
- Takeda Development Center Americas, Inc.; Cambridge MA USA
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Plassman BL, Chanti-Ketterl M, Hayden KM, Potter GG, Burke JR, Parks CG, Chen H, Shrestha S, Lutz MW, Keil AP, Kuchibhatla M. P2-566: LONG-TERM PESTICIDE USE AND RISK OF DEMENTIA IN THE AGRICULTURAL HEALTH STUDY OF MEMORY IN AGING. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.2975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | | | | | | | - Christine G. Parks
- National Institute of Environmental Health Sciences; Research Triangle Park NC USA
| | | | - Srishti Shrestha
- National Institute of Environmental Health Sciences; Research Triangle Park NC USA
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