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Yi H, Yang Q, Repaci C, Lee CM, Heo G, Timsina J, Gorijala P, Yang C, Budde J, Wang L, Cruchaga C, Sung YJ. TOPMed imputed genomics enhances genomic atlas of the human proteome in brain, cerebrospinal fluid, and plasma. Sci Data 2024; 11:387. [PMID: 38627416 PMCID: PMC11021418 DOI: 10.1038/s41597-024-03140-3] [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: 08/22/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Comprehensive expression quantitative trait loci studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein quantitative trait loci in brain, cerebrospinal fluid, and plasma. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in cerebrospinal fluid, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 loci in brain, 30 loci in cerebrospinal fluid, and 22 loci in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These resources are accessible through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer for use by the scientific community.
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Affiliation(s)
- Heng Yi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Qijun Yang
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Charlie Repaci
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cheolmin Matthew Lee
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gyujin Heo
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengran Yang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University, St. Louis, MO, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA.
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Timsina J, Dinasarapu A, Kilic-Berkmen G, Budde J, Sung YJ, Klein AM, Cruchaga C, Jinnah HA. Blood-Based Proteomics for Adult-Onset Focal Dystonias. Ann Neurol 2024. [PMID: 38578115 DOI: 10.1002/ana.26929] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES The adult-onset focal dystonias are characterized by over-active muscles leading to abnormal movements. For most cases, the etiology and pathogenesis remain unknown. In the current study, unbiased proteomics methods were used to identify potential changes in blood plasma proteins. METHODS A large-scale unbiased proteomics screen was used to compare proteins (N = 6,345) in blood plasma of normal healthy controls (N = 49) with adult-onset focal dystonia (N = 143) consisting of specific subpopulations of cervical dystonia (N = 45), laryngeal dystonia (N = 49), and blepharospasm (N = 49). Pathway analyses were conducted to identify relevant biological pathways. Finally, protein changes were used to build a prediction model for dystonia. RESULTS After correction for multiple comparisons, 15 proteins were associated with adult-onset focal dystonia. Subgroup analyses revealed some proteins were shared across the dystonia subgroups while others were unique to 1 subgroup. The top biological pathways involved changes in the immune system, metal ion transport, and reactive oxygen species. A 4-protein model showed high accuracy in discriminating control individuals from dystonia cases [average area under the curve (AUC) = 0.89]. INTERPRETATION These studies provide novel insights into the etiopathogenesis of dystonia, as well as novel potential biomarkers. ANN NEUROL 2024.
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Affiliation(s)
- Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashok Dinasarapu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Gamze Kilic-Berkmen
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam M Klein
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
| | - H A Jinnah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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Cruchaga C, Ali M, Shen Y, Do A, Wang L, Western D, Liu M, Beric A, Budde J, Gentsch J, Schindler S, Morris J, Holtzman D, Fernández M, Ruiz A, Alvarez I, Aguilar M, Pastor P, Rutledge J, Oh H, Wilson E, Le Guen Y, Khalid R, Robins C, Pulford D, Ibanez L, Wyss-Coray T, Ju Sung Y. Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures for asymptomatic and symptomatic Alzheimer's disease. Res Sq 2024:rs.3.rs-3631708. [PMID: 38410465 PMCID: PMC10896368 DOI: 10.21203/rs.3.rs-3631708/v1] [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: 02/28/2024]
Abstract
Changes in Amyloid-β (A), hyperphosphorylated Tau (T) in brain and cerebrospinal fluid (CSF) precedes AD symptoms, making CSF proteome a potential avenue to understand the pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 proteins dysregulated in AD, that were further validated in a third totally independent cohort. Machine learning was implemented to create and validate highly accurate and replicable (AUC>0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD and those AD cases with faster progression. The associated proteins cluster in four different protein pseudo-trajectories groups spanning the AD continuum and were enrichment in specific pathways including neuronal death, apoptosis and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfuncton(mid-stages), brain plasticity and longevity (mid-stages) and late microglia-neuron crosstalk (late stages).
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Affiliation(s)
| | | | | | - Anh Do
- Washington University School of Medicine
| | - Lihua Wang
- Washington University School of Medicine
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca MútuaTerrassa, Terrassa, Barcelona, Spain
| | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
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Shen Y, Ali M, Timsina J, Wang C, Do A, Western D, Liu M, Gorijala P, Budde J, Liu H, Gordon B, McDade E, Morris JC, Llibre-Guerra JJ, Bateman RJ, Joseph-Mathurin N, Perrin RJ, Maschi D, Wyss-Coray T, Pastor P, Goate A, Renton AE, Surace EI, Johnson ECB, Levey AI, Alvarez I, Levin J, Ringman JM, Allegri RF, Seyfried N, Day GS, Wu Q, Fernández MV, Ibanez L, Sung YJ, Cruchaga C. Systematic proteomics in Autosomal dominant Alzheimer's disease reveals decades-early changes of CSF proteins in neuronal death, and immune pathways. medRxiv 2024:2024.01.12.24301242. [PMID: 38260583 PMCID: PMC10802763 DOI: 10.1101/2024.01.12.24301242] [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: 01/24/2024]
Abstract
Background To date, there is no high throughput proteomic study in the context of Autosomal Dominant Alzheimer's disease (ADAD). Here, we aimed to characterize early CSF proteome changes in ADAD and leverage them as potential biomarkers for disease monitoring and therapeutic strategies. Methods We utilized Somascan® 7K assay to quantify protein levels in the CSF from 291 mutation carriers (MCs) and 185 non-carriers (NCs). We employed a multi-layer regression model to identify proteins with different pseudo-trajectories between MCs and NCs. We replicated the results using publicly available ADAD datasets as well as proteomic data from sporadic Alzheimer's disease (sAD). To biologically contextualize the results, we performed network and pathway enrichment analyses. Machine learning was applied to create and validate predictive models. Findings We identified 125 proteins with significantly different pseudo-trajectories between MCs and NCs. Twelve proteins showed changes even before the traditional AD biomarkers (Aβ42, tau, ptau). These 125 proteins belong to three different modules that are associated with age at onset: 1) early stage module associated with stress response, glutamate metabolism, and mitochondria damage; 2) the middle stage module, enriched in neuronal death and apoptosis; and 3) the presymptomatic stage module was characterized by changes in microglia, and cell-to-cell communication processes, indicating an attempt of rebuilding and establishing new connections to maintain functionality. Machine learning identified a subset of nine proteins that can differentiate MCs from NCs better than traditional AD biomarkers (AUC>0.89). Interpretation Our findings comprehensively described early proteomic changes associated with ADAD and captured specific biological processes that happen in the early phases of the disease, fifteen to five years before clinical onset. We identified a small subset of proteins with the potentials to become therapy-monitoring biomarkers of ADAD MCs. Funding Proteomic data generation was supported by NIH: RF1AG044546.
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5
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Cisterna-García A, Beric A, Ali M, Pardo JA, Chen HH, Fernandez MV, Norton J, Gentsch J, Bergmann K, Budde J, Perlmutter JS, Morris JC, Cruchaga C, Botia JA, Ibanez L. Cell-free RNA signatures predict Alzheimer's disease. iScience 2023; 26:108534. [PMID: 38089583 PMCID: PMC10711471 DOI: 10.1016/j.isci.2023.108534] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
There is a need for affordable, scalable, and specific blood-based biomarkers for Alzheimer's disease that can be applied to a population level. We have developed and validated disease-specific cell-free transcriptomic blood-based biomarkers composed by a scalable number of transcripts that capture AD pathobiology even in the presymptomatic stages of the disease. Accuracies are in the range of the current CSF and plasma biomarkers, and specificities are high against other neurodegenerative diseases.
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Affiliation(s)
- Alejandro Cisterna-García
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Muhammad Ali
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Jose Adrian Pardo
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Hsiang-Han Chen
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Joel S. Perlmutter
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Radiology, Neuroscience, Physical Therapy, and Occupational Therapy, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - John C. Morris
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | - Juan A. Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
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6
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Oh HSH, Rutledge J, Nachun D, Pálovics R, Abiose O, Moran-Losada P, Channappa D, Urey DY, Kim K, Sung YJ, Wang L, Timsina J, Western D, Liu M, Kohlfeld P, Budde J, Wilson EN, Guen Y, Maurer TM, Haney M, Yang AC, He Z, Greicius MD, Andreasson KI, Sathyan S, Weiss EF, Milman S, Barzilai N, Cruchaga C, Wagner AD, Mormino E, Lehallier B, Henderson VW, Longo FM, Montgomery SB, Wyss-Coray T. Organ aging signatures in the plasma proteome track health and disease. Nature 2023; 624:164-172. [PMID: 38057571 PMCID: PMC10700136 DOI: 10.1038/s41586-023-06802-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 10/19/2022] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
Animal studies show aging varies between individuals as well as between organs within an individual1-4, but whether this is true in humans and its effect on age-related diseases is unknown. We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20-50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer's disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. We introduce a simple and interpretable method to study organ aging using plasma proteomics data, predicting diseases and aging effects.
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Affiliation(s)
- Hamilton Se-Hwee Oh
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Jarod Rutledge
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Graduate Program in Genetics, Stanford University, Stanford, CA, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Róbert Pálovics
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Olamide Abiose
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Moran-Losada
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Divya Channappa
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Deniz Yagmur Urey
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University School of Engineering, Stanford, CA, USA
| | - Kate Kim
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Dan Western
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Menghan Liu
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Edward N Wilson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Yann Guen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Taylor M Maurer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Haney
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew C Yang
- Departments of Neurology and Anatomy, University of California San Francisco, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Katrin I Andreasson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sanish Sathyan
- Departments of Medicine and Genetics, Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, USA
| | - Erica F Weiss
- Department of Neurology, Montefiore Medical Center, New York, NY, USA
| | - Sofiya Milman
- Departments of Medicine and Genetics, Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, USA
| | - Nir Barzilai
- Departments of Medicine and Genetics, Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anthony D Wagner
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Elizabeth Mormino
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Victor W Henderson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Frank M Longo
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Tony Wyss-Coray
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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7
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Cruchaga C, Western D, Timsina J, Wang L, Wang C, Yang C, Ali M, Beric A, Gorijala P, Kohlfeld P, Budde J, Levey A, Morris J, Perrin R, Ruiz A, Marquié M, Boada M, de Rojas I, Rutledge J, Oh H, Wilson E, Guen YL, Alvarez I, Aguilar M, Greicius M, Pastor P, Pulford D, Ibanez L, Wyss-Coray T, Sung YJ, Phillips B. Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and informs causal proteins for Alzheimer's disease. Res Sq 2023:rs.3.rs-2814616. [PMID: 37333337 PMCID: PMC10275048 DOI: 10.21203/rs.3.rs-2814616/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The integration of quantitative trait loci (QTL) with disease genome-wide association studies (GWAS) has proven successful at prioritizing candidate genes at disease-associated loci. QTL mapping has mainly been focused on multi-tissue expression QTL or plasma protein QTL (pQTL). Here we generated the largest-to-date cerebrospinal fluid (CSF) pQTL atlas by analyzing 7,028 proteins in 3,107 samples. We identified 3,373 independent study-wide associations for 1,961 proteins, including 2,448 novel pQTLs of which 1,585 are unique to CSF, demonstrating unique genetic regulation of the CSF proteome. In addition to the established chr6p22.2-21.32 HLA region, we identified pleiotropic regions on chr3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron-specificity and neurological development. We also integrated this pQTL atlas with the latest Alzheimer's disease (AD) GWAS through PWAS, colocalization and Mendelian Randomization and identified 42 putative causal proteins for AD, 15 of which have drugs available. Finally, we developed a proteomics-based risk score for AD that outperforms genetics-based polygenic risk scores. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.
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Affiliation(s)
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Washington University School of Medicine
| | | | | | | | | | | | - Patsy Kohlfeld
- Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | | | | | | | - Mercè Boada
- Memory Clinic of Fundaciò ACE, Catalan Institute of Applied Neurosciences
| | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca Mútua Terrassa, Terrassa, Barcelona, Spain
| | | | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
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8
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer's and coronary disease pathways. iScience 2023; 26:106408. [PMID: 36974157 PMCID: PMC10010831 DOI: 10.1016/j.isci.2023.106408] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/21/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Identification of proteins dysregulated by COVID-19 infection is critically important for better understanding of its pathophysiology, building prognostic models, and identifying new targets. Plasma proteomic profiling of 4,301 proteins was performed in two independent datasets and tested for the association for three COVID-19 outcomes (infection, ventilation, and death). We identified 1,449 proteins consistently associated in both datasets with any of these three outcomes. We subsequently created highly accurate models that distinctively predict infection, ventilation, and death. These proteins were enriched in specific biological processes including cytokine signaling, Alzheimer's disease, and coronary artery disease. Mendelian randomization and gene network analyses identified eight causal proteins and 141 highly connected hub proteins including 35 with known drug targets. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes, reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R. Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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9
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Minaya MA, Mahali S, Iyer AK, Eteleeb AM, Martinez R, Huang G, Budde J, Temple S, Nana AL, Seeley WW, Spina S, Grinberg LT, Harari O, Karch CM. Conserved gene signatures shared among MAPT mutations reveal defects in calcium signaling. Front Mol Biosci 2023; 10:1051494. [PMID: 36845551 PMCID: PMC9948093 DOI: 10.3389/fmolb.2023.1051494] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: More than 50 mutations in the MAPT gene result in heterogeneous forms of frontotemporal lobar dementia with tau inclusions (FTLD-Tau). However, early pathogenic events that lead to disease and the degree to which they are common across MAPT mutations remain poorly understood. The goal of this study is to determine whether there is a common molecular signature of FTLD-Tau. Methods: We analyzed genes differentially expressed in induced pluripotent stem cell-derived neurons (iPSC-neurons) that represent the three major categories of MAPT mutations: splicing (IVS10 + 16), exon 10 (p.P301L), and C-terminal (p.R406W) compared with isogenic controls. The genes that were commonly differentially expressed in MAPT IVS10 + 16, p.P301L, and p.R406W neurons were enriched in trans-synaptic signaling, neuronal processes, and lysosomal function. Many of these pathways are sensitive to disruptions in calcium homeostasis. One gene, CALB1, was significantly reduced across the three MAPT mutant iPSC-neurons and in a mouse model of tau accumulation. We observed a significant reduction in calcium levels in MAPT mutant neurons compared with isogenic controls, pointing to a functional consequence of this disrupted gene expression. Finally, a subset of genes commonly differentially expressed across MAPT mutations were also dysregulated in brains from MAPT mutation carriers and to a lesser extent in brains from sporadic Alzheimer disease and progressive supranuclear palsy, suggesting that molecular signatures relevant to genetic and sporadic forms of tauopathy are captured in a dish. The results from this study demonstrate that iPSC-neurons capture molecular processes that occur in human brains and can be used to pinpoint common molecular pathways involving synaptic and lysosomal function and neuronal development, which may be regulated by disruptions in calcium homeostasis.
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Affiliation(s)
- Miguel A. Minaya
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Sidhartha Mahali
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Abhirami K. Iyer
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Abdallah M. Eteleeb
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Rita Martinez
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Guangming Huang
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - John Budde
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Sally Temple
- Neural Stem Cell Institute, Rensselaer, NY, United States
| | - Alissa L. Nana
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - William W. Seeley
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Salvatore Spina
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Lea T. Grinberg
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil
| | - Oscar Harari
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University in St Louis, St Louis, MO, United States
- NeuroGenomics and Informatics Center, Washington University in St Louis, St Louis, MO, United States
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University in St Louis, St Louis, MO, United States
- NeuroGenomics and Informatics Center, Washington University in St Louis, St Louis, MO, United States
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10
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You SF, Brase L, Filipello F, Iyer AK, Del-Aguila J, He J, D’Oliveira Albanus R, Budde J, Norton J, Gentsch J, Dräger NM, Sattler SM, Kampmann M, Piccio L, Morris JC, Perrin RJ, McDade E, Paul SM, Cashikar AG, Benitez BA, Harari O, Karch CM. MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state. medRxiv 2023:2023.02.06.23285545. [PMID: 36798226 PMCID: PMC9934804 DOI: 10.1101/2023.02.06.23285545] [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] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Genome-wide association studies (GWAS) have identified many modifiers of Alzheimer disease (AD) risk enriched in microglia. Two of these modifiers are common variants in the MS4A locus (rs1582763: protective and rs6591561: risk) and serve as major regulators of CSF sTREM2 levels. To understand their functional impact on AD, we used single nucleus transcriptomics to profile brains from carriers of these variants. We discovered a "chemokine" microglial subpopulation that is altered in MS4A variant carriers and for which MS4A4A is the major regulator. The protective variant increases MS4A4A expression and shifts the chemokine microglia subpopulation to an interferon state, while the risk variant suppresses MS4A4A expression and reduces this subpopulation of microglia. Our findings provide a mechanistic explanation for the AD variants in the MS4A locus. Further, they pave the way for future mechanistic studies of AD variants and potential therapeutic strategies for enhancing microglia resilience in AD pathogenesis.
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Affiliation(s)
- Shih-Feng You
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Logan Brase
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Fabia Filipello
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Abhirami K. Iyer
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Jorge Del-Aguila
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - June He
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | | | - John Budde
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Nina M. Dräger
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sydney M. Sattler
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Piccio
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- Charles Perkins Centre and Brain and Mind Centre, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - John C. Morris
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J. Perrin
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric McDade
- Department of Neurology, Washington University in St. Louis School of Medicine, USA
| | | | - Steven M. Paul
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Anil G. Cashikar
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
| | - Bruno A. Benitez
- Department of Neurology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, Missouri, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, Missouri, USA
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11
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer and coronary disease pathways. medRxiv 2022:2022.07.25.22278025. [PMID: 35923315 PMCID: PMC9347279 DOI: 10.1101/2022.07.25.22278025] [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] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of the plasma proteomic changes of Coronavirus disease 2019 (COVID-19) is essential to understanding the pathophysiology of the disease and developing predictive models and novel therapeutics. We performed plasma deep proteomic profiling from 332 COVID-19 patients and 150 controls and pursued replication in an independent cohort (297 cases and 76 controls) to find potential biomarkers and causal proteins for three COVID-19 outcomes (infection, ventilation, and death). We identified and replicated 1,449 proteins associated with any of the three outcomes (841 for infection, 833 for ventilation, and 253 for death) that can be query on a web portal ( https://covid.proteomics.wustl.edu/ ). Using those proteins and machine learning approached we created and validated specific prediction models for ventilation (AUC>0.91), death (AUC>0.95) and either outcome (AUC>0.80). These proteins were also enriched in specific biological processes, including immune and cytokine signaling (FDR ≤ 3.72×10 -14 ), Alzheimer's disease (FDR ≤ 5.46×10 -10 ) and coronary artery disease (FDR ≤ 4.64×10 -2 ). Mendelian randomization using pQTL as instrumental variants nominated BCAT2 and GOLM1 as a causal proteins for COVID-19. Causal gene network analyses identified 141 highly connected key proteins, of which 35 have known drug targets with FDA-approved compounds. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes (ventilation and death), reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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12
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Ibanez L, Heitsch L, Carrera C, Farias FHG, Del Aguila JL, Dhar R, Budde J, Bergmann K, Bradley J, Harari O, Phuah CL, Lemmens R, Viana Oliveira Souza AA, Moniche F, Cabezas-Juan A, Arenillas JF, Krupinksi J, Cullell N, Torres-Aguila N, Muiño E, Cárcel-Márquez J, Marti-Fabregas J, Delgado-Mederos R, Marin-Bueno R, Hornick A, Vives-Bauza C, Navarro RD, Tur S, Jimenez C, Obach V, Segura T, Serrano-Heras G, Chung JW, Roquer J, Soriano-Tarraga C, Giralt-Steinhauer E, Mola-Caminal M, Pera J, Lapicka-Bodzioch K, Derbisz J, Davalos A, Lopez-Cancio E, Muñoz L, Tatlisumak T, Molina C, Ribo M, Bustamante A, Sobrino T, Castillo-Sanchez J, Campos F, Rodriguez-Castro E, Arias-Rivas S, Rodríguez-Yáñez M, Herbosa C, Ford AL, Gutierrez-Romero A, Uribe-Pacheco R, Arauz A, Lopes-Cendes I, Lowenkopf T, Barboza MA, Amini H, Stamova B, Ander BP, Sharp FR, Kim GM, Bang OY, Jimenez-Conde J, Slowik A, Stribian D, Tsai EA, Burkly LC, Montaner J, Fernandez-Cadenas I, Lee JM, Cruchaga C. Multi-ancestry GWAS reveals excitotoxicity associated with outcome after ischaemic stroke. Brain 2022; 145:2394-2406. [PMID: 35213696 PMCID: PMC9890452 DOI: 10.1093/brain/awac080] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/14/2021] [Revised: 01/14/2022] [Accepted: 02/06/2022] [Indexed: 02/05/2023] Open
Abstract
During the first hours after stroke onset, neurological deficits can be highly unstable: some patients rapidly improve, while others deteriorate. This early neurological instability has a major impact on long-term outcome. Here, we aimed to determine the genetic architecture of early neurological instability measured by the difference between the National Institutes of Health Stroke Scale (NIHSS) within 6 h of stroke onset and NIHSS at 24 h. A total of 5876 individuals from seven countries (Spain, Finland, Poland, USA, Costa Rica, Mexico and Korea) were studied using a multi-ancestry meta-analyses. We found that 8.7% of NIHSS at 24 h of variance was explained by common genetic variations, and also that early neurological instability has a different genetic architecture from that of stroke risk. Eight loci (1p21.1, 1q42.2, 2p25.1, 2q31.2, 2q33.3, 5q33.2, 7p21.2 and 13q31.1) were genome-wide significant and explained 1.8% of the variability suggesting that additional variants influence early change in neurological deficits. We used functional genomics and bioinformatic annotation to identify the genes driving the association from each locus. Expression quantitative trait loci mapping and summary data-based Mendelian randomization indicate that ADAM23 (log Bayes factor = 5.41) was driving the association for 2q33.3. Gene-based analyses suggested that GRIA1 (log Bayes factor = 5.19), which is predominantly expressed in the brain, is the gene driving the association for the 5q33.2 locus. These analyses also nominated GNPAT (log Bayes factor = 7.64) ABCB5 (log Bayes factor = 5.97) for the 1p21.1 and 7p21.1 loci. Human brain single-nuclei RNA-sequencing indicates that the gene expression of ADAM23 and GRIA1 is enriched in neurons. ADAM23, a presynaptic protein and GRIA1, a protein subunit of the AMPA receptor, are part of a synaptic protein complex that modulates neuronal excitability. These data provide the first genetic evidence in humans that excitotoxicity may contribute to early neurological instability after acute ischaemic stroke.
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Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Laura Heitsch
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Department of Emergency Medicine, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Caty Carrera
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
| | - Fabiana H G Farias
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Jorge L Del Aguila
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Rajat Dhar
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - John Budde
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Joseph Bradley
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Oscar Harari
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Hope Center for Neurological Disorders, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Chia Ling Phuah
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Robin Lemmens
- Department of Neuroscience, Katholieke Universiteit Leuven, Campus Gasthuisberg O&N2, Leuven BE-3000, Belgium
| | - Alessandro A Viana Oliveira Souza
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Cidade Universitaria, Campinas 13083-887, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), R. Tessalia Viera de Camargo, Campinas 13083-887, Brazil
| | - Francisco Moniche
- Department of Neurology, Hospital Virgen del Rocio, University of Seville, Seville 41013, Spain
| | - Antonio Cabezas-Juan
- Department of Neurology, Hospital Virgen del Rocio, University of Seville, Seville 41013, Spain
- Hospital Virgen de la Macarena, University of Seville, Seville 41009, Spain
| | - Juan Francisco Arenillas
- Department of Neurology, Hospital Clinico Universitario Valladolid, Valladolid University, Valladolid 47003, Spain
| | - Jerzy Krupinksi
- Department of Neurology, Mutua Terrassa University Hospital, Universitat de Barcelona, Terrassa 08221, Spain
- Fundacio Docencia i Recerca Mutua Terrassa, Universitat de Barcelona, Terrassa 08221, Spain
| | - Natalia Cullell
- Fundacio Docencia i Recerca Mutua Terrassa, Universitat de Barcelona, Terrassa 08221, Spain
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Nuria Torres-Aguila
- Fundacio Docencia i Recerca Mutua Terrassa, Universitat de Barcelona, Terrassa 08221, Spain
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Elena Muiño
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Jara Cárcel-Márquez
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Joan Marti-Fabregas
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Raquel Delgado-Mederos
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Rebeca Marin-Bueno
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Alejandro Hornick
- Department of Neurology, Southern Illinois Healthcare Memorial Hospital of Carbondale, Carbondale 62901, IL, USA
| | | | - Rosa Diaz Navarro
- Department of Neurology, Hospital Universitari Son Espases, Universitat de les Illes Balears, Palma 07120, Spain
| | - Silvia Tur
- Department of Neurology, Hospital Universitari Son Espases, Universitat de les Illes Balears, Palma 07120, Spain
| | - Carmen Jimenez
- Department of Neurology, Hospital Universitari Son Espases, Universitat de les Illes Balears, Palma 07120, Spain
| | - Victor Obach
- Department of Neurology, Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona 08036, Spain
| | - Tomas Segura
- Research Unit, Complejo Hospitalario Universitario de Albacete, Albacete 02008, Spain
| | - Gemma Serrano-Heras
- Research Unit, Complejo Hospitalario Universitario de Albacete, Albacete 02008, Spain
| | - Jong Won Chung
- Department of Neurology, Samsung Medical Center, Seoul, South Korea
| | - Jaume Roquer
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Carol Soriano-Tarraga
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- NeuroGenomics and Informatics, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Eva Giralt-Steinhauer
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Marina Mola-Caminal
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
- Department of Surgical Sciences, Orthopedics, Uppsala University, Uppsala 75185, Sweden
| | - Joanna Pera
- Department of Neurology, Jagiellonian University, Krakow 31-007, Poland
| | | | - Justyna Derbisz
- Department of Neurology, Jagiellonian University, Krakow 31-007, Poland
| | - Antoni Davalos
- Department of Neurology, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona 08916, Spain
| | - Elena Lopez-Cancio
- Department of Neurology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Lucia Muñoz
- Department of Neurology, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona 08916, Spain
| | - Turgut Tatlisumak
- Department of Neurology, Sahlgrenska University Hospital, University of Gothenburg, Gothenburg 413 45, Sweden
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Carlos Molina
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
| | - Marc Ribo
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
| | - Alejandro Bustamante
- Department of Neurology, Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona 08916, Spain
| | - Tomas Sobrino
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Jose Castillo-Sanchez
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Francisco Campos
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Emilio Rodriguez-Castro
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Susana Arias-Rivas
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Manuel Rodríguez-Yáñez
- Clinical Neurosciences Research Laboratory, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15706, Spain
| | - Christina Herbosa
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | - Andria L Ford
- Department of Neurology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Hope Center for Neurological Disorders, School of Medicine, Washington University, Saint Louis 63110, MO, USA
- Department of Radiology, School of Medicine, Washington University, Saint Louis 63110, MO, USA
| | | | - Rodrigo Uribe-Pacheco
- Instituto Nacional de Neurologia y Neurocirurgia de Mexico, Ciudad de Mexico 14269, Mexico
| | - Antonio Arauz
- Instituto Nacional de Neurologia y Neurocirurgia de Mexico, Ciudad de Mexico 14269, Mexico
| | - Iscia Lopes-Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Cidade Universitaria, Campinas 13083-887, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), R. Tessalia Viera de Camargo, Campinas 13083-887, Brazil
| | - Theodore Lowenkopf
- Department of Neurology, Providence St. Vincent Medical Center, Portland 97225, OR, USA
| | - Miguel A Barboza
- Neurosciences Department, Hospital Rafael A. Calderon Guardia, Aranjuez, San José, Costa Rica
| | - Hajar Amini
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Boryana Stamova
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Bradley P Ander
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Frank R Sharp
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento 95817, CA, USA
| | - Gyeong Moon Kim
- Department of Neurology, Samsung Medical Center, Seoul, South Korea
| | - Oh Young Bang
- Department of Neurology, Samsung Medical Center, Seoul, South Korea
| | - Jordi Jimenez-Conde
- Neurovascular Research Group, Institut Hospital del Mar de Investigacions Mediques, Barcelona 08003, Spain
| | - Agnieszka Slowik
- Department of Neurology, Jagiellonian University, Krakow 31-007, Poland
| | - Daniel Stribian
- Department of Neurology, Helsinki University Hospital, Helsinki 00290, Finland
| | - Ellen A Tsai
- Translational Biology, Biogen, Inc., Cambridge 02142, MA, USA
| | - Linda C Burkly
- Genetics and Neurodevelopmental Disease Research Unit, Biogen, Inc., Cambridge 02142, MA, USA
| | - Joan Montaner
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
- Department of Neurology, Hospital Virgen del Rocio, University of Seville, Seville 41013, Spain
- Hospital Virgen de la Macarena, University of Seville, Seville 41009, Spain
| | - Israel Fernandez-Cadenas
- Stroke Unit, Vall d’Hebron University Hospital, Universitat de Barcelona, Barcelona 08035, Spain
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona 08041, Spain
| | - Jin Moo Lee
- Correspondence may also be addressed to: Jin-Moo Lee School of Medicine, Washington University 660 South Euclid Avenue Campus Box 8111 St. Louis, MO 63110, USA E-mail:
| | - Carlos Cruchaga
- Correspondence to: Carlos Cruchaga School of Medicine, Washington University 660 South Euclid Avenue Campus Box 8134 Saint Louis, MO 63110, USA E-mail:
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13
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Deming Y, Filipello F, Cignarella F, Cantoni C, Hsu S, Mikesell R, Li Z, Del-Aguila JL, Dube U, Farias FG, Bradley J, Budde J, Ibanez L, Fernandez MV, Blennow K, Zetterberg H, Heslegrave A, Johansson PM, Svensson J, Nellgård B, Lleo A, Alcolea D, Clarimon J, Rami L, Molinuevo JL, Suárez-Calvet M, Morenas-Rodríguez E, Kleinberger G, Ewers M, Harari O, Haass C, Brett TJ, Benitez BA, Karch CM, Piccio L, Cruchaga C. The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer's disease risk. Sci Transl Med 2019; 11:eaau2291. [PMID: 31413141 PMCID: PMC6697053 DOI: 10.1126/scitranslmed.aau2291] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [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: 05/24/2018] [Accepted: 04/05/2019] [Indexed: 12/13/2022]
Abstract
Soluble triggering receptor expressed on myeloid cells 2 (sTREM2) in cerebrospinal fluid (CSF) has been associated with Alzheimer's disease (AD). TREM2 plays a critical role in microglial activation, survival, and phagocytosis; however, the pathophysiological role of sTREM2 in AD is not well understood. Understanding the role of sTREM2 in AD may reveal new pathological mechanisms and lead to the identification of therapeutic targets. We performed a genome-wide association study (GWAS) to identify genetic modifiers of CSF sTREM2 obtained from the Alzheimer's Disease Neuroimaging Initiative. Common variants in the membrane-spanning 4-domains subfamily A (MS4A) gene region were associated with CSF sTREM2 concentrations (rs1582763; P = 1.15 × 10-15); this was replicated in independent datasets. The variants associated with increased CSF sTREM2 concentrations were associated with reduced AD risk and delayed age at onset of disease. The single-nucleotide polymorphism rs1582763 modified expression of the MS4A4A and MS4A6A genes in multiple tissues, suggesting that one or both of these genes are important for modulating sTREM2 production. Using human macrophages as a proxy for microglia, we found that MS4A4A and TREM2 colocalized on lipid rafts at the plasma membrane, that sTREM2 increased with MS4A4A overexpression, and that silencing of MS4A4A reduced sTREM2 production. These genetic, molecular, and cellular findings suggest that MS4A4A modulates sTREM2. These findings also provide a mechanistic explanation for the original GWAS signal in the MS4A locus for AD risk and indicate that TREM2 may be involved in AD pathogenesis not only in TREM2 risk-variant carriers but also in those with sporadic disease.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Fabia Filipello
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Francesca Cignarella
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Claudia Cantoni
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Simon Hsu
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Mikesell
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fabiana Geraldo Farias
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph Bradley
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
| | - Amanda Heslegrave
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Per M Johansson
- Department of Clinical Sciences Helsingborg, Lund University, Lund, Sweden
| | - Johan Svensson
- Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
| | - Bengt Nellgård
- Department of Anesthesiology, Sahlgrenska University Hospital, Department of Internal Medicine, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
| | - Alberto Lleo
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Daniel Alcolea
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jordi Clarimon
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Lorena Rami
- IDIBAPS, Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic, Barcelona, Spain
| | - José Luis Molinuevo
- IDIBAPS, Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, ICN Hospital Clinic, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
| | - Marc Suárez-Calvet
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Estrella Morenas-Rodríguez
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Gernot Kleinberger
- Biomedical Center (BMC), Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- ISAR Bioscience GmbH, 2152 Planegg, Germany
| | - Michael Ewers
- Institute for Stroke and Dementia Research, University Hospital, LMU, Munich, Germany
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Chair of Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Thomas J Brett
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Brain and Mind Centre, University of Sydney, Sydney, NSW 2050, Australia
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
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14
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Ibanez L, Heitsch L, Dube U, Farias FHG, Budde J, Bergmann K, Davenport R, Bradley J, Carrera C, Kinnunen J, Sallinen H, Strbian D, Slowik A, Fernandez-Cadenas I, Montaner J, Lee JM, Cruchaga C. Overlap in the Genetic Architecture of Stroke Risk, Early Neurological Changes, and Cardiovascular Risk Factors. Stroke 2019; 50:1339-1345. [PMID: 31084338 DOI: 10.1161/strokeaha.118.023097] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background and Purpose- The genetic relationships between stroke risk, stroke severity, and early neurological changes are complex and not completely understood. Genetic studies have identified 32 all stroke risk loci. Polygenic risk scores can be used to compare the genetic architecture of related traits. In this study, we compare the genetic architecture of stroke risk, stroke severity, and early neurological changes with that of 2 stroke risk factors: type 2 diabetes mellitus (T2DM) and hypertension. Methods- We assessed the degree of overlap in the genetic architecture of stroke risk, T2DM, hypertension, and 2 acute stroke phenotypes based on the National Institutes of Health Stroke Scale (NIHSS), which ranges from 0 for no stroke symptoms to 21 to 42 for a severe stroke: baseline (within 6 hours after onset) and change in NIHSS (ΔNIHSS=NIHSS at baseline-NIHSS at 24 hours). This was done by (1) single-nucleotide polymorphism by single-nucleotide polymorphism comparison, (2) weighted polygenic risk scores with sentinel variants, and (3) whole-genome polygenic risk scores using multiple P thresholds. Results- We found evidence of genetic architecture overlap between stroke risk and T2DM ( P=2.53×10-169), hypertension ( P=3.93×10-04), and baseline NIHSS ( P=0.03). However, there was no evidence of overlap between ΔNIHSS and stroke risk, T2DM, or hypertension. Conclusions- The genetic architecture of stroke risk is correlated with that of T2DM, hypertension, and initial stroke severity (NIHSS within 6 hours of stroke onset). However, the genetic architecture of early neurological change after stroke (ΔNIHSS) is not correlated with that of ischemic stroke risk, T2DM, or hypertension. Thus, stroke risk and early neurological change after stroke have distinct genetic architectures.
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Affiliation(s)
- Laura Ibanez
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - Laura Heitsch
- Division of Emergency Medicine (L.H.), Washington University School of Medicine, St. Louis, MO.,Department of Neurology (L.H., J.-M.L.), Washington University School of Medicine, St. Louis, MO
| | - Umber Dube
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - Fabiana H G Farias
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - John Budde
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - Kristy Bergmann
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - Rich Davenport
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - Joseph Bradley
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
| | - Caty Carrera
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain (C. Carrera, I.F.-C., J.M.)
| | - Janne Kinnunen
- Department of Neurology, Helsinki University Hospital, Finland (J.K., H.S., D.S.)
| | - Hanne Sallinen
- Department of Neurology, Helsinki University Hospital, Finland (J.K., H.S., D.S.)
| | - Daniel Strbian
- Department of Neurology, Helsinki University Hospital, Finland (J.K., H.S., D.S.)
| | - Agnieszka Slowik
- Department of Neurology, Jagiellonian University Medical College, Kraków, Poland (A.S.)
| | - Israel Fernandez-Cadenas
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain (C. Carrera, I.F.-C., J.M.)
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain (C. Carrera, I.F.-C., J.M.).,Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, Consejo Superior de Investigaciones Cientificas (CSIC), University of Seville, Spain (J.M.).,Department of Neurology, Hospital Universitario Virgen Macarena, Seville, Spain (J.M.)
| | - Jin-Moo Lee
- Department of Neurology (L.H., J.-M.L.), Washington University School of Medicine, St. Louis, MO
| | - Carlos Cruchaga
- From the Department of Psychiatry (L.I., U.D., F.H.G.F., J. Budde, K.B., R.D., J. Bradley, C. Cruchaga), Washington University School of Medicine, St. Louis, MO
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15
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Jiang S, Wen N, Li Z, Dube U, Del Aguila J, Budde J, Martinez R, Hsu S, Fernandez MV, Cairns NJ, Harari O, Cruchaga C, Karch CM. Integrative system biology analyses of CRISPR-edited iPSC-derived neurons and human brains reveal deficiencies of presynaptic signaling in FTLD and PSP. Transl Psychiatry 2018; 8:265. [PMID: 30546007 PMCID: PMC6293323 DOI: 10.1038/s41398-018-0319-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 01/12/2023] Open
Abstract
Mutations in the microtubule-associated protein tau (MAPT) gene cause autosomal dominant frontotemporal lobar degeneration with tau inclusions (FTLD-tau). MAPT p.R406W carriers present clinically with progressive memory loss and neuropathologically with neuronal and glial tauopathy. However, the pathogenic events triggered by the expression of the mutant tau protein remain poorly understood. To identify the genes and pathways that are dysregulated in FTLD-tau, we performed transcriptomic analyses in induced pluripotent stem cell (iPSC)-derived neurons carrying MAPT p.R406W and CRISPR/Cas9-corrected isogenic controls. We found that the expression of the MAPT p.R406W mutation was sufficient to create a significantly different transcriptomic profile compared with that of the isogeneic controls and to cause the differential expression of 328 genes. Sixty-one of these genes were also differentially expressed in the same direction between MAPT p.R406W carriers and pathology-free human control brains. We found that genes differentially expressed in the stem cell models and human brains were enriched for pathways involving gamma-aminobutyric acid (GABA) receptors and pre-synaptic function. The expression of GABA receptor genes, including GABRB2 and GABRG2, were consistently reduced in iPSC-derived neurons and brains from MAPT p.R406W carriers. Interestingly, we found that GABA receptor genes, including GABRB2 and GABRG2, are significantly lower in symptomatic mouse models of tauopathy, as well as in brains with progressive supranuclear palsy. Genome wide association analyses reveal that common variants within GABRB2 are associated with increased risk for frontotemporal dementia (P < 1 × 10-3). Thus, our systems biology approach, which leverages molecular data from stem cells, animal models, and human brain tissue can reveal novel disease mechanisms. Here, we demonstrate that MAPT p.R406W is sufficient to induce changes in GABA-mediated signaling and synaptic function, which may contribute to the pathogenesis of FTLD-tau and other primary tauopathies.
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Affiliation(s)
- Shan Jiang
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Natalie Wen
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Zeran Li
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Umber Dube
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Jorge Del Aguila
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - John Budde
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Rita Martinez
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Simon Hsu
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Maria V. Fernandez
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
| | - Nigel J. Cairns
- 0000 0001 2355 7002grid.4367.6Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, 660S. Euclid Ave, Campus Box 8118, Saint Louis, MO 63110 USA
| | | | | | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Celeste M. Karch
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8134, St. Louis, MO 63110 USA ,0000 0001 2355 7002grid.4367.6Hope Center for Neurological Disorders, Washington University School of Medicine, 660S. Euclid Ave. Campus Box 8111, St. Louis, MO 63110 USA
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Deming Y, Dumitrescu L, Barnes LL, Thambisetty M, Kunkle B, Gifford KA, Bush WS, Chibnik LB, Mukherjee S, De Jager PL, Kukull W, Huentelman M, Crane PK, Resnick SM, Keene CD, Montine TJ, Schellenberg GD, Haines JL, Zetterberg H, Blennow K, Larson EB, Johnson SC, Albert M, Moghekar A, Del Aguila JL, Fernandez MV, Budde J, Hassenstab J, Fagan AM, Riemenschneider M, Petersen RC, Minthon L, Chao MJ, Van Deerlin VM, Lee VMY, Shaw LM, Trojanowski JQ, Peskind ER, Li G, Davis LK, Sealock JM, Cox NJ, Goate AM, Bennett DA, Schneider JA, Jefferson AL, Cruchaga C, Hohman TJ. Sex-specific genetic predictors of Alzheimer's disease biomarkers. Acta Neuropathol 2018; 136:857-872. [PMID: 29967939 PMCID: PMC6280657 DOI: 10.1007/s00401-018-1881-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [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] [Received: 05/01/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022]
Abstract
Cerebrospinal fluid (CSF) levels of amyloid-β 42 (Aβ42) and tau have been evaluated as endophenotypes in Alzheimer's disease (AD) genetic studies. Although there are sex differences in AD risk, sex differences have not been evaluated in genetic studies of AD endophenotypes. We performed sex-stratified and sex interaction genetic analyses of CSF biomarkers to identify sex-specific associations. Data came from a previous genome-wide association study (GWAS) of CSF Aβ42 and tau (1527 males, 1509 females). We evaluated sex interactions at previous loci, performed sex-stratified GWAS to identify sex-specific associations, and evaluated sex interactions at sex-specific GWAS loci. We then evaluated sex-specific associations between prefrontal cortex (PFC) gene expression at relevant loci and autopsy measures of plaques and tangles using data from the Religious Orders Study and Rush Memory and Aging Project. In Aβ42, we observed sex interactions at one previous and one novel locus: rs316341 within SERPINB1 (p = 0.04) and rs13115400 near LINC00290 (p = 0.002). These loci showed stronger associations among females (β = - 0.03, p = 4.25 × 10-8; β = 0.03, p = 3.97 × 10-8) than males (β = - 0.02, p = 0.009; β = 0.01, p = 0.20). Higher levels of expression of SERPINB1, SERPINB6, and SERPINB9 in PFC was associated with higher levels of amyloidosis among females (corrected p values < 0.02) but not males (p > 0.38). In total tau, we observed a sex interaction at a previous locus, rs1393060 proximal to GMNC (p = 0.004), driven by a stronger association among females (β = 0.05, p = 4.57 × 10-10) compared to males (β = 0.02, p = 0.03). There was also a sex-specific association between rs1393060 and tangle density at autopsy (pfemale = 0.047; pmale = 0.96), and higher levels of expression of two genes within this locus were associated with lower tangle density among females (OSTN p = 0.006; CLDN16 p = 0.002) but not males (p ≥ 0.32). Results suggest a female-specific role for SERPINB1 in amyloidosis and for OSTN and CLDN16 in tau pathology. Sex-specific genetic analyses may improve understanding of AD's genetic architecture.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 1207 17th Avenue S, Nashville, TN, 37212, USA
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Madhav Thambisetty
- Unit of Clinical and Translational Neuroscience, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Brian Kunkle
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Katherine A Gifford
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 1207 17th Avenue S, Nashville, TN, 37212, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Lori B Chibnik
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Walter Kukull
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Matt Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Susan M Resnick
- Unit of Clinical and Translational Neuroscience, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Eric B Larson
- Department of Medicine, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Sterling C Johnson
- Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Geriatric Research Education and Clinical Center of the Wm. S. Middleton Memorial VA Hospital, Madison, WI, USA
| | - Marilyn Albert
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jorge L Del Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Jason Hassenstab
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Anne M Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Lennart Minthon
- Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Michael J Chao
- Ronald M Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Elaine R Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Gail Li
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Lea K Davis
- Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julia M Sealock
- Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alison M Goate
- Ronald M Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Angela L Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 1207 17th Avenue S, Nashville, TN, 37212, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Vanderbilt University School of Medicine, 1207 17th Avenue S, Nashville, TN, 37212, USA.
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17
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Gilbert B, Hill E, Aragon M, Frentzel S, Hoeng J, Ito S, Ishikawa S, Budde J, Maione A, Hayden P, Fields W, Keyser B, Haswell L, Azzopardi D, Behrsing H. Human In Vitro models for respiratory toxicology: evaluation of goblet cell hyperplasia, mucus production, and ciliary beating assays. Toxicol Lett 2018. [DOI: 10.1016/j.toxlet.2018.06.536] [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: 11/28/2022]
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18
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Li Z, Del-Aguila JL, Dube U, Budde J, Martinez R, Black K, Xiao Q, Cairns NJ, Dougherty JD, Lee JM, Morris JC, Bateman RJ, Karch CM, Cruchaga C, Harari O. Genetic variants associated with Alzheimer's disease confer different cerebral cortex cell-type population structure. Genome Med 2018; 10:43. [PMID: 29880032 PMCID: PMC5992755 DOI: 10.1186/s13073-018-0551-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 03/05/2018] [Accepted: 05/15/2018] [Indexed: 12/13/2022] Open
Abstract
Background Alzheimer’s disease (AD) is characterized by neuronal loss and astrocytosis in the cerebral cortex. However, the specific effects that pathological mutations and coding variants associated with AD have on the cellular composition of the brain are often ignored. Methods We developed and optimized a cell-type-specific expression reference panel and employed digital deconvolution methods to determine brain cellular distribution in three independent transcriptomic studies. Results We found that neuronal and astrocyte relative proportions differ between healthy and diseased brains and also among AD cases that carry specific genetic risk variants. Brain carriers of pathogenic mutations in APP, PSEN1, or PSEN2 presented lower neuron and higher astrocyte relative proportions compared to sporadic AD. Similarly, the APOE ε4 allele also showed decreased neuronal and increased astrocyte relative proportions compared to AD non-carriers. In contrast, carriers of variants in TREM2 risk showed a lower degree of neuronal loss compared to matched AD cases in multiple independent studies. Conclusions These findings suggest that genetic risk factors associated with AD etiology have a specific imprinting in the cellular composition of AD brains. Our digital deconvolution reference panel provides an enhanced understanding of the fundamental molecular mechanisms underlying neurodegeneration, enabling the analysis of large bulk RNA-sequencing studies for cell composition and suggests that correcting for the cellular structure when performing transcriptomic analysis will lead to novel insights of AD. Electronic supplementary material The online version of this article (10.1186/s13073-018-0551-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zeran Li
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.,Medical Scientist Training Program, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Rita Martinez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Qingli Xiao
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Nigel J Cairns
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.,Department of Pathology & Immunology, Washington University in St. Louis, School of Medicine, 510 S. Kingshighway, MC 8131, Saint Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | | | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.,Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA. .,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA.
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.
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19
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Ibanez L, Dube U, Davis AA, Fernandez MV, Budde J, Cooper B, Diez-Fairen M, Ortega-Cubero S, Pastor P, Perlmutter JS, Cruchaga C, Benitez BA. Pleiotropic Effects of Variants in Dementia Genes in Parkinson Disease. Front Neurosci 2018; 12:230. [PMID: 29692703 PMCID: PMC5902712 DOI: 10.3389/fnins.2018.00230] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/23/2018] [Indexed: 12/17/2022] Open
Abstract
Background: The prevalence of dementia in Parkinson disease (PD) increases dramatically with advancing age, approaching 80% in patients who survive 20 years with the disease. Increasing evidence suggests clinical, pathological and genetic overlap between Alzheimer disease, dementia with Lewy bodies and frontotemporal dementia with PD. However, the contribution of the dementia-causing genes to PD risk, cognitive impairment and dementia in PD is not fully established. Objective: To assess the contribution of coding variants in Mendelian dementia-causing genes on the risk of developing PD and the effect on cognitive performance of PD patients. Methods: We analyzed the coding regions of the amyloid-beta precursor protein (APP), Presenilin 1 and 2 (PSEN1, PSEN2), and Granulin (GRN) genes from 1,374 PD cases and 973 controls using pooled-DNA targeted sequence, human exome-chip and whole-exome sequencing (WES) data by single variant and gene base (SKAT-O and burden tests) analyses. Global cognitive function was assessed using the Mini-Mental State Examination (MMSE) or the Montreal Cognitive Assessment (MoCA). The effect of coding variants in dementia-causing genes on cognitive performance was tested by multiple regression analysis adjusting for gender, disease duration, age at dementia assessment, study site and APOE carrier status. Results: Known AD pathogenic mutations in the PSEN1 (p.A79V) and PSEN2 (p.V148I) genes were found in 0.3% of all PD patients. There was a significant burden of rare, likely damaging variants in the GRN and PSEN1 genes in PD patients when compared with frequencies in the European population from the ExAC database. Multiple regression analysis revealed that PD patients carrying rare variants in the APP, PSEN1, PSEN2, and GRN genes exhibit lower cognitive tests scores than non-carrier PD patients (p = 2.0 × 10-4), independent of age at PD diagnosis, age at evaluation, APOE status or recruitment site. Conclusions: Pathogenic mutations in the Alzheimer disease-causing genes (PSEN1 and PSEN2) are found in sporadic PD patients. PD patients with cognitive decline carry rare variants in dementia-causing genes. Variants in genes causing Mendelian neurodegenerative diseases exhibit pleiotropic effects.
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Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Umber Dube
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Albert A Davis
- Department of Neurology, Washington University, Saint Louis, MO, United States
| | - Maria V Fernandez
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - John Budde
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Breanna Cooper
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Monica Diez-Fairen
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain.,Movement Disorders Unit, Department of Neurology, University Hospital Mutua de Terrassa, Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
| | - Sara Ortega-Cubero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain.,Department of Neurology and Neurosurgery, Hospital Universitario de Burgos, Burgos, Spain
| | - Pau Pastor
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain.,Movement Disorders Unit, Department of Neurology, University Hospital Mutua de Terrassa, Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
| | - Joel S Perlmutter
- Department of Neurology, Washington University, Saint Louis, MO, United States.,Departments of Radiology, Neuroscience, Physical Therapy, and Occupational Therapy, Washington University, Saint Louis, MO, United States
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, Saint Louis, MO, United States
| | - Bruno A Benitez
- Department of Medicine, Washington University, Saint Louis, MO, United States
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20
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Fernández MV, Budde J, Del-Aguila JL, Ibañez L, Deming Y, Harari O, Norton J, Morris JC, Goate AM, Cruchaga C. Evaluation of Gene-Based Family-Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease. Front Neurosci 2018; 12:209. [PMID: 29670507 PMCID: PMC5893779 DOI: 10.3389/fnins.2018.00209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/15/2018] [Indexed: 12/22/2022] Open
Abstract
Gene-based tests to study the combined effect of rare variants on a particular phenotype have been widely developed for case-control studies, but their evolution and adaptation for family-based studies, especially studies of complex incomplete families, has been slower. In this study, we have performed a practical examination of all the latest gene-based methods available for family-based study designs using both simulated and real datasets. We examined the performance of several collapsing, variance-component, and transmission disequilibrium tests across eight different software packages and 22 models utilizing a cohort of 285 families (N = 1,235) with late-onset Alzheimer disease (LOAD). After a thorough examination of each of these tests, we propose a methodological approach to identify, with high confidence, genes associated with the tested phenotype and we provide recommendations to select the best software and model for family-based gene-based analyses. Additionally, in our dataset, we identified PTK2B, a GWAS candidate gene for sporadic AD, along with six novel genes (CHRD, CLCN2, HDLBP, CPAMD8, NLRP9, and MAS1L) as candidate genes for familial LOAD.
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Affiliation(s)
- Maria V. Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - Laura Ibañez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Alison M. Goate
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | | | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United States
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21
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Cruchaga C, Del-Aguila JL, Saef B, Black K, Fernandez MV, Budde J, Ibanez L, Deming Y, Kapoor M, Tosto G, Mayeux RP, Holtzman DM, Fagan AM, Morris JC, Bateman RJ, Goate AM, Harari O. Polygenic risk score of sporadic late-onset Alzheimer's disease reveals a shared architecture with the familial and early-onset forms. Alzheimers Dement 2018; 14:205-214. [PMID: 28943286 PMCID: PMC5803427 DOI: 10.1016/j.jalz.2017.08.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [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: 12/02/2016] [Revised: 07/31/2017] [Accepted: 08/18/2017] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To determine whether the extent of overlap of the genetic architecture among the sporadic late-onset Alzheimer's Disease (sLOAD), familial late-onset AD (fLOAD), sporadic early-onset AD (sEOAD), and autosomal dominant early-onset AD (eADAD). METHODS Polygenic risk scores (PRSs) were constructed using previously identified 21 genome-wide significant loci for LOAD risk. RESULTS We found that there is an overlap in the genetic architecture among sEOAD, fLOAD, and sLOAD. The highest association of the PRS and risk (odds ratio [OR] = 2.27; P = 1.29 × 10-7) was observed in sEOAD, followed by fLOAD (OR = 1.75; P = 1.12 × 10-7) and sLOAD (OR = 1.40; P = 1.21 × 10-3). The PRS was associated with cerebrospinal fluid ptau181-Aβ42 on eADAD (P = 4.36 × 10-2). CONCLUSION Our analysis confirms that the genetic factors identified for LOAD modulate risk in sLOAD and fLOAD and also sEOAD cohorts. Specifically, our results suggest that the burden of these risk variants is associated with familial clustering and earlier onset of AD. Although these variants are not associated with risk in the eADAD, they may be modulating age at onset.
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Affiliation(s)
- Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Manav Kapoor
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University College of Physicians and Surgeons, New York, NY, USA; Department of Neurology, Columbia University College of Physicians and Surgeons, New York-Presbyterian Hospital, New York, NY, USA
| | - Richard P Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University College of Physicians and Surgeons, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University College of Physicians and Surgeons, New York, NY, USA; School of Medicine, Mother and Teacher Pontifical Catholic University, Santiago, Dominican Republic
| | - David M Holtzman
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne M Fagan
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Randall J Bateman
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Del-Aguila JL, Fernández MV, Schindler S, Ibanez L, Deming Y, Ma S, Saef B, Black K, Budde J, Norton J, Chasse R, Harari O, Goate A, Xiong C, Morris JC, Cruchaga C. Assessment of the Genetic Architecture of Alzheimer's Disease Risk in Rate of Memory Decline. J Alzheimers Dis 2018; 62:745-756. [PMID: 29480181 PMCID: PMC5989565 DOI: 10.3233/jad-170834] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 12/16/2022]
Abstract
Many genetic studies for Alzheimer's disease (AD) have been focused on the identification of common genetic variants associated with AD risk and not on other aspects of the disease, such as age at onset or rate of dementia progression. There are multiple approaches to untangling the genetic architecture of these phenotypes. We hypothesized that the genetic architecture of rate of progression is different than the risk for developing AD dementia. To test this hypothesis, we used longitudinal clinical data from ADNI and the Knight-ADRC at Washington University, and we calculated PRS (polygenic risk score) based on the IGAP study to compare the genetic architecture of AD risk and dementia progression. Dementia progression was measured by the change of Clinical Dementia Rating Sum of Boxes (CDR)-SB per year. Out of the 21 loci for AD risk, no association with the rate of dementia progression was found. The PRS rate was significantly associated with the rate of dementia progression (β= 0.146, p = 0.03). In the case of rare variants, TREM2 (β= 0.309, p = 0.02) was also associated with the rate of dementia progression. TREM2 variant carriers showed a 23% faster rate of dementia compared with non-variant carriers. In conclusion, our results indicate that the recently identified common and rare variants for AD susceptibility have a limited impact on the rate of dementia progression in AD patients.
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Affiliation(s)
- Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne Schindler
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Shengmei Ma
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Ben Saef
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel Chasse
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison Goate
- Mount Sinai School of Medicine, New York, NY, USA
| | - Chengjie Xiong
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
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23
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Ibanez L, Dube U, Saef B, Budde J, Black K, Medvedeva A, Del-Aguila JL, Davis AA, Perlmutter JS, Harari O, Benitez BA, Cruchaga C. Parkinson disease polygenic risk score is associated with Parkinson disease status and age at onset but not with alpha-synuclein cerebrospinal fluid levels. BMC Neurol 2017; 17:198. [PMID: 29141588 PMCID: PMC5688622 DOI: 10.1186/s12883-017-0978-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 05/04/2017] [Accepted: 11/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic architecture of Parkinson's Disease (PD) is complex and not completely understood. Multiple genetic studies to date have identified multiple causal genes and risk loci. Nevertheless, most of the expected genetic heritability remains unexplained. Polygenic risk scores (PRS) may provide greater statistical power and inform about the genetic architecture of multiple phenotypes. The aim of this study was to test the association between PRS and PD risk, age at onset and cerebrospinal fluid (CSF) biomarkers (α-synuclein, Aβ1-42, t-tau and p-tau). METHODS The weighted PRS was created using the genome-wide loci from Nalls et al., 2014 PD GWAs meta-analysis. The PRS was tested for association with PD status, age at onset and CSF biomarker levels in 829 cases and 432 controls of European ancestry. RESULTS The PRS was associated with PD status (p = 5.83×10-08) and age at onset (p = 5.70×10-07). The CSF t-tau levels showed a nominal association with the PRS (p = 0.02). However, CSF α-synuclein, amyloid beta and phosphorylated tau were not found to be associated with the PRS. CONCLUSION Our study suggests that there is an overlap in the genetic architecture of PD risk and onset, although the different loci present different weights for those phenotypes. In our dataset we found a marginal association of the PRS with CSF t-tau but not with α-synuclein CSF levels, suggesting that the genetic architecture for the CSF biomarker levels is different from that of PD risk.
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Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Umber Dube
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA.,Medical Scientist Training Program, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Benjamin Saef
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - John Budde
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Kathleen Black
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Alexandra Medvedeva
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Albert A Davis
- Department of Neurology, School of Medicine, Washington University in St Louis, Saint Louis, MO, USA
| | - Joel S Perlmutter
- Department of Neurology, School of Medicine, Washington University in St Louis, Saint Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA.,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Bruno A Benitez
- Department of Medicine, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, School of Medicine, Washington University in Saint Louis, Saint Louis, MO, USA. .,Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University in Saint Louis, Saint Louis, MO, USA.
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24
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Huang KL, Marcora E, Pimenova AA, Di Narzo AF, Kapoor M, Jin SC, Harari O, Bertelsen S, Fairfax BP, Czajkowski J, Chouraki V, Grenier-Boley B, Bellenguez C, Deming Y, McKenzie A, Raj T, Renton AE, Budde J, Smith A, Fitzpatrick A, Bis JC, DeStefano A, Adams HHH, Ikram MA, van der Lee S, Del-Aguila JL, Fernandez MV, Ibañez L, Sims R, Escott-Price V, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Lambert JC, van Duijn C, Launer L, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe JSK, Cruchaga C, Hao K, Goate AM. A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease. Nat Neurosci 2017; 20:1052-1061. [PMID: 28628103 PMCID: PMC5759334 DOI: 10.1038/nn.4587] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [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: 06/30/2016] [Accepted: 05/20/2017] [Indexed: 12/12/2022]
Abstract
A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function. AD heritability was enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network in AD. Finally, experimentally altered PU.1 levels affected the expression of mouse orthologs of many AD risk genes and the phagocytic activity of mouse microglial cells. Our results suggest that lower SPI1 expression reduces AD risk by regulating myeloid gene expression and cell function.
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Affiliation(s)
- Kuan-lin Huang
- Department of Medicine, Washington University in St. Louis, Saint
Louis, MO, USA
- Department of McDonnell Genome Institute, Washington University in
St. Louis, Saint Louis, MO, USA
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Anna A Pimenova
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Manav Kapoor
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New
Haven, CT, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Sarah Bertelsen
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, Nuffield Department of
Medicine, University of Oxford, Oxford, United Kingdom
| | - Jake Czajkowski
- Department of Genetics, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Vincent Chouraki
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA
| | - Benjamin Grenier-Boley
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
| | - Céline Bellenguez
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
| | - Yuetiva Deming
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Andrew McKenzie
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Alan E Renton
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - John Budde
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | | | - Annette Fitzpatrick
- Department of Epidemiology, University of Washington, Seattle,
Washington, USA
| | - Joshua C Bis
- Department of Medicine, University of Washington, Seattle,
Washington, USA
| | - Anita DeStefano
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - Hieab HH Adams
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Sven van der Lee
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | | | - Laura Ibañez
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | | | | | - Rebecca Sims
- Psychological Medicine and Clinical Neurosciences, Medical Research
Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Cardiff University,
Cardiff, UK
| | - Valentina Escott-Price
- Psychological Medicine and Clinical Neurosciences, Medical Research
Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Cardiff University,
Cardiff, UK
| | - Richard Mayeux
- Taub Institute on Alzheimer’s Disease and the Aging Brain,
Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY,
USA
- Department of Neurology, Columbia University, New York, NY,
USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve
University, Cleveland, OH, USA; Department of Ophthalmology, Boston University
School of Medicine, Boston, MA, USA
| | - Lindsay A Farrer
- Institut Pasteur de Lille, F-59000 Lille, France
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University
School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public
Health, Boston, MA, USA
- The John P. Hussman Institute for Human Genomics, University of
Miami, Miami, FL, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of
Miami, Miami, FL, USA
- Macdonald Foundation Department of Human Genetics, University of
Miami, Miami, FL, USA
| | - Jean Charles Lambert
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Lenore Launer
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, Maryland, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA
| | - Julie Williams
- Psychological Medicine and Clinical Neurosciences, Medical Research
Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Cardiff University,
Cardiff, UK
| | - Philippe Amouyel
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
- Centre Hospitalier Universitaire de Lille, U1167, F-59000 Lille,
France
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of
Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | | | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, Utah,
USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
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25
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Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Huang KL, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O'Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VMY, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF, Kauwe JSK, Goate AM, Cruchaga C. Genome-wide association study identifies four novel loci associated with Alzheimer's endophenotypes and disease modifiers. Acta Neuropathol 2017; 133:839-856. [PMID: 28247064 PMCID: PMC5613285 DOI: 10.1007/s00401-017-1685-y] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [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] [Received: 12/01/2016] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 01/20/2023]
Abstract
More than 20 genetic loci have been associated with risk for Alzheimer's disease (AD), but reported genome-wide significant loci do not account for all the estimated heritability and provide little information about underlying biological mechanisms. Genetic studies using intermediate quantitative traits such as biomarkers, or endophenotypes, benefit from increased statistical power to identify variants that may not pass the stringent multiple test correction in case-control studies. Endophenotypes also contain additional information helpful for identifying variants and genes associated with other aspects of disease, such as rate of progression or onset, and provide context to interpret the results from genome-wide association studies (GWAS). We conducted GWAS of amyloid beta (Aβ42), tau, and phosphorylated tau (ptau181) levels in cerebrospinal fluid (CSF) from 3146 participants across nine studies to identify novel variants associated with AD. Five genome-wide significant loci (two novel) were associated with ptau181, including loci that have also been associated with AD risk or brain-related phenotypes. Two novel loci associated with Aβ42 near GLIS1 on 1p32.3 (β = -0.059, P = 2.08 × 10-8) and within SERPINB1 on 6p25 (β = -0.025, P = 1.72 × 10-8) were also associated with AD risk (GLIS1: OR = 1.105, P = 3.43 × 10-2), disease progression (GLIS1: β = 0.277, P = 1.92 × 10-2), and age at onset (SERPINB1: β = 0.043, P = 4.62 × 10-3). Bioinformatics indicate that the intronic SERPINB1 variant (rs316341) affects expression of SERPINB1 in various tissues, including the hippocampus, suggesting that SERPINB1 influences AD through an Aβ-associated mechanism. Analyses of known AD risk loci suggest CLU and FERMT2 may influence CSF Aβ42 (P = 0.001 and P = 0.009, respectively) and the INPP5D locus may affect ptau181 levels (P = 0.009); larger studies are necessary to verify these results. Together the findings from this study can be used to inform future AD studies.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Manav Kapoor
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Shengmei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kuan-Lin Huang
- Department of Medicine, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Sarah Bertelsen
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anne M Fagan
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Sungeun Kim
- Indiana Alzheimer Disease Center and Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Electrical and Computer Engineering, State University of New York, Oswego, NY, 13126, USA
| | - Andrew J Saykin
- Indiana Alzheimer Disease Center and Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Institute for the Neurosciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard University and M.I.T., Cambridge, MA, 02142, USA
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard O'Brien
- Department of Neurology, Duke Medical Center, Box 2900, Durham, NC, 27710, USA
| | | | | | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Department of Neuroscience and Physiology, Sahlgrenska University Hospital, University of Gothenburg, Mölndal, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Lennart Minthon
- Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia Man-Yee Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan L Haines
- Department of Molecular Physiology and Biophysics, Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Richard Mayeux
- Department of Neurology, Taub Institute on Alzheimer's Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, and Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Lindsay A Farrer
- Departments of Biostatistics, Medicine (Genetics Program), Ophthalmology, Epidemiology, and Neurology, Boston University, Boston, MA, USA
| | - Elaine R Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- VISN-20 Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Ge Li
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- VISN-20 Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Alison M Goate
- Department of Neuroscience, Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.
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Budde J, Fischer K, Menz W, Sauerwald F. Viskositätemessungen XIV. Z PHYS CHEM 2017. [DOI: 10.1515/zpch-1962-21812] [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: 11/15/2022]
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Deming Y, Black K, Carrell D, Cai Y, Del-Aguila JL, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Huang KL, Sutphen CL, Tarawneh R, Fagan AM, Holtzman DM, Morris JC, Goate AM, Dougherty JD, Cruchaga C. Chitinase-3-like 1 protein (CHI3L1) locus influences cerebrospinal fluid levels of YKL-40. BMC Neurol 2016; 16:217. [PMID: 27832767 PMCID: PMC5105244 DOI: 10.1186/s12883-016-0742-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 07/15/2016] [Accepted: 11/03/2016] [Indexed: 11/27/2022] Open
Abstract
Background Alzheimer’s disease (AD) pathology appears several years before clinical symptoms, so identifying ways to detect individuals in the preclinical stage is imperative. The cerebrospinal fluid (CSF) Tau/Aβ42 ratio is currently the best known predictor of AD status and cognitive decline, and the ratio of CSF levels of chitinase-3-like 1 protein (CHI3L1, YKL-40) and amyloid beta (Aβ42) were reported as predictive, but individual variability and group overlap inhibits their utility for individual diagnosis making it necessary to find ways to improve sensitivity of these biomarkers. Methods We used linear regression to identify genetic loci associated with CSF YKL-40 levels in 379 individuals (80 cognitively impaired and 299 cognitively normal) from the Charles F and Joanne Knight Alzheimer’s Disease Research Center. We tested correlations between YKL-40 and CSF Tau/Aβ42 ratio, Aβ42, tau, and phosphorylated tau (ptau181). We used studentized residuals from a linear regression model of the log-transformed, standardized protein levels and the additive reference allele counts from the most significant locus to adjust YKL-40 values and tested the differences in correlations with CSF Tau/Aβ42 ratio, Aβ42, tau, and ptau181. Results We found that genetic variants on the CH13L1 locus were significantly associated with CSF YKL-40 levels, but not AD risk, age at onset, or disease progression. The most significant variant is a reported expression quantitative trait locus for CHI3L1, the gene which encodes YKL-40, and explained 12.74 % of the variance in CSF YKL-40 in our study. YKL-40 was positively correlated with ptau181 (r = 0.521) and the strength of the correlation significantly increased with the addition of genetic information (r = 0.573, p = 0.006). Conclusions CSF YKL-40 levels are likely a biomarker for AD, but we found no evidence that they are an AD endophenotype. YKL-40 levels are highly regulated by genetic variation, and by including genetic information the strength of the correlation between YKL-40 and ptau181 levels is significantly improved. Our results suggest that studies of potential biomarkers may benefit from including genetic information. Electronic supplementary material The online version of this article (doi:10.1186/s12883-016-0742-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - ShengMei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA
| | - Sarah Bertelsen
- Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kuan-Lin Huang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Courtney L Sutphen
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Rawan Tarawneh
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Anne M Fagan
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA.,Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO, 63110, USA. .,Hope Center for Neurological Disorders, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA.
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Deming Y, Harari O, Black K, Carrell D, Cai Y, Del-Aguila JL, Fernandez V, Budde J, Ma S, Saef B, Bertelsen S, Kauwe J, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, Jager P, Goate AM, Cruchaga C, Albert MS, Moghekar A, O'Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, M-Y Lee V, Shaw LM, Trojanowski JQ, Peskind ER, Li G. O2‐10‐05: Cerebrospinal Fluid Levels of Amyloid Beta and Tau as Endophenotypes Reveal Novel Variants Potentially Informative for Alzheimer's Disease. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.452] [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: 11/27/2022]
Affiliation(s)
- Yuetiva Deming
- Washington University School of MedicineSaint LouisMO USA
| | - Oscar Harari
- Washington University in St. LouisSaint LouisMO USA
| | - Kathleen Black
- Washington University School of MedicineSaint LouisMO USA
| | - David Carrell
- Washington University School of MedicineSaint LouisMO USA
| | - Yefei Cai
- Washington University School of MedicineSt LouisMO USA
| | | | | | - John Budde
- Washington University School of MedicineSaint LouisMO USA
| | - Shengmei Ma
- Washington University School of MedicineSaint LouisMO USA
| | - Ben Saef
- Washington University School of MedicineSaint LouisMO USA
| | | | | | - Anne M. Fagan
- Washington University School of MedicineSt. LouisMO USA
- Knight Alzheimer's Disease Research CenterSt. LouisMO USA
| | - David M. Holtzman
- Washington University School of MedicineSt. LouisMO USA
- Knight Alzheimer's Disease Research CenterSt. LouisMO USA
| | - John C. Morris
- Knight Alzheimer's Disease Research CenterSt. LouisMO USA
- Washington University in St. LouisSt. LouisMO USA
| | - Sungeun Kim
- Indiana University School of MedicineIndianapolisIN USA
| | | | | | | | - Carlos Cruchaga
- Washington University School of MedicineSt. LouisMO USA
- Knight Alzheimer Disease CenterSt. LouisMO USA
| | | | - Abhay Moghekar
- Johns Hopkins University School of MedicineBaltimoreMD USA
| | | | | | | | - Kaj Blennow
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Lennart Minthon
- Clinical Memory Research Unit Department of Clinical Sciences Lund UniversityMalmoSweden
| | | | - Virginia M-Y Lee
- Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaPA USA
| | - Leslie M. Shaw
- Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaPA USA
| | | | | | - Gail Li
- University of WashingtonSeattleWA USA
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Huang KL, Jin SC, Harari O, Kapoor M, Bertelsen S, Czajkowski J, Lambert JC, Chouraki V, Bellenguez C, Grenier-Boley B, Deming Y, McKenzie A, Renton AE, Budde J, Del-Aguila JL, Fernandez MV, Ibanez L, Harold D, Hollingworth P, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe J, Marcora E, Cruchaga C, Goate AM. O2‐10‐06: A Common Allele in
SPI1
Lowers Risk and Delays Age at Onset for Alzheimer's Disease. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.453] [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: 10/20/2022]
Affiliation(s)
| | | | - Oscar Harari
- Washington University in St. LouisSaint LouisMO USA
| | - Manav Kapoor
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | | | | | | | | | | | | | - Yuetiva Deming
- Washington University School of MedicineSaint LouisMO USA
| | | | | | - John Budde
- Washington University School of MedicineSaint LouisMO USA
| | | | | | - Laura Ibanez
- Washington University in St. LouisSaint LouisMO USA
| | | | | | | | | | | | | | | | - Julie Williams
- MRC Centre for Neuropsychiatric Genetics & Genomics Institute of Psychological Medicine and Clinical Neurosciences, Cardiff UniversityCardiff United Kingdom
| | | | | | - Bin Zhang
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
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Fernández MV, Black K, Carrell D, Saef B, Budde J, Deming Y, Howells B, Del-Aguila JL, Ma S, Norton J, Chasse R, Morris JC, Goate A, Cruchaga C. P3‐097:
SORL1
Variants Across Alzheimer’s Disease Cohorts in European Americans. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.1756] [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: 11/25/2022]
Affiliation(s)
| | - Kathleen Black
- Washington University School of MedicineSaint LouisMO USA
| | - David Carrell
- Washington University School of MedicineSaint LouisMO USA
| | - Ben Saef
- Washington University School of MedicineSaint LouisMO USA
| | - John Budde
- Washington University School of MedicineSaint LouisMO USA
| | - Yuetiva Deming
- Washington University School of MedicineSaint LouisMO USA
| | - Bill Howells
- Washington University School of MedicineSaint LouisMO USA
| | | | - Shengmei Ma
- Washington University School of MedicineSaint LouisMO USA
| | - Joanne Norton
- Washington University School of MedicineSaint LouisMO USA
| | - Rachel Chasse
- Washington University School of MedicineSaint LouisMO USA
| | - John C. Morris
- Knight Alzheimer's Disease Research CenterSt. LouisMO USA
- Washington University School of MedicineSt. LouisMO USA
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Robat C, Budde J. Potency and stability of compounded cyclophosphamide: a pilot study. Vet Comp Oncol 2016; 15:706-709. [DOI: 10.1111/vco.12210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/04/2015] [Accepted: 12/14/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Robat
- Department of Medical Sciences; School of Veterinary Medicine, University of Wisconsin-Madison; Madison WI USA
| | - J. Budde
- UW Veterinary Care Pharmacy; University of Wisconsin-Madison; Madison WI USA
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Deming Y, Xia J, Cai Y, Lord J, Del-Aguila JL, Fernandez MV, Carrell D, Black K, Budde J, Ma S, Saef B, Howells B, Bertelsen S, Bailey M, Ridge PG, Holtzman D, Morris JC, Bales K, Pickering EH, Lee JM, Heitsch L, Kauwe J, Goate A, Piccio L, Cruchaga C. Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits. Sci Rep 2016; 6:18092. [PMID: 36647296 PMCID: PMC4698720 DOI: 10.1038/srep18092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 07/23/2015] [Accepted: 11/11/2015] [Indexed: 01/23/2023] Open
Abstract
Genome-wide association studies of 146 plasma protein levels in 818 individuals revealed 56 genome-wide significant associations (28 novel) with 47 analytes. Loci associated with plasma levels of 39 proteins tested have been previously associated with various complex traits such as heart disease, inflammatory bowel disease, Type 2 diabetes and multiple sclerosis. These data suggest that these plasma protein levels may constitute informative endophenotypes for these complex traits. We found three potential pleiotropic genes: ABO for plasma SELE and ACE levels, FUT2 for CA19-9 and CEA plasma levels and APOE for ApoE and CRP levels. We also found multiple independent signals in loci associated with plasma levels of ApoH, CA19-9, FetuinA, IL6r and LPa. Our study highlights the power of biological traits for genetic studies to identify genetic variants influencing clinically relevant traits, potential pleiotropic effects and complex disease associations in the same locus.
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Affiliation(s)
- Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Jian Xia
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yefei Cai
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Jenny Lord
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Human Genetics Programme, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - ShengMei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Benjamin Saef
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Sarah Bertelsen
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
| | - Matthew Bailey
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - David Holtzman
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Kelly Bales
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Eve H. Pickering
- Neuroscience Research Unit, Worldwide Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Laura Heitsch
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - John Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Alison Goate
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, 4488 Forest Park Ave., St Louis, MO 63108, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders. Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO 63110, USA
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Del-Aguila JL, Fernández MV, Jimenez J, Black K, Ma S, Deming Y, Carrell D, Saef B, Howells B, Budde J, Cruchaga C. Role of ABCA7 loss-of-function variant in Alzheimer's disease: a replication study in European-Americans. Alzheimers Res Ther 2015; 7:73. [PMID: 26654793 PMCID: PMC4675010 DOI: 10.1186/s13195-015-0154-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/12/2015] [Indexed: 11/10/2022]
Abstract
INTRODUCTION A recent study found a significant increase of ABCA7 loss-of-function variants in Alzheimer's disease (AD) cases compared to controls. Some variants were located on noncoding regions, but it was demonstrated that they affect splicing. Here, we try to replicate the association between AD risk and ABCA7 loss-of-function variants at both the single-variant and gene level in a large and well-characterized European American dataset. METHODS We genotyped the GWAS common variant and four rare variants previously reported for ABCA7 in 3476 European-Americans. RESULTS We were not able to replicate the association at the single-variant level, likely due to a lower effect size on the European American population which led to limited statistical power. However, we did replicate the association at the gene level; we found a significant enrichment of ABCA7 loss-of-function variants in AD cases compared to controls (P = 0.0388; odds ratio =1.54). We also confirmed that the association of the loss-of-function variants is independent of the previously reported genome-wide association study signal. CONCLUSIONS Although the effect size for the association of ABCA7 loss-of-function variants with AD risk is lower in our study (odds ratio = 1.54) compared to the original report (odds ratio = 2.2), the replication of the findings of the original report provides a stronger foundation for future functional applications. The data indicate that different independent signals that modify risk for complex traits may exist on the same locus. Additionally, our results suggest that replication of rare-variant studies should be performed at the gene level rather than focusing on a single variant.
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Affiliation(s)
- Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Jessica Jimenez
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Kathleen Black
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Shengmei Ma
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Yuetiva Deming
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - David Carrell
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA
| | - Ben Saef
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | | | - Bill Howells
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA.,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO, 63110, USA. .,The Hope Center for Neurological Disorders, BJC Institute of Health, 425 S. Euclid Ave, St. Louis, MO, 63110, USA.
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Kapoor M, Wang JC, Wetherill L, Le N, Bertelsen S, Hinrichs AL, Budde J, Agrawal A, Almasy L, Bucholz K, Dick DM, Harari O, Xiaoling X, Hesselbrock V, Kramer J, Nurnberger JI, Rice J, Schuckit M, Tischfield J, Porjesz B, Edenberg HJ, Bierut L, Foroud T, Goate A. Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families. Drug Alcohol Depend 2014; 142:56-62. [PMID: 24962325 PMCID: PMC4127128 DOI: 10.1016/j.drugalcdep.2014.05.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/24/2014] [Accepted: 05/29/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND The age at onset of alcohol dependence (AD) is a critical moderator of genetic associations for alcohol dependence. The present study evaluated whether single nucleotide polymorphisms (SNPs) can influence the age at onset of AD in large high-risk families from the Collaborative Study on the Genetics of Alcoholism (COGA). METHODS Genomewide SNP genotyping was performed in 1788 regular drinkers from 118 large European American families densely affected with alcoholism. We used a genome-wide Cox proportional hazards regression model to test for association between age at onset of AD and SNPs. RESULTS This family-based analysis identified an intergenic SNP, rs2168784 on chromosome 3 that showed strong evidence of association (P=5×10(-9)) with age at onset of AD among regular drinkers. Carriers of the minor allele of rs2168784 had 1.5 times the hazard of AD onset as compared with those homozygous for the major allele. By the age of 20 years, nearly 30% of subjects homozygous for the minor allele were alcohol dependent while only 19% of those homozygous for the major allele were. We also identified intronic SNPs in the ADP-ribosylation factor like 15 (ARL15) gene on chromosome 5 (P=1.11×10(-8)) and the UTP20 small subunit (UTP20) gene on chromosome 12 (P=4.32×10(-8)) that were associated with age at onset of AD. CONCLUSIONS This extended family based genome-wide cox-proportional hazards analysis identified several loci that might be associated with age at onset of AD.
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Affiliation(s)
- Manav Kapoor
- Washington University School of Medicine, United States
| | | | | | - Nhung Le
- Washington University School of Medicine, United States
| | | | | | - John Budde
- Washington University School of Medicine, United States
| | | | - Laura Almasy
- Southwest Foundation for Biomedical Research, United States
| | | | | | - Oscar Harari
- Washington University School of Medicine, United States
| | - Xuei Xiaoling
- Indiana University School of Medicine, United States
| | | | - John Kramer
- University of Iowa Carver College of Medicine, United States
| | | | - John Rice
- Washington University School of Medicine, United States
| | | | | | | | | | - Laura Bierut
- Washington University School of Medicine, United States
| | | | - Alison Goate
- Washington University School of Medicine, United States.
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Haller G, Kapoor M, Budde J, Xuei X, Edenberg H, Nurnberger J, Kramer J, Brooks A, Tischfield J, Almasy L, Agrawal A, Bucholz K, Rice J, Saccone N, Bierut L, Goate A. Rare missense variants in CHRNB3 and CHRNA3 are associated with risk of alcohol and cocaine dependence. Hum Mol Genet 2013; 23:810-9. [PMID: 24057674 DOI: 10.1093/hmg/ddt463] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Previous findings have demonstrated that variants in nicotinic receptor genes are associated with nicotine, alcohol and cocaine dependence. Because of the substantial comorbidity, it has often been unclear whether a variant is associated with multiple substances or whether the association is actually with a single substance. To investigate the possible contribution of rare variants to the development of substance dependencies other than nicotine dependence, specifically alcohol and cocaine dependence, we undertook pooled sequencing of the coding regions and flanking sequence of CHRNA5, CHRNA3, CHRNB4, CHRNA6 and CHRNB3 in 287 African American and 1028 European American individuals from the Collaborative Study of the Genetics of Alcoholism (COGA). All members of families for whom any individual was sequenced (2504 African Americans and 7318 European Americans) were then genotyped for all variants identified by sequencing. For each gene, we then tested for association using FamSKAT. For European Americans, we find increased DSM-IV cocaine dependence symptoms (FamSKAT P = 2 × 10(-4)) and increased DSM-IV alcohol dependence symptoms (FamSKAT P = 5 × 10(-4)) among carriers of missense variants in CHRNB3. Additionally, one variant (rs149775276; H329Y) shows association with both cocaine dependence symptoms (P = 7.4 × 10(-5), β = 2.04) and alcohol dependence symptoms (P = 2.6 × 10(-4), β = 2.04). For African Americans, we find decreased cocaine dependence symptoms among carriers of missense variants in CHRNA3 (FamSKAT P = 0.005). Replication in an independent sample supports the role of rare variants in CHRNB3 and alcohol dependence (P = 0.006). These are the first results to implicate rare variants in CHRNB3 or CHRNA3 in risk for alcohol dependence or cocaine dependence.
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Zelinka L, McCann S, Budde J, Sethi S, Guidos M, Giles R, Walker GR. Characterization of the in vitro expressed autoimmune rippling muscle disease immunogenic domain of human titin encoded by TTN exons 248-249. Biochem Biophys Res Commun 2011; 411:501-505. [PMID: 21741357 DOI: 10.1016/j.bbrc.2011.06.139] [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] [Received: 06/15/2011] [Accepted: 06/20/2011] [Indexed: 05/31/2023]
Abstract
Autoimmune rippling muscle disease (ARMD) is an autoimmune neuromuscular disease associated with myasthenia gravis (MG). Past studies in our laboratory recognized a very high molecular weight skeletal muscle protein antigen identified by ARMD patient antisera as the titin isoform. These past studies used antisera from ARMD and MG patients as probes to screen a human skeletal muscle cDNA library and several pBluescript clones revealed supporting expression of immunoreactive peptides. This study characterizes the products of subcloning the titin immunoreactive domain into pGEX-3X and the subsequent fusion protein. Sequence analysis of the fusion gene indicates the cloned titin domain (GenBank ID: EU428784) is in frame and is derived from a sequence of N2-A spanning the exons 248-250 an area that encodes the fibronectin III domain. PCR and EcoR1 restriction mapping studies have demonstrated that the inserted cDNA is of a size that is predicted by bioinformatics analysis of the subclone. Expression of the fusion protein result in the isolation of a polypeptide of 52 kDa consistent with the predicted inferred amino acid sequence. Immunoblot experiments of the fusion protein, using rippling muscle/myasthenia gravis antisera, demonstrate that only the titin domain is immunoreactive.
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Affiliation(s)
- L Zelinka
- Biomedical Sciences Program, Kent State University, Kent, OH, United States
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Dick DM, Meyers JL, Latendresse SJ, Creemers HE, Lansford JE, Pettit GS, Bates JE, Dodge KA, Budde J, Goate A, Buitelaar JK, Ormel J, Verhulst FC, Huizink AC. CHRM2, parental monitoring, and adolescent externalizing behavior: evidence for gene-environment interaction. Psychol Sci 2011; 22:481-9. [PMID: 21441226 DOI: 10.1177/0956797611403318] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Psychologists, with their long-standing tradition of studying mechanistic processes, can make important contributions to further characterizing the risk associated with genes identified as influencing risk for psychiatric disorders. We report one such effort with respect to CHRM2, which codes for the cholinergic muscarinic 2 receptor and was of interest originally for its association with alcohol dependence. We tested for association between CHRM2 and prospectively measured externalizing behavior in a longitudinal, community-based sample of adolescents, as well as for moderation of this association by parental monitoring. We found evidence for an interaction in which the association between the genotype and externalizing behavior was stronger in environments with lower parental monitoring. There was also suggestion of a crossover effect, in which the genotype associated with the highest levels of externalizing behavior under low parental monitoring had the lowest levels of externalizing behavior at the extreme high end of parental monitoring. The difficulties involved in distinguishing mechanisms of gene-environment interaction are discussed.
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Affiliation(s)
- Danielle M Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298-0126, USA.
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Saccone NL, Wang JC, Breslau N, Johnson EO, Hatsukami D, Saccone SF, Grucza RA, Sun L, Duan W, Budde J, Culverhouse RC, Fox L, Hinrichs AL, Steinbach JH, Wu M, Rice JP, Goate AM, Bierut LJ. The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans. Cancer Res 2009; 69:6848-56. [PMID: 19706762 DOI: 10.1158/0008-5472.can-09-0786] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genetic association studies have shown the importance of variants in the CHRNA5-CHRNA3-CHRNB4 cholinergic nicotinic receptor subunit gene cluster on chromosome 15q24-25.1 for the risk of nicotine dependence, smoking, and lung cancer in populations of European descent. We have carried out a detailed study of this region using dense genotyping in both European-Americans and African-Americans. We genotyped 75 known single nucleotide polymorphisms (SNPs) and one sequencing-discovered SNP in an African-American sample (N = 710) and in a European-American sample (N = 2,062). Cases were nicotine-dependent and controls were nondependent smokers. The nonsynonymous CHRNA5 SNP rs16969968 is the most significant SNP associated with nicotine dependence in the full sample of 2,772 subjects [P = 4.49 x 10(-8); odds ratio (OR), 1.42; 95% confidence interval (CI), 1.25-1.61] as well as in African-Americans only (P = 0.015; OR, 2.04; 1.15-3.62) and in European-Americans only (P = 4.14 x 10(-7); OR, 1.40; 1.23-1.59). Other SNPs that have been shown to affect the mRNA levels of CHRNA5 in European-Americans are associated with nicotine dependence in African-Americans but not in European-Americans. The CHRNA3 SNP rs578776, which has a low correlation with rs16969968, is associated with nicotine dependence in European-Americans but not in African-Americans. Less common SNPs (frequency <or= 5%) are also associated with nicotine dependence. In summary, multiple variants in this gene cluster contribute to nicotine dependence risk, and some are also associated with functional effects on CHRNA5. The nonsynonymous SNP rs16969968, a known risk variant in populations of European-descent, is also significantly associated with risk in African-Americans. Additional SNPs contribute to risk in distinct ways in these two populations.
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Affiliation(s)
- Nancy L Saccone
- Department of Genetics, Washington University, St. Louis, Missouri 63110, UA.
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Bierut LJ, Stitzel JA, Wang JC, Hinrichs AL, Grucza RA, Xuei X, Saccone NL, Saccone SF, Bertelsen S, Fox L, Horton WJ, Morgan SD, Breslau N, Budde J, Cloninger CR, Dick DM, Foroud T, Hatsukami D, Hesselbrock V, Johnson EO, Kramer J, Kuperman S, Madden PAF, Mayo K, Nurnberger J, Pomerleau O, Porjesz B, Reyes O, Schuckit M, Swan G, Tischfield JA, Edenberg HJ, Rice JP, Goate AM. Variants in nicotinic receptors and risk for nicotine dependence. Am J Psychiatry 2008; 165:1163-71. [PMID: 18519524 PMCID: PMC2574742 DOI: 10.1176/appi.ajp.2008.07111711] [Citation(s) in RCA: 471] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE A recent study provisionally identified numerous genetic variants as risk factors for the transition from smoking to the development of nicotine dependence, including an amino acid change in the alpha5 nicotinic cholinergic receptor (CHRNA5). The purpose of this study was to replicate these findings in an independent data set and more thoroughly investigate the role of genetic variation in the cluster of physically linked nicotinic receptors, CHRNA5-CHRNA3-CHRNB4, and the risk of smoking. METHOD Individuals from 219 European American families (N=2,284) were genotyped across this gene cluster to test the genetic association with smoking. The frequency of the amino acid variant (rs16969968) was studied in 995 individuals from diverse ethnic populations. In vitro studies were performed to directly test whether the amino acid variant in the CHRNA5 influences receptor function. RESULTS A genetic variant marking an amino acid change showed association with the smoking phenotype (p=0.007). This variant is within a highly conserved region across nonhuman species, but its frequency varied across human populations (0% in African populations to 37% in European populations). Furthermore, functional studies demonstrated that the risk allele decreased response to a nicotine agonist. A second independent finding was seen at rs578776 (p=0.003), and the functional significance of this association remains unknown. CONCLUSIONS This study confirms that at least two independent variants in this nicotinic receptor gene cluster contribute to the development of habitual smoking in some populations, and it underscores the importance of multiple genetic variants contributing to the development of common diseases in various populations.
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Affiliation(s)
- Laura Jean Bierut
- Department of Psychiatry, Washington University School of Medicine, Box 8134, 660 South Euclid Ave., St. Louis, MO 63110, USA.
| | | | - Jen C. Wang
- Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | - Sarah Bertelsen
- Washington University School of Medicine, St. Louis, MO, USA
| | - Louis Fox
- Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | - John Budde
- Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Tatiana Foroud
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | | - Eric O. Johnson
- Research Triangle Institute International, Research Triangle Park, NC, USA
| | | | | | | | - Kevin Mayo
- Washington University School of Medicine, St. Louis, MO, USA
| | - John Nurnberger
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Bernice Porjesz
- State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Oliver Reyes
- Washington University School of Medicine, St. Louis, MO, USA
| | - Marc Schuckit
- University of California-San Diego, San Diego, CA, USA
| | - Gary Swan
- SRI International, Menlo Park, CA, USA
| | | | | | - John P. Rice
- Washington University School of Medicine, St. Louis, MO, USA
| | - Alison M. Goate
- Washington University School of Medicine, St. Louis, MO, USA
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Dick DM, Aliev F, Wang JC, Saccone S, Hinrichs A, Bertelsen S, Budde J, Saccone N, Foroud T, Nurnberger J, Xuei X, Conneally PM, Schuckit M, Almasy L, Crowe R, Kuperman S, Kramer J, Tischfield JA, Hesselbrock V, Edenberg HJ, Porjesz B, Rice JP, Bierut L, Goate A. A Systematic single nucleotide polymorphism screen to fine-map alcohol dependence genes on chromosome 7 identifies association with a novel susceptibility gene ACN9. Biol Psychiatry 2008; 63:1047-53. [PMID: 18163977 PMCID: PMC3823371 DOI: 10.1016/j.biopsych.2007.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 11/06/2007] [Accepted: 11/07/2007] [Indexed: 10/22/2022]
Abstract
BACKGROUND Chromosome 7 has shown consistent evidence of linkage with a variety of phenotypes related to alcohol dependence in the Collaborative Study on the Genetics of Alcoholism (COGA) project. With a sample of 262 densely affected families, a peak logarithm of odds (LOD) score for alcohol dependence of 2.9 was observed at D7S1799. The LOD score in the region increased to 4.1 when a subset of the sample was genotyped with the Illumina Linkage III panel for the Genetic Analysis Workshop 14 (GAW14). To follow up on this linkage region, we systematically screened single nucleotide polymorphisms (SNPs) across a 2 LOD support interval surrounding the alcohol dependence peak. METHODS The SNPs were selected from the HapMap Phase I CEPH data to tag linkage disequilibrium bins across the region. Across the 18-Mb region, genotyped by the Center for Inherited Disease Research (CIDR), 1340 SNPs were analyzed. Family-based association analyses were performed on a sample of 1172 individuals from 217 Caucasian families. RESULTS Eight SNPs showed association with alcohol dependence at p < .01. Four of the eight most significant SNPs were located in or very near the ACN9 gene. We conducted additional genotyping across ACN9 and identified multiple variants with significant evidence of association with alcohol dependence. CONCLUSIONS These analyses suggest that ACN9 is involved in the predisposition to alcohol dependence. Data from yeast suggest that ACN9 is involved in gluconeogenesis and the assimilation of ethanol or acetate into carbohydrate.
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Affiliation(s)
- Danielle M Dick
- Washington University in St. Louis, St. Louis, Missouri, USA.
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Mukherjee O, Pastor P, Cairns NJ, Chakraverty S, Kauwe JSK, Shears S, Behrens MI, Budde J, Hinrichs AL, Norton J, Levitch D, Taylor-Reinwald L, Gitcho M, Tu PH, Tenenholz Grinberg L, Liscic RM, Armendariz J, Morris JC, Goate AM. HDDD2 is a familial frontotemporal lobar degeneration with ubiquitin-positive, tau-negative inclusions caused by a missense mutation in the signal peptide of progranulin. Ann Neurol 2006; 60:314-22. [PMID: 16983685 PMCID: PMC2803024 DOI: 10.1002/ana.20963] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [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] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Familial autosomal dominant frontotemporal dementia with ubiquitin-positive, tau-negative inclusions in the brain linked to 17q21-22 recently has been reported to carry null mutations in the progranulin gene (PGRN). Hereditary dysphasic disinhibition dementia (HDDD) is a frontotemporal dementia with prominent changes in behavior and language deficits. A previous study found significant linkage to chromosome 17 in a HDDD family (HDDD2), but no mutation in the MAPT gene. Longitudinal follow-up has enabled us to identify new cases and to further characterize the dementia in this family. The goals of this study were to develop research criteria to classify the different clinical expressions of dementia observed in this large kindred, to identify the causal mutation in affected individuals and correlate this with phenotypic characteristics in this pedigree, and to assess the neuropathological characteristics using immunohistochemical techniques. METHODS In this study we describe a detailed clinical, pathological and mutation analysis of the HDDD2 kindred. RESULTS Neuropathologically, HDDD2 represents a familial frontotemporal lobar degeneration with ubiquitin-positive, tau-negative inclusions (FTLD-U). We developed research classification criteria and identified three distinct diagnostic thresholds, which helped localize the disease locus. The chromosomal region with the strongest evidence of linkage lies within the minimum critical region for FTLD-U. Sequencing of each exon of the PGRN gene led to the identification of a novel missense mutation, Ala-9 Asp, within the signal peptide. INTERPRETATION HDDD2 is an FTLD-U caused by a missense mutation in the PGRN gene that cosegregates with the disease and with the disease haplotype in at-risk individuals. This mutation is the first reported pathogenic missense mutation in the signal peptide of the PGRN gene causing FTLD-U. In light of the previous reports of null mutations and its position in the gene, two possible pathological mechanisms are proposed: (1) the protein may accumulate within the endoplasmic reticulum due to inefficient secretion; and (2) mutant RNA may have a lower expression because of degradation via nonsense-mediated decay.
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Affiliation(s)
- Odity Mukherjee
- Washington University Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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Schram-Bijkerk D, Doekes G, Boeve M, Douwes J, Riedler J, Ublagger E, von Mutius E, Budde J, Pershagen G, van Hage M, Wickman M, Braun-Fahrländer C, Waser M, Brunekreef B. Nonlinear relations between house dust mite allergen levels and mite sensitization in farm and nonfarm children. Allergy 2006; 61:640-7. [PMID: 16629797 DOI: 10.1111/j.1398-9995.2006.01079.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [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: 11/29/2022]
Abstract
BACKGROUND Low sensitization rates to common allergens have been observed in farm children, which might be due to high exposure to microbial agents. It is not known how microbial agents modify the association between specific allergen exposure and sensitization. OBJECTIVE To examine the relations between house dust mite allergen exposure and mite sensitization in farm and nonfarm children and to assess the effects of microbial agents levels on this association. METHODS Major mite allergens of Dermatophagoides pteronyssinus (Der p 1) and Dermatophagoides farinae (Der f 1), endotoxin, beta(1,3)-glucans and fungal extracellular polysaccharides were measured in mattress dust of 402 children participating in a cross-sectional study in five European countries. Mite allergen (Der p 1 + Der f 1) levels were divided into tertiles with cut-offs 1.4 and 10.4 microg/g. Sensitization was assessed by measurement of allergen-specific immunoglobulin E against house dust mite. RESULTS Prevalence ratios of mite sensitization for medium and high when compared with low mite allergen levels were 3.1 [1.7-5.7] and 1.4 [0.7-2.8] respectively. Highest mite sensitization rates at intermediate exposure levels were consistently observed across country (except for Sweden) and in both farm and nonfarm children. The shape of the dose-response curve was similar for above and below median mattress microbial agent levels, but the 'sensitization peak' appeared to be lower for above median levels. CONCLUSIONS Our data suggest a bell-shaped dose-response relationship between mite allergen exposure and sensitization to mite allergens. In populations with high microbial agent levels and low sensitization rates, the curve is shifted down.
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Affiliation(s)
- D Schram-Bijkerk
- Institute for Risk Assessment Sciences, University of Utrecht, Utrecht, the Netherlands
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Alfvén T, Braun-Fahrländer C, Brunekreef B, von Mutius E, Riedler J, Scheynius A, van Hage M, Wickman M, Benz MR, Budde J, Michels KB, Schram D, Ublagger E, Waser M, Pershagen G. Allergic diseases and atopic sensitization in children related to farming and anthroposophic lifestyle--the PARSIFAL study. Allergy 2006; 61:414-21. [PMID: 16512802 DOI: 10.1111/j.1398-9995.2005.00939.x] [Citation(s) in RCA: 229] [Impact Index Per Article: 12.7] [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: 11/29/2022]
Abstract
BACKGROUND The prevalence of allergic diseases has increased rapidly in recent decades, particularly in children. For adequate prevention it is important not only to identify risk factors, but also possible protective factors. The aim of this study was to compare the prevalence of allergic diseases and sensitization between farm children, children in anthroposophic families, and reference children, with the aim to identify factors that may protect against allergic disease. METHODS The study was of cross-sectional design and included 14,893 children, aged 5-13 years, from farm families, anthroposophic families (recruited from Steiner schools) and reference children in Austria, Germany, The Netherlands, Sweden and Switzerland. A detailed questionnaire was completed and allergen-specific IgE was measured in blood. RESULTS Growing up on a farm was found to have a protective effect against all outcomes studied, both self-reported, such as rhinoconjunctivitis, wheezing, atopic eczema and asthma and sensitization (allergen specific IgE > or = 0.35 kU/l). The adjusted odds ratio (OR) for current rhinoconjunctivitis symptoms was 0.50 (95% confidence interval (CI) 0.38-0.65) and for atopic sensitization 0.53 (95% CI 0.42-0.67) for the farm children compared to their references. The prevalence of allergic symptoms and sensitization was also lower among Steiner school children compared to reference children, but the difference was less pronounced and not as consistent between countries, adjusted OR for current rhinoconjunctivitis symptoms was 0.69 (95% CI 0.56-0.86) and for atopic sensitization 0.73 (95% CI 0.58-0.92). CONCLUSIONS This study indicates that growing up on a farm, and to a lesser extent leading an anthroposophic life style may confer protection from both sensitization and allergic diseases in childhood.
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Affiliation(s)
- T Alfvén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Hinrichs AL, Wang JC, Bufe B, Kwon JM, Budde J, Allen R, Bertelsen S, Evans W, Dick D, Rice J, Foroud T, Nurnberger J, Tischfield JA, Kuperman S, Crowe R, Hesselbrock V, Schuckit M, Almasy L, Porjesz B, Edenberg HJ, Begleiter H, Meyerhof W, Bierut LJ, Goate AM. Functional variant in a bitter-taste receptor (hTAS2R16) influences risk of alcohol dependence. Am J Hum Genet 2006; 78:103-11. [PMID: 16385453 PMCID: PMC1380207 DOI: 10.1086/499253] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [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: 08/26/2005] [Accepted: 10/11/2005] [Indexed: 11/03/2022] Open
Abstract
A coding single-nucleotide polymorphism (cSNP), K172N, in hTAS2R16, a gene encoding a taste receptor for bitter beta -glucopyranosides, shows significant association with alcohol dependence (P = .00018). This gene is located on chromosome 7q in a region reported elsewhere to exhibit linkage with alcohol dependence. The SNP is located in the putative ligand-binding domain and is associated with an increased sensitivity to many bitter beta -glucopyranosides in the presence of the N172 allele. Individuals with the ancestral allele K172 are at increased risk of alcohol dependence, regardless of ethnicity. However, this risk allele is uncommon in European Americans (minor-allele frequency [MAF] 0.6%), whereas 45% of African Americans carry the allele (MAF 26%), which makes it a much more significant risk factor in the African American population.
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Affiliation(s)
- Anthony L. Hinrichs
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Jen C. Wang
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Bernd Bufe
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Jennifer M. Kwon
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - John Budde
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Rebecca Allen
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Sarah Bertelsen
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Whitney Evans
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Danielle Dick
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - John Rice
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Tatiana Foroud
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - John Nurnberger
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Jay A. Tischfield
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Samuel Kuperman
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Raymond Crowe
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Victor Hesselbrock
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Marc Schuckit
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Laura Almasy
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Bernice Porjesz
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Howard J. Edenberg
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Henri Begleiter
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Wolfgang Meyerhof
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Laura J. Bierut
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
| | - Alison M. Goate
- Washington University School of Medicine, St. Louis; German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda; Indiana University School of Medicine, Indianapolis; Rutgers University, Piscataway, NJ; University of Iowa School of Medicine, Iowa City; University of Connecticut School of Medicine, Farmington; University of California at San Diego School of Medicine, La Jolla; Southwest Foundation, San Antonio; and State University of New York Health Science Center at Brooklyn, Brooklyn
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Schram D, Doekes G, Boeve M, Douwes J, Riedler J, Ublagger E, von Mutius E, Budde J, Pershagen G, Nyberg F, Alm J, Braun-Fahrländer C, Waser M, Brunekreef B. Bacterial and fungal components in house dust of farm children, Rudolf Steiner school children and reference children--the PARSIFAL Study. Allergy 2005; 60:611-8. [PMID: 15813805 DOI: 10.1111/j.1398-9995.2005.00748.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [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: 11/28/2022]
Abstract
BACKGROUND Growing up on a farm and an anthroposophic lifestyle are associated with a lower prevalence of allergic diseases in childhood. It has been suggested that the enhanced exposure to endotoxin is an important protective factor of farm environments. Little is known about exposure to other microbial components on farms and exposure in anthroposophic families. OBJECTIVE To assess the levels and determinants of bacterial endotoxin, mould beta(1,3)-glucans and fungal extracellular polysaccharides (EPS) in house dust of farm children, Steiner school children and reference children. METHODS Mattress and living room dust was collected in the homes of 229 farm children, 122 Steiner children and 60 and 67 of their respective reference children in five European countries. Stable dust was collected as well. All samples were analysed in one central laboratory. Determinants were assessed by questionnaire. RESULTS Levels of endotoxin, EPS and glucans per gram of house dust in farm homes were 1.2- to 3.2-fold higher than levels in reference homes. For Steiner children, 1.1- to 1.6-fold higher levels were observed compared with their reference children. These differences were consistently found across countries, although mean levels varied considerably. Differences between groups and between countries were also significant after adjustment for home and family characteristics. CONCLUSION Farm children are not only consistently exposed to higher levels of endotoxin, but also to higher levels of mould components. Steiner school children may also be exposed to higher levels of microbial agents, but differences with reference children are much less pronounced than for farm children. Further analyses are, however, required to assess the association between exposure to these various microbial agents and allergic and airway diseases in the PARSIFAL population.
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Affiliation(s)
- D Schram
- Institute for Risk Assessment Sciences, University of Utrecht, Utrecht, The Netherlands
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Wang JC, Hinrichs AL, Stock H, Budde J, Allen R, Bertelsen S, Kwon JM, Wu W, Dick DM, Rice J, Jones K, Nurnberger JI, Tischfield J, Porjesz B, Edenberg HJ, Hesselbrock V, Crowe R, Schuckit M, Begleiter H, Reich T, Goate AM, Bierut LJ. Evidence of common and specific genetic effects: association of the muscarinic acetylcholine receptor M2 (CHRM2) gene with alcohol dependence and major depressive syndrome. Hum Mol Genet 2004; 13:1903-11. [PMID: 15229186 DOI: 10.1093/hmg/ddh194] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.4] [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] [Indexed: 11/13/2022] Open
Abstract
Several correlated phenotypes, alcohol dependence, major depressive syndrome, and an endophenotype of electrophysiological measurements, event-related oscillations (EROs), have demonstrated linkage on the long arm of chromosome 7. Recently, we reported both linkage and association between polymorphisms in the gene encoding the muscarinic acetylcholine receptor M2 (CHRM2) and EROs. In this study, we evaluated whether genetic variation in the CHRM2 gene is also a risk factor for the correlated clinical characteristics of alcoholism and depression. The CHRM2 gene contains a single coding exon and a large 5' untranslated region encoded by multiple exons that can be alternatively spliced. Families were recruited through an alcohol dependent proband, and multiplex pedigrees were selected for genetic analyses. We examined 11 single nucleotide polymorphisms (SNPs) spanning the CHRM2 gene in these families. Using the UNPHASED pedigree disequilibrium test (PDTPHASE), three SNPs (one in intron 4 and two in intron 5) showed highly significant association with alcoholism (P=0.004-0.007). Two SNPs (both in intron 4) were significantly associated with major depressive syndrome (P=0.004 and 0.017). Haplotype analyses revealed that the most common haplotype (>40% frequency), T-T-T (rs1824024-rs2061174-rs324650), was under-transmitted to affected individuals with alcohol dependence and major depressive syndrome. Different complementary haplotypes were over-transmitted in alcohol dependent and depressed individuals. These findings provide strong evidence that variants within or close to the CHRM2 locus influence risk for two common psychiatric disorders.
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Affiliation(s)
- Jen C Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA
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48
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Willig TN, Niemeyer CM, Leblanc T, Tiemann C, Robert A, Budde J, Lambiliotte A, Kohne E, Souillet G, Eber S, Stephan JL, Girot R, Bordigoni P, Cornu G, Blanche S, Guillard JM, Mohandas N, Tchernia G. Identification of new prognosis factors from the clinical and epidemiologic analysis of a registry of 229 Diamond-Blackfan anemia patients. DBA group of Société d'Hématologie et d'Immunologie Pédiatrique (SHIP), Gesellshaft für Pädiatrische Onkologie und Hämatologie (GPOH), and the European Society for Pediatric Hematology and Immunology (ESPHI). Pediatr Res 1999; 46:553-61. [PMID: 10541318 DOI: 10.1203/00006450-199911000-00011] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a constitutional disease characterized by a specific maturation defect in cells of erythroid lineage. We have assembled a registry of 229 DBA patients, which includes 151 patients from France, 70 from Germany, and eight from other countries. Presence of malformations was significantly and independently associated with familial history of DBA, short stature at presentation (before any steroid therapy), and absence of hypotrophy at birth. Two hundred twenty-two patients were available for long-term follow-up analysis (median, 111.5 mo). Of these individuals, 62.6% initially responded to steroid therapy. Initial steroid responsiveness was found significantly and independently associated with older age at presentation, familial history of DBA, and a normal platelet count at the time of diagnosis. Severe evolution of the disease (transfusion dependence or death) was significantly and independently associated with a younger age at presentation and with a history of premature birth. In contrast, patients with a familial history of the disease experienced a better outcome. Outcome analysis revealed the benefit of reassessing steroid responsiveness during the course of the disease for initially nonresponsive patients. Bone marrow transplantation was successful in 11/13 cases; HLA typing of probands and siblings should be performed early if patients are transfusion dependent, and cord blood should be preserved. Incidence of DBA (assessed for France over a 13-y period) is 7.3 cases per million live births without effect of seasonality on incidence of the disease or on malformative status. Similarly, no parental imprinting effect or anticipation phenomenon could be documented in families with dominant inheritance.
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Affiliation(s)
- T N Willig
- Département de Pédiatrie et Laboratoire d'Hématologie, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, Université Paris XI, France
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Bushnell S, Budde J, Catino T, Cole J, Derti A, Kelso R, Collins ML, Molino G, Sheridan P, Monahan J, Urdea M. ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays. Bioinformatics 1999; 15:348-55. [PMID: 10366654 DOI: 10.1093/bioinformatics/15.5.348] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [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: 11/13/2022] Open
Abstract
MOTIVATION The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay. RESULTS We present a software application which allows for rapid and flexible design of bDNA probesets for novel targets. It includes an algorithm for estimating the magnitude of NSH contribution to background, a mechanism for removing probes with elevated contributions, a methodology for the simultaneous design of probesets for multiple targets, and a graphical user interface which guides the user through the design steps. AVAILABILITY The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.
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Affiliation(s)
- S Bushnell
- Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA
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50
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Quilty MJ, Budde J. St. Vincent de Paul Senior Services: meeting the needs of Chicago's elderly. Continuum 1998; 18:17-9. [PMID: 10182855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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