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Brase L, You SF, D'Oliveira Albanus R, Del-Aguila JL, Dai Y, Novotny BC, Soriano-Tarraga C, Dykstra T, Fernandez MV, Budde JP, Bergmann K, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Goate AM, Farlow M, Sutherland GT, Kipnis J, Karch CM, Benitez BA, Harari O. Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers. Nat Commun 2023; 14:2314. [PMID: 37085492 PMCID: PMC10121712 DOI: 10.1038/s41467-023-37437-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 10/04/2022] [Accepted: 03/15/2023] [Indexed: 04/23/2023] Open
Abstract
Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell-specific effect of variants in these genes is not fully understood. Here, we perform single-nucleus RNA-sequencing (snRNA-seq) on nearly 300,000 nuclei from the parietal cortex of AD autosomal dominant (APP and PSEN1) and risk-modifying variant (APOE, TREM2 and MS4A) carriers. Within individual cell types, we capture genes commonly dysregulated across variant groups. However, specific transcriptional states are more prevalent within variant carriers. TREM2 oligodendrocytes show a dysregulated autophagy-lysosomal pathway, MS4A microglia have dysregulated complement cascade genes, and APOEε4 inhibitory neurons display signs of ferroptosis. All cell types have enriched states in autosomal dominant carriers. We leverage differential expression and single-nucleus ATAC-seq to map GWAS signals to effector cell types including the NCK2 signal to neurons in addition to the initially proposed microglia. Overall, our results provide insights into the transcriptional diversity resulting from AD genetic architecture and cellular heterogeneity. The data can be explored on the online browser ( http://web.hararilab.org/SNARE/ ).
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Affiliation(s)
- Logan Brase
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Shih-Feng You
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Ricardo D'Oliveira Albanus
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Yaoyi Dai
- Baylor College of Medicine, Houston, TX, USA
| | - Brenna C Novotny
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Carolina Soriano-Tarraga
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Taitea Dykstra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John C Morris
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Randall J Bateman
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Richard J Perrin
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Eric McDade
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Chengjie Xiong
- Knight Alzheimer Disease Research Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Alison M Goate
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Greg T Sutherland
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jonathan Kipnis
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- NeuroGenomics and Informatics, Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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2
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Lananna BV, McKee CA, King MW, Del-Aguila JL, Dimitry JM, Farias FHG, Nadarajah CJ, Xiong DD, Guo C, Cammack AJ, Elias JA, Zhang J, Cruchaga C, Musiek ES. Chi3l1/YKL-40 is controlled by the astrocyte circadian clock and regulates neuroinflammation and Alzheimer's disease pathogenesis. Sci Transl Med 2021; 12:12/574/eaax3519. [PMID: 33328329 DOI: 10.1126/scitranslmed.aax3519] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/21/2020] [Accepted: 08/29/2020] [Indexed: 12/12/2022]
Abstract
Regulation of glial activation and neuroinflammation are critical factors in the pathogenesis of Alzheimer's disease (AD). YKL-40, a primarily astrocytic protein encoded by the gene Chi3l1, is a widely studied cerebrospinal fluid biomarker that increases with aging and early in AD. However, the function of Chi3l1/YKL-40 in AD is unknown. In a cohort of patients with AD, we observed that a variant in the human CHI3L1 gene, which results in decreased CSF YKL-40 expression, was associated with slower AD progression. At baseline, Chi3l1 deletion in mice had no effect on astrocyte activation while modestly promoting microglial activation. In a mouse APP/PS1 model of AD, Chi3l1 deletion decreased amyloid plaque burden and increased periplaque expression of the microglial lysosomal marker CD68, suggesting that Chi3l1 may suppress glial phagocytic activation and promote amyloid accumulation. Accordingly, Chi3l1 knockdown increased phagocytosis of zymosan particles and of β-amyloid peptide in both astrocytes and microglia in vitro. We further observed that expression of Chi3l1 is regulated by the circadian clock, as deletion of the core clock proteins BMAL1 or CLOCK/NPAS2 strongly suppresses basal Chi3l1 expression, whereas deletion of the negative clock regulators PER1/PER2 increased Chi3l1 expression. Basal Chi3l1 mRNA was nonrhythmic because of a long mRNA half-life in astrocytes. However, inflammatory induction of Chi3l1 was gated by the clock. Our findings reveal Chi3l1/YKL-40 as a modulator of glial phagocytic activation and AD pathogenesis in both mice and humans and suggest that the astrocyte circadian clock regulates inflammatory Chi3l1 induction.
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Affiliation(s)
- Brian V Lananna
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Celia A McKee
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Melvin W King
- Department of Neurology, 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
| | - Julie M Dimitry
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fabiana H G Farias
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Collin J Nadarajah
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David D Xiong
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chun Guo
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alexander J Cammack
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jack A Elias
- Division of Medicine and Biological Sciences, Brown University, Providence, RI 02903, USA
| | - Jinsong Zhang
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.,Knight Alzheimer's Disease Research Center and Hope Center for Neurological Disease, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Erik S Musiek
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Knight Alzheimer's Disease Research Center and Hope Center for Neurological Disease, Washington University School of Medicine, St. Louis, MO 63108, USA
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3
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Li Z, Farias FHG, Dube U, Del-Aguila JL, Mihindukulasuriya KA, Fernandez MV, Ibanez L, Budde JP, Wang F, Lake AM, Deming Y, Perez J, Yang C, Bahena JA, Qin W, Bradley JL, Davenport R, Bergmann K, Morris JC, Perrin RJ, Benitez BA, Dougherty JD, Harari O, Cruchaga C. The TMEM106B FTLD-protective variant, rs1990621, is also associated with increased neuronal proportion. Acta Neuropathol 2020; 139:45-61. [PMID: 31456032 PMCID: PMC6942643 DOI: 10.1007/s00401-019-02066-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 05/17/2019] [Revised: 08/03/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022]
Abstract
Apart from amyloid β deposition and tau neurofibrillary tangles, Alzheimer's disease (AD) is a neurodegenerative disorder characterized by neuronal loss and astrocytosis in the cerebral cortex. The goal of this study is to investigate genetic factors associated with the neuronal proportion in health and disease. To identify cell-autonomous genetic variants associated with neuronal proportion in cortical tissues, we inferred cellular population structure from bulk RNA-Seq derived from 1536 individuals. We identified the variant rs1990621 located in the TMEM106B gene region as significantly associated with neuronal proportion (p value = 6.40 × 10-07) and replicated this finding in an independent dataset (p value = 7.41 × 10-04) surpassing the genome-wide threshold in the meta-analysis (p value = 9.42 × 10-09). This variant is in high LD with the TMEM106B non-synonymous variant p.T185S (rs3173615; r2 = 0.98) which was previously identified as a protective variant for frontotemporal lobar degeneration (FTLD). We stratified the samples by disease status, and discovered that this variant modulates neuronal proportion not only in AD cases, but also several neurodegenerative diseases and in elderly cognitively healthy controls. Furthermore, we did not find a significant association in younger controls or schizophrenia patients, suggesting that this variant might increase neuronal survival or confer resilience to the neurodegenerative process. The single variant and gene-based analyses also identified an overall genetic association between neuronal proportion, AD and FTLD risk. These results suggest that common pathways are implicated in these neurodegenerative diseases, that implicate neuronal survival. In summary, we identified a protective variant in the TMEM106B gene that may have a neuronal protection effect against general aging, independent of disease status, which could help elucidate the relationship between aging and neuronal survival in the presence or absence of neurodegenerative disorders. Our findings suggest that TMEM106B could be a potential target for neuronal protection therapies to ameliorate cognitive and functional deficits.
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Affiliation(s)
- Zeran Li
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Fabiana H G Farias
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Umber Dube
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, 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, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathie A Mihindukulasuriya
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, 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 Fernandez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Allison M Lake
- Vanderbilt University Medical Scientist Training Program, Nashville, TN, USA
| | - Yuetiva Deming
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - James Perez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengran Yang
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Jorge A Bahena
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Qin
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Joseph L Bradley
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard Davenport
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard J Perrin
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph D Dougherty
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
| | - Oscar Harari
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, BJC Institute of Heath, Washington University School of Medicine, 425 S. Euclid Ave., Box 8134, St. Louis, MO, 63110, USA.
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
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4
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Dube U, Del-Aguila JL, Li Z, Budde JP, Jiang S, Hsu S, Ibanez L, Fernandez MV, Farias F, Norton J, Gentsch J, Wang F, Salloway S, Masters CL, Lee JH, Graff-Radford NR, Chhatwal JP, Bateman RJ, Morris JC, Karch CM, Harari O, Cruchaga C. An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations. Nat Neurosci 2019; 22:1903-1912. [PMID: 31591557 PMCID: PMC6858549 DOI: 10.1038/s41593-019-0501-5] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 08/20/2019] [Indexed: 01/05/2023]
Abstract
We generated parietal cortex RNA-seq data from individuals with and without Alzheimer disease (AD; ncontrol = 13; nAD = 83) from the Knight-ADRC. Using this and an independent (MSBB) AD RNA-seq dataset, we quantified cortical circular RNA (circRNA) expression in the context of AD. We identified significant associations between circRNA expression and AD diagnosis, clinical dementia severity, and neuropathological severity. We demonstrated that a majority of circRNA AD-associations are independent from changes in cognate linear mRNA expression or brain cell-type proportions. We provided evidence for circRNA expression changes occurring early in pre-symptomatic AD, and in autosomal dominant AD. We also observed AD-associated circRNAs co-expressing with known AD genes. Finally, we identified potential microRNA binding sites in AD-associated circRNAs for microRNAs predicted to target AD genes. Together, these results highlight the importance of analyzing non-linear RNAs and support future studies exploring the potential roles of circRNAs in AD pathogenesis.
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Affiliation(s)
- Umber Dube
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA.,Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA.,Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Shan Jiang
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Simon Hsu
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Fabiana Farias
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | | | - Stephen Salloway
- Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, USA
| | - Colin L Masters
- The Florey Institute, the University of Melbourne. Level 1, Howard Florey Laboratories, Royal Parade, Parkville, VIC, Australia
| | - Jae-Hong Lee
- Department of Neurology, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Jasmeer P Chhatwal
- Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, 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, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, USA. .,Department of Neurology, Washington University School of Medicine, St Louis, MO, USA. .,Hope Center for Neurological Disorders. Washington University School of Medicine, St. Louis, MO, USA. .,NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, USA.
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5
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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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6
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Del-Aguila JL, Li Z, Dube U, Mihindukulasuriya KA, Budde JP, Fernandez MV, Ibanez L, Bradley J, Wang F, Bergmann K, Davenport R, Morris JC, Holtzman DM, Perrin RJ, Benitez BA, Dougherty J, Cruchaga C, Harari O. A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain. Alzheimers Res Ther 2019; 11:71. [PMID: 31399126 PMCID: PMC6689177 DOI: 10.1186/s13195-019-0524-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022]
Abstract
Background Alzheimer’s disease (AD) is the most common form of dementia. This neurodegenerative disorder is associated with neuronal death and gliosis heavily impacting the cerebral cortex. AD has a substantial but heterogeneous genetic component, presenting both Mendelian and complex genetic architectures. Using bulk RNA-seq from the parietal lobes and deconvolution methods, we previously reported that brains exhibiting different AD genetic architecture exhibit different cellular proportions. Here, we sought to directly investigate AD brain changes in cell proportion and gene expression using single-cell resolution. Methods We generated unsorted single-nuclei RNA sequencing data from brain tissue. We leveraged the tissue donated from a carrier of a Mendelian genetic mutation, PSEN1 p.A79V, and two family members who suffer from sporadic AD, but do not carry any autosomal mutations. We evaluated alternative alignment approaches to maximize the titer of reads, genes, and cells with high quality. In addition, we employed distinct clustering strategies to determine the best approach to identify cell clusters that reveal neuronal and glial cell types and avoid artifacts such as sample and batch effects. We propose an approach to cluster cells that reduces biases and enable further analyses. Results We identified distinct types of neurons, both excitatory and inhibitory, and glial cells, including astrocytes, oligodendrocytes, and microglia, among others. In particular, we identified a reduced proportion of excitatory neurons in the Mendelian mutation carrier, but a similar distribution of inhibitory neurons. Furthermore, we investigated whether single-nuclei RNA-seq from the human brains recapitulate the expression profile of disease-associated microglia (DAM) discovered in mouse models. We also determined that when analyzing human single-nuclei data, it is critical to control for biases introduced by donor-specific expression profiles. Conclusion We propose a collection of best practices to generate a highly detailed molecular cell atlas of highly informative frozen tissue stored in brain banks. Importantly, we have developed a new web application to make this unique single-nuclei molecular atlas publicly available. Electronic supplementary material The online version of this article (10.1186/s13195-019-0524-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge L Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Kathie A Mihindukulasuriya
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Joseph Bradley
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard Davenport
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John C Morris
- 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.,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - David M Holtzman
- 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.,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard J Perrin
- 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.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, USA.,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Joseph Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, 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. .,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, Campus Box 8134, 425 S. Euclid Ave, BJC Institute of Health, Office: 9607, St. Louis, MO, 63110, 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. .,NeuroGenomics and Informatics, Department of Psychiatry, Washington University, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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Wang Q, Del-Aguila JL, Cruchaga C, Reiman EM, Su Y. P1-400: IMPACT OF REFERENCE REGION USED TO QUANTIFY AMYLOID BURDEN ON INTERPRETING THE RELATIONSHIP BETWEEN AMYLOID BURDEN AND GENETIC RISK FACTORS OF AD. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.1005] [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: 12/01/2022]
Affiliation(s)
- Qi Wang
- Arizona State University; Tempe AZ USA
| | | | | | | | - Yi Su
- Banner Alzheimer's Institute; Phoenix AZ USA
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Fernandez V, Del-Aguila JL, Li Z, Dube U, Davenport R, Bradley J, Mihindukulasuriya KA, Farias FH, Budde JP, Norton J, Gentsch J, Morris JC, Harari O, Cruchaga C. P4-106: INTEGRATIVE ANALYSIS POINTS TO AGFG2
AS A NOVEL PLAYER IN THE PATHOLOGY OF ALZHEIMER DISEASE. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.3767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Victoria Fernandez
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Jorge L. Del-Aguila
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Zeran Li
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Umber Dube
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Richard Davenport
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Joseph Bradley
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Kathie A. Mihindukulasuriya
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Fabiana H.G. Farias
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - John P. Budde
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Joanne Norton
- Washington University School of Medicine; St. Louis MO USA
- Knight Alzheimer Disease Research Center; St. Louis MO USA
| | - Jen Gentsch
- Washington University School of Medicine; St. Louis MO USA
- Knight Alzheimer Disease Research Center; St. Louis MO USA
| | - John C. Morris
- Knight Alzheimer Disease Research Center; St. Louis MO USA
- Washington University School of Medicine; St. Louis MO USA
| | - Oscar Harari
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; St. Louis MO USA
| | - Carlos Cruchaga
- Washington University School of Medicine; St. Louis MO USA
- Hope Center for Neurological Disorders; Washington University School of Medicine; St. Louis MO USA
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Del-Aguila JL, Benitez BA, Li Z, Dube U, Mihindukulasuriya KA, Budde JP, Farias FHG, Fernández MV, Ibanez L, Jiang S, Perrin RJ, Cairns NJ, Morris JC, Harari O, Cruchaga C. TREM2 brain transcript-specific studies in AD and TREM2 mutation carriers. Mol Neurodegener 2019; 14:18. [PMID: 31068200 PMCID: PMC6505298 DOI: 10.1186/s13024-019-0319-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Low frequency coding variants in TREM2 are associated with Alzheimer disease (AD) risk and cerebrospinal fluid (CSF) TREM2 protein levels are different between AD cases and controls. Similarly, TREM2 risk variant carriers also exhibit differential CSF TREM2 levels. TREM2 has three different alternative transcripts, but most of the functional studies only model the longest transcript. No studies have analyzed TREM2 expression levels or alternative splicing in brains from AD and cognitively normal individuals. We wanted to determine whether there was differential expression of TREM2 in sporadic-AD cases versus AD-TREM2 carriers vs sex- and aged-matched normal controls; and if this differential expression was due to a particular TREM2 transcript. METHODS We analyzed RNA-Seq data from parietal lobe brain tissue from AD cases with TREM2 variants (n = 33), AD cases (n = 195) and healthy controls (n = 118), from three independent datasets using Kallisto and the R package tximport to determine the read count for each transcript and quantified transcript abundance as transcripts per million. RESULTS The three TREM2 transcripts were expressed in brain cortex in the three datasets. We demonstrate for the first time that the transcript that lacks the transmembrane domain and encodes a soluble form of TREM2 (sTREM2) has an expression level around 60% of the canonical transcript, suggesting that around 25% of the sTREM2 protein levels could be explained by this transcript. We did not observe a difference in the overall TREM2 expression level between cases and controls. However, the isoform which lacks the 5' exon, but includes the transmembrane domain, was significantly lower in TREM2- p.R62H carriers than in AD cases (p = 0.007). CONCLUSION Using bulk RNA-Seq data from three different cohorts, we were able to quantify the expression level of the three TREM2 transcripts, demonstrating: (1) all three transcripts of them are highly expressed in the human cortex, (2) that up to 25% of the sTREM2 may be due to the expression of a specific isoform and not TREM2 cleavage; and (3) that TREM2 risk variants do not affect expression levels, suggesting that the effect of the TREM2 variants on CSF levels occurs at post-transcriptional level.
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Affiliation(s)
- Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Bruno A. Benitez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Zeran Li
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Umber Dube
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Kathie A. Mihindukulasuriya
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - John P. Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Fabiana H. G. Farias
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, 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
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
| | - Shan Jiang
- 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
| | - Richard J. Perrin
- 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
- Department of Neurology, Washington University School of Medicine, St. Louis, MO USA
| | - Nigel J. Cairns
- 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
- Department of Neurology, Washington University School of Medicine, St. Louis, MO USA
- Department of Pathology and Immunology, 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
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, 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
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics, 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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10
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Fernandez MV, Budde JP, Del-Aguila JL, Ibanez L, Deming Y, Harari O, Li Z, Dube U, Norton J, Morris JC, Goate AM, Cruchaga C. P2‐105: NOMINATION OF NOVEL CANDIDATE GENES FOR FAMILIAL LATE ONSET ALZHEIMER DISEASE AFTER EVALUATION OF GENE‐BASED FAMILY‐BASED METHODS. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.791] [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: 11/16/2022]
Affiliation(s)
- Maria Victoria Fernandez
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - John P. Budde
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Jorge L. Del-Aguila
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Laura Ibanez
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Yuetiva Deming
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Oscar Harari
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Zeran Li
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Umber Dube
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
| | - Joanne Norton
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
- Knight Alzheimer's Disease Research CenterSaint LouisMOUSA
| | - John C. Morris
- Washington University School of MedicineSaint LouisMOUSA
- Knight Alzheimer's Disease Research CenterSaint LouisMOUSA
| | | | - Carlos Cruchaga
- Washington University School of MedicineSaint LouisMOUSA
- Hope Center for Neurological DisordersSaint LouisMOUSA
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11
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Del-Aguila JL, Li Z, Dube U, Budde JP, Morris JC, Harari O, Cruchaga C. P1‐173: BRAIN TRANSCRIPTOMICS STUDY REVEALS DIFFERENTIAL EXPRESSION OF THE THREE
TREM2
TRANSCRIPT IN AD AND
TREM2
MUTATION CARRIERS. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.177] [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)
| | - Zeran Li
- Hope Center for Neurological DisordersSt. LouisMOUSA
| | - Umber Dube
- Hope Center for Neurological DisordersSt. LouisMOUSA
| | - John P. Budde
- Hope Center for Neurological DisordersSt. LouisMOUSA
| | | | - Oscar Harari
- Hope Center for Neurological DisordersSt. LouisMOUSA
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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Shi Y, Yamada K, Liddelow SA, Smith ST, Zhao L, Luo W, Tsai RM, Spina S, Grinberg LT, Rojas JC, Gallardo G, Wang K, Roh J, Robinson G, Finn MB, Jiang H, Sullivan PM, Baufeld C, Wood MW, Sutphen C, McCue L, Xiong C, Del-Aguila JL, Morris JC, Cruchaga C, Fagan AM, Miller BL, Boxer AL, Seeley WW, Butovsky O, Barres BA, Paul SM, Holtzman DM. ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy. Nature 2017; 549:523-527. [PMID: 28959956 PMCID: PMC5641217 DOI: 10.1038/nature24016] [Citation(s) in RCA: 746] [Impact Index Per Article: 106.6] [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: 11/25/2016] [Accepted: 08/17/2017] [Indexed: 12/21/2022]
Abstract
APOE4 is the strongest genetic risk factor for late-onset Alzheimer disease. ApoE4 increases brain amyloid-β pathology relative to other ApoE isoforms. However, whether APOE independently influences tau pathology, the other major proteinopathy of Alzheimer disease and other tauopathies, or tau-mediated neurodegeneration, is not clear. By generating P301S tau transgenic mice on either a human ApoE knock-in (KI) or ApoE knockout (KO) background, here we show that P301S/E4 mice have significantly higher tau levels in the brain and a greater extent of somatodendritic tau redistribution by three months of age compared with P301S/E2, P301S/E3, and P301S/EKO mice. By nine months of age, P301S mice with different ApoE genotypes display distinct phosphorylated tau protein (p-tau) staining patterns. P301S/E4 mice develop markedly more brain atrophy and neuroinflammation than P301S/E2 and P301S/E3 mice, whereas P301S/EKO mice are largely protected from these changes. In vitro, E4-expressing microglia exhibit higher innate immune reactivity after lipopolysaccharide treatment. Co-culturing P301S tau-expressing neurons with E4-expressing mixed glia results in a significantly higher level of tumour-necrosis factor-α (TNF-α) secretion and markedly reduced neuronal viability compared with neuron/E2 and neuron/E3 co-cultures. Neurons co-cultured with EKO glia showed the greatest viability with the lowest level of secreted TNF-α. Treatment of P301S neurons with recombinant ApoE (E2, E3, E4) also leads to some neuronal damage and death compared with the absence of ApoE, with ApoE4 exacerbating the effect. In individuals with a sporadic primary tauopathy, the presence of an ε4 allele is associated with more severe regional neurodegeneration. In individuals who are positive for amyloid-β pathology with symptomatic Alzheimer disease who usually have tau pathology, ε4-carriers demonstrate greater rates of disease progression. Our results demonstrate that ApoE affects tau pathogenesis, neuroinflammation, and tau-mediated neurodegeneration independently of amyloid-β pathology. ApoE4 exerts a 'toxic' gain of function whereas the absence of ApoE is protective.
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Affiliation(s)
- Yang Shi
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Kaoru Yamada
- Department of Neuropathology, Graduate School of Medicine, The
University of Tokyo, Tokyo, Japan
| | - Shane Antony Liddelow
- Department of Neurobiology, School of Medicine, Stanford University,
Stanford, CA, USA
- Department of Pharmacology and Therapeutics, The University of
Melbourne, Melbourne, Australia
| | - Scott T Smith
- Brigham and Women’s Hospital, Harvard Medical School,
Boston, MA, USA
| | - Lingzhi Zhao
- Appel Alzheimer’s Disease Research Institute, Feil Family
Brain and Mind Research Institute, Weill Cornell Medical College of Cornell
University, New York, NY, USA
| | - Wenjie Luo
- Appel Alzheimer’s Disease Research Institute, Feil Family
Brain and Mind Research Institute, Weill Cornell Medical College of Cornell
University, New York, NY, USA
| | - Richard M. Tsai
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
| | - Salvatore Spina
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
| | - Lea T. Grinberg
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco,
CA, USA
| | - Julio C. Rojas
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
| | - Gilbert Gallardo
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Kairuo Wang
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Joseph Roh
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Grace Robinson
- Department of Ophthalmology, University of Missouri School of
Medicine, Columbia, Missouri, USA
| | - Mary Beth Finn
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Hong Jiang
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Patrick M Sullivan
- Department of Medicine, Duke University Medical Center, Durham
Veterans Health Administration Medical Center’s Geriatric Research,
Education and Clinical Center, Durham, NC, USA
| | - Caroline Baufeld
- Brigham and Women’s Hospital, Harvard Medical School,
Boston, MA, USA
| | | | - Courtney Sutphen
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Lena McCue
- Division of Biostatistics, Washington University in St Louis, St
Louis, Missouri, USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University in St Louis, St
Louis, Missouri, USA
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University School of Medicine,
660 S. Euclid Ave. B8134, St. Louis, MO, USA
| | - John C. Morris
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine,
660 S. Euclid Ave. B8134, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School
of Medicine, 660 S. Euclid Ave., St. Louis, MO, USA
| | | | - Anne M. Fagan
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
| | - Bruce L. Miller
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
| | - Adam L. Boxer
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
| | - William W. Seeley
- Memory and Aging Center, Department of Neurology, University of
California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco,
CA, USA
| | - Oleg Butovsky
- Brigham and Women’s Hospital, Harvard Medical School,
Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Brigham and
Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Ben A. Barres
- Department of Neurobiology, School of Medicine, Stanford University,
Stanford, CA, USA
| | - Steven M. Paul
- Appel Alzheimer’s Disease Research Institute, Feil Family
Brain and Mind Research Institute, Weill Cornell Medical College of Cornell
University, New York, NY, USA
- Voyager Therapeutics, Cambridge, MA, USA
| | - David M. Holtzman
- Department of Neurology, Hope Center for Neurological Disorders,
Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington
University School of Medicine, St. Louis, Missouri, USA
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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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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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25
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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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26
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Del-Aguila JL, Koboldt DC, Black K, Chasse R, Norton J, Wilson RK, Cruchaga C. Alzheimer's disease: rare variants with large effect sizes. Curr Opin Genet Dev 2015; 33:49-55. [PMID: 26311074 DOI: 10.1016/j.gde.2015.07.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/27/2022]
Abstract
Recent advances in sequencing technology and novel genotyping arrays (focused on low-frequency and coding variants) have made it possible to identify novel coding variants with large effect sizes and also novel genes (TREM2, PLD3, UNC5C, and AKAP9) associated with Alzheimer's disease (AD) risk. The major advantages of these studies over the classic genome-wide association studies (GWAS) include the identification of the functional variant and the gene-driven association. In addition to the large effect size, these studies make it possible to model these variants and genes using cell and animal systems. On the other hand, the underlying population-variability of these very low allele frequency variants poses a great challenge to replicating results. Studies that include very large datasets (>10,000 cases and controls) and combine sequencing and genotyping approaches will lead to the identification of novel genes for Alzheimer's disease.
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Affiliation(s)
- Jorge L Del-Aguila
- 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
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Kathleen Black
- 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
| | - Rachel Chasse
- 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
| | - Joanne Norton
- 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
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, 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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27
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Del-Aguila JL, Cooper-DeHoff RM, Chapman AB, Gums JG, Beitelshees AL, Bailey K, Turner ST, Johnson JA, Boerwinkle E. Transethnic meta-analysis suggests genetic variation in the HEME pathway influences potassium response in patients treated with hydrochlorothiazide. Pharmacogenomics J 2014; 15:153-7. [PMID: 25201287 DOI: 10.1038/tpj.2014.46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 01/22/2023]
Abstract
Hypokalemia is a recognized adverse effect of thiazide diuretic treatment. This phenomenon, which may impair insulin secretion, has been suggested to be a reason for the adverse effects on glucose metabolism associated with thiazide diuretic treatment of hypertension. However, the mechanisms underlying thiazide diuretic-induced hypokalemia are not well understood. In an effort to identify genes or genomic regions associated with potassium response to hydrochlorothiazide, without a priori knowledge of biologic effects, we performed a genome-wide association study and a multiethnic meta-analysis in 718 European- and African-American hypertensive participants from two different pharmacogenetic studies. Single-nucleotide polymorphisms rs10845697 (Bayes factor=5.560) on chromosome 12, near to the HEME binding protein 1 gene, and rs11135740 (Bayes factor=5.258) on chromosome 8, near to the Mitoferrin-1 gene, reached genome-wide association study significance (Bayes factor >5). These results, if replicated, suggest a novel mechanism involving effects of genes in the HEME pathway influencing hydrochlorothiazide-induced renal potassium loss.
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Affiliation(s)
- J L Del-Aguila
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - R M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - A B Chapman
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - J G Gums
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - A L Beitelshees
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - K Bailey
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - S T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - J A Johnson
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - E Boerwinkle
- 1] Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA [2] Human Genome Sequencing Center at Baylor College of Medicine, Houston, TX, USA
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28
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Del-Aguila JL, Beitelshees AL, Cooper-Dehoff RM, Chapman AB, Gums JG, Bailey K, Gong Y, Turner ST, Johnson JA, Boerwinkle E. Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. Pharmacogenomics J 2013; 14:35-40. [PMID: 23400010 PMCID: PMC3812324 DOI: 10.1038/tpj.2013.3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/13/2012] [Accepted: 01/03/2013] [Indexed: 12/02/2022]
Abstract
Hydrochlorothiazide (HCTZ) is one of the most widely prescribed antihypertensive medications. Although it is well known that HCTZ is associated with hyperglycemia and hypertriglyceridemia, the mechanisms underlying these adverse effects are not well understood. We performed a genome-wide association study and meta-analysis of the change in fasting plasma glucose and triglycerides in response to HCTZ from two different clinical trials: the Pharmacogenomic Evaluation of Antihypertensive Responses and the Genetic Epidemiology of Responses to Antihypertensive studies. Two single-nucleotide polymorphisms (rs12279250 and rs4319515 (r2=0.73)), located at 11p15.1 in the NELL1 gene, achieved genome-wide significance for association with change in fasting plasma triglycerides in African Americans, whereby each variant allele was associated with a 28 mg dl−1 increase in the change in triglycerides. NELL1 encodes a cytoplasmic protein that contains epidermal growth factor-like repeats and has been shown to represses adipogenic differentiation. These findings may represent a novel mechanism underlying HCTZ-induced adverse metabolic effects.
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Affiliation(s)
- J L Del-Aguila
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - A L Beitelshees
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland, Baltimore, MD, USA
| | - R M Cooper-Dehoff
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - A B Chapman
- Renal Division, Emory University School of Medicine, Atlanta, GA, USA
| | - J G Gums
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - K Bailey
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Y Gong
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - S T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - J A Johnson
- Department of Pharmacotherapy and Translational Research and Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, FL, USA
| | - E Boerwinkle
- 1] Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA [2] Human Genome Sequencing Center at Baylor College of Medicine, Houston, TX, USA
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