101
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Urnikyte A, Molyte A, Kučinskas V. Genome-Wide Landscape of North-Eastern European Populations: A View from Lithuania. Genes (Basel) 2021; 12:genes12111730. [PMID: 34828336 PMCID: PMC8623362 DOI: 10.3390/genes12111730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 01/15/2023] Open
Abstract
There are still several unanswered questions regarding about ancient events in the Lithuanian population. The Lithuanians, as the subject of this study, are of great interest as they represent a partially isolated population maintaining an ancient genetic composition and show genetic uniqueness in European comparisons. To elucidate the genetic relationships between the Lithuania and North-Eastern European and West Siberian populations, we analyzed the population structure, effective population size, and recent positive selection from genome-wide single nucleotide polymorphism (SNP) data. We identified the close genetic proximity of Lithuanians to neighboring populations (Latvians, Estonians, Belarusians) and in part with West and South Slavs (Poles, Slovaks, and Slovenians), however, with particular genetic distinctiveness. The estimated long-term Ne values ranged from ~5900 in the Estonian population to ~2400 in the South Russian population. The divergence times between the Lithuanian and study populations ranged from 240 to 12,871 YBP. We also found evidence of selection in 24 regions, 21 of which have not been discovered in previous analyses of selection. Undoubtedly, the genetic diversity analysis of geographically specific regions may provide new insights into microevolutionary processes affecting local human populations.
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Affiliation(s)
- Alina Urnikyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškiu St. 2, LT-08661 Vilnius, Lithuania; (A.M.); (V.K.)
- Correspondence: ; Tel.: +370-698-55292
| | - Alma Molyte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškiu St. 2, LT-08661 Vilnius, Lithuania; (A.M.); (V.K.)
- Department of Information Systems, Faculty of Fundamentals Sciences, Vilnius Gediminas Technical University, Saulėtekio Al. 11, LT-10223 Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškiu St. 2, LT-08661 Vilnius, Lithuania; (A.M.); (V.K.)
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102
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Phospholipase Cγ2 regulates endocannabinoid and eicosanoid networks in innate immune cells. Proc Natl Acad Sci U S A 2021; 118:2112971118. [PMID: 34607960 DOI: 10.1073/pnas.2112971118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Human genetic studies have pointed to a prominent role for innate immunity and lipid pathways in immunological and neurodegenerative disorders. Our understanding of the composition and function of immunomodulatory lipid networks in innate immune cells, however, remains incomplete. Here, we show that phospholipase Cγ2 (PLCγ2 or PLCG2)-mutations in which are associated with autoinflammatory disorders and Alzheimer's disease-serves as a principal source of diacylglycerol (DAG) pools that are converted into a cascade of bioactive endocannabinoid and eicosanoid lipids by DAG lipase (DAGL) and monoacylglycerol lipase (MGLL) enzymes in innate immune cells. We show that this lipid network is tonically stimulated by disease-relevant human mutations in PLCγ2, as well as Fc receptor activation in primary human and mouse macrophages. Genetic disruption of PLCγ2 in mouse microglia suppressed DAGL/MGLL-mediated endocannabinoid-eicosanoid cross-talk and also caused widespread transcriptional and proteomic changes, including the reorganization of immune-relevant lipid pathways reflected in reductions in DAGLB and elevations in PLA2G4A. Despite these changes, Plcg2 -/- mice showed generally normal proinflammatory cytokine and chemokine responses to lipopolysaccharide treatment, instead displaying a more restricted deficit in microglial activation that included impairments in prostaglandin production and CD68 expression. Our findings enhance the understanding of PLCγ2 function in innate immune cells, delineating a role in cross-talk with endocannabinoid/eicosanoid pathways and modulation of subsets of cellular responses to inflammatory stimuli.
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103
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Baloni P, Funk CC, Readhead B, Price ND. Systems modeling of metabolic dysregulation in neurodegenerative diseases. Curr Opin Pharmacol 2021; 60:59-65. [PMID: 34352486 PMCID: PMC8511060 DOI: 10.1016/j.coph.2021.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Neurodegenerative diseases (NDDs) encompass a wide range of conditions that arise owing to progressive degeneration and the ultimate loss of nerve cells in the brain and peripheral nervous system. NDDs such as Alzheimer's, Parkinson's, and Huntington's diseases negatively impact both length and quality of life, due to lack of effective disease-modifying treatments. Herein, we review the use of genome-scale metabolic models, network-based approaches, and integration with multiomics data to identify key biological processes that characterize NDDs. We describe powerful systems biology approaches for modeling NDD pathophysiology by leveraging in silico models that are informed by patient-derived multiomics data. These approaches can enable mechanistic insights into NDD-specific metabolic dysregulations that can be leveraged to identify potential metabolic markers of disease and predisease states.
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Affiliation(s)
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | - Ben Readhead
- Onegevity, a Division of Thorne HealthTech, New York, NY, USA; Arizona State University-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA; Onegevity, a Division of Thorne HealthTech, New York, NY, USA.
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104
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Han R, Yuan T, Yang Z, Zhang Q, Wang WW, Lin LB, Zhu MQ, Gao JM. Ulmoidol, an unusual nortriterpenoid from Eucommia ulmoides Oliv. Leaves prevents neuroinflammation by targeting the PU.1 transcriptional signaling pathway. Bioorg Chem 2021; 116:105345. [PMID: 34560559 DOI: 10.1016/j.bioorg.2021.105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/19/2022]
Abstract
Chronic neuroinflammation is closely associated with the development of neurodegenerative diseases, including Alzheimer's disease (AD). In the current study, 13 anti-neuroinflammatory compounds were isolated from Eucommia ulmoides Oliv. leaves. Among these compounds, trans-sinapaldehyde (6), 3',4',5,7-tetrahydroxy-3-methylflavone (7), and amarusine A (13) were isolated from E. ulmoides leaves for the first time. The ursane-type C29-triterpenoid, ulmoidol (ULM, 9), significantly inhibited the production of proinflammatory mediators and reduced the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, ULM inhibited the cluster of differentiation 14 (CD14)/Toll-like receptor 4 (TLR4) signaling pathway and consequently limited the activation of nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways. Notably, electrophoretic mobility shift assay (EMSA) and molecular docking analyses indicated that ULM could prevent PU box binding-1 (PU.1) from binding to DNA, suggesting that PU.1 might be a potential ULM target. In conclusion, ULM alleviates neuroinflammatory responses in microglia, which could be partly explained by its targeting of PU.1 and the resulting suppression of the TLR4/MAPK/NF-κB signaling pathways. These results suggested that ULM may have therapeutic potential as an agent for treating neuroinflammation-related neurodegenerative diseases.
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Affiliation(s)
- Rui Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Tian Yuan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Zhi Yang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Wei-Wei Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Li-Bin Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Ming-Qiang Zhu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China.
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China.
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105
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Salminen A, Kaarniranta K, Kauppinen A. Hypoxia/ischemia impairs CD33 (Siglec-3)/TREM2 signaling: Potential role in Alzheimer's pathogenesis. Neurochem Int 2021; 150:105186. [PMID: 34530055 DOI: 10.1016/j.neuint.2021.105186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/22/2022]
Abstract
Recent genetic and molecular studies have indicated that the innate immune system, especially microglia, have a crucial role in the accumulation of β-amyloid plaques in Alzheimer's disease (AD). In particular, the CD33 receptor, also called Siglec-3, inhibits the TREM2 receptor-induced phagocytic activity of microglia. CD33 receptors recognize the α2,3 and α2,6-linked sialic groups in tissue glycocalyx, especially sialylated gangliosides in human brain. The CD33 receptor triggers cell-type specific responses, e.g., in microglia, CD33 inhibits phagocytosis, whereas in natural killer cells, it inhibits the cytotoxic activity of the NKG2D receptor. Nonetheless, the regulation of the activity of CD33 receptor needs to be clarified. For example, it seems that hypoxia/ischemia, a potential cause of AD pathology, increases the expression of CD33 and its downstream target SHP-1, a tyrosine phosphatase which suppresses the phagocytosis driven by TREM2. Moreover, hypoxia/ischemia increases the deposition of sialylated gangliosides, e.g., GM1, GM2, GM3, and GD1, which are ligands for inhibitory CD33/Siglec-3 receptors. In addition, β-amyloid peptides bind to the sialylated gangliosides in raft-like clusters and subsequently these gangliosides act as seeds for the formation of β-amyloid plaques in AD pathology. It is known that senile plaques contain sialylated GM1, GM2, and GM3 gangliosides, i.e., the same species induced by hypoxia/ischemia treatment. Sialylated gangliosides in plaques might stimulate the CD33/Siglec-3 receptors of microglia and thus impede TREM2-driven phagocytosis. We propose that hypoxia/ischemia, e.g., via the accumulation of sialylated gangliosides, prevents the phagocytosis of β-amyloid deposits by inhibiting CD33/TREM2 signaling.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 100, FI-70029, KYS, Finland
| | - Anu Kauppinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
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106
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Zhang Y, Lu Q, Ye Y, Huang K, Liu W, Wu Y, Zhong X, Li B, Yu Z, Travers BG, Werling DM, Li JJ, Zhao H. SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits. Genome Biol 2021; 22:262. [PMID: 34493297 PMCID: PMC8422619 DOI: 10.1186/s13059-021-02478-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Local genetic correlation quantifies the genetic similarity of complex traits in specific genomic regions. However, accurate estimation of local genetic correlation remains challenging, due to linkage disequilibrium in local genomic regions and sample overlap across studies. We introduce SUPERGNOVA, a statistical framework to estimate local genetic correlations using summary statistics from genome-wide association studies. We demonstrate that SUPERGNOVA outperforms existing methods through simulations and analyses of 30 complex traits. In particular, we show that the positive yet paradoxical genetic correlation between autism spectrum disorder and cognitive performance could be explained by two etiologically distinct genetic signatures with bidirectional local genetic correlations.
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Affiliation(s)
- Yiliang Zhang
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yixuan Ye
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Kunling Huang
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Wei Liu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Yuchang Wu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xiaoyuan Zhong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Zhaolong Yu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA
| | - Brittany G Travers
- Occupational Therapy Program in the Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Donna M Werling
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - James J Li
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Psychology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06510, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
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107
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Yang C, Farias FHG, Ibanez L, Suhy A, Sadler B, Fernandez MV, Wang F, Bradley JL, Eiffert B, Bahena JA, Budde JP, Li Z, Dube U, Sung YJ, Mihindukulasuriya KA, Morris JC, Fagan AM, Perrin RJ, Benitez BA, Rhinn H, Harari O, Cruchaga C. Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders. Nat Neurosci 2021; 24:1302-1312. [PMID: 34239129 PMCID: PMC8521603 DOI: 10.1038/s41593-021-00886-6] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Understanding the tissue-specific genetic controls of protein levels is essential to uncover mechanisms of post-transcriptional gene regulation. In this study, we generated a genomic atlas of protein levels in three tissues relevant to neurological disorders (brain, cerebrospinal fluid and plasma) by profiling thousands of proteins from participants with and without Alzheimer's disease. We identified 274, 127 and 32 protein quantitative trait loci (pQTLs) for cerebrospinal fluid, plasma and brain, respectively. cis-pQTLs were more likely to be tissue shared, but trans-pQTLs tended to be tissue specific. Between 48.0% and 76.6% of pQTLs did not co-localize with expression, splicing, DNA methylation or histone acetylation QTLs. Using Mendelian randomization, we nominated proteins implicated in neurological diseases, including Alzheimer's disease, Parkinson's disease and stroke. This first multi-tissue study will be instrumental to map signals from genome-wide association studies onto functional genes, to discover pathways and to identify drug targets for neurological diseases.
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Affiliation(s)
- Chengran Yang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- 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 Center, 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 Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Adam Suhy
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Brooke Sadler
- Pediatrics Hematology/Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Joseph L Bradley
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Brett Eiffert
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Jorge A Bahena
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, 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 Center, 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 Center, 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 Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- 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 Center, 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
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne M Fagan
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, 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
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne 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, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Herve Rhinn
- Department of Bioinformatics, Alector, Inc., South San Francisco, CA, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne 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 Center, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA.
- The Charles F. and Joanne Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.
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108
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Zhan L, Li J, Jew B, Sul JH. Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. PLoS Genet 2021; 17:e1009772. [PMID: 34516545 PMCID: PMC8460036 DOI: 10.1371/journal.pgen.1009772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/23/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.
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Affiliation(s)
- Lingyu Zhan
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jiajin Li
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Brandon Jew
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, California, United States of America
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109
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Kapoor M, Chao MJ, Johnson EC, Novikova G, Lai D, Meyers JL, Schulman J, Nurnberger JI, Porjesz B, Liu Y, Foroud T, Edenberg HJ, Marcora E, Agrawal A, Goate A. Multi-omics integration analysis identifies novel genes for alcoholism with potential overlap with neurodegenerative diseases. Nat Commun 2021; 12:5071. [PMID: 34417470 PMCID: PMC8379159 DOI: 10.1038/s41467-021-25392-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/03/2021] [Indexed: 11/27/2022] Open
Abstract
Identification of causal variants and genes underlying genome-wide association study (GWAS) loci is essential to understand the biology of alcohol use disorder (AUD) and drinks per week (DPW). Multi-omics integration approaches have shown potential for fine mapping complex loci to obtain biological insights to disease mechanisms. In this study, we use multi-omics approaches, to fine-map AUD and DPW associations at single SNP resolution to demonstrate that rs56030824 on chromosome 11 significantly reduces SPI1 mRNA expression in myeloid cells and lowers risk for AUD and DPW. Our analysis also identifies MAPT as a candidate causal gene specifically associated with DPW. Genes prioritized in this study show overlap with causal genes associated with neurodegenerative disorders. Multi-omics integration analyses highlight, genetic similarities and differences between alcohol intake and disordered drinking, suggesting molecular heterogeneity that might inform future targeted functional and cross-species studies.
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Affiliation(s)
- Manav Kapoor
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Michael J Chao
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Gloriia Novikova
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Jessica Schulman
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernice Porjesz
- Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Howard J Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edoardo Marcora
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison Goate
- Departments of Genetics and Genomic Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Ibanez L, Cruchaga C, Fernández MV. Advances in Genetic and Molecular Understanding of Alzheimer's Disease. Genes (Basel) 2021; 12:1247. [PMID: 34440421 PMCID: PMC8394321 DOI: 10.3390/genes12081247] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 01/19/2023] Open
Abstract
Alzheimer's disease (AD) has become a common disease of the elderly for which no cure currently exists. After over 30 years of intensive research, we have gained extensive knowledge of the genetic and molecular factors involved and their interplay in disease. These findings suggest that different subgroups of AD may exist. Not only are we starting to treat autosomal dominant cases differently from sporadic cases, but we could be observing different underlying pathological mechanisms related to the amyloid cascade hypothesis, immune dysfunction, and a tau-dependent pathology. Genetic, molecular, and, more recently, multi-omic evidence support each of these scenarios, which are highly interconnected but can also point to the different subgroups of AD. The identification of the pathologic triggers and order of events in the disease processes are key to the design of treatments and therapies. Prevention and treatment of AD cannot be attempted using a single approach; different therapeutic strategies at specific disease stages may be appropriate. For successful prevention and treatment, biomarker assays must be designed so that patients can be more accurately monitored at specific points during the course of the disease and potential treatment. In addition, to advance the development of therapeutic drugs, models that better mimic the complexity of the human brain are needed; there have been several advances in this arena. Here, we review significant, recent developments in genetics, omics, and molecular studies that have contributed to the understanding of this disease. We also discuss the implications that these contributions have on medicine.
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Affiliation(s)
- Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; (L.I.); (C.C.)
- Neurogenomics and Informatics Center, 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; (L.I.); (C.C.)
- Neurogenomics and Informatics Center, 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
| | - Maria Victoria Fernández
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA; (L.I.); (C.C.)
- Neurogenomics and Informatics Center, Washington University School of Medicine, 660 S. Euclid Ave. B8134, St. Louis, MO 63110, USA
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111
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Jones RE, Andrews R, Holmans P, Hill M, Taylor PR. Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer's disease. Sci Rep 2021; 11:14935. [PMID: 34294785 PMCID: PMC8298495 DOI: 10.1038/s41598-021-94324-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Genetic association studies have identified multiple variants at the SPI1 locus that modify risk and age of onset for Alzheimer's Disease (AD). Reports linking risk variants to gene expression suggest that variants denoting higher SPI1 expression are likely to have an earlier AD onset, and several other AD risk genes contain PU.1 binding sites in the promoter region. Overall, this suggests the level of SPI1 may alter microglial phenotype potentially impacting AD. This study determined how the microglial transcriptome was altered following modest changes to Spi1 expression in primary mouse microglia. RNA-sequencing was performed on microglia with reduced or increased Spi1/PU.1 expression to provide an unbiased approach to determine transcriptomic changes affected by Spi1. In summary, a reduction in microglial Spi1 resulted in the dysregulation of transcripts encoding proteins involved in DNA replication pathways while an increased Spi1 results in an upregulation of genes associated with immune response pathways. Additionally, a subset of 194 Spi1 dose-sensitive genes was identified and pathway analysis suggests that several innate immune and interferon response pathways are impacted by the concentration of Spi1. Together these results suggest Spi1 levels can alter the microglial transcriptome and suggests interferon pathways may be altered in individuals with AD related Spi1 risk SNPs.
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Affiliation(s)
- Ruth E Jones
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Robert Andrews
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Matthew Hill
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Philip R Taylor
- Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- UK Dementia Research Institute at Cardiff, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK.
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK.
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112
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Kretzschmar GC, Alencar NM, da Silva SSL, Sulzbach CD, Meissner CG, Petzl-Erler ML, Souza RLR, Boldt ABW. GWAS-Top Polymorphisms Associated With Late-Onset Alzheimer Disease in Brazil: Pointing Out Possible New Culprits Among Non-Coding RNAs. Front Mol Biosci 2021; 8:632314. [PMID: 34291080 PMCID: PMC8287568 DOI: 10.3389/fmolb.2021.632314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 01/06/2023] Open
Abstract
Several genome-wide association studies (GWAS) have been carried out with late-onset Alzheimer's disease (LOAD), mainly in European and Asian populations. Different polymorphisms were associated, but several of them without a functional explanation. GWAS are fundamental for identifying loci associated with diseases, although they often do not point to causal polymorphisms. In this sense, functional investigations are a fundamental tool for discovering causality, although the failure of this validation does not necessarily indicate a non-causality. Furthermore, the allele frequency of associated genetic variants may vary widely between populations, requiring replication of these associations in other ethnicities. In this sense, our study sought to replicate in 150 AD patients and 114 elderly controls from the South Brazilian population 18 single-nucleotide polymorphisms (SNPs) associated with AD in European GWAS, with further functional investigation using bioinformatic tools for the associated SNPs. Of the 18 SNPs investigated, only four were associated in our population: rs769449 (APOE), rs10838725 (CELF1), rs6733839, and rs744373 (BIN1-CYP27C1). We identified 54 variants in linkage disequilibrium (LD) with the associated SNPs, most of which act as expression or splicing quantitative trait loci (eQTLs/sQTLs) in genes previously associated with AD or with a possible functional role in the disease, such as CELF1, MADD, MYBPC3, NR1H3, NUP160, SPI1, and TOMM40. Interestingly, eight of these variants are located within long non-coding RNA (lncRNA) genes that have not been previously investigated regarding AD. Some of these polymorphisms can result in changes in these lncRNAs' secondary structures, leading to either loss or gain of microRNA (miRNA)-binding sites, deregulating downstream pathways. Our pioneering work not only replicated LOAD association with polymorphisms not yet associated in the Brazilian population but also identified six possible lncRNAs that may interfere in LOAD development. The results lead us to emphasize the importance of functional exploration of associations found in large-scale association studies in different populations to base personalized and inclusive medicine in the future.
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Affiliation(s)
- Gabriela Canalli Kretzschmar
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Nina Moura Alencar
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Saritha Suellen Lopes da Silva
- Laboratory of Polymorphism and Linkage, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Carla Daniela Sulzbach
- Laboratory of Polymorphism and Linkage, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Caroline Grisbach Meissner
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Ricardo Lehtonen R. Souza
- Laboratory of Polymorphism and Linkage, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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113
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Martínez M, Inestrosa NC. The transcriptional landscape of Alzheimer's disease and its association with Wnt signaling pathway. Neurosci Biobehav Rev 2021; 128:454-466. [PMID: 34224789 DOI: 10.1016/j.neubiorev.2021.06.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/31/2021] [Accepted: 06/20/2021] [Indexed: 12/26/2022]
Abstract
Alzheimer's disease (AD) is a neurological disorder primarily affecting the elderly. The disease manifests as progressive deterioration in cognitive functions, leading to a loss of autonomy. The identification of transcriptional changes in susceptible signaling pathways has provided clues to the origin and progression of AD and has pinpointed synapse loss as the prominent event in early stages of the disease. Synapse failure represents a key pathological correlate of cognitive decline in patients. Genetics and transcriptomics studies have also identified novel genes, processes, and pathways associated with AD. This evidence suggests that a deficiency in Wnt signaling pathway contributes to AD pathogenesis by inducing synaptic dysfunction and neuronal degeneration. In the adult nervous system, Wnt signaling plays a crucial role in synaptic physiology, modulating the synaptic vesicle cycle, trafficking neurotransmitter receptors, and modulating the expression of different genes associated with these processes. In this review, we describe the general transcriptional landscape associated with AD, specifically transcriptional changes associated with the Wnt signaling pathway and their effects in the context of disease.
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Affiliation(s)
- Milka Martínez
- Centro de Envejecimiento y Regeneración (CARE UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nibaldo C Inestrosa
- Centro de Envejecimiento y Regeneración (CARE UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; Centro de Excelencia en Biomedicina de Magallanes (CEBIMA), Universidad de Magallanes, Punta Arenas, Chile.
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114
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Treur JL, Munafò MR, Logtenberg E, Wiers RW, Verweij KJH. Using Mendelian randomization analysis to better understand the relationship between mental health and substance use: a systematic review. Psychol Med 2021; 51:1593-1624. [PMID: 34030749 PMCID: PMC8327626 DOI: 10.1017/s003329172100180x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/17/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Poor mental health has consistently been associated with substance use (smoking, alcohol drinking, cannabis use, and consumption of caffeinated drinks). To properly inform public health policy it is crucial to understand the mechanisms underlying these associations, and most importantly, whether or not they are causal. METHODS In this pre-registered systematic review, we assessed the evidence for causal relationships between mental health and substance use from Mendelian randomization (MR) studies, following PRISMA. We rated the quality of included studies using a scoring system that incorporates important indices of quality, such as the quality of phenotype measurement, instrument strength, and use of sensitivity methods. RESULTS Sixty-three studies were included for qualitative synthesis. The final quality rating was '-' for 16 studies, '- +' for 37 studies, and '+'for 10 studies. There was robust evidence that higher educational attainment decreases smoking and that there is a bi-directional, increasing relationship between smoking and (symptoms of) mental disorders. Another robust finding was that higher educational attainment increases alcohol use frequency, but decreases binge-drinking and alcohol use problems, and that mental disorders causally lead to more alcohol drinking without evidence for the reverse. CONCLUSIONS The current MR literature increases our understanding of the relationship between mental health and substance use. Bi-directional causal relationships are indicated, especially for smoking, providing further incentive to strengthen public health efforts to decrease substance use. Future MR studies should make use of large(r) samples in combination with detailed phenotypes, a wide range of sensitivity methods, and triangulate with other research methods.
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Affiliation(s)
- Jorien L. Treur
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Addiction Development and Psychopathology (ADAPT) Lab, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands
| | - Marcus R. Munafò
- School of Psychological Science, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, the University of Bristol, Bristol, UK
| | - Emma Logtenberg
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Reinout W. Wiers
- Addiction Development and Psychopathology (ADAPT) Lab, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands
- Center for Urban Mental Health, University of Amsterdam, Amsterdam, the Netherlands
| | - Karin J. H. Verweij
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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115
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Sharma VK, Mehta V, Singh TG. Alzheimer's Disorder: Epigenetic Connection and Associated Risk Factors. Curr Neuropharmacol 2021; 18:740-753. [PMID: 31989902 PMCID: PMC7536832 DOI: 10.2174/1570159x18666200128125641] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/26/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
The gene based therapeutics and drug targets have shown incredible and appreciable advances in alleviating human sufferings and complexities. Epigenetics simply means above genetics or which controls the organism beyond genetics. At present it is very clear that all characteristics of an individual are not determined by DNA alone, rather the environment, stress, life style and nutrition play a vital part in determining the response of an organism. Thus, nature (genetic makeup) and nurture (exposure) play equally important roles in the responses observed, both at the cellular and organism levels. Epigenetics influence plethora of complications at cellular and molecular levels that includes cancer, metabolic and cardiovascular complications including neurological (psychosis) and neurodegenerative disorders (Alzheimer’s disease, Parkinson disease etc.). The epigenetic mechanisms include DNA methylation, histone modification and non coding RNA which have substantial impact on progression and pathways linked to Alzheimer’s disease. The epigenetic mechanism gets deregulated in Alzheimer’s disease and is characterized by DNA hyper methylation, deacetylation of histones and general repressed chromatin state which alter gene expression at the transcription level by upregulation, downregulation or silencing of genes. Thus, the processes or modulators of these epigenetic processes have shown vast potential as a therapeutic target in Alzheimer’s disease.
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Affiliation(s)
| | - Vineet Mehta
- Govt. College of Pharmacy, Rohru, District Shimla, Himachal Pradesh-171207, India
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116
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Saunders AM, Burns DK, Gottschalk WK. Reassessment of Pioglitazone for Alzheimer's Disease. Front Neurosci 2021; 15:666958. [PMID: 34220427 PMCID: PMC8243371 DOI: 10.3389/fnins.2021.666958] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/18/2021] [Indexed: 01/01/2023] Open
Abstract
Alzheimer's disease is a quintessential 'unmet medical need', accounting for ∼65% of progressive cognitive impairment among the elderly, and 700,000 deaths in the United States in 2020. In 2019, the cost of caring for Alzheimer's sufferers was $244B, not including the emotional and physical toll on caregivers. In spite of this dismal reality, no treatments are available that reduce the risk of developing AD or that offer prolonged mitiagation of its most devestating symptoms. This review summarizes key aspects of the biology and genetics of Alzheimer's disease, and we describe how pioglitazone improves many of the patholophysiological determinants of AD. We also summarize the results of pre-clinical experiments, longitudinal observational studies, and clinical trials. The results of animal testing suggest that pioglitazone can be corrective as well as protective, and that its efficacy is enhanced in a time- and dose-dependent manner, but the dose-effect relations are not monotonic or sigmoid. Longitudinal cohort studies suggests that it delays the onset of dementia in individuals with pre-existing type 2 diabetes mellitus, which small scale, unblinded pilot studies seem to confirm. However, the results of placebo-controlled, blinded clinical trials have not borne this out, and we discuss possible explanations for these discrepancies.
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Affiliation(s)
- Ann M. Saunders
- Zinfandel Pharmaceuticals, Inc., Chapel Hill, NC, United States
| | - Daniel K. Burns
- Zinfandel Pharmaceuticals, Inc., Chapel Hill, NC, United States
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117
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Bandyopadhyay S. Role of Neuron and Glia in Alzheimer's Disease and Associated Vascular Dysfunction. Front Aging Neurosci 2021; 13:653334. [PMID: 34211387 PMCID: PMC8239194 DOI: 10.3389/fnagi.2021.653334] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Amyloidogenicity and vascular dysfunction are the key players in the pathogenesis of Alzheimer’s disease (AD), involving dysregulated cellular interactions. An intricate balance between neurons, astrocytes, microglia, oligodendrocytes and vascular cells sustains the normal neuronal circuits. Conversely, cerebrovascular diseases overlap neuropathologically with AD, and glial dyshomeostasis promotes AD-associated neurodegenerative cascade. While pathological hallmarks of AD primarily include amyloid-β (Aβ) plaques and neurofibrillary tangles, microvascular disorders, altered cerebral blood flow (CBF), and blood-brain barrier (BBB) permeability induce neuronal loss and synaptic atrophy. Accordingly, microglia-mediated inflammation and astrogliosis disrupt the homeostasis of the neuro-vascular unit and stimulate infiltration of circulating leukocytes into the brain. Large-scale genetic and epidemiological studies demonstrate a critical role of cellular crosstalk for altered immune response, metabolism, and vasculature in AD. The glia associated genetic risk factors include APOE, TREM2, CD33, PGRN, CR1, and NLRP3, which correlate with the deposition and altered phagocytosis of Aβ. Moreover, aging-dependent downregulation of astrocyte and microglial Aβ-degrading enzymes limits the neurotrophic and neurogenic role of glial cells and inhibits lysosomal degradation and clearance of Aβ. Microglial cells secrete IGF-1, and neurons show a reduced responsiveness to the neurotrophic IGF-1R/IRS-2/PI3K signaling pathway, generating amyloidogenic and vascular dyshomeostasis in AD. Glial signals connect to neural stem cells, and a shift in glial phenotype over the AD trajectory even affects adult neurogenesis and the neurovascular niche. Overall, the current review informs about the interaction of neuronal and glial cell types in AD pathogenesis and its critical association with cerebrovascular dysfunction.
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Affiliation(s)
- Sanghamitra Bandyopadhyay
- Developmental Toxicology Laboratory, Systems Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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118
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Jaladanki SK, Elmas A, Malave GS, Huang KL. Genetic dependency of Alzheimer's disease-associated genes across cells and tissue types. Sci Rep 2021; 11:12107. [PMID: 34103633 PMCID: PMC8187448 DOI: 10.1038/s41598-021-91713-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/28/2021] [Indexed: 11/09/2022] Open
Abstract
Effective treatments targeting disease etiology are urgently needed for Alzheimer's disease (AD). Although candidate AD genes have been identified and altering their levels may serve as therapeutic strategies, the consequence of such alterations remain largely unknown. Herein, we analyzed CRISPR knockout/RNAi knockdown screen data for over 700 cell lines and evaluated cellular dependencies of 104 AD-associated genes previously identified by genome-wide association studies (GWAS) and gene expression network studies. Multiple genes showed widespread cell dependencies across tissue lineages, suggesting their inhibition may yield off-target effects. Meanwhile, several genes including SPI1, MEF2C, GAB2, ABCC11, ATCG1 were identified as genes of interest since their genetic knockouts specifically affected high-expressing cells whose tissue lineages are relevant to cell types found in AD. Overall, analyses of genetic screen data identified AD-associated genes whose knockout or knockdown selectively affected cell lines of relevant tissue lineages, prioritizing targets for potential AD treatments.
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Affiliation(s)
- Suraj K Jaladanki
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Abdulkadir Elmas
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriel Santos Malave
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kuan-Lin Huang
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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119
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Süß P, Schlachetzki JCM. Microglia in Alzheimer's Disease. Curr Alzheimer Res 2021; 17:29-43. [PMID: 32048973 DOI: 10.2174/1567205017666200212155234] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 12/31/2019] [Accepted: 01/20/2020] [Indexed: 11/22/2022]
Abstract
Alzheimer's Disease (AD) is the most frequent neurodegenerative disorder. Although proteinaceous aggregates of extracellular Amyloid-β (Aβ) and intracellular hyperphosphorylated microtubule- associated tau have long been identified as characteristic neuropathological hallmarks of AD, a disease- modifying therapy against these targets has not been successful. An emerging concept is that microglia, the innate immune cells of the brain, are major players in AD pathogenesis. Microglia are longlived tissue-resident professional phagocytes that survey and rapidly respond to changes in their microenvironment. Subpopulations of microglia cluster around Aβ plaques and adopt a transcriptomic signature specifically linked to neurodegeneration. A plethora of molecules and pathways associated with microglia function and dysfunction has been identified as important players in mediating neurodegeneration. However, whether microglia exert either beneficial or detrimental effects in AD pathology may depend on the disease stage. In this review, we summarize the current knowledge about the stage-dependent role of microglia in AD, including recent insights from genetic and gene expression profiling studies as well as novel imaging techniques focusing on microglia in human AD pathology and AD mouse models.
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Affiliation(s)
- Patrick Süß
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universitat, Erlangen- Nürnberg, Germany
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, United States
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120
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Cullell N, Cárcel-Márquez J, Gallego-Fábrega C, Muiño E, Llucià-Carol L, Lledós M, Amaut KEU, Krupinski J, Fernández-Cadenas I. Sleep/wake cycle alterations as a cause of neurodegenerative diseases: A Mendelian randomization study. Neurobiol Aging 2021; 106:320.e1-320.e12. [PMID: 34130902 DOI: 10.1016/j.neurobiolaging.2021.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/30/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022]
Abstract
Sleep and/or wake cycle alterations are common in neurodegenerative diseases (ND). Our aim was to determine whether there is a causal relationship between sleep and/or wake cycle patterns and ND (Parkinson's disease (PD) age at onset (AAO), Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS)) using two-sample Mendelian Randomization (MR). We selected 12 sleep traits with available Genome-Wide Association Study (GWAS) to evaluate their causal relationship with the ND risk through Inverse-Variance Weighted regression as main analysis. We used as outcome the latest ND GWAS with available summary-statistics: PD-AAO (N = 17,996), AD (N = 21,235) and ALS (N = 40,136). MR results pointed to a causal effect of subjective and objective-measured morning chronotype on later PD-AAO (95%CI:0.33-1.81, p = 8.47×10-09 and 95%CI:-7.28 to -4.44, p = 5.87×10-16, respectively). Sleep efficiency was causally associated with a decreased AD risk (95%CI:-20.408 to -0.66, p = 0.04) and daytime sleepiness with an increased ALS risk (95%CI:0.15 to 1.61, p = 0.01). Our study suggests that sleep and/or wake patterns have causal relationship with ND. Given that sleep and/or wake patterns are modifiable risk factors, sleep interventions should be investigated as a potential treatment in PD-AAO, AD and ALS.
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Affiliation(s)
- Natalia Cullell
- Department of Neurology, Hospital Universitari MútuaTerrassa / Fundació Docència i Recerca MútuaTerrassa, Terrassa, Spain // Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain // Faculty of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain
| | - Cristina Gallego-Fábrega
- Department of Neurology, Hospital Universitari MútuaTerrassa / Fundació Docència i Recerca MútuaTerrassa, Terrassa, Spain // Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain
| | - Elena Muiño
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spainn
| | - Miquel Lledós
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain
| | | | - Jerzy Krupinski
- Department of Neurology, Hospital Universitari MútuaTerrassa / Fundació Docència i Recerca MútuaTerrassa, Terrassa, Spain // Centre for bioscience, School of HealthCare Science, Manchester Metropolitan University, Manchester, UK
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics, Biomedical Research Institute Sant Pau, Sant Pau Hospital, Barcelona, Spain // Department of Neurology, Hospital Universitari MútuaTerrassa / Fundació Docència i Recerca MútuaTerrassa, Terrassa, Spain.
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Lau SF, Chen C, Fu WY, Qu JY, Cheung TH, Fu AKY, Ip NY. IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer's Disease. Cell Rep 2021; 31:107530. [PMID: 32320664 DOI: 10.1016/j.celrep.2020.107530] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/11/2020] [Accepted: 03/27/2020] [Indexed: 02/06/2023] Open
Abstract
Impairment of microglial clearance activity contributes to beta-amyloid (Aβ) pathology in Alzheimer's disease (AD). While the transcriptome profile of microglia directs microglial functions, how the microglial transcriptome can be regulated to alleviate AD pathology is largely unknown. Here, we show that injection of interleukin (IL)-33 in an AD transgenic mouse model ameliorates Aβ pathology by reprogramming microglial epigenetic and transcriptomic profiles to induce a microglial subpopulation with enhanced phagocytic activity. These IL-33-responsive microglia (IL-33RMs) express a distinct transcriptome signature that is highlighted by increased major histocompatibility complex class II genes and restored homeostatic signature genes. IL-33-induced remodeling of chromatin accessibility and PU.1 transcription factor binding at the signature genes of IL-33RM control their transcriptome reprogramming. Specifically, disrupting PU.1-DNA interaction abolishes the microglial state transition and Aβ clearance that is induced by IL-33. Thus, we define a PU.1-dependent transcriptional pathway that drives the IL-33-induced functional state transition of microglia, resulting in enhanced Aβ clearance.
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Affiliation(s)
- Shun-Fat Lau
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Congping Chen
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Biophotonics Research Laboratory, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wing-Yu Fu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianan Y Qu
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Biophotonics Research Laboratory, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tom H Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Amy K Y Fu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong 518057, China
| | - Nancy Y Ip
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, Guangdong 518057, China.
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122
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Gockley J, Montgomery KS, Poehlman WL, Wiley JC, Liu Y, Gerasimov E, Greenwood AK, Sieberts SK, Wingo AP, Wingo TS, Mangravite LM, Logsdon BA. Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer's disease. Genome Med 2021; 13:76. [PMID: 33947463 PMCID: PMC8094491 DOI: 10.1186/s13073-021-00890-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 04/17/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is an incurable neurodegenerative disease currently affecting 1.75% of the US population, with projected growth to 3.46% by 2050. Identifying common genetic variants driving differences in transcript expression that confer AD risk is necessary to elucidate AD mechanism and develop therapeutic interventions. We modify the FUSION transcriptome-wide association study (TWAS) pipeline to ingest gene expression values from multiple neocortical regions. METHODS A combined dataset of 2003 genotypes clustered to 1000 Genomes individuals from Utah with Northern and Western European ancestry (CEU) was used to construct a training set of 790 genotypes paired to 888 RNASeq profiles from temporal cortex (TCX = 248), prefrontal cortex (FP = 50), inferior frontal gyrus (IFG = 41), superior temporal gyrus (STG = 34), parahippocampal cortex (PHG = 34), and dorsolateral prefrontal cortex (DLPFC = 461). Following within-tissue normalization and covariate adjustment, predictive weights to impute expression components based on a gene's surrounding cis-variants were trained. The FUSION pipeline was modified to support input of pre-scaled expression values and support cross validation with a repeated measure design arising from the presence of multiple transcriptome samples from the same individual across different tissues. RESULTS Cis-variant architecture alone was informative to train weights and impute expression for 6780 (49.67%) autosomal genes, the majority of which significantly correlated with gene expression; FDR < 5%: N = 6775 (99.92%), Bonferroni: N = 6716 (99.06%). Validation of weights in 515 matched genotype to RNASeq profiles from the CommonMind Consortium (CMC) was (72.14%) in DLPFC profiles. Association of imputed expression components from all 2003 genotype profiles yielded 8 genes significantly associated with AD (FDR < 0.05): APOC1, EED, CD2AP, CEACAM19, CLPTM1, MTCH2, TREM2, and KNOP1. CONCLUSIONS We provide evidence of cis-genetic variation conferring AD risk through 8 genes across six distinct genomic loci. Moreover, we provide expression weights for 6780 genes as a valuable resource to the community, which can be abstracted across the neocortex and a wide range of neuronal phenotypes.
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Affiliation(s)
| | | | | | | | - Yue Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ekaterina Gerasimov
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | | | - Aliza P Wingo
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Benjamin A Logsdon
- Cajal Neuroscience, 1616 Eastlake Avenue East, Suite 208, Seattle, WA, 98102, USA.
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Da Mesquita S, Papadopoulos Z, Dykstra T, Brase L, Farias FG, Wall M, Jiang H, Kodira CD, de Lima KA, Herz J, Louveau A, Goldman DH, Salvador AF, Onengut-Gumuscu S, Farber E, Dabhi N, Kennedy T, Milam MG, Baker W, Smirnov I, Rich SS, Benitez BA, Karch CM, Perrin RJ, Farlow M, Chhatwal JP, Holtzman DM, Cruchaga C, Harari O, Kipnis J. Meningeal lymphatics affect microglia responses and anti-Aβ immunotherapy. Nature 2021; 593:255-260. [PMID: 33911285 PMCID: PMC8817786 DOI: 10.1038/s41586-021-03489-0] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/25/2021] [Indexed: 02/02/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent cause of dementia1. Although there is no effective treatment for AD, passive immunotherapy with monoclonal antibodies against amyloid beta (Aβ) is a promising therapeutic strategy2,3. Meningeal lymphatic drainage has an important role in the accumulation of Aβ in the brain4, but it is not known whether modulation of meningeal lymphatic function can influence the outcome of immunotherapy in AD. Here we show that ablation of meningeal lymphatic vessels in 5xFAD mice (a mouse model of amyloid deposition that expresses five mutations found in familial AD) worsened the outcome of mice treated with anti-Aβ passive immunotherapy by exacerbating the deposition of Aβ, microgliosis, neurovascular dysfunction, and behavioural deficits. By contrast, therapeutic delivery of vascular endothelial growth factor C improved clearance of Aβ by monoclonal antibodies. Notably, there was a substantial overlap between the gene signature of microglia from 5xFAD mice with impaired meningeal lymphatic function and the transcriptional profile of activated microglia from the brains of individuals with AD. Overall, our data demonstrate that impaired meningeal lymphatic drainage exacerbates the microglial inflammatory response in AD and that enhancement of meningeal lymphatic function combined with immunotherapies could lead to better clinical outcomes.
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Affiliation(s)
- Sandro Da Mesquita
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA.
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
| | - Zachary Papadopoulos
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Neuroscience Graduate Program, Washington University in St. Louis, St. Louis, MO, USA
| | - Taitea Dykstra
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Logan Brase
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Morgan Wall
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Hong Jiang
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Kalil Alves de Lima
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jasmin Herz
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Antoine Louveau
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Dylan H Goldman
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Andrea Francesca Salvador
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Nisha Dabhi
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Tatiana Kennedy
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Mary Grace Milam
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Wendy Baker
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
| | - Igor Smirnov
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Richard J Perrin
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Jasmeer P Chhatwal
- Massachusetts General Hospital, Harvard Medical School, Department of Neurology, Boston, MA, USA
| | - David M Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Jonathan Kipnis
- Department of Neuroscience, University of Virginia, Charlottesville, VA, USA.
- Center for Brain Immunology and Glia (BIG), Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA.
- Neuroscience Graduate Program, Washington University in St. Louis, St. Louis, MO, USA.
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA.
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Patel D, Zhang X, Farrell JJ, Chung J, Stein TD, Lunetta KL, Farrer LA. Cell-type-specific expression quantitative trait loci associated with Alzheimer disease in blood and brain tissue. Transl Psychiatry 2021; 11:250. [PMID: 33907181 PMCID: PMC8079392 DOI: 10.1038/s41398-021-01373-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/24/2021] [Accepted: 04/08/2021] [Indexed: 02/02/2023] Open
Abstract
Because regulation of gene expression is heritable and context-dependent, we investigated AD-related gene expression patterns in cell types in blood and brain. Cis-expression quantitative trait locus (eQTL) mapping was performed genome-wide in blood from 5257 Framingham Heart Study (FHS) participants and in brain donated by 475 Religious Orders Study/Memory & Aging Project (ROSMAP) participants. The association of gene expression with genotypes for all cis SNPs within 1 Mb of genes was evaluated using linear regression models for unrelated subjects and linear-mixed models for related subjects. Cell-type-specific eQTL (ct-eQTL) models included an interaction term for the expression of "proxy" genes that discriminate particular cell type. Ct-eQTL analysis identified 11,649 and 2533 additional significant gene-SNP eQTL pairs in brain and blood, respectively, that were not detected in generic eQTL analysis. Of note, 386 unique target eGenes of significant eQTLs shared between blood and brain were enriched in apoptosis and Wnt signaling pathways. Five of these shared genes are established AD loci. The potential importance and relevance to AD of significant results in myeloid cell types is supported by the observation that a large portion of GWS ct-eQTLs map within 1 Mb of established AD loci and 58% (23/40) of the most significant eGenes in these eQTLs have previously been implicated in AD. This study identified cell-type-specific expression patterns for established and potentially novel AD genes, found additional evidence for the role of myeloid cells in AD risk, and discovered potential novel blood and brain AD biomarkers that highlight the importance of cell-type-specific analysis.
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Affiliation(s)
- Devanshi Patel
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Lindsay A Farrer
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
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125
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Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen X, Martin ER, Wang L. Sex-specific DNA methylation differences in Alzheimer's disease pathology. Acta Neuropathol Commun 2021; 9:77. [PMID: 33902726 PMCID: PMC8074512 DOI: 10.1186/s40478-021-01177-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022] Open
Abstract
Sex is an important factor that contributes to the clinical and biological heterogeneities in Alzheimer's disease (AD), but the regulatory mechanisms underlying sex disparity in AD are still not well understood. DNA methylation is an important epigenetic modification that regulates gene transcription and is known to be involved in AD. We performed the first large-scale sex-specific meta-analysis of DNA methylation differences in AD neuropathology, by re-analyzing four recent epigenome-wide association studies totaling more than 1000 postmortem prefrontal cortex brain samples using a uniform analytical pipeline. For each cohort, we employed two complementary analytical strategies, a sex-stratified analysis that examined methylation-Braak stage associations in male and female samples separately, and a sex-by-Braak stage interaction analysis that compared the magnitude of these associations between different sexes. Our analysis uncovered 14 novel CpGs, mapped to genes such as TMEM39A and TNXB that are associated with the AD Braak stage in a sex-specific manner. TMEM39A is known to be involved in inflammation, dysregulated type I interferon responses, and other immune processes. TNXB encodes tenascin proteins, which are extracellular matrix glycoproteins demonstrated to modulate synaptic plasticity in the brain. Moreover, for many previously implicated genes in AD neuropathology, such as MBP and AZU1, our analysis provided the new insights that they were predominately driven by effects in only one sex. These sex-specific DNA methylation differences were enriched in divergent biological processes such as integrin activation in females and complement activation in males. Our study implicated multiple new loci and biological processes that affected AD neuropathology in a sex-specific manner.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Jesse Cai
- Brentwood High School, 5304 Murray Ln, Brentwood, TN, 37027, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
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126
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Dehghani N, Bras J, Guerreiro R. How understudied populations have contributed to our understanding of Alzheimer's disease genetics. Brain 2021; 144:1067-1081. [PMID: 33889936 DOI: 10.1093/brain/awab028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
The majority of genome-wide association studies have been conducted using samples with a broadly European genetic background. As a field, we acknowledge this limitation and the need to increase the diversity of populations studied. A major challenge when designing and conducting such studies is to assimilate large samples sizes so that we attain enough statistical power to detect variants associated with disease, particularly when trying to identify variants with low and rare minor allele frequencies. In this review, we aimed to illustrate the benefits to genetic characterization of Alzheimer's disease, in researching currently understudied populations. This is important for both fair representation of world populations and the translatability of findings. To that end, we conducted a literature search to understand the contributions of studies, on different populations, to Alzheimer's disease genetics. Using both PubMed and Alzforum Mutation Database, we systematically quantified the number of studies reporting variants in known disease-causing genes, in a worldwide manner, and discuss the contributions of research in understudied populations to the identification of novel genetic factors in this disease. Additionally, we compared the effects of genome-wide significant single nucleotide polymorphisms across populations by focusing on loci that show different association profiles between populations (a key example being APOE). Reports of variants in APP, PSEN1 and PSEN2 can initially determine whether patients from a country have been studied for Alzheimer's disease genetics. Most genome-wide significant associations in non-Hispanic white genome-wide association studies do not reach genome-wide significance in such studies of other populations, with some suggesting an opposite effect direction; this is likely due to much smaller sample sizes attained. There are, however, genome-wide significant associations first identified in understudied populations which have yet to be replicated. Familial studies in understudied populations have identified rare, high effect variants, which have been replicated in other populations. This work functions to both highlight how understudied populations have furthered our understanding of Alzheimer's disease genetics, and to help us gauge our progress in understanding the genetic architecture of this disease in all populations.
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Affiliation(s)
- Nadia Dehghani
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
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127
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Novikova G, Andrews SJ, Renton AE, Marcora E. Beyond association: successes and challenges in linking non-coding genetic variation to functional consequences that modulate Alzheimer's disease risk. Mol Neurodegener 2021; 16:27. [PMID: 33882988 PMCID: PMC8061035 DOI: 10.1186/s13024-021-00449-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is the most common type of dementia, affecting millions of people worldwide; however, no disease-modifying treatments are currently available. Genome-wide association studies (GWASs) have identified more than 40 loci associated with AD risk. However, most of the disease-associated variants reside in non-coding regions of the genome, making it difficult to elucidate how they affect disease susceptibility. Nonetheless, identification of the regulatory elements, genes, pathways and cell type/tissue(s) impacted by these variants to modulate AD risk is critical to our understanding of disease pathogenesis and ability to develop effective therapeutics. In this review, we provide an overview of the methods and approaches used in the field to identify the functional effects of AD risk variants in the causal path to disease risk modification as well as describe the most recent findings. We first discuss efforts in cell type/tissue prioritization followed by recent progress in candidate causal variant and gene nomination. We discuss statistical methods for fine-mapping as well as approaches that integrate multiple levels of evidence, such as epigenomic and transcriptomic data, to identify causal variants and risk mechanisms of AD-associated loci. Additionally, we discuss experimental approaches and data resources that will be needed to validate and further elucidate the effects of these variants and genes on biological pathways, cellular phenotypes and disease risk. Finally, we discuss future steps that need to be taken to ensure that AD GWAS functional mapping efforts lead to novel findings and bring us closer to finding effective treatments for this devastating disease.
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Affiliation(s)
- Gloriia Novikova
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shea J Andrews
- 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
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Edoardo Marcora
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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128
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Harwood JC, Leonenko G, Sims R, Escott-Price V, Williams J, Holmans P. Defining functional variants associated with Alzheimer's disease in the induced immune response. Brain Commun 2021; 3:fcab083. [PMID: 33959712 PMCID: PMC8087896 DOI: 10.1093/braincomms/fcab083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Defining the mechanisms involved in the aetiology of Alzheimer’s disease from genome-wide association studies alone is challenging since Alzheimer’s disease is polygenic and most genetic variants are non-coding. Non-coding Alzheimer’s disease risk variants can influence gene expression by affecting miRNA binding and those located within enhancers and within CTCF sites may influence gene expression through alterations in chromatin states. In addition, their function can be cell-type specific. They can function specifically in microglial enhancers thus affecting gene expression in the brain. Hence, transcriptome-wide association studies have been applied to test the genetic association between disease risk and cell-/tissue-specific gene expression. Many Alzheimer’s disease-associated loci are involved in the pathways of the innate immune system. Both microglia, the primary immune cells of the brain, and monocytes which can infiltrate the brain and differentiate into activated macrophages, have roles in neuroinflammation and β‐amyloid clearance through phagocytosis. In monocytes the function of regulatory variants can be context-specific after immune stimulation. To dissect the variants associated with Alzheimer’s disease in the context of monocytes, we utilized data from naïve monocytes and following immune stimulation in vitro, in combination with genome-wide association studies of Alzheimer’s disease in transcriptome-wide association studies. Of the nine genes with statistically independent transcriptome-wide association signals, seven are located in known Alzheimer’s disease risk loci: BIN1, PTK2B, SPI1, MS4A4A, MS4A6E, APOE and PVR. The transcriptome-wide association signal for MS4A6E, PTK2B and PVR and the direction of effect replicated in an independent genome-wide association studies. Our analysis identified two novel candidate genes for Alzheimer’s disease risk, LACTB2 and PLIN2/ADRP. LACTB2 replicated in a transcriptome-wide association study using independent expression weights. LACTB2 and PLIN2/ADRP are involved in mitochondrial function and lipid metabolism, respectively. Comparison of transcriptome-wide association study results from monocytes, whole blood and brain showed that the signal for PTK2B is specific to blood and MS4A6E is specific to LPS stimulated monocytes.
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Affiliation(s)
- Janet C Harwood
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Ganna Leonenko
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Julie Williams
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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129
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Wickstead ES, Irving MA, Getting SJ, McArthur S. Exploiting formyl peptide receptor 2 to promote microglial resolution: a new approach to Alzheimer's disease treatment. FEBS J 2021; 289:1801-1822. [PMID: 33811735 DOI: 10.1111/febs.15861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/09/2021] [Accepted: 03/29/2021] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease and dementia are among the most significant current healthcare challenges given the rapidly growing elderly population, and the almost total lack of effective therapeutic interventions. Alzheimer's disease pathology has long been considered in terms of accumulation of amyloid beta and hyperphosphorylated tau, but the importance of neuroinflammation in driving disease has taken greater precedence over the last 15-20 years. Inflammatory activation of the primary brain immune cells, the microglia, has been implicated in Alzheimer's pathogenesis through genetic, preclinical, imaging and postmortem human studies, and strategies to regulate microglial activity may hold great promise for disease modification. Neuroinflammation is necessary for defence of the brain against pathogen invasion or damage but is normally self-limiting due to the engagement of endogenous pro-resolving circuitry that terminates inflammatory activity, a process that appears to fail in Alzheimer's disease. Here, we discuss the potential for a major regulator and promoter of resolution, the receptor FPR2, to restrain pro-inflammatory microglial activity, and propose that it may serve as a valuable target for therapeutic investigation in Alzheimer's disease.
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Affiliation(s)
| | - Murray A Irving
- Institute of Dentistry, Barts and the London School of Medicine & Dentistry, Blizard Institute, Queen Mary, University of London, UK
| | - Stephen J Getting
- College of Liberal Arts & Sciences, School of Life Sciences, University of Westminster, London, UK
| | - Simon McArthur
- Institute of Dentistry, Barts and the London School of Medicine & Dentistry, Blizard Institute, Queen Mary, University of London, UK
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130
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Le Guen Y, Belloy ME, Napolioni V, Eger SJ, Kennedy G, Tao R, He Z, Greicius MD. A novel age-informed approach for genetic association analysis in Alzheimer's disease. Alzheimers Res Ther 2021; 13:72. [PMID: 33794991 PMCID: PMC8017764 DOI: 10.1186/s13195-021-00808-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/11/2021] [Indexed: 01/17/2023]
Abstract
BACKGROUND Many Alzheimer's disease (AD) genetic association studies disregard age or incorrectly account for it, hampering variant discovery. METHODS Using simulated data, we compared the statistical power of several models: logistic regression on AD diagnosis adjusted and not adjusted for age; linear regression on a score integrating case-control status and age; and multivariate Cox regression on age-at-onset. We applied these models to real exome-wide data of 11,127 sequenced individuals (54% cases) and replicated suggestive associations in 21,631 genotype-imputed individuals (51% cases). RESULTS Modeling variable AD risk across age results in 5-10% statistical power gain compared to logistic regression without age adjustment, while incorrect age adjustment leads to critical power loss. Applying our novel AD-age score and/or Cox regression, we discovered and replicated novel variants associated with AD on KIF21B, USH2A, RAB10, RIN3, and TAOK2 genes. CONCLUSION Our AD-age score provides a simple means for statistical power gain and is recommended for future AD studies.
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Affiliation(s)
- Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94304, USA.
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94304, USA
| | - Valerio Napolioni
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, Italy
| | - Sarah J Eger
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94304, USA
| | - Gabriel Kennedy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94304, USA
| | - Ran Tao
- Department of Biostatistics and Vanderbilt Genetic Institute, Vanderbilt University, Nashville, TN, 37203, USA
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94304, USA
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, 94304, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94304, USA
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131
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Zimmer TS, Korotkov A, Zwakenberg S, Jansen FE, Zwartkruis FJT, Rensing NR, Wong M, Mühlebner A, van Vliet EA, Aronica E, Mills JD. Upregulation of the pathogenic transcription factor SPI1/PU.1 in tuberous sclerosis complex and focal cortical dysplasia by oxidative stress. Brain Pathol 2021; 31:e12949. [PMID: 33786950 PMCID: PMC8412124 DOI: 10.1111/bpa.12949] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a congenital disorder characterized by cortical malformations and concomitant epilepsy caused by loss‐of‐function mutations in the mTOR suppressors TSC1 or TSC2. While the underlying molecular changes caused by mTOR activation in TSC have previously been investigated, the drivers of these transcriptional change have not been fully elucidated. A better understanding of the perturbed transcriptional regulation could lead to the identification of novel pathways for therapeutic intervention not only in TSC, but other genetic epilepsies in which mTOR activation plays a key role, such as focal cortical dysplasia 2b (FCD). Here, we analyzed RNA sequencing data from cortical tubers and a tsc2−/− zebrafish. We identified differential expression of the transcription factors (TFs) SPI1/PU.1, IRF8, GBX2, and IKZF1 of which SPI1/PU.1 and IRF8 targets were enriched among the differentially expressed genes. Furthermore, for SPI1/PU.1 these findings were conserved in TSC zebrafish model. Next, we confirmed overexpression of SPI1/PU.1 on the RNA and protein level in a separate cohort of surgically resected TSC tubers and FCD tissue, in fetal TSC tissue, and a Tsc1GFAP−/− mouse model of TSC. Subsequently, we validated the expression of SPI1/PU.1 in dysmorphic cells with mTOR activation in TSC tubers. In fetal TSC, we detected SPI1/PU.1 expression prenatally and elevated RNA Spi1 expression in Tsc1GFAP−/− mice before the development of seizures. Finally, in vitro, we identified that in astrocytes and neurons SPI1 transcription was driven by H2O2‐induced oxidative stress, independent of mTOR. We identified SPI1/PU.1 as a novel TF involved in the pro‐inflammatory gene expression of malformed cells in TSC and FCD 2b. This transcriptional program is activated in response to oxidative stress and already present prenatally. Importantly, SPI1/PU.1 protein appears to be strictly limited to malformed cells, as we did not find SPI1/PU.1 protein expression in mice nor in our in vitro models.
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Affiliation(s)
- Till S Zimmer
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anatoly Korotkov
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Susan Zwakenberg
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Floor E Jansen
- Department of Pediatric Neurology, Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fried J T Zwartkruis
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Michael Wong
- Department of Neurology, Washington University, Saint Louis, MO, USA
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.,Department of Clinical and Experimental Epilepsy, UCL, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
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132
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Vogrinc D, Goričar K, Dolžan V. Genetic Variability in Molecular Pathways Implicated in Alzheimer's Disease: A Comprehensive Review. Front Aging Neurosci 2021; 13:646901. [PMID: 33815092 PMCID: PMC8012500 DOI: 10.3389/fnagi.2021.646901] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disease, affecting a significant part of the population. The majority of AD cases occur in the elderly with a typical age of onset of the disease above 65 years. AD presents a major burden for the healthcare system and since population is rapidly aging, the burden of the disease will increase in the future. However, no effective drug treatment for a full-blown disease has been developed to date. The genetic background of AD is extensively studied; numerous genome-wide association studies (GWAS) identified significant genes associated with increased risk of AD development. This review summarizes more than 100 risk loci. Many of them may serve as biomarkers of AD progression, even in the preclinical stage of the disease. Furthermore, we used GWAS data to identify key pathways of AD pathogenesis: cellular processes, metabolic processes, biological regulation, localization, transport, regulation of cellular processes, and neurological system processes. Gene clustering into molecular pathways can provide background for identification of novel molecular targets and may support the development of tailored and personalized treatment of AD.
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Affiliation(s)
| | | | - Vita Dolžan
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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133
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Chen Y, Ding X, Wang S, Ding P, Xu Z, Li J, Wang M, Xiang R, Wang X, Wang H, Feng Q, Qiu J, Wang F, Huang Z, Zhang X, Tang G, Tang S. A single-cell atlas of mouse olfactory bulb chromatin accessibility. J Genet Genomics 2021; 48:147-162. [PMID: 33926839 DOI: 10.1016/j.jgg.2021.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 10/21/2022]
Abstract
Olfaction, the sense of smell, is a fundamental trait crucial to many species. The olfactory bulb (OB) plays pivotal roles in processing and transmitting odor information from the environment to the brain. The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing. However, the epigenetic landscape of the mOB remains mostly unexplored. Herein, we apply single-cell assay for transposase-accessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the mOB. Based on single-cell epigenetic signatures, mOB cells are classified into 21 clusters corresponding to 11 cell types. We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred. In addition, the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage. Our study provides a valuable epigenetic data set for the mOB at single-cell resolution, and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.
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Affiliation(s)
- Yin Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiangning Ding
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyou Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Peiwen Ding
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Zaoxu Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiankang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Mingyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Rong Xiang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoling Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Qikai Feng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiaying Qiu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Feiyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China; School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhen Huang
- Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Xingliang Zhang
- Shenzhen Children's Hospital, Shenzhen 518083, China; Department of Pediatrics, the Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China.
| | - Gen Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China.
| | - Shengping Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China; Zunyi Medical University, Zunyi, Guizhou 563099, China; China Medical University, Shenyang, Liaoning 110122, China.
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134
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Novikova G, Kapoor M, Tcw J, Abud EM, Efthymiou AG, Chen SX, Cheng H, Fullard JF, Bendl J, Liu Y, Roussos P, Björkegren JL, Liu Y, Poon WW, Hao K, Marcora E, Goate AM. Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes. Nat Commun 2021; 12:1610. [PMID: 33712570 PMCID: PMC7955030 DOI: 10.1038/s41467-021-21823-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer's disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD pathogenesis. Previously, we showed that AD risk alleles are enriched in myeloid-specific epigenomic annotations. Here, we show that they are specifically enriched in active enhancers of monocytes, macrophages and microglia. We integrated AD GWAS with myeloid epigenomic and transcriptomic datasets using analytical approaches to link myeloid enhancer activity to target gene expression regulation and AD risk modification. We identify AD risk enhancers and nominate candidate causal genes among their likely targets (including AP4E1, AP4M1, APBB3, BIN1, MS4A4A, MS4A6A, PILRA, RABEP1, SPI1, TP53INP1, and ZYX) in twenty loci. Fine-mapping of these enhancers nominates candidate functional variants that likely modify AD risk by regulating gene expression in myeloid cells. In the MS4A locus we identified a single candidate functional variant and validated it in human induced pluripotent stem cell (hiPSC)-derived microglia and brain. Taken together, this study integrates AD GWAS with multiple myeloid genomic datasets to investigate the mechanisms of AD risk alleles and nominates candidate functional variants, regulatory elements and genes that likely modulate disease susceptibility.
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Affiliation(s)
- Gloriia Novikova
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manav Kapoor
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julia Tcw
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edsel M Abud
- Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, USA
| | - Anastasia G Efthymiou
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven X Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiyuan Liu
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan Lm Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wayne W Poon
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Ronald M. Loeb Center for Alzheimer's Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 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.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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135
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Lu RJ, Wang EK, Benayoun BA. Functional genomics of inflamm-aging and immunosenescence. Brief Funct Genomics 2021; 21:43-55. [PMID: 33690792 DOI: 10.1093/bfgp/elab009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
The aging population is at a higher risk for age-related diseases and infections. This observation could be due to immunosenescence: the decline in immune efficacy of both the innate and the adaptive immune systems. Age-related immune decline also links to the concept of 'inflamm-aging,' whereby aging is accompanied by sterile chronic inflammation. Along with a decline in immune function, aging is accompanied by a widespread of 'omics' remodeling. Transcriptional landscape changes linked to key pathways of immune function have been identified across studies, such as macrophages having decreased expression of genes associated to phagocytosis, a major function of macrophages. Therefore, a key mechanism underlying innate immune cell dysfunction during aging may stem from dysregulation of youthful genomic networks. In this review, we discuss both molecular and cellular phenotypes of innate immune cells that contribute to age-related inflammation.
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Affiliation(s)
- Ryan J Lu
- Leonard Davis School of Gerontology at the University of Southern California
| | - Emily K Wang
- Leonard Davis School of Gerontology at the University of Southern California
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology at the University of Southern California
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136
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Si Z, Wang X. Stem Cell Therapies in Alzheimer's Disease: Applications for Disease Modeling. J Pharmacol Exp Ther 2021; 377:207-217. [PMID: 33558427 DOI: 10.1124/jpet.120.000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease with complex pathologic and biologic characteristics. Extracellular β-amyloid deposits, such as senile plaques, and intracellular aggregation of hyperphosphorylated tau, such as neurofibrillary tangles, remain the main neuropathological criteria for the diagnosis of AD. There is currently no effective treatment of the disease, and many clinical trials have failed to prove any benefits of new therapeutics. More recently, there has been increasing interest in harnessing the potential of stem cell technologies for drug discovery, disease modeling, and cell therapies, which have been used to study an array of human conditions, including AD. The recently developed and optimized induced pluripotent stem cell (iPSC) technology is a critical platform for screening anti-AD drugs and understanding mutations that modify AD. Neural stem cell (NSC) transplantation has been investigated as a new therapeutic approach to treat neurodegenerative diseases. Mesenchymal stem cells (MSCs) also exhibit considerable potential to treat neurodegenerative diseases by secreting growth factors and exosomes, attenuating neuroinflammation. This review highlights recent progress in stem cell research and the translational applications and challenges of iPSCs, NSCs, and MSCs as treatment strategies for AD. Even though these treatments are still in relative infancy, these developing stem cell technologies hold considerable promise to combat AD and other neurodegenerative disorders. SIGNIFICANCE STATEMENT: Alzheimer's disease (AD) is a neurodegenerative disease that results in learning and memory defects. Although some drugs have been approved for AD treatment, fewer than 20% of patients with AD benefit from these drugs. Therapies based on stem cells, including induced pluripotent stem cells, neural stem cells, and mesenchymal stem cells, provide promising therapeutic strategies for AD.
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Affiliation(s)
- Zizhen Si
- Department of Physiology and Pharmacology, School of Medicine, Ningbo University, Ningbo, China (Z.S.) and Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China (X.W.)
| | - Xidi Wang
- Department of Physiology and Pharmacology, School of Medicine, Ningbo University, Ningbo, China (Z.S.) and Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China (X.W.)
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137
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Pan Q, Liu YJ, Bai XF, Han XL, Jiang Y, Ai B, Shi SS, Wang F, Xu MC, Wang YZ, Zhao J, Chen JX, Zhang J, Li XC, Zhu J, Zhang GR, Wang QY, Li CQ. VARAdb: a comprehensive variation annotation database for human. Nucleic Acids Res 2021; 49:D1431-D1444. [PMID: 33095866 PMCID: PMC7779011 DOI: 10.1093/nar/gkaa922] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/28/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023] Open
Abstract
With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include ‘Variation information’, ‘Regulatory information’, ‘Related genes’, ‘Chromatin accessibility’ and ‘Chromatin interaction’. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.
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Affiliation(s)
- Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yue-Juan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xue-Feng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xiao-Le Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Shan-Shan Shi
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Ming-Cong Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Yue-Zhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jia-Xin Chen
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Xue-Cang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Guo-Rui Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Qiu-Yu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
| | - Chun-Quan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University. Daqing 163319, China
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Tajbakhsh A, Read M, Barreto GE, Ávila-Rodriguez M, Gheibi-Hayat SM, Sahebkar A. Apoptotic neurons and amyloid-beta clearance by phagocytosis in Alzheimer's disease: Pathological mechanisms and therapeutic outlooks. Eur J Pharmacol 2021; 895:173873. [PMID: 33460611 DOI: 10.1016/j.ejphar.2021.173873] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Neuronal survival and axonal renewal following central nervous system damage and in neurodegenerative illnesses, such as Alzheimer's disease (AD), can be enhanced by fast clearance of neuronal apoptotic debris, as well as the removal of amyloid beta (Aβ) by phagocytic cells through the process of efferocytosis. This process quickly inhibits the release of proinflammatory and antigenic autoimmune constituents, enhancing the formation of a microenvironment vital for neuronal survival and axonal regeneration. Therefore, the detrimental features associated with microglial phagocytosis uncoupling, such as the accumulation of apoptotic cells, inflammation and phagoptosis, could exacerbate the pathology in brain disease. Some mechanisms of efferocytosis could be targeted by several promising agents, such as curcumin, URMC-099 and Y-P30, which have emerged as potential treatments for AD. This review aims to investigate and update the current research regarding the signaling molecules and pathways involved in efferocytosis and how these could be targeted as a potential therapy in AD.
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Affiliation(s)
- Amir Tajbakhsh
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Morgayn Read
- Department of Pharmacology, School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Health Research Institute, University of Limerick, Limerick, Ireland
| | | | - Seyed Mohammad Gheibi-Hayat
- Department of Medical Biotechnology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Polish Mother's Memorial Hospital Research Institute (PMMHRI), Lodz, Poland.
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139
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Patrick E, Olah M, Taga M, Klein HU, Xu J, White CC, Felsky D, Agrawal S, Gaiteri C, Chibnik LB, Mostafavi S, Schneider JA, Bennett DA, Bradshaw EM, De Jager PL. A cortical immune network map identifies distinct microglial transcriptional programs associated with β-amyloid and Tau pathologies. Transl Psychiatry 2021; 11:50. [PMID: 33446646 PMCID: PMC7809035 DOI: 10.1038/s41398-020-01175-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/16/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023] Open
Abstract
Microglial dysfunction has been proposed as one of the many cellular mechanisms that can contribute to the development of Alzheimer's disease (AD). Here, using a transcriptional network map of the human frontal cortex, we identify five modules of co-expressed genes related to microglia and assess their role in the neuropathologic features of AD in 540 subjects from two cohort studies of brain aging. Two of these transcriptional programs-modules 113 and 114-relate to the accumulation of β-amyloid, while module 5 relates to tau pathology. We replicate these associations in brain epigenomic data and in two independent datasets. In terms of tau, we propose that module 5, a marker of activated microglia, may lead to tau accumulation and subsequent cognitive decline. We validate our model further by showing that three representative module 5 genes (ACADVL, TRABD, and VASP) encode proteins that are upregulated in activated microglia in AD.
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Affiliation(s)
- Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Marta Olah
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Mariko Taga
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | | | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry & Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Sonal Agrawal
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lori B Chibnik
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Mostafavi
- Paul Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Elizabeth M Bradshaw
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA.
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA.
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140
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Tan MS, Yang YX, Xu W, Wang HF, Tan L, Zuo CT, Dong Q, Tan L, Suckling J, Yu JT. Associations of Alzheimer's disease risk variants with gene expression, amyloidosis, tauopathy, and neurodegeneration. Alzheimers Res Ther 2021; 13:15. [PMID: 33419465 PMCID: PMC7792349 DOI: 10.1186/s13195-020-00755-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Genome-wide association studies have identified more than 30 Alzheimer's disease (AD) risk genes, although the detailed mechanism through which all these genes are associated with AD pathogenesis remains unknown. We comprehensively evaluate the roles of the variants in top 30 non-APOE AD risk genes, based on whether these variants were associated with altered mRNA transcript levels, as well as brain amyloidosis, tauopathy, and neurodegeneration. METHODS Human brain gene expression data were obtained from the UK Brain Expression Consortium (UKBEC), while other data used in our study were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. We examined the association of AD risk allele carrier status with the levels of gene expression in blood and brain regions and tested the association with brain amyloidosis, tauopathy, and neurodegeneration at baseline, using a multivariable linear regression model. Next, we analyzed the longitudinal effects of these variants on the change rates of pathology using a mixed effect model. RESULTS Altogether, 27 variants were detected to be associated with the altered expression of 21 nearby genes in blood and brain regions. Eleven variants (especially novel variants in ADAM10, IGHV1-68, and SLC24A4/RIN3) were associated with brain amyloidosis, 7 variants (especially in INPP5D, PTK2B) with brain tauopathy, and 8 variants (especially in ECHDC3, HS3ST1) with brain neurodegeneration. Variants in ADAMTS1, BZRAP1-AS1, CELF1, CD2AP, and SLC24A4/RIN3 participated in more than one cerebral pathological process. CONCLUSIONS Genetic variants might play functional roles and suggest potential mechanisms in AD pathogenesis, which opens doors to uncover novel targets for AD treatment.
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Affiliation(s)
- Meng-Shan Tan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Yu-Xiang Yang
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, 12th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Wei Xu
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Hui-Fu Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Lin Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Chuan-Tao Zuo
- PET Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, 12th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - John Suckling
- Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, 12th Wulumuqi Zhong Road, Shanghai, 200040, China.
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141
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Farias FHG, Benitez BA, Cruchaga C. Quantitative endophenotypes as an alternative approach to understanding genetic risk in neurodegenerative diseases. Neurobiol Dis 2021; 151:105247. [PMID: 33429041 DOI: 10.1016/j.nbd.2020.105247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 01/02/2023] Open
Abstract
Endophenotypes, as measurable intermediate features of human diseases, reflect underlying molecular mechanisms. The use of quantitative endophenotypes in genetic studies has improved our understanding of pathophysiological changes associated with diseases. The main advantage of the quantitative endophenotypes approach to study human diseases over a classic case-control study design is the inferred biological context that can enable the development of effective disease-modifying treatments. Here, we summarize recent progress on biomarkers for neurodegenerative diseases, including cerebrospinal fluid and blood-based, neuroimaging, neuropathological, and clinical studies. This review focuses on how endophenotypic studies have successfully linked genetic modifiers to disease risk, disease onset, or progression rate and provided biological context to genes identified in genome-wide association studies. Finally, we review critical methodological considerations for implementing this approach and future directions.
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Affiliation(s)
- Fabiana H G Farias
- Department of Psychiatry, Washington University, St. Louis, MO 63110, United States of America; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, United States of America
| | - Bruno A Benitez
- Department of Psychiatry, Washington University, St. Louis, MO 63110, United States of America; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, United States of America
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO 63110, United States of America; NeuroGenomics and Informatics, Washington University, St. Louis, MO 63110, United States of America; Hope Center for Neurologic Diseases, Washington University, St. Louis, MO 63110, United States of America; The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, 63110, United States of America; Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, United States of America.
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142
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Pimenova AA, Herbinet M, Gupta I, Machlovi SI, Bowles KR, Marcora E, Goate AM. Alzheimer's-associated PU.1 expression levels regulate microglial inflammatory response. Neurobiol Dis 2021; 148:105217. [PMID: 33301878 PMCID: PMC7808757 DOI: 10.1016/j.nbd.2020.105217] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/09/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
More than forty loci contribute to genetic risk for Alzheimer's disease (AD). These risk alleles are enriched in myeloid cell enhancers suggesting that microglia, the brain-resident macrophages, contribute to AD risk. We have previously identified SPI1/PU.1, a master regulator of myeloid cell development in the brain and periphery, as a genetic risk factor for AD. Higher expression of SPI1 is associated with increased risk for AD, while lower expression is protective. To investigate the molecular and cellular phenotypes associated with higher and lower expression of PU.1 in microglia, we used stable overexpression and knock-down of PU.1 in BV2, an immortalized mouse microglial cell line. Transcriptome analysis suggests that reduced PU.1 expression suppresses expression of homeostatic genes similar to the disease-associated microglia response to amyloid plaques in mouse models of AD. Moreover, PU.1 knock-down resulted in activation of protein translation, antioxidant action and cholesterol/lipid metabolism pathways with a concomitant decrease of pro-inflammatory gene expression. PU.1 overexpression upregulated and knock-down downregulated phagocytic uptake in BV2 cells independent of the nature of the engulfed material. However, cells with reduced PU.1 expression retained their ability to internalize myelin similar to control albeit with a delay, which aligns with their anti-inflammatory profile. Here we identified several microglial responses that are modulated by PU.1 expression levels and propose that risk association of PU.1 to AD is driven by increased pro-inflammatory response due to increased viability of cells under cytotoxic conditions. In contrast, low expression of PU.1 leads to increased cell death under cytotoxic conditions accompanied by reduced pro-inflammatory signaling that decreased A1 reactive astrocytes signature supporting the protective effect of SPI1 genotype in AD. These findings inform future in vivo validation studies and design of small molecule screens for therapeutic discovery in AD.
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Affiliation(s)
- Anna A Pimenova
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manon Herbinet
- Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, India
| | - Saima I Machlovi
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn R Bowles
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Ronald M. Loeb Center for Alzheimer's disease, Department of Neuroscience, 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; 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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143
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Andrews SJ, Fulton-Howard B, O'Reilly P, Marcora E, Goate AM. Causal Associations Between Modifiable Risk Factors and the Alzheimer's Phenome. Ann Neurol 2021; 89:54-65. [PMID: 32996171 PMCID: PMC8088901 DOI: 10.1002/ana.25918] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The purpose of this study was to infer causal relationships between 22 previously reported risk factors for Alzheimer's disease (AD) and the "AD phenome": AD, AD age of onset (AAOS), hippocampal volume, cortical surface area and thickness, cerebrospinal fluid (CSF) levels of amyloid-β (Aβ42 ), tau, and ptau181 , and the neuropathological burden of neuritic plaques, neurofibrillary tangles (NFTs), and vascular brain injury (VBI). METHODS Polygenic risk scores (PRS) for the 22 risk factors were computed in 26,431 AD cases/controls and the association with AD was evaluated using logistic regression. Two-sample Mendelian randomization (MR) was used to infer the causal effect of risk factors on the AD phenome. RESULTS PRS for increased education and diastolic blood pressure were associated with reduced risk for AD. MR indicated that only education was causally associated with reduced risk of AD, delayed AAOS, and increased cortical surface area and thickness. Total- and LDL-cholesterol levels were causally associated with increased neuritic plaque burden, although the effects were driven by single nucleotide polymorphisms (SNPs) within the APOE locus. Diastolic blood pressure and pulse pressure are causally associated with increased risk of VBI. Furthermore, total cholesterol was associated with decreased hippocampal volume; smoking initiation with decreased cortical thickness; type 2 diabetes with an earlier AAOS; and sleep duration with increased cortical thickness. INTERPRETATION Our comprehensive examination of the genetic evidence for the causal relationships between previously reported risk factors in AD using PRS and MR supports a causal role for education, blood pressure, cholesterol levels, smoking, and diabetes with the AD phenome. ANN NEUROL 2021;89:54-65.
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Affiliation(s)
- Shea J Andrews
- 'Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- 'Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Edoardo Marcora
- 'Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 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
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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144
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How wide is the application of genetic big data in biomedicine. Biomed Pharmacother 2020; 133:111074. [PMID: 33378973 DOI: 10.1016/j.biopha.2020.111074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the era of big data, massive genetic data, as a new industry, has quickly swept almost all industries, especially the pharmaceutical industry. As countries around the world start to build their own gene banks, scientists study the data to explore the origins and migration of humans. Moreover, big data encourage the development of cancer therapy and bring good news to cancer patients. Big datum has been involved in the study of many diseases, and it has been found that analyzing diseases at the gene level can lead to more beneficial treatment options than ordinary treatments. This review will introduce the development of extensive data in medical research from the perspective of big data and tumor, neurological and psychiatric diseases, cardiovascular diseases, other applications and the development direction of big data in medicine.
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145
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Doostparast Torshizi A, Ionita-Laza I, Wang K. Cell Type-Specific Annotation and Fine Mapping of Variants Associated With Brain Disorders. Front Genet 2020; 11:575928. [PMID: 33343624 PMCID: PMC7744805 DOI: 10.3389/fgene.2020.575928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Common genetic variants confer susceptibility to a large number of complex brain disorders. Given that such variants predominantly localize in non-coding regions of the human genome, there is a significant challenge to predict and characterize their functional consequences. More importantly, most available computational methods, generally defined as context-free methods, output prediction scores regarding the functionality of genetic variants irrespective of the context, i.e., the tissue or cell-type affected by a disease, limiting the ability to predict the functional consequences of common variants on brain disorders. In this study, we introduce a comparative multi-step pipeline to investigate the relative effectiveness of context-specific and context-free approaches to prioritize disease causal variants. As an experimental case, we focused on schizophrenia (SCZ), a debilitating neuropsychiatric disease for which a large number of susceptibility variants is identified from genome-wide association studies. We tested over two dozen available methods and examined potential associations between the cell/tissue-specific mapping scores and open chromatin accessibility, and provided a prioritized map of SCZ risk loci for in vitro or in-vivo functional analysis. We found extensive differences between context-free and tissue-specific approaches and showed how they may play complementary roles. As a proof of concept, we found a few sets of genes, through a consensus mapping of both categories, including FURIN to be among the top hits. We showed that the genetic variants in this gene and related genes collectively dysregulate gene expression patterns in stem cell-derived neurons and characterize SCZ phenotypic manifestations, while genes which were not shared among highly prioritized candidates in both approaches did not demonstrate such characteristics. In conclusion, by combining context-free and tissue-specific predictions, our pipeline enables prioritization of the most likely disease-causal common variants in complex brain disorders.
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Affiliation(s)
- Abolfazl Doostparast Torshizi
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Columbia University, New York, NY, United States
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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146
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Lewcock JW, Schlepckow K, Di Paolo G, Tahirovic S, Monroe KM, Haass C. Emerging Microglia Biology Defines Novel Therapeutic Approaches for Alzheimer’s Disease. Neuron 2020; 108:801-821. [DOI: 10.1016/j.neuron.2020.09.029] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 02/01/2023]
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147
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Podleśny-Drabiniok A, Marcora E, Goate AM. Microglial Phagocytosis: A Disease-Associated Process Emerging from Alzheimer’s Disease Genetics. Trends Neurosci 2020; 43:965-979. [DOI: 10.1016/j.tins.2020.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/02/2020] [Accepted: 10/05/2020] [Indexed: 01/02/2023]
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148
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Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L. Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease. Nat Commun 2020; 11:6114. [PMID: 33257653 PMCID: PMC7704686 DOI: 10.1038/s41467-020-19791-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
DNA methylation differences in Alzheimer's disease (AD) have been reported. Here, we conducted a meta-analysis of more than 1000 prefrontal cortex brain samples to prioritize the most consistent methylation differences in multiple cohorts. Using a uniform analysis pipeline, we identified 3751 CpGs and 119 differentially methylated regions (DMRs) significantly associated with Braak stage. Our analysis identified differentially methylated genes such as MAMSTR, AGAP2, and AZU1. The most significant DMR identified is located on the MAMSTR gene, which encodes a cofactor that stimulates MEF2C. Notably, MEF2C cooperates with another transcription factor, PU.1, a central hub in the AD gene network. Our enrichment analysis highlighted the potential roles of the immune system and polycomb repressive complex 2 in pathological AD. These results may help facilitate future mechanistic and biomarker discovery studies in AD.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Brian W Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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149
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Schartz ND, Tenner AJ. The good, the bad, and the opportunities of the complement system in neurodegenerative disease. J Neuroinflammation 2020; 17:354. [PMID: 33239010 PMCID: PMC7690210 DOI: 10.1186/s12974-020-02024-8] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
The complement cascade is a critical effector mechanism of the innate immune system that contributes to the rapid clearance of pathogens and dead or dying cells, as well as contributing to the extent and limit of the inflammatory immune response. In addition, some of the early components of this cascade have been clearly shown to play a beneficial role in synapse elimination during the development of the nervous system, although excessive complement-mediated synaptic pruning in the adult or injured brain may be detrimental in multiple neurogenerative disorders. While many of these later studies have been in mouse models, observations consistent with this notion have been reported in human postmortem examination of brain tissue. Increasing awareness of distinct roles of C1q, the initial recognition component of the classical complement pathway, that are independent of the rest of the complement cascade, as well as the relationship with other signaling pathways of inflammation (in the periphery as well as the central nervous system), highlights the need for a thorough understanding of these molecular entities and pathways to facilitate successful therapeutic design, including target identification, disease stage for treatment, and delivery in specific neurologic disorders. Here, we review the evidence for both beneficial and detrimental effects of complement components and activation products in multiple neurodegenerative disorders. Evidence for requisite co-factors for the diverse consequences are reviewed, as well as the recent studies that support the possibility of successful pharmacological approaches to suppress excessive and detrimental complement-mediated chronic inflammation, while preserving beneficial effects of complement components, to slow the progression of neurodegenerative disease.
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Affiliation(s)
- Nicole D. Schartz
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697 USA
| | - Andrea J. Tenner
- Department of Molecular Biology and Biochemistry, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697 USA
- Department of Neurobiology and Behavior, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697 USA
- Department of Pathology and Laboratory Medicine, University of California Irvine, 3205 McGaugh Hall, Irvine, CA 92697 USA
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150
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Liu W, Taso O, Wang R, Bayram S, Graham AC, Garcia-Reitboeck P, Mallach A, Andrews WD, Piers TM, Botia JA, Pocock JM, Cummings DM, Hardy J, Edwards FA, Salih DA. Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions. Hum Mol Genet 2020; 29:3224-3248. [PMID: 32959884 PMCID: PMC7689298 DOI: 10.1093/hmg/ddaa209] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies have reported that, amongst other microglial genes, variants in TREM2 can profoundly increase the incidence of developing Alzheimer's disease (AD). We have investigated the role of TREM2 in primary microglial cultures from wild type mice by using siRNA to decrease Trem2 expression, and in parallel from knock-in mice heterozygous or homozygous for the Trem2 R47H AD risk variant. The prevailing phenotype of Trem2 R47H knock-in mice was decreased expression levels of Trem2 in microglia, which resulted in decreased density of microglia in the hippocampus. Overall, primary microglia with reduced Trem2 expression, either by siRNA or from the R47H knock-in mice, displayed a similar phenotype. Comparison of the effects of decreased Trem2 expression under conditions of lipopolysaccharide (LPS) pro-inflammatory or IL-4 anti-inflammatory stimulation revealed the importance of Trem2 in driving a number of the genes up-regulated in the anti-inflammatory phenotype. RNA-seq analysis showed that IL-4 induced the expression of a program of genes including Arg1 and Ap1b1 in microglia, which showed an attenuated response to IL-4 when Trem2 expression was decreased. Genes showing a similar expression profile to Arg1 were enriched for STAT6 transcription factor recognition elements in their promoter, and Trem2 knockdown decreased levels of STAT6. LPS-induced pro-inflammatory stimulation suppressed Trem2 expression, thus preventing TREM2's anti-inflammatory drive. Given that anti-inflammatory signaling is associated with tissue repair, understanding the signaling mechanisms downstream of Trem2 in coordinating the pro- and anti-inflammatory balance of microglia, particularly mediating effects of the IL-4-regulated anti-inflammatory pathway, has important implications for fighting neurodegenerative disease.
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Affiliation(s)
- Wenfei Liu
- Department of Neuroscience, Physiology and Pharmacology, UCL, London WC1E 6BT, UK
| | - Orjona Taso
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
| | - Rui Wang
- Department of Neuroscience, Physiology and Pharmacology, UCL, London WC1E 6BT, UK
| | | | | | | | - Anna Mallach
- Department of Neuroinflammation, Institute of Neurology, UCL, London WC1N 1PJ, UK
| | - William D Andrews
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
| | - Thomas M Piers
- Department of Neuroinflammation, Institute of Neurology, UCL, London WC1N 1PJ, UK
| | - Juan A Botia
- Department of Information and Communications Engineering, Universidad de Murcia, Murcia E-30100, Spain
- Department of Neurodegenerative Diseases, Institute of Neurology, UCL, London WC1N 1PJ, UK
| | - Jennifer M Pocock
- Department of Neuroinflammation, Institute of Neurology, UCL, London WC1N 1PJ, UK
| | - Damian M Cummings
- Department of Neuroscience, Physiology and Pharmacology, UCL, London WC1E 6BT, UK
| | - John Hardy
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
- Department of Neurodegenerative Diseases, Institute of Neurology, UCL, London WC1N 1PJ, UK
| | - Frances A Edwards
- Department of Neuroscience, Physiology and Pharmacology, UCL, London WC1E 6BT, UK
| | - Dervis A Salih
- Department of Neuroscience, Physiology and Pharmacology, UCL, London WC1E 6BT, UK
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
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