151
|
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]
|
152
|
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.
Collapse
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.
| |
Collapse
|
153
|
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.
Collapse
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
| |
Collapse
|
154
|
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: 78] [Impact Index Per Article: 19.5] [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.
Collapse
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
| |
Collapse
|
155
|
Elmaleh DR, Farlow MR, Conti PS, Tompkins RG, Kundakovic L, Tanzi RE. Developing Effective Alzheimer's Disease Therapies: Clinical Experience and Future Directions. J Alzheimers Dis 2020; 71:715-732. [PMID: 31476157 PMCID: PMC6839593 DOI: 10.3233/jad-190507] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) clinical trials, focused on disease modifying drugs and conducted in patients with mild to moderate AD, as well as prodromal (early) AD, have failed to reach efficacy endpoints in improving cognitive function in most cases to date or have been terminated due to adverse events. Drugs that have reached clinical stage were reviewed using web resources (such as clinicaltrials.gov, alzforum.org, company press releases, and peer reviewed literature) to identify late stage (Phase II and Phase III) efficacy clinical trials and summarize reasons for their failure. For each drug, only the latest clinical trials and ongoing trials that aimed at improving cognitive function were included in the analysis. Here we highlight the potential reasons that have hindered clinical success, including clinical trial design and choice of outcome measures, heterogeneity of patient populations, difficulties in diagnosing and staging the disease, drug design, mechanism of action, and toxicity related to the long-term use. We review and suggest approaches for AD clinical trial design aimed at improving our ability to identify novel therapies for this devastating disease.
Collapse
Affiliation(s)
- David R Elmaleh
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA.,AZTherapies Inc., Boston, MA, USA
| | - Martin R Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter S Conti
- Molecular Imaging Center, Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ronald G Tompkins
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Rudolph E Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Diseases (MIND), Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| |
Collapse
|
156
|
Manzali SB, Ravona-Springer R, Alkelai A, Yu E, Gan-Or Z, Ganmore I, Heymann A, Beeri MS, Greenbaum L. Association of the CD2AP locus with cognitive functioning among middle-aged individuals with a family history of Alzheimer's disease. Neurobiol Aging 2020; 101:50-56. [PMID: 33578194 DOI: 10.1016/j.neurobiolaging.2020.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/19/2022]
Abstract
First-degree family history is an established risk factor for Alzheimer's disease (AD). We investigated the association of late-onset AD risk loci with cognitive functioning among 315 offspring of AD patients. Participants were cognitively normal Jewish individuals, aged 40-65 years, from the Israel Registry for Alzheimer's Prevention (IRAP) study. Twenty-two single-nucleotide polymorphisms (SNPs) within these loci and the APOE E4 allele were included in the final analyses, and a polygenic risk score was also calculated. Using linear regression (assuming an additive genetic model), we found a significant association only for SNP rs9473117, located near the CD2-associated protein (CD2AP) gene, with global cognition. Controlling for demographic variables (age, sex, years of education, and ancestry), the late-onset AD risk allele C was associated with lower global cognitive functioning (p = 0.0005), and withstood correction for multiple testing. After adjusting for additional characteristics (APOE E4 status and then also for cardiovascular factors), the results remained essentially unchanged (p = 0.0003 and p = 0.0005, respectively). In secondary analyses examining specific cognitive domains, rs9473117 was similarly associated with episodic memory (p = 0.005), language (p = 0.009), and working memory/attention (p = 0.018) but not with executive functions (p = 0.27). Again, the results were similar after adjusting for APOE E4 status and cardiovascular factors. The polygenic risk score was not associated with global cognitive functioning or with any of the 4 domains. In conclusion, our findings suggest a contribution of the CD2AP locus to cognitive functioning in middle-aged individuals with a parental history of AD. Further validations, including in longitudinal studies, are required.
Collapse
Affiliation(s)
- Sigalit Batia Manzali
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Ithamar Ganmore
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.
| |
Collapse
|
157
|
Roy ER, Cao W. Antiviral Immune Response in Alzheimer's Disease: Connecting the Dots. Front Neurosci 2020; 14:577744. [PMID: 33132831 PMCID: PMC7561672 DOI: 10.3389/fnins.2020.577744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/08/2020] [Indexed: 11/15/2022] Open
Abstract
Alzheimer’s disease (AD) represents an enormous public health challenge currently and with increasing urgency in the coming decades. Our understanding of the etiology and pathogenesis of AD is rather incomplete, which is manifested in stagnated therapeutic developments. Apart from the well-established Amyloid Hypothesis of AD, gaining traction in recent years is the Pathogen Hypothesis, which postulates a causal role of infectious agents in the development of AD. Particularly, infection by viruses, among a diverse range of microorganisms, has been implicated. Recently, we described a prominent antiviral immune response in human AD brains as well as murine amyloid beta models, which has consequential effects on neuropathology. Such findings expectedly allude to the question about viral infections and AD. In this Perspective, we would like to discuss the molecular mechanism underlying the antiviral immune response, highlight how such pathway directly promotes AD pathogenesis, and depict a multilayered connection between antiviral immune response and other agents and factors relevant to AD. By tying together these threads of evidence, we provide a cohesive perspective on the uprising of antiviral immune response in AD.
Collapse
Affiliation(s)
- Ethan R Roy
- Huffington Center on Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Wei Cao
- Huffington Center on Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
158
|
CELF2 regulates the species-specific alternative splicing of TREM2. Sci Rep 2020; 10:17995. [PMID: 33093587 PMCID: PMC7582162 DOI: 10.1038/s41598-020-75057-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/12/2020] [Indexed: 11/08/2022] Open
Abstract
Genetic variations of TREM2 have been implicated as a risk factor of Alzheimer’s disease (AD). Recent studies suggest that the loss of TREM2 function compromises microglial responses to the accumulation of amyloid beta. Previously, we found that exon 3 of TREM2 is an alternative exon whose skipping leads to a reduction in full-length TREM2 protein by inducing nonsense-mediated mRNA decay. Here, we aimed to identify factors regulating TREM2 splicing. Using a panel of RNA-binding proteins, we found that exon 3 skipping of TREM2 was promoted by two paralogous proteins, CELF1 and CELF2, which were both linked previously with risk loci of AD. Although the overexpression of both CELF1 and CELF2 enhanced exon 3 skipping, only CELF2 reduced the expression of full-length TREM2 protein. Notably, the TREM2 ortholog in the green monkey, but not in the mouse, showed alternative splicing of exon 3 like human TREM2. Similarly, splicing regulation of exon 3 by CELF1/2 was found to be common to humans and monkeys. Using chimeric minigenes of human and mouse TREM2, we mapped a CELF-responsive sequence within intron 3 of human TREM2. Collectively, our results revealed a novel regulatory factor of TREM2 expression and highlighted a species-dependent difference of its regulation.
Collapse
|
159
|
Xiao X, Liu X, Jiao B. Epigenetics: Recent Advances and Its Role in the Treatment of Alzheimer's Disease. Front Neurol 2020; 11:538301. [PMID: 33178099 PMCID: PMC7594522 DOI: 10.3389/fneur.2020.538301] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Objective: This review summarizes recent findings on the epigenetics of Alzheimer's disease (AD) and provides therapeutic strategies for AD. Methods: We searched the following keywords: “genetics,” “epigenetics,” “Alzheimer's disease,” “DNA methylation,” “DNA hydroxymethylation,” “histone modifications,” “non-coding RNAs,” and “therapeutic strategies” in PubMed. Results: In this review, we summarizes recent studies of epigenetics in AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs. There are no consistent results of global DNA methylation/hydroxymethylation in AD. Epigenetic genome-wide association studies show that many differentially methylated sites exist in AD. Several studies investigate the role of histone modifications in AD; for example, histone acetylation decreases, whereas H3 phosphorylation increases significantly in AD. In addition, non-coding RNAs, such as microRNA-16 and BACE1-antisense transcript (BACE1-AS), are associated with the pathology of AD. These epigenetic changes provide us with novel insights into the pathogenesis of AD and may be potential therapeutic strategies for AD. Conclusion: Epigenetics is associated with the pathogenesis of AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs, which provide potential therapeutic strategies for AD.
Collapse
Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| |
Collapse
|
160
|
Morabito S, Miyoshi E, Michael N, Swarup V. Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease. Hum Mol Genet 2020; 29:2899-2919. [PMID: 32803238 PMCID: PMC7566321 DOI: 10.1093/hmg/ddaa182] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/10/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Alzheimer's disease (AD) is a devastating neurological disorder characterized by changes in cell-type proportions and consequently marked alterations of the transcriptome. Here we use a data-driven systems biology meta-analytical approach across three human AD cohorts, encompassing six cortical brain regions, and integrate with multi-scale datasets comprising of DNA methylation, histone acetylation, transcriptome- and genome-wide association studies and quantitative trait loci to further characterize the genetic architecture of AD. We perform co-expression network analysis across more than 1200 human brain samples, identifying robust AD-associated dysregulation of the transcriptome, unaltered in normal human aging. We assess the cell-type specificity of AD gene co-expression changes and estimate cell-type proportion changes in human AD by integrating co-expression modules with single-cell transcriptome data generated from 27 321 nuclei from human postmortem prefrontal cortical tissue. We also show that genetic variants of AD are enriched in a microglial AD-associated module and identify key transcription factors regulating co-expressed modules. Additionally, we validate our results in multiple published human AD gene expression datasets, which can be easily accessed using our online resource (https://swaruplab.bio.uci.edu/consensusAD).
Collapse
Affiliation(s)
- Samuel Morabito
- Mathematical, Computational and Systems Biology (MCSB) Program, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| | - Emily Miyoshi
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| | - Neethu Michael
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, CA 92697, USA
| |
Collapse
|
161
|
Sierksma A, Escott-Price V, De Strooper B. Translating genetic risk of Alzheimer’s disease into mechanistic insight and drug targets. Science 2020; 370:61-66. [DOI: 10.1126/science.abb8575] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To provide better prevention and treatment, we need to understand the environmental and genetic risks of Alzheimer’s disease (AD). However, the definition of AD has been confounded with dementia in many studies. Thus, overinterpretation of genetic findings with regard to mechanisms and drug targets may explain, in part, controversies in the field. Here, we analyze the different forms of genetic risk of AD and how these can be used to model disease. We stress the importance of studying gene variants in the right cell types and in the right pathological context. The lack of mechanistic understanding of genetic variation has become the major bottleneck in the search for new drug targets for AD.
Collapse
Affiliation(s)
- Annerieke Sierksma
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- UK Dementia Research Institute, Cardiff University, Cardiff, UK
| | - Bart De Strooper
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven (University of Leuven), Leuven, Belgium
- UK Dementia Research Institute, University College London, London, UK
| |
Collapse
|
162
|
Dragunow M. Human Brain Neuropharmacology: A Platform for Translational Neuroscience. Trends Pharmacol Sci 2020; 41:777-792. [PMID: 32994050 DOI: 10.1016/j.tips.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/10/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022]
Abstract
Central nervous system (CNS) drug development has been plagued by a failure to translate effective therapies from the lab to the clinic. There are many potential reasons for this, including poor understanding of brain pharmacokinetic (PK) and pharmacodynamic (PD) factors, preclinical study flaws, clinical trial design issues, the complexity and variability of human brain diseases, as well as species differences. To address some of these problems, we have developed a platform for CNS drug discovery comprising: drug screening of primary adult human brain cells; human brain tissue microarray analysis of drug targets; and high-content phenotypic screening methods. In this opinion, I summarise the theoretical basis and the practical development and use of this platform in CNS drug discovery.
Collapse
Affiliation(s)
- Mike Dragunow
- Department of Pharmacology and Hugh Green Biobank, Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
| |
Collapse
|
163
|
Zhang Q, Sidorenko J, Couvy-Duchesne B, Marioni RE, Wright MJ, Goate AM, Marcora E, Huang KL, Porter T, Laws SM, Sachdev PS, Mather KA, Armstrong NJ, Thalamuthu A, Brodaty H, Yengo L, Yang J, Wray NR, McRae AF, Visscher PM. Risk prediction of late-onset Alzheimer's disease implies an oligogenic architecture. Nat Commun 2020; 11:4799. [PMID: 32968074 PMCID: PMC7511365 DOI: 10.1038/s41467-020-18534-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/25/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic association studies have identified 44 common genome-wide significant risk loci for late-onset Alzheimer's disease (LOAD). However, LOAD genetic architecture and prediction are unclear. Here we estimate the optimal P-threshold (Poptimal) of a genetic risk score (GRS) for prediction of LOAD in three independent datasets comprising 676 cases and 35,675 family history proxy cases. We show that the discriminative ability of GRS in LOAD prediction is maximised when selecting a small number of SNPs. Both simulation results and direct estimation indicate that the number of causal common SNPs for LOAD may be less than 100, suggesting LOAD is more oligogenic than polygenic. The best GRS explains approximately 75% of SNP-heritability, and individuals in the top decile of GRS have ten-fold increased odds when compared to those in the bottom decile. In addition, 14 variants are identified that contribute to both LOAD risk and age at onset of LOAD.
Collapse
Affiliation(s)
- Qian Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Baptiste Couvy-Duchesne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Alison M Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Edoardo Marcora
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kuan-Lin Huang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tenielle Porter
- Collaborative Genomics Group, Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Simon M Laws
- Collaborative Genomics Group, Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, Sydney, NSW, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Murdoch University, Perth, WA, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Neuroscience Research Australia, Sydney, NSW, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
- Dementia Centre for Research Collaboration, University of New South Wales, Sydney, NSW, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
164
|
Finkbeiner S. Functional genomics, genetic risk profiling and cell phenotypes in neurodegenerative disease. Neurobiol Dis 2020; 146:105088. [PMID: 32977020 PMCID: PMC7686089 DOI: 10.1016/j.nbd.2020.105088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 12/03/2022] Open
Abstract
Human genetics provides unbiased insights into the causes of human disease, which can be used to create a foundation for effective ways to more accurately diagnose patients, stratify patients for more successful clinical trials, discover and develop new therapies, and ultimately help patients choose the safest and most promising therapeutic option based on their risk profile. But the process for translating basic observations from human genetics studies into pathogenic disease mechanisms and treatments is laborious and complex, and this challenge has particularly slowed the development of interventions for neurodegenerative disease. In this review, we discuss the many steps in the process, the important considerations at each stage, and some of the latest tools and technologies that are available to help investigators translate insights from human genetics into diagnostic and therapeutic strategies that will lead to the sort of advances in clinical care that make a difference for patients.
Collapse
Affiliation(s)
- Steven Finkbeiner
- Center for Systems and Therapeutics, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of Califorina, San Francisco, CA 94158, USA.
| |
Collapse
|
165
|
Sun J, Chen J, Li T, Huang P, Li J, Shen M, Gao M, Sun Y, Liang J, Li X, Wang Y, Xiao Y, Shi X, Hu Y, Feng J, Jia H, Liu T, Sun X. ROS production and mitochondrial dysfunction driven by PU.1-regulated NOX4-p22 phox activation in Aβ-induced retinal pigment epithelial cell injury. Am J Cancer Res 2020; 10:11637-11655. [PMID: 33052238 PMCID: PMC7546003 DOI: 10.7150/thno.48064] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Rationale: Amyloid β (Aβ) deposition, an essential pathological process in age-related macular degeneration (AMD), causes retinal pigment epithelium (RPE) degeneration driven mostly by oxidative stress. However, despite intense investigations, the extent to which overoxidation contributes to Aβ-mediated RPE damage and its potential mechanism has not been fully elucidated. Methods: We performed tandem mass-tagged (TMT) mass spectrometry (MS) and bioinformatic analysis of the RPE-choroid complex in an Aβ1-40-induced mouse model of retinal degeneration to obtain a comprehensive proteomic profile. Key regulators in this model were confirmed by reactive oxygen species (ROS) detection, mitochondrial ROS assay, oxygen consumption rate (OCR) measurement, gene knockout experiment, chromatin immunoprecipitation (ChIP), and luciferase assay. Results: A total of 4243 proteins were identified, 1069 of which were significantly affected by Aβ1-40 and found to be enriched in oxidation-related pathways by bioinformatic analysis. Moreover, NADPH oxidases were identified as hub proteins in Aβ1-40-mediated oxidative stress, as evidenced by mitochondrial dysfunction and reactive oxygen species overproduction. By motif and binding site analyses, we found that the transcription factor PU.1/Spi1 acted as a master regulator of the activation of NADPH oxidases, especially the NOX4-p22phox complex. Also, PU.1 silencing impeded RPE oxidative stress and mitochondrial dysfunction and rescued the retinal structure and function. Conclusion: Our study suggests that PU.1 is a novel therapeutic target for AMD, and the regulation of PU.1 expression represents a potentially novel approach against excessive oxidative stress in Aβ-driven RPE injury.
Collapse
|
166
|
Li C, Wu D, Lu Q. Set-based genetic association and interaction tests for survival outcomes based on weighted V statistics. Genet Epidemiol 2020; 45:46-63. [PMID: 32896012 DOI: 10.1002/gepi.22353] [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: 04/10/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 01/07/2023]
Abstract
With advancements in high-throughout technologies, studies have been conducted to investigate the role of massive genetic variants in human diseases. While set-based tests have been developed for binary and continuous disease outcomes, there are few computationally efficient set-based tests available for time-to-event outcomes. To facilitate the genetic association and interaction analyses of time-to-event outcomes, We develop a suite of multivariant tests based on weighted V statistics with or without considering potential genetic heterogeneity. In addition to the computation efficiency and nice asymptotic properties, all the new tests can deal with left truncation and competing risks in the survival data, and adjust for covariates. Simulation studies show that the new tests run faster, are more accurate in small samples, and account for confounding effect better than the existing multivariant survival tests. When the genetic effect is heterogeneous across individuals/subpopulations, the association test considering genetic heterogeneity is more powerful than the existing tests that do not account for genetic heterogeneity. Using the new methods, we perform a genome-wide association analysis of the genotype and age-to-Alzheimer's data from the Rush Memory and Aging Project and the Religious Orders Study. The analysis identifies two genes, APOE and APOC1, associated with age to Alzheimer's disease onset.
Collapse
Affiliation(s)
- Chenxi Li
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Di Wu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Qing Lu
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
167
|
Neuner SM, Tcw J, Goate AM. Genetic architecture of Alzheimer's disease. Neurobiol Dis 2020; 143:104976. [PMID: 32565066 PMCID: PMC7409822 DOI: 10.1016/j.nbd.2020.104976] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Advances in genetic and genomic technologies over the last thirty years have greatly enhanced our knowledge concerning the genetic architecture of Alzheimer's disease (AD). Several genes including APP, PSEN1, PSEN2, and APOE have been shown to exhibit large effects on disease susceptibility, with the remaining risk loci having much smaller effects on AD risk. Notably, common genetic variants impacting AD are not randomly distributed across the genome. Instead, these variants are enriched within regulatory elements active in human myeloid cells, and to a lesser extent liver cells, implicating these cell and tissue types as critical to disease etiology. Integrative approaches are emerging as highly effective for identifying the specific target genes through which AD risk variants act and will likely yield important insights related to potential therapeutic targets in the coming years. In the future, additional consideration of sex- and ethnicity-specific contributions to risk as well as the contribution of complex gene-gene and gene-environment interactions will likely be necessary to further improve our understanding of AD genetic architecture.
Collapse
Affiliation(s)
- Sarah M Neuner
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Julia Tcw
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Alison M Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
| |
Collapse
|
168
|
Kalra G, Milon B, Casella AM, Herb BR, Humphries E, Song Y, Rose KP, Hertzano R, Ament SA. Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty. PLoS Genet 2020; 16:e1009025. [PMID: 32986727 PMCID: PMC7544108 DOI: 10.1371/journal.pgen.1009025] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/08/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 330,759) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5x10-8), of which eight have not been reported previously in the peer-reviewed literature. We investigated the regulatory and cell specific expression for these loci by generating mRNA-seq, ATAC-seq, and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were most strongly enriched for expression in cochlear epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. Regions of the human genome homologous to open chromatin in epithelial cells from the mouse were strongly enriched for heritable risk for hearing difficulty, even after adjusting for baseline effects of evolutionary conservation and cell-type non-specific regulatory regions. Epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. Of these, 39 were expressed robustly in mouse cochlea and 16 were enriched specifically in sensory hair cells. These results reveal new risk loci and risk genes for hearing difficulty and suggest an important role for altered gene regulation in the cochlear sensory epithelium.
Collapse
Affiliation(s)
- Gurmannat Kalra
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Beatrice Milon
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Alex M. Casella
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Physician Scientist Training Program, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Elizabeth Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Kevin P. Rose
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Ronna Hertzano
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Seth A. Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States of America
| |
Collapse
|
169
|
Baggiani M, Dell’Anno MT, Pistello M, Conti L, Onorati M. Human Neural Stem Cell Systems to Explore Pathogen-Related Neurodevelopmental and Neurodegenerative Disorders. Cells 2020; 9:E1893. [PMID: 32806773 PMCID: PMC7464299 DOI: 10.3390/cells9081893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 12/18/2022] Open
Abstract
Building and functioning of the human brain requires the precise orchestration and execution of myriad molecular and cellular processes, across a multitude of cell types and over an extended period of time. Dysregulation of these processes affects structure and function of the brain and can lead to neurodevelopmental, neurological, or psychiatric disorders. Multiple environmental stimuli affect neural stem cells (NSCs) at several levels, thus impairing the normal human neurodevelopmental program. In this review article, we will delineate the main mechanisms of infection adopted by several neurotropic pathogens, and the selective NSC vulnerability. In particular, TORCH agents, i.e., Toxoplasma gondii, others (including Zika virus and Coxsackie virus), Rubella virus, Cytomegalovirus, and Herpes simplex virus, will be considered for their devastating effects on NSC self-renewal with the consequent neural progenitor depletion, the cellular substrate of microcephaly. Moreover, new evidence suggests that some of these agents may also affect the NSC progeny, producing long-term effects in the neuronal lineage. This is evident in the paradigmatic example of the neurodegeneration occurring in Alzheimer's disease.
Collapse
Affiliation(s)
- Matteo Baggiani
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, 56126 Pisa, Italy;
| | - Maria Teresa Dell’Anno
- Cellular Engineering Laboratory, Fondazione Pisana per la Scienza ONLUS, 56017 Pisa, Italy;
| | - Mauro Pistello
- Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa and Virology Division, Pisa University Hospital, 56100 Pisa, Italy;
| | - Luciano Conti
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38122 Trento, Italy;
| | - Marco Onorati
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, 56126 Pisa, Italy;
| |
Collapse
|
170
|
Zhou X, Chen Y, Ip FCF, Lai NCH, Li YYT, Jiang Y, Zhong H, Chen Y, Zhang Y, Ma S, Lo RMN, Cheung K, Tong EPS, Ko H, Shoai M, Mok KY, Hardy J, Mok VCT, Kwok TCY, Fu AKY, Ip NY. Genetic and polygenic risk score analysis for Alzheimer's disease in the Chinese population. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2020; 12:e12074. [PMID: 32775599 PMCID: PMC7403835 DOI: 10.1002/dad2.12074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Dozens of Alzheimer's disease (AD)-associated loci have been identified in European-descent populations, but their effects have not been thoroughly investigated in the Hong Kong Chinese population. METHODS TaqMan array genotyping was performed for known AD-associated variants in a Hong Kong Chinese cohort. Regression analysis was conducted to study the associations of variants with AD-associated traits and biomarkers. Lasso regression was applied to establish a polygenic risk score (PRS) model for AD risk prediction. RESULTS SORL1 is associated with AD in the Hong Kong Chinese population. Meta-analysis corroborates the AD-protective effect of the SORL1 rs11218343 C allele. The PRS is developed and associated with AD risk, cognitive status, and AD-related endophenotypes. TREM2 H157Y might influence the amyloid beta 42/40 ratio and levels of immune-associated proteins in plasma. DISCUSSION SORL1 is associated with AD in the Hong Kong Chinese population. The PRS model can predict AD risk and cognitive status in this population.
Collapse
Affiliation(s)
- Xiaopu Zhou
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Yu Chen
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
- The Brain Cognition and Brain Disease InstituteShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
| | - Fanny C. F. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Nicole C. H. Lai
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Yolanda Y. T. Li
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Yuanbing Jiang
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Huan Zhong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Yuewen Chen
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Yulin Zhang
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Shuangshuang Ma
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Ronnie M. N. Lo
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Kit Cheung
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Estella P. S. Tong
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Ho Ko
- Division of NeurologyDepartment of Medicine and TherapeuticsLi Ka Shing Institute of Health SciencesSchool of Biomedical SciencesGerald Choa Neuroscience CenterFaculty of MedicineThe Chinese University of Hong KongShatinHong KongChina
| | - Maryam Shoai
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - Kin Y. Mok
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - John Hardy
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
- Institute for Advanced StudyThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
| | - Vincent C. T. Mok
- Gerald Choa Neuroscience CentreLui Che Woo Institute of Innovative MedicineTherese Pei Fong Chow Research Centre for Prevention of DementiaDivision of NeurologyDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongShatinHong KongChina
| | - Timothy C. Y. Kwok
- Therese Pei Fong Chow Research Centre for Prevention of DementiaDivision of GeriatricsDepartment of Medicine and TherapeuticsThe Chinese University of Hong KongShatinHong KongChina
| | - Amy K. Y. Fu
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| | - Nancy Y. Ip
- Division of Life ScienceState Key Laboratory of Molecular Neuroscience and Molecular Neuroscience CenterThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong KongChina
- Hong Kong Center for Neurodegenerative DiseasesHong Kong Science ParkHong KongChina
- Guangdong Provincial Key Laboratory of Brain ScienceDisease and Drug DevelopmentHKUST Shenzhen Research InstituteShenzhen‐Hong Kong Institute of Brain ScienceShenzhenGuangdongChina
| |
Collapse
|
171
|
Dumitrescu L, Mahoney ER, Mukherjee S, Lee ML, Bush WS, Engelman CD, Lu Q, Fardo DW, Trittschuh EH, Mez J, Kaczorowski C, Hernandez Saucedo H, Widaman KF, Buckley R, Properzi M, Mormino E, Yang HS, Harrison T, Hedden T, Nho K, Andrews SJ, Tommet D, Hadad N, Sanders RE, Ruderfer DM, Gifford KA, Moore AM, Cambronero F, Zhong X, Raghavan NS, Vardarajan B, Pericak-Vance MA, Farrer LA, Wang LS, Cruchaga C, Schellenberg G, Cox NJ, Haines JL, Keene CD, Saykin AJ, Larson EB, Sperling RA, Mayeux R, Bennett DA, Schneider JA, Crane PK, Jefferson AL, Hohman TJ. Genetic variants and functional pathways associated with resilience to Alzheimer's disease. Brain 2020; 143:2561-2575. [PMID: 32844198 PMCID: PMC7447518 DOI: 10.1093/brain/awaa209] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/22/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
Approximately 30% of older adults exhibit the neuropathological features of Alzheimer's disease without signs of cognitive impairment. Yet, little is known about the genetic factors that allow these potentially resilient individuals to remain cognitively unimpaired in the face of substantial neuropathology. We performed a large, genome-wide association study (GWAS) of two previously validated metrics of cognitive resilience quantified using a latent variable modelling approach and representing better-than-predicted cognitive performance for a given level of neuropathology. Data were harmonized across 5108 participants from a clinical trial of Alzheimer's disease and three longitudinal cohort studies of cognitive ageing. All analyses were run across all participants and repeated restricting the sample to individuals with unimpaired cognition to identify variants at the earliest stages of disease. As expected, all resilience metrics were genetically correlated with cognitive performance and education attainment traits (P-values < 2.5 × 10-20), and we observed novel correlations with neuropsychiatric conditions (P-values < 7.9 × 10-4). Notably, neither resilience metric was genetically correlated with clinical Alzheimer's disease (P-values > 0.42) nor associated with APOE (P-values > 0.13). In single variant analyses, we observed a genome-wide significant locus among participants with unimpaired cognition on chromosome 18 upstream of ATP8B1 (index single nucleotide polymorphism rs2571244, minor allele frequency = 0.08, P = 2.3 × 10-8). The top variant at this locus (rs2571244) was significantly associated with methylation in prefrontal cortex tissue at multiple CpG sites, including one just upstream of ATPB81 (cg19596477; P = 2 × 10-13). Overall, this comprehensive genetic analysis of resilience implicates a putative role of vascular risk, metabolism, and mental health in protection from the cognitive consequences of neuropathology, while also providing evidence for a novel resilience gene along the bile acid metabolism pathway. Furthermore, the genetic architecture of resilience appears to be distinct from that of clinical Alzheimer's disease, suggesting that a shift in focus to molecular contributors to resilience may identify novel pathways for therapeutic targets.
Collapse
Affiliation(s)
- Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily R Mahoney
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Michael L Lee
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Corinne D Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Qiongshi Lu
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - David W Fardo
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Emily H Trittschuh
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
- VA Puget Sound Health Care System, GRECC, Seattle, WA, USA
| | - Jesse Mez
- Deparment of Neurology, Boston University School of Medicine, Boston, MA, USA
| | | | - Hector Hernandez Saucedo
- UC Davis Alzheimer’s Disease Research Center, Department of Neurology, University of California Davis Medical Center, Sacramento, CA, USA
| | | | - Rachel Buckley
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
- Center for Alzheimer’s Research and Treatment, Department of Neurology, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
- Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, Australia
| | - Michael Properzi
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Elizabeth Mormino
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Hyun-Sik Yang
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
- Center for Alzheimer’s Research and Treatment, Department of Neurology, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA, USA
| | - Tessa Harrison
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Trey Hedden
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shea J Andrews
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Doug Tommet
- Department of Psychiatry and Human Behavior, Brown University School of Medicine, Providence, RI, USA
| | | | | | - Douglas M Ruderfer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Katherine A Gifford
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Annah M Moore
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Francis Cambronero
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaoyuan Zhong
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Neha S Raghavan
- Department of Neurology, Columbia University, New York, NY, USA
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University, New York, NY, USA
- The Institute for Genomic Medicine, Columbia University Medical Center and The New York Presbyterian Hospital, New York, NY, USA
| | - Badri Vardarajan
- Department of Neurology, Columbia University, New York, NY, USA
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University, New York, NY, USA
- The Institute for Genomic Medicine, Columbia University Medical Center and The New York Presbyterian Hospital, New York, NY, USA
| | | | | | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami School of Medicine, Miami, FL, USA
| | - Lindsay A Farrer
- Deparment of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Eric B Larson
- Department of Medicine, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Reisa A Sperling
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University, New York, NY, USA
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University, New York, NY, USA
- The Institute for Genomic Medicine, Columbia University Medical Center and The New York Presbyterian Hospital, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Angela L Jefferson
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
172
|
Guo T, Zhang D, Zeng Y, Huang TY, Xu H, Zhao Y. Molecular and cellular mechanisms underlying the pathogenesis of Alzheimer's disease. Mol Neurodegener 2020; 15:40. [PMID: 32677986 PMCID: PMC7364557 DOI: 10.1186/s13024-020-00391-7] [Citation(s) in RCA: 431] [Impact Index Per Article: 107.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disorder seen in age-dependent dementia. There is currently no effective treatment for AD, which may be attributed in part to lack of a clear underlying mechanism. Studies within the last few decades provide growing evidence for a central role of amyloid β (Aβ) and tau, as well as glial contributions to various molecular and cellular pathways in AD pathogenesis. Herein, we review recent progress with respect to Aβ- and tau-associated mechanisms, and discuss glial dysfunction in AD with emphasis on neuronal and glial receptors that mediate Aβ-induced toxicity. We also discuss other critical factors that may affect AD pathogenesis, including genetics, aging, variables related to environment, lifestyle habits, and describe the potential role of apolipoprotein E (APOE), viral and bacterial infection, sleep, and microbiota. Although we have gained much towards understanding various aspects underlying this devastating neurodegenerative disorder, greater commitment towards research in molecular mechanism, diagnostics and treatment will be needed in future AD research.
Collapse
Affiliation(s)
- Tiantian Guo
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Denghong Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Yuzhe Zeng
- Department of Orthopaedics, Orthopaedic Center of People's Liberation Army, The Affiliated Southeast Hospital of Xiamen University, Zhangzhou, China
| | - Timothy Y Huang
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| | - Huaxi Xu
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| | - Yingjun Zhao
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China.
| |
Collapse
|
173
|
Abstract
Neurodegenerative, neurodevelopmental and neuropsychiatric disorders are among the greatest public health challenges, as many lack disease-modifying treatments. A major reason for the absence of effective therapies is our limited understanding of the causative molecular and cellular mechanisms. Genome-wide association studies are providing a growing catalogue of disease-associated genetic variants, and the next challenge is to elucidate how these variants cause disease and to translate this understanding into therapies. This Review describes how new CRISPR-based functional genomics approaches can uncover disease mechanisms and therapeutic targets in neurological diseases. The bacterial CRISPR system can be used in experimental disease models to edit genomes and to control gene expression levels through CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa). These genetic perturbations can be implemented in massively parallel genetic screens to evaluate the functional consequences for human cells. CRISPR screens are particularly powerful in combination with induced pluripotent stem cell technology, which enables the derivation of differentiated cell types, such as neurons and glia, and brain organoids from cells obtained from patients. Modelling of disease-associated changes in gene expression via CRISPRi and CRISPRa can pinpoint causal changes. In addition, genetic modifier screens can be used to elucidate disease mechanisms and causal determinants of cell type-selective vulnerability and to identify therapeutic targets.
Collapse
|
174
|
Griswold AJ, Sivasankaran SK, Van Booven D, Gardner OK, Rajabli F, Whitehead PL, Hamilton-Nelson KL, Adams LD, Scott AM, Hofmann NK, Vance JM, Cuccaro ML, Bush WS, Martin ER, Byrd GS, Haines JL, Pericak-Vance MA, Beecham GW. Immune and Inflammatory Pathways Implicated by Whole Blood Transcriptomic Analysis in a Diverse Ancestry Alzheimer's Disease Cohort. J Alzheimers Dis 2020; 76:1047-1060. [PMID: 32597797 DOI: 10.3233/jad-190855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Significant work has identified genetic variants conferring risk and protection for Alzheimer's disease (AD), but functional effects of these variants is lacking, particularly in under-represented ancestral populations. Expression studies performed in easily accessible tissue, such as whole blood, can recapitulate some transcriptional changes occurring in brain and help to identify mechanisms underlying neurodegenerative processes. OBJECTIVE We aimed to identify transcriptional differences between AD cases and controls in a cohort of diverse ancestry. METHODS We analyzed the protein coding transcriptome using RNA sequencing from peripheral blood collected from 234 African American (AA) (115 AD, 119 controls) and 240 non-Hispanic Whites (NHW) (121 AD, 119 controls). To identify case-control differentially expressed genes and pathways, we performed stratified, joint, and interaction analyses using linear regression models within and across ancestral groups followed by pathway and gene set enrichment analyses. RESULTS Overall, we identified 418 (291 upregulated, 127 downregulated) and 488 genes (352 upregulated, 136 downregulated) differentially expressed in the AA and NHW datasets, respectively, with only 16 genes commonly differentially expressed in both ancestral groups. Joint analyses provided greater power to detect case-control differences and identified 1,102 differentially expressed genes between cases and controls (812 upregulated, 290 downregulated). Interaction analysis identified only 27 genes with different effects in AA compared to NHW. Pathway and gene-set enrichment analyses revealed differences in immune response-related pathways that were enriched across the analyses despite different underlying gene sets. CONCLUSION These results support the hypothesis of converging underlying pathophysiological processes in AD across ancestral groups.
Collapse
Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | | | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Olivia K Gardner
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | | | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Aja M Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Goldie S Byrd
- Department of Public Health Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| |
Collapse
|
175
|
Srinivasan K, Friedman BA, Etxeberria A, Huntley MA, van der Brug MP, Foreman O, Paw JS, Modrusan Z, Beach TG, Serrano GE, Hansen DV. Alzheimer's Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation. Cell Rep 2020; 31:107843. [PMID: 32610143 PMCID: PMC7422733 DOI: 10.1016/j.celrep.2020.107843] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/22/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Damage-associated microglia (DAM) profiles observed in Alzheimer's disease (AD)-related mouse models reflect an activation state that could modulate AD risk or progression. To learn whether human AD microglia (HAM) display a similar profile, we develop a method for purifying cell types from frozen cerebrocortical tissues for RNA-seq analysis, allowing better transcriptome coverage than typical single-nucleus RNA-seq approaches. The HAM profile we observe bears little resemblance to the DAM profile. Instead, HAM display an enhanced human aging profile, in addition to other disease-related changes such as APOE upregulation. Analyses of whole-tissue RNA-seq and single-cell/nucleus RNA-seq datasets corroborate our findings and suggest that the lack of DAM response in human microglia occurs specifically in AD tissues, not other neurodegenerative settings. These results, which can be browsed at http://research-pub.gene.com/BrainMyeloidLandscape, provide a genome-wide picture of microglial activation in human AD and highlight considerable differences between mouse models and human disease.
Collapse
Affiliation(s)
| | - Brad A Friedman
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA.
| | - Ainhoa Etxeberria
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA
| | - Melanie A Huntley
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Marcel P van der Brug
- Department of Biomarker Discovery OMNI, Genentech, Inc., South San Francisco, CA, USA
| | - Oded Foreman
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Jonathan S Paw
- Department of Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | | | | | - David V Hansen
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA.
| |
Collapse
|
176
|
Lutz MW, Luo S, Williamson DE, Chiba-Falek O. Shared genetic etiology underlying late-onset Alzheimer's disease and posttraumatic stress syndrome. Alzheimers Dement 2020; 16:1280-1292. [PMID: 32588970 DOI: 10.1002/alz.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Late-onset Alzheimer's disease (LOAD) manifests comorbid neuropsychiatric symptoms and posttraumatic stress disorder (PTSD) is associated with an increased risk for dementia in late life, suggesting the two disorders may share genetic etiologies. METHODS We performed genetic pleiotropy analysis using LOAD and PTSD genome-wide association study (GWAS) datasets from white and African-American populations, followed by functional-genomic analyses. RESULTS We found an enrichment for LOAD across increasingly stringent levels of significance with the PTSD GWAS association (LOAD|PTSD) in the discovery and replication cohorts and a modest enrichment for the reverse conditional association (PTSD|LOAD). LOAD|PTSD association analysis identified and replicated the MS4A genes region. These genes showed similar expression pattern in brain regions affected in LOAD, and across-brain-tissue analysis identified a significant association for MS4A6A. The African-American samples showed moderate enrichment; however, no false discovery rate-significant associations. DISCUSSION We demonstrated common genetic signatures for LOAD and PTSD and suggested immune response as a common pathway for these diseases.
Collapse
Affiliation(s)
- Michael W Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Douglas E Williamson
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina, USA.,Research Service, Durham VA Medical Center, Durham, North Carolina, USA.,Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|
177
|
Martin-Estebane M, Gomez-Nicola D. Targeting Microglial Population Dynamics in Alzheimer's Disease: Are We Ready for a Potential Impact on Immune Function? Front Cell Neurosci 2020; 14:149. [PMID: 32581720 PMCID: PMC7289918 DOI: 10.3389/fncel.2020.00149] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia, affecting two-thirds of people with dementia in the world. To date, no disease-modifying treatments are available to stop or delay the progression of AD. This chronic neurodegenerative disease is dominated by a strong innate immune response, whereby microglia plays a central role as the main resident macrophage of the brain. Recent genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) located in microglial genes and associated with a delayed onset of AD, highlighting the important role of these cells on the onset and/or progression of the disease. These findings have increased the interest in targeting microglia-associated neuroinflammation as a potentially disease-modifying therapeutic approach for AD. In this review we provide an overview on the contribution of microglia to the pathophysiology of AD, focusing on the main regulatory pathways controlling microglial population dynamics during the neuroinflammatory response, such as the colony-stimulating factor 1 receptor (CSF1R), its ligands (the colony-stimulating factor 1 and interleukin 34) and the transcription factor PU.1. We also discuss the current therapeutic strategies targeting proliferation to modulate microglia-associated neuroinflammation and their potential impact on peripheral immune cell populations in the short and long-term. Understanding the effects of immunomodulatory approaches on microglia and other immune cell types might be critical for developing specific, effective, and safe therapies for neurodegenerative diseases.
Collapse
Affiliation(s)
- Maria Martin-Estebane
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| |
Collapse
|
178
|
Kun C, Feiyi S, Jian D, Feng C, Guihua W, Jiangping Z, Jianwu J, Hong L, Xiaowei H. Network pharmacology-based study on the mechanism of Schisandra chinensis for treating Alzheimer's disease. Indian J Pharmacol 2020; 52:94-101. [PMID: 32565596 PMCID: PMC7282681 DOI: 10.4103/ijp.ijp_515_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/20/2019] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND: Alzheimer's disease (AD) is a mental illness that poses a serious threat to human health worldwide. Schisandra chinensis is a natural herb that can treat the effects of AD, but its specific mechanism is still unclear. The purpose of this study was to explore the potential components and pharmacological pathways of S. chinensis in the treatment of AD. MATERIALS AND METHODS: In this study, we investigated the compound of S. chinensis and the effects of it on AD by network pharmacology. Meanwhile, the potential mechanism was proved in vitro. RESULTS: The results showed that S. chinensis contained 173 compounds. Compound-target network confirmed that (E)-9-Isopropyl-6-Methyl-5,9-Decadiene-2-One, 1-Phenyl-1,3-Butanedion, nootkatone and phenyl-2-Propanone were the main chemical constituents which highly aimed at APOE, CACNA1D, GRIN2A, and PTGS2. KEGG and GO enrichment analysis indicated that the main pathways involved neural-related signaling pathways and functions, such as nicotine addiction, GABAergic synapse, Ca2+ signaling pathway, AD, and so on. Validation experiments showed that nootkatone was able to exert anti-apoptotic effects related to Ca2+ signaling pathway by inhibiting nitric oxide production, enhancing the activity of antioxidant enzymes, upregulating the expression of anti-oxidation and anti-apoptotic proteins in vitro. CONCLUSIONS: These results illustrated that S. chinensis could regulate neuronal apoptosis through the calcium signaling pathway to exert anti-AD by integrating multi-component, multi-target and multi-pathway.
Collapse
Affiliation(s)
- Cheng Kun
- Department of Neurology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi, China
| | - Sun Feiyi
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Dong Jian
- Graduate School of Southern Anhui Medical College, Anhui, China
| | - Chen Feng
- Department of Neurology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi, China
| | - Wu Guihua
- Department of Neurology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi, China
| | - Zhu Jiangping
- Department of Radiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi Province, China
| | - Ji Jianwu
- Department of Radiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi Province, China
| | - Liu Hong
- Department of Neurology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi, China
| | - Han Xiaowei
- Department of Radiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shangxi Province, China
| |
Collapse
|
179
|
Gupta I, Dandavate R, Gupta P, Agrawal V, Kapoor M. Recent advances in genetic studies of alcohol use disorders. CURRENT GENETIC MEDICINE REPORTS 2020; 8:27-34. [PMID: 33344068 PMCID: PMC7748121 DOI: 10.1007/s40142-020-00185-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Alcohol use disorder (AUD) is a complex genetic disorder with very high heritability. This polygenic disorder not only results in increased morbidity and mortality, it is also a substantial social and economic burden on families and the nation. For past three decades, several genetic studies were conducted to identify genes and pathways associated with AUD. This review aims to summarize past efforts and recent advances in genetic association studies of AUD and related traits. RECENT FINDINGS Initial genetic association studies achieved a limted success and suffered from low power due to small sample sizes. AUD is a polygenic trait and data from several thousands individuals was required to identify the genetic factors of small effect sizes. The scenario changed recently with technological advances and significant reduction in cost of the genome wide association analyses (GWAS). This enabled researchers to generate genomic data on mega biobanks and cohorts with access to extensive clinical and non-clinical phenotypes. Public access to data from biobanks and collaborative efforts of researchers lead to identification of several novel loci associated with AUDs and related traits. Efforts are now underway to identify the causal variants under the GWAS loci to identify target genes and biological mechanisms underpining AUDs. Many GWAS variants occur in promoter or enhancer regions of the genes and are involved in regulation of gene expression of causal genes. This, large amounts of "omics" data from projects such as "ENCODE", RoadMap and GTEx is also helping researchers to integrate "multi-omics" data to interpret functional significance of GWAS variants. SUMMARY With current review, we aim to present the recent advances in genetic and molecular studies of AUDs. Recent successes in genetic studies of AUDs will definetely motivate researchers and lead to better therapeutic interventions for this complex disorder.
Collapse
Affiliation(s)
| | - Rohan Dandavate
- Indian Institute of Science Education and Research, Bhopal, India
| | - Pallavi Gupta
- Indian Institute of Science Education and Research, Bhopal, India
| | - Viplav Agrawal
- Indian Institute of Science Education and Research, Bhopal, India
| | - Manav Kapoor
- Icahn School of Medicine at Mount Sinai, New york, USA
| |
Collapse
|
180
|
Kumar S, Fritz Z, Sulakhiya K, Theis T, Berthiaume F. Transcriptional Factors and Protein Biomarkers as Target Therapeutics in Traumatic Spinal Cord and Brain Injury. Curr Neuropharmacol 2020; 18:1092-1105. [PMID: 32442086 PMCID: PMC7709155 DOI: 10.2174/1570159x18666200522203542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/19/2020] [Accepted: 05/07/2020] [Indexed: 12/04/2022] Open
Abstract
Traumatic injury to the spinal cord (SCI) and brain (TBI) are serious health problems and affect many people every year throughout the world. These devastating injuries are affecting not only patients but also their families socially as well as financially. SCI and TBI lead to neurological dysfunction besides continuous inflammation, ischemia, and necrosis followed by progressive neurodegeneration. There are well-established changes in several other processes such as gene expression as well as protein levels that are the important key factors to control the progression of these diseases. We are not yet able to collect enough knowledge on the underlying mechanisms leading to the altered gene expression profiles and protein levels in SCI and TBI. Cell loss is hastened by the induction or imbalance of pro- or anti-inflammatory expression profiles and transcription factors for cell survival after or during trauma. There is a sequence of events of dysregulation of these factors from early to late stages of trauma that opens a therapeutic window for new interventions to prevent/restrict the progression of these diseases. There has been increasing interest in the modulation of these factors for improving the patient’s quality of life by targeting both SCI and TBI. Here, we review some of the recent transcriptional factors and protein biomarkers that have been developed and discovered in the last decade in the context of targeted therapeutics for SCI and TBI patients.
Collapse
Affiliation(s)
- Suneel Kumar
- Department of Biomedical Engineering, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Zachary Fritz
- Department of Biomedical Engineering, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Kunjbihari Sulakhiya
- Department of Pharmacy, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Thomas Theis
- W. M. Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers, The
State University of New Jersey, Piscataway, New Jersey, USA
| | - Francois Berthiaume
- Department of Biomedical Engineering, The State University of New Jersey, Piscataway, New Jersey, USA
| |
Collapse
|
181
|
Scheiblich H, Trombly M, Ramirez A, Heneka MT. Neuroimmune Connections in Aging and Neurodegenerative Diseases. Trends Immunol 2020; 41:300-312. [DOI: 10.1016/j.it.2020.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 11/26/2022]
|
182
|
Bellenguez C, Grenier-Boley B, Lambert JC. Genetics of Alzheimer’s disease: where we are, and where we are going. Curr Opin Neurobiol 2020; 61:40-48. [DOI: 10.1016/j.conb.2019.11.024] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
|
183
|
Shared genetic etiology underlying Alzheimer's disease and major depressive disorder. Transl Psychiatry 2020; 10:88. [PMID: 32152295 PMCID: PMC7062839 DOI: 10.1038/s41398-020-0769-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 01/22/2023] Open
Abstract
Patients with late-onset Alzheimer's disease (LOAD) frequently manifest comorbid neuropsychiatric symptoms with depression and anxiety being most frequent, and individuals with major depressive disorder (MDD) have an increased prevalence of LOAD. This suggests shared etiologies and intersecting pathways between LOAD and MDD. We performed pleiotropy analyses using LOAD and MDD GWAS data sets from the International Genomics of Alzheimer's Project (IGAP) and the Psychiatric Genomics Consortium (PGC), respectively. We found a moderate enrichment for SNPs associated with LOAD across increasingly stringent levels of significance with the MDD GWAS association (LOAD|MDD), of maximum four and eightfolds, including and excluding the APOE-region, respectively. Association analysis excluding the APOE-region identified numerous SNPs corresponding to 40 genes, 9 of which are known LOAD-risk loci primarily in chromosome 11 regions that contain the SPI1 gene and MS4A genes cluster, and others were novel pleiotropic risk-loci for LOAD conditional with MDD. The most significant associated SNPs on chromosome 11 overlapped with eQTLs found in whole-blood and monocytes, suggesting functional roles in gene regulation. The reverse conditional association analysis (MDD|LOAD) showed a moderate level, ~sevenfold, of polygenic overlap, however, no SNP showed significant association. Pathway analyses replicated previously reported LOAD biological pathways related to immune response and regulation of endocytosis. In conclusion, we provide insights into the overlapping genetic signatures underpinning the common phenotypic manifestations and inter-relationship between LOAD and MDD. This knowledge is crucial to the development of actionable targets for novel therapies to treat depression preceding dementia, in an effort to delay or ultimately prevent the onset of LOAD.
Collapse
|
184
|
Sierksma A, Lu A, Mancuso R, Fattorelli N, Thrupp N, Salta E, Zoco J, Blum D, Buée L, De Strooper B, Fiers M. Novel Alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology. EMBO Mol Med 2020; 12:e10606. [PMID: 31951107 PMCID: PMC7059012 DOI: 10.15252/emmm.201910606] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Polygenic risk scores have identified that genetic variants without genome-wide significance still add to the genetic risk of developing Alzheimer's disease (AD). Whether and how subthreshold risk loci translate into relevant disease pathways is unknown. We investigate here the involvement of AD risk variants in the transcriptional responses of two mouse models: APPswe/PS1L166P and Thy-TAU22. A unique gene expression module, highly enriched for AD risk genes, is specifically responsive to Aβ but not TAU pathology. We identify in this module 7 established AD risk genes (APOE, CLU, INPP5D, CD33, PLCG2, SPI1, and FCER1G) and 11 AD GWAS genes below the genome-wide significance threshold (GPC2, TREML2, SYK, GRN, SLC2A5, SAMSN1, PYDC1, HEXB, RRBP1, LYN, and BLNK), that become significantly upregulated when exposed to Aβ. Single microglia sequencing confirms that Aβ, not TAU, pathology induces marked transcriptional changes in microglia, including increased proportions of activated microglia. We conclude that genetic risk of AD functionally translates into different microglia pathway responses to Aβ pathology, placing AD genetic risk downstream of the amyloid pathway but upstream of TAU pathology.
Collapse
Affiliation(s)
- Annerieke Sierksma
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Ashley Lu
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Renzo Mancuso
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Nicola Fattorelli
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Nicola Thrupp
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Evgenia Salta
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Jesus Zoco
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - David Blum
- INSERM, CHU Lille, LabEx DISTALZ, UMR‐S 1172, Alzheimer & TauopathiesUniversité LilleLilleFrance
| | - Luc Buée
- INSERM, CHU Lille, LabEx DISTALZ, UMR‐S 1172, Alzheimer & TauopathiesUniversité LilleLilleFrance
| | - Bart De Strooper
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
- UK Dementia Research InstituteUniversity College LondonLondonUK
| | - Mark Fiers
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| |
Collapse
|
185
|
Birnbaum R, Weinberger DR. A Genetics Perspective on the Role of the (Neuro)Immune System in Schizophrenia. Schizophr Res 2020; 217:105-113. [PMID: 30850283 PMCID: PMC6728242 DOI: 10.1016/j.schres.2019.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/11/2019] [Accepted: 02/14/2019] [Indexed: 12/30/2022]
Abstract
The immune system has long been hypothesized to play a role in schizophrenia pathogenesis based on data from diverse disciplines. Recent reports of the identification of schizophrenia-associated genetic variants and their initial biological characterization have renewed investigation of the role of the immune system in schizophrenia. In the current review, the plausibility of a role of the immune system in schizophrenia pathogenesis is examined, by revisiting epidemiology, neuroimaging, pharmacology, and developmental biology from a genetics perspective, as well as by synthesizing diverse findings from the emerging and dynamic schizophrenia genomics field. Genetic correlations between schizophrenia and immunological disorders are inconsistent and often contradictory, as are neuroimaging studies of microglia markers. Small therapeutic trials of anti-inflammatory agents targeting immune function have been consistently negative. Some gene expression analyses of post-mortem brains of patients with schizophrenia have reported an upregulation of genes of immune function though others report downregulation, and overall transcriptome profiling to date does not support an upregulation of immune pathways associated with schizophrenia genetic risk. The currently reviewed genetic data do not converge to reveal consistent evidence of the neuroimmune system in schizophrenia pathogenesis, and indeed, a substantive role for the neuroimmune system in schizophrenia has yet to be established.
Collapse
Affiliation(s)
- Rebecca Birnbaum
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, United States of America
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States of America; Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, United States of America; Johns Hopkins University School of Medicine, Department of Neurology, Baltimore, MD, United States of America; Johns Hopkins University School of Medicine, Institute of Genomics Medicine, Baltimore, MD, United States of America; Johns Hopkins University School of Medicine, Department of Neuroscience, Baltimore, MD, United States of America.
| |
Collapse
|
186
|
Sims R, Hill M, Williams J. The multiplex model of the genetics of Alzheimer's disease. Nat Neurosci 2020; 23:311-322. [PMID: 32112059 DOI: 10.1038/s41593-020-0599-5] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/24/2020] [Indexed: 12/25/2022]
Abstract
Genes play a strong role in Alzheimer's disease (AD), with late-onset AD showing heritability of 58-79% and early-onset AD showing over 90%. Genetic association provides a robust platform to build our understanding of the etiology of this complex disease. Over 50 loci are now implicated for AD, suggesting that AD is a disease of multiple components, as supported by pathway analyses (immunity, endocytosis, cholesterol transport, ubiquitination, amyloid-β and tau processing). Over 50% of late-onset AD heritability has been captured, allowing researchers to calculate the accumulation of AD genetic risk through polygenic risk scores. A polygenic risk score predicts disease with up to 90% accuracy and is an exciting tool in our research armory that could allow selection of those with high polygenic risk scores for clinical trials and precision medicine. It could also allow cellular modelling of the combined risk. Here we propose the multiplex model as a new perspective from which to understand AD. The multiplex model reflects the combination of some, or all, of these model components (genetic and environmental), in a tissue-specific manner, to trigger or sustain a disease cascade, which ultimately results in the cell and synaptic loss observed in AD.
Collapse
Affiliation(s)
- Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Matthew Hill
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- UK Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Julie Williams
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
- UK Dementia Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
| |
Collapse
|
187
|
Parikh IJ, Estus JL, Zajac DJ, Malik M, Maldonado Weng J, Tai LM, Chlipala GE, LaDu MJ, Green SJ, Estus S. Murine Gut Microbiome Association With APOE Alleles. Front Immunol 2020; 11:200. [PMID: 32117315 PMCID: PMC7034241 DOI: 10.3389/fimmu.2020.00200] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Since APOE alleles represent the most impactful genetic risk factors for Alzheimer's disease (AD), their differential mechanism(s) of action are under intense scrutiny. APOE4 is robustly associated with increased AD risk compared to the neutral APOE3 and protective APOE2. APOE alleles have also been associated with differential inflammation and gastrointestinal recovery after insult in human and murine studies, leading us to hypothesize that APOE alleles impact the gut microbiome. Methods: To assess this hypothesis, we compared 16S ribosomal RNA gene amplicon-based microbiome profiles in a cohort of mice that were homozygous for APOE2, APOE3, or APOE4, and included both males and females as well as carriers and non-carriers of five familial AD (5xFAD) mutations. Fecal samples were analyzed from mice at 4 and 6 months of age. APOE genotype, as well as sex and 5xFAD status, was then tested for influence on alpha diversity (Shannon H index) and beta diversity (principal coordinate analyses and PERMANOVA). A Random Forest analysis was used to identify features that predicted APOE, sex and 5xFAD status. Results: The richness and evenness (alpha diversity) of the fecal microbiome was not robustly associated with APOE genotype, 5xFAD status or sex. In contrast, microbial community composition (beta-diversity) was consistently and strongly associated with APOE genotype. The association between beta-diversity and sex or 5xFAD status was less consistent and more modest. Comparison of the differences underlying APOE effects showed that the relative abundance of multiple bacterial taxa was significantly different as a function of APOE genotype. Conclusions: The structure of the gut microbiome was strongly and significantly associated with APOE alleles in this murine model. Further evaluation of these findings in humans, as well as studies evaluating the impact of the APOE-associated microbiota on AD-relevant phenotypes in murine models, will be necessary to determine if alterations in the gut microbiome represent a novel mechanism whereby APOE genotype impacts AD.
Collapse
Affiliation(s)
- Ishita J. Parikh
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Janice L. Estus
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Diana J. Zajac
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Manasi Malik
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| | - Juan Maldonado Weng
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Leon M. Tai
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - George E. Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Mary Jo LaDu
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Stefan J. Green
- Research Resources Center, University of Illinois at Chicago, Chicago, IL, United States
| | - Steven Estus
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
188
|
Ramdhani S, Navarro E, Udine E, Efthymiou AG, Schilder BM, Parks M, Goate A, Raj T. Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs. PLoS Genet 2020; 16:e1008549. [PMID: 32012164 PMCID: PMC7018232 DOI: 10.1371/journal.pgen.1008549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 02/13/2020] [Accepted: 12/02/2019] [Indexed: 01/10/2023] Open
Abstract
Recent human genetic studies suggest that cells of the innate immune system have a primary role in the pathogenesis of neurodegenerative diseases. However, the results from these studies often do not elucidate how the genetic variants affect the biology of these cells to modulate disease risk. Here, we applied a tensor decomposition method to uncover disease associated gene networks linked to distal genetic variation in stimulated human monocyte and macrophage gene expression profiles. We report robust evidence that some disease associated genetic variants affect the expression of multiple genes in trans. These include a Parkinson's disease locus influencing the expression of genes mediated by a protease that controls lysosomal function, and Alzheimer's disease loci influencing the expression of genes involved in type 1 interferon signaling, myeloid phagocytosis, and complement cascade pathways. Overall, we uncover gene networks in induced innate immune cells linked to disease associated genetic variants, which may help elucidate the underlying biology of disease.
Collapse
Affiliation(s)
- Satesh Ramdhani
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Elisa Navarro
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Evan Udine
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Anastasia G. Efthymiou
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brian M. Schilder
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Madison Parks
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Alison Goate
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Towfique Raj
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| |
Collapse
|
189
|
Gosselin D. Epigenomic and transcriptional determinants of microglial cell identity. Glia 2020; 68:1643-1654. [PMID: 31994799 DOI: 10.1002/glia.23787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Microglia perform multiple tasks that are essential to ensure proper cerebral functions, including synaptic remodeling, clearance of molecular debris, prevention of infections, and so forth. Furthermore, accumulating genetic and pathological evidence implicates microglial cell activity in the etiology of numerous neurodegenerative diseases and psychiatric disorders. Given this, efforts aimed at understanding the molecular mechanisms underlying microglial cell functions hold great potential for the development of novel therapies for various conditions affecting the central nervous system. In that regard, the application of paradigms in epigenomics to study transcription in microglia has provided significant insights into the molecular mechanisms that control the ontogeny and functions of these cells. With a focus on the roles of genomic regulatory elements and the epigenetic marks that control microglial gene expression, we review here recent key advancements in our comprehension of the epigenomic and transcriptional mechanisms that enable microglial cell development and activity.
Collapse
Affiliation(s)
- David Gosselin
- Department of Molecular Medicine, Faculty of Medicine, CHU de Québec Research Center, Université Laval, Quebec City, Quebec, Canada
| |
Collapse
|
190
|
Hasselmann J, Blurton-Jones M. Human iPSC-derived microglia: A growing toolset to study the brain's innate immune cells. Glia 2020; 68:721-739. [PMID: 31926038 DOI: 10.1002/glia.23781] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/21/2019] [Accepted: 12/30/2019] [Indexed: 12/11/2022]
Abstract
Recent advances in the generation of microglia from human induced pluripotent stem cells (iPSCs) have provided exciting new approaches to examine and decipher the biology of microglia. As these techniques continue to evolve to encompass more complex in situ and in vivo paradigms, so too have they begun to yield novel scientific insight into the genetics and function of human microglia. As such, researchers now have access to a toolset comprised of three unique "flavors" of iPSC-derived microglia: in vitro microglia (iMGs), organoid microglia (oMGs), and xenotransplanted microglia (xMGs). The goal of this review is to discuss the variety of research applications that each of these techniques enables and to highlight recent discoveries that these methods have begun to uncover. By presenting the research paradigms in which each model has been successful, as well as the key benefits and limitations of each approach, it is our hope that this review will help interested researchers to incorporate these techniques into their studies, collectively advancing our understanding of human microglia biology.
Collapse
Affiliation(s)
- Jonathan Hasselmann
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California.,Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California.,Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, California
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California.,Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California.,Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, California
| |
Collapse
|
191
|
Taguchi YH, Turki T. Neurological Disorder Drug Discovery from Gene Expression with Tensor Decomposition. Curr Pharm Des 2020; 25:4589-4599. [PMID: 31820695 DOI: 10.2174/1381612825666191210160906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/30/2019] [Indexed: 02/06/2023]
Abstract
Background:
Identifying effective candidate drug compounds in patients with neurological disorders
based on gene expression data is of great importance to the neurology field. By identifying effective candidate
drugs to a given neurological disorder, neurologists would (1) reduce the time searching for effective treatments;
and (2) gain additional useful information that leads to a better treatment outcome. Although there are many
strategies to screen drug candidate in pre-clinical stage, it is not easy to check if candidate drug compounds can
also be effective to human.
Objective:
We tried to propose a strategy to screen genes whose expression is altered in model animal
experiments to be compared with gene expressed differentially with drug treatment to human cell lines.
Methods:
Recently proposed tensor decomposition (TD) based unsupervised feature extraction (FE) is applied to
single cell (sc) RNA-seq experiments of Alzheimer’s disease model animal mouse brain.
Results:
Four hundreds and one genes are screened as those differentially expressed during A946 accumulation as
age progresses. These genes are significantly overlapped with those expressed differentially with the known drug
treatments for three independent data sets: LINCS, DrugMatrix, and GEO.
Conclusion:
Our strategy, application of TD based unsupervised FE, is useful one to screen drug candidate
compounds using scRNA-seq data set.
Collapse
Affiliation(s)
- Y-h. Taguchi
- Department of Physics, Chuo University, Tokyo 112-8551, Japan
| | - Turki Turki
- Department of Computer Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
192
|
Association between alcohol consumption and Alzheimer's disease: A Mendelian randomization study. Alzheimers Dement 2020; 16:345-353. [PMID: 31786126 DOI: 10.1016/j.jalz.2019.09.086] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Observational studies have suggested that light-to-moderate alcohol consumption decreases the risk of Alzheimer's disease, but it is unclear if this association is causal. METHODS Two-sample Mendelian randomization (MR) analysis was used to examine whether alcohol consumption, alcohol dependence, or Alcohol Use Disorder Identification Test (AUDIT) scores were causally associated with the risk of Late-Onset Alzheimer's disease (LOAD) or Alzheimer's disease age of onset survival (AAOS). Additionally, γ-glutamyltransferase levels were included as a positive control. RESULTS There was no evidence of a causal association between alcohol consumption, alcohol dependence, or AUDIT, and LOAD. Alcohol consumption was associated with an earlier AAOS and increased γ-glutamyltransferase blood concentrations. Alcohol dependence was associated with a delayed AAOS. DISCUSSION MR found robust evidence of a causal association between alcohol consumption and an earlier AAOS, but not alcohol intake and LOAD risk. The protective effect of alcohol dependence is potentially due to survivor bias.
Collapse
|
193
|
Penney J, Ralvenius WT, Tsai LH. Modeling Alzheimer's disease with iPSC-derived brain cells. Mol Psychiatry 2020; 25:148-167. [PMID: 31391546 PMCID: PMC6906186 DOI: 10.1038/s41380-019-0468-3] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/10/2019] [Accepted: 05/13/2019] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease is a devastating neurodegenerative disorder with no cure. Countless promising therapeutics have shown efficacy in rodent Alzheimer's disease models yet failed to benefit human patients. While hope remains that earlier intervention with existing therapeutics will improve outcomes, it is becoming increasingly clear that new approaches to understand and combat the pathophysiology of Alzheimer's disease are needed. Human induced pluripotent stem cell (iPSC) technologies have changed the face of preclinical research and iPSC-derived cell types are being utilized to study an array of human conditions, including neurodegenerative disease. All major brain cell types can now be differentiated from iPSCs, while increasingly complex co-culture systems are being developed to facilitate neuroscience research. Many cellular functions perturbed in Alzheimer's disease can be recapitulated using iPSC-derived cells in vitro, and co-culture platforms are beginning to yield insights into the complex interactions that occur between brain cell types during neurodegeneration. Further, iPSC-based systems and genome editing tools will be critical in understanding the roles of the numerous new genes and mutations found to modify Alzheimer's disease risk in the past decade. While still in their relative infancy, these developing iPSC-based technologies hold considerable promise to push forward efforts to combat Alzheimer's disease and other neurodegenerative disorders.
Collapse
Affiliation(s)
- Jay Penney
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - William T Ralvenius
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
194
|
Dharshini SAP, Taguchi YH, Gromiha MM. Investigating the energy crisis in Alzheimer disease using transcriptome study. Sci Rep 2019; 9:18509. [PMID: 31811163 PMCID: PMC6898285 DOI: 10.1038/s41598-019-54782-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/09/2019] [Indexed: 01/01/2023] Open
Abstract
Alzheimer disease (AD) is a devastating neurological disorder, which initiates from hippocampus and proliferates to cortical regions. The neurons of hippocampus require higher energy to preserve the firing pattern. In AD, aberrant energy metabolism is the critical factor for neurodegeneration. However, the reason for the energy crisis in hippocampus neurons is still unresolved. Transcriptome analysis enables us in understanding the underlying mechanism of energy crisis. In this study, we identified variants/differential gene/transcript expression profiles from hippocampus RNA-seq data. We predicted the effect of variants in transcription factor (TF) binding using in silico tools. Further, a hippocampus-specific co-expression and functional interaction network were designed to decipher the relationships between TF and differentially expressed genes (DG). Identified variants predominantly influence TF binding, which subsequently regulates the DG. From the results, we hypothesize that the loss of vascular integrity is the fundamental attribute for the energy crisis, which leads to neurodegeneration.
Collapse
Affiliation(s)
- S Akila Parvathy Dharshini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - Y-H Taguchi
- Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India.
| |
Collapse
|
195
|
Hardy J. Failures in Protein Clearance Partly Underlie Late Onset Neurodegenerative Diseases and Link Pathology to Genetic Risk. Front Neurosci 2019; 13:1304. [PMID: 31866813 PMCID: PMC6906158 DOI: 10.3389/fnins.2019.01304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/20/2019] [Indexed: 01/29/2023] Open
Abstract
As we identify the loci involved in late onset neurodegenerative disease, we are finding that the majority of them are involved in damage response processes. In this short review, I propose that it is partly a failure in these damage response processes which underlie late onset disease and that the resultant pathology is a marker of the type of damage response which has failed: microglial clearance of damaged neuronal membranes in Alzheimer's disease (AD), ubiquitin proteasome clearance in the tauopathies, and lysosomal clearance in Parkinson's disease (PD). In this review, I outline this relationship. This article is not intended as a comprehensive review of the cell biology of any of these disorders but rather a summary of the evidence that the genetics and pathology of these disorders appear to point, in each case, to the removal of misfolded proteins as a critical process in disease pathogenesis.
Collapse
Affiliation(s)
- John Hardy
- Department of Neurodegenerative Disease and Reta Lila Weston Laboratories, UCL Queen Square Institute of Neurology, London, United Kingdom
- UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, United Kingdom
| |
Collapse
|
196
|
Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci 2019; 22:2087-2097. [PMID: 31768052 DOI: 10.1038/s41593-019-0539-4] [Citation(s) in RCA: 491] [Impact Index Per Article: 98.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is currently little information available about how individual cell types contribute to Alzheimer's disease. Here we applied single-nucleus RNA sequencing to entorhinal cortex samples from control and Alzheimer's disease brains (n = 6 per group), yielding a total of 13,214 high-quality nuclei. We detail cell-type-specific gene expression patterns, unveiling how transcriptional changes in specific cell subpopulations are associated with Alzheimer's disease. We report that the Alzheimer's disease risk gene APOE is specifically repressed in Alzheimer's disease oligodendrocyte progenitor cells and astrocyte subpopulations and upregulated in an Alzheimer's disease-specific microglial subopulation. Integrating transcription factor regulatory modules with Alzheimer's disease risk loci revealed drivers of cell-type-specific state transitions towards Alzheimer's disease. For example, transcription factor EB, a master regulator of lysosomal function, regulates multiple disease genes in a specific Alzheimer's disease astrocyte subpopulation. These results provide insights into the coordinated control of Alzheimer's disease risk genes and their cell-type-specific contribution to disease susceptibility. These results are available at http://adsn.ddnetbio.com.
Collapse
Affiliation(s)
- Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Gabriel Chew
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xin Yi Choo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Catriona McLean
- Victorian Brain Bank, Florey Institute of Neurosciences, Parkville, Victoria, Australia
| | - Rebecca K Simmons
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Sam Buckberry
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landin
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Daniel Poppe
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
- The Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
197
|
Hardy J, Escott-Price V. Genes, pathways and risk prediction in Alzheimer's disease. Hum Mol Genet 2019; 28:R235-R240. [PMID: 31332445 DOI: 10.1093/hmg/ddz163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 11/12/2022] Open
Abstract
The failure of recent clinical trials in Alzheimer's disease has highlighted the need for the development of a more complete understanding of the pathogenesis of the disorder and also a belief that therapies may only work if given very early in the disease process before overt symptoms occur. The rare, early onset forms of the disease are all caused by mutations which make amyloid deposition a more likely event. Here we discuss the recent data showing that, in contrast, much of the risk of late onset disease is encoded by loci involved in lipid metabolism and/or encoded by microglia. We discuss these finding and suggest that amyloid induced membrane damage may be a key factor in disease and also review the evidence that genome wide genetic analysis can substantially help in the prediction of those individuals at high risk of disease in the general population.
Collapse
Affiliation(s)
- John Hardy
- Reta Lilla Research Laboratories, Department of Molecular Neuroscience, University College London Institute of Neurology and UK Dementia Research Institute, University College London, London, UK
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences and Dementia Research Institute, Cardiff University, Cardiff, UK
| |
Collapse
|
198
|
Nott A, Holtman IR, Coufal NG, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiao J, Wu Y, Keulen Z, Pasillas MP, O'Connor C, Nickl CK, Schafer ST, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK. Brain cell type-specific enhancer-promoter interactome maps and disease -risk association. Science 2019; 366:1134-1139. [PMID: 31727856 DOI: 10.1126/science.aay0793] [Citation(s) in RCA: 392] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022]
Abstract
Noncoding genetic variation is a major driver of phenotypic diversity, but functional interpretation is challenging. To better understand common genetic variation associated with brain diseases, we defined noncoding regulatory regions for major cell types of the human brain. Whereas psychiatric disorders were primarily associated with variants in transcriptional enhancers and promoters in neurons, sporadic Alzheimer's disease (AD) variants were largely confined to microglia enhancers. Interactome maps connecting disease-risk variants in cell-type-specific enhancers to promoters revealed an extended microglia gene network in AD. Deletion of a microglia-specific enhancer harboring AD-risk variants ablated BIN1 expression in microglia, but not in neurons or astrocytes. These findings revise and expand the list of genes likely to be influenced by noncoding variants in AD and suggest the probable cell types in which they function.
Collapse
Affiliation(s)
- Alexi Nott
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Section Molecular Neurobiology, Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands
| | - Nicole G Coufal
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Monique Pena
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jiayang Xiao
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yin Wu
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Zahara Keulen
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christian K Nickl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Zeyang Shen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert A Rissman
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA
| | - James B Brewer
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec G1V 4G2, Canada
| | - David D Gonda
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Michael L Levy
- Department of Neurosurgery, University of California, San Diego-Rady Children's Hospital, San Diego, CA 92123, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Graham McVicker
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Fred H Gage
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells & Systems, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands
| | - Bing Ren
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.,The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA. .,Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| |
Collapse
|
199
|
Golde TE. Harnessing Immunoproteostasis to Treat Neurodegenerative Disorders. Neuron 2019; 101:1003-1015. [PMID: 30897353 DOI: 10.1016/j.neuron.2019.02.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/05/2019] [Accepted: 02/15/2019] [Indexed: 12/12/2022]
Abstract
Immunoproteostasis is a term used to reflect interactions between the immune system and the proteinopathies that are presumptive "triggers" of many neurodegenerative disorders. The study of immunoproteostasis is bolstered by several observations. Mutations or rare variants in genes expressed in microglial cells, known to regulate immune functions, or both can cause, or alter risk for, various neurodegenerative disorders. Additionally, genetic association studies identify numerous loci harboring genes that encode proteins of known immune function that alter risk of developing Alzheimer's disease (AD) and other neurodegenerative proteinopathies. Further, preclinical studies reveal beneficial effects and liabilities of manipulating immune pathways in various neurodegenerative disease models. Although there are concerns that manipulation of the immune system may cause more harm than good, there is considerable interest in developing immune modulatory therapies for neurodegenerative disorders. Herein, I highlight the promise and challenges of harnessing immunoproteostasis to treat neurodegenerative proteinopathies.
Collapse
Affiliation(s)
- Todd E Golde
- McKnight Brain Institute, Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience and Neurology, University of Florida, Gainesville, FL 32607, USA.
| |
Collapse
|
200
|
Liu G, Zhang H, Liu B, Ji X. Rs2293871 regulates HTRA1 expression and affects cerebral small vessel stroke and Alzheimer's disease. Brain 2019; 142:e61. [PMID: 31603204 PMCID: PMC6821345 DOI: 10.1093/brain/awz305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Guiyou Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| | - Haihua Zhang
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| | - Bian Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xunming Ji
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| |
Collapse
|