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Patel T, Carnwath TP, Wang X, Allen M, Lincoln SJ, Lewis‐Tuffin L, Quicksall ZS, Lin S, Tutor‐New FQ, Ho CC, Min Y, Malphrus KG, Nguyen TT, Martin E, Garcia CA, Alkharboosh RM, Grewal S, Chaichana K, Wharen R, Guerrero‐Cazares H, Quinones‐Hinojosa A, Ertekin‐Taner N. Transcriptional landscape of human microglia implicates age, sex, and APOE-related immunometabolic pathway perturbations. Aging Cell 2022; 21:e13606. [PMID: 35388616 PMCID: PMC9124307 DOI: 10.1111/acel.13606] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/20/2022] Open
Abstract
Microglia have fundamental roles in health and disease; however, effects of age, sex, and genetic factors on human microglia have not been fully explored. We applied bulk and single-cell approaches to comprehensively characterize human microglia transcriptomes and their associations with age, sex, and APOE. We identified a novel microglial signature, characterized its expression in bulk tissue and single-cell microglia transcriptomes. We discovered microglial co-expression network modules associated with age, sex, and APOE-ε4 that are enriched for lipid and carbohydrate metabolism genes. Integrated analyses of modules with single-cell transcriptomes revealed significant overlap between age-associated module genes and both pro-inflammatory and disease-associated microglial clusters. These modules and clusters harbor known neurodegenerative disease genes including APOE, PLCG2, and BIN1. Meta-analyses with published bulk and single-cell microglial datasets further supported our findings. Thus, these data represent a well-characterized human microglial transcriptome resource and highlight age, sex, and APOE-related microglial immunometabolism perturbations with potential relevance in neurodegeneration.
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Affiliation(s)
- Tulsi Patel
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | - Xue Wang
- Department of Quantitative Health SciencesMayo ClinicJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | - Shu Lin
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Yuhao Min
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | - Thuy T. Nguyen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Rawan M. Alkharboosh
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
- Neuroscience Graduate ProgramMayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMinnesotaUSA
- Regenerative Sciences Training ProgramCenter for Regenerative MedicineMayo ClinicRochesterMinnesotaUSA
| | - Sanjeet Grewal
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
| | | | - Robert Wharen
- Department of NeurosurgeryMayo ClinicJacksonvilleFloridaUSA
| | | | | | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Department of NeurologyMayo ClinicJacksonvilleFloridaUSA
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2
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Min Y, Wang X, Reddy JS, Nguyen T, Malphrus KG, Crook JE, Carrasquillo MM, Dickson DW, Allen M, Ertekin‐Taner N. Understanding the transcriptional (dys)regulation in progressive supranuclear palsy. Alzheimers Dement 2021. [DOI: 10.1002/alz.050985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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3
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Carrasquillo MM, Jin J, Reddy JS, Crook JE, Lincoln SJ, Ho CC, Malphrus KG, Nguyen T, Greig‐Custo MT, Lucas JA, Graff‐Radford NR, Ertekin‐Taner N. Plasma transcript profiling identifies significant differentially expressed genes and expression of quantitative trait loci in African Americans. Alzheimers Dement 2021. [DOI: 10.1002/alz.055643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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4
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Wang X, Allen M, İş Ö, Reddy JS, Tutor-New FQ, Castanedes Casey M, Carrasquillo MM, Oatman SR, Min Y, Asmann YW, Funk C, Nguyen T, Ho CC, Malphrus KG, Seyfried NT, Levey AI, Younkin SG, Murray ME, Dickson DW, Price ND, Golde TE, Ertekin-Taner N. Alzheimer's disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions. J Clin Invest 2021; 132:149904. [PMID: 34813500 PMCID: PMC8759790 DOI: 10.1172/jci149904] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Vast numbers of differentially expressed genes and perturbed networks have been identified in Alzheimer’s disease (AD), however, neither disease nor brain region specificity of these transcriptome alterations has been explored. Using RNA-Seq data from 231 temporal cortex and 224 cerebellum samples from patients with AD and progressive supranuclear palsy (PSP), a tauopathy, we identified a striking correlation in the directionality and magnitude of gene expression changes between these 2 neurodegenerative proteinopathies. Further, the transcriptomic changes in AD and PSP brains ware highly conserved between the temporal and cerebellar cortices, indicating that highly similar transcriptional changes occur in pathologically affected and grossly less affected, albeit functionally connected, areas of the brain. Shared up- or downregulated genes in AD and PSP are enriched in biological pathways. Many of these genes also have concordant protein changes and evidence of epigenetic control. These conserved transcriptomic alterations of 2 distinct proteinopathies in brain regions with and without significant gross neuropathology have broad implications. AD and other neurodegenerative diseases are likely characterized by common disease or compensatory pathways with widespread perturbations in the whole brain. These findings can be leveraged to develop multifaceted therapies and biomarkers that address these common, complex, and ubiquitous molecular alterations in neurodegenerative diseases.
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Affiliation(s)
- Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, United States of America
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Özkan İş
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, United States of America
| | - Frederick Q Tutor-New
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | | | | | - Stephanie R Oatman
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Yuhao Min
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Yan W Asmann
- Department of Quantitative Health Sciences, Mayo Clinic Florida, Jacksonville, United States of America
| | - Cory Funk
- Systems Biology, Institute of Systems Biology, Seattle, United States of America
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Charlotte Cg Ho
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Kimberly G Malphrus
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory Univeristy, Atlanta, United States of America
| | | | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, United States of America
| | - Nathan D Price
- Systems Biology, Institute for Systems Biology, Seattle, United States of America
| | - Todd E Golde
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, United States of America
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Reddy JS, Allen M, Ho CCG, Oatman SR, İş Ö, Quicksall ZS, Wang X, Jin J, Patel TA, Carnwath TP, Nguyen TT, Malphrus KG, Lincoln SJ, Carrasquillo MM, Crook JE, Kanekiyo T, Murray ME, Bu G, Dickson DW, Ertekin-Taner N. Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. Acta Neuropathol Commun 2021; 9:93. [PMID: 34020725 PMCID: PMC8147512 DOI: 10.1186/s40478-021-01199-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 01/09/2023] Open
Abstract
Cerebral amyloid angiopathy (CAA) contributes to accelerated cognitive decline in Alzheimer’s disease (AD) dementia and is a common finding at autopsy. The APOEε4 allele and male sex have previously been reported to associate with increased CAA in AD. To inform biomarker and therapeutic target discovery, we aimed to identify additional genetic risk factors and biological pathways involved in this vascular component of AD etiology. We present a genome-wide association study of CAA pathology in AD cases and report sex- and APOE-stratified assessment of this phenotype. Genome-wide genotypes were collected from 853 neuropathology-confirmed AD cases scored for CAA across five brain regions, and imputed to the Haplotype Reference Consortium panel. Key variables and genome-wide genotypes were tested for association with CAA in all individuals and in sex and APOEε4 stratified subsets. Pathway enrichment was run for each of the genetic analyses. Implicated loci were further investigated for functional consequences using brain transcriptome data from 1,186 samples representing seven brain regions profiled as part of the AMP-AD consortium. We confirmed association of male sex, AD neuropathology and APOEε4 with increased CAA, and identified a novel locus, LINC-PINT, associated with lower CAA amongst APOEε4-negative individuals (rs10234094-C, beta = −3.70 [95% CI −0.49—−0.24]; p = 1.63E-08). Transcriptome profiling revealed higher LINC-PINT expression levels in AD cases, and association of rs10234094-C with altered LINC-PINT splicing. Pathway analysis indicates variation in genes involved in neuronal health and function are linked to CAA in AD patients. Further studies in additional and diverse cohorts are needed to assess broader translation of our findings.
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Deniz K, Ho CCG, Malphrus KG, Reddy JS, Nguyen T, Carnwath TP, Crook JE, Lucas JA, Graff-Radford NR, Carrasquillo MM, Ertekin-Taner N. Plasma Biomarkers of Alzheimer's Disease in African Americans. J Alzheimers Dis 2021; 79:323-334. [PMID: 33252078 PMCID: PMC7902984 DOI: 10.3233/jad-200828] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background/Objective: The aim of this study was to determine if plasma concentrations of 5 surrogate markers of Alzheimer’s disease (AD) pathology and neuroinflammation are associated with disease status in African Americans. Methods: We evaluated 321 African Americans (159 AD, 162 controls) from the Florida Consortium for African-American Alzheimer’s Disease Studies (FCA3DS). Five plasma proteins reflecting AD neuropathology or inflammation (Aβ42, tau, IL6, IL10, TNFα) were tested for associations with AD, age, sex, APOE and MAPT genotypes, and for pairwise correlations. Results: Plasma tau levels were higher in AD when adjusted for biological and technical covariates. APOEɛ4 was associated with lower plasma Aβ42 and tau levels. Older age was associated with higher plasma Aβ42, tau, and TNFα. Females had lower IL10 levels. Inflammatory proteins had strong pairwise correlations amongst themselves and with Aβ42. Conclusion: We identified effects of demographic and genetic variants on five potential plasma biomarkers in African Americans. Plasma inflammatory biomarkers and Aβ42 may reflect correlated pathologies and elevated plasma tau may be a biomarker of AD in this population.
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Affiliation(s)
- Kaancan Deniz
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA
| | | | | | - Joseph S Reddy
- Mayo Clinic, Department of Health Science Research, Jacksonville, FL, USA
| | - Thuy Nguyen
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA
| | - Troy P Carnwath
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA
| | - Julia E Crook
- Mayo Clinic, Department of Health Science Research, Jacksonville, FL, USA
| | - John A Lucas
- Mayo Clinic, Department of Psychiatry and Psychology, Jacksonville, FL, USA
| | | | | | - Nilüfer Ertekin-Taner
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA.,Mayo Clinic, Department of Neurology, Jacksonville, FL, USA
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Strickland SL, Morel H, Prusinski C, Allen M, Patel TA, Carrasquillo MM, Conway OJ, Lincoln SJ, Reddy JS, Nguyen T, Malphrus KG, Soto AI, Walton RL, Crook JE, Murray ME, Boeve BF, Petersen RC, Lucas JA, Ferman TJ, Uitti RJ, Wszolek ZK, Ross OA, Graff-Radford NR, Dickson DW, Ertekin-Taner N. Association of ABI3 and PLCG2 missense variants with disease risk and neuropathology in Lewy body disease and progressive supranuclear palsy. Acta Neuropathol Commun 2020; 8:172. [PMID: 33092647 PMCID: PMC7579984 DOI: 10.1186/s40478-020-01050-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Missense variants ABI3_rs616338-T and PLCG2_rs72824905-G were previously associated with elevated or reduced risk of Alzheimer's disease (AD), respectively. Despite reports of associations with other neurodegenerative diseases, there are few studies of these variants in purely neuropathologically diagnosed cohorts. Further, the effect of these mutations on neurodegenerative disease pathologies is unknown. In this study, we tested the effects of ABI3_rs616338-T and PLCG2_rs72824905-G on disease risk in autopsy cohorts comprised of 973 patients diagnosed neuropathologically with Lewy body disease (LBD-NP) and 1040 with progressive supranuclear palsy (PSP), compared to 3351 controls. LBD-NP patients were further categorized as high, intermediate and low likelihood of clinical dementia with Lewy bodies (DLB-CL) based on DLB Consortium criteria. We also tested for association with both Braak neurofibrillary tau tangle (nTotal = 2008, nPSP = 1037, nLBD-NP = 971) and Thal phase amyloid plaque scores (nTotal = 1786, nPSP = 1018, nLBD-NP = 768). Additionally, 841 PSP patients had quantitative tau neuropathology measures that were assessed for genetic associations. There was no statistically significant association with disease risk for either LBD-NP or PSP in our study. LBD intermediate category disease risk was significantly associated with ABI3_rs616338-T (OR = 2.65, 95% CI 1.46-4.83, p = 0.001). PLCG2_rs72824905-G was associated with lower Braak stage (ß = - 0.822, 95% CI - 1.439 to - 0.204, p = 0.009). This effect was more pronounced in the PSP (ß = - 0.995, 95% CI - 1.773 to - 0.218, p = 0.012) than LBD-NP patients (ß = - 0.292, 95% CI - 1.283 to 0.698, p = 0.563). PLCG2_rs72824905-G also showed association with reduced quantitative tau pathology for each lesion type and overall tau burden in PSP (ß = - 0.638, 95% CI - 1.139 to - 0.136, p = 0.013). These findings support a role for PLCG2_rs72824905-G in suppressing tau neuropathology. ABI3_rs616338-T may influence disease risk specifically in the LBD-NP intermediate category comprised of patients with diffuse neocortical or limbic LB, concurrently with moderate or high AD neuropathology, respectively. Our study provides a potential mechanism of action for the missense PLCG2 variant and suggests a differential disease risk effect for ABI3 in a distinct LBD-NP neuropathologic category.
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Wang X, Allen M, Li S, Quicksall ZS, Patel TA, Carnwath TP, Reddy JS, Carrasquillo MM, Lincoln SJ, Nguyen TT, Malphrus KG, Dickson DW, Crook JE, Asmann YW, Ertekin-Taner N. Correction to: Deciphering cellular transcriptional alterations in Alzheimer's disease brains. Mol Neurodegener 2020; 15:54. [PMID: 32928256 PMCID: PMC7490892 DOI: 10.1186/s13024-020-00403-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA.
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Shaoyu Li
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary S Quicksall
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Troy P Carnwath
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Sarah J Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Thuy T Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA. .,Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA.
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Wang X, Allen M, Li S, Quicksall ZS, Patel TA, Carnwath TP, Reddy JS, Carrasquillo MM, Lincoln SJ, Nguyen TT, Malphrus KG, Dickson DW, Crook JE, Asmann YW, Ertekin-Taner N. Deciphering cellular transcriptional alterations in Alzheimer's disease brains. Mol Neurodegener 2020; 15:38. [PMID: 32660529 PMCID: PMC7359236 DOI: 10.1186/s13024-020-00392-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/27/2020] [Indexed: 02/06/2023] Open
Abstract
Large-scale brain bulk-RNAseq studies identified molecular pathways implicated in Alzheimer's disease (AD), however these findings can be confounded by cellular composition changes in bulk-tissue. To identify cell intrinsic gene expression alterations of individual cell types, we designed a bioinformatics pipeline and analyzed three AD and control bulk-RNAseq datasets of temporal and dorsolateral prefrontal cortex from 685 brain samples. We detected cell-proportion changes in AD brains that are robustly replicable across the three independently assessed cohorts. We applied three different algorithms including our in-house algorithm to identify cell intrinsic differentially expressed genes in individual cell types (CI-DEGs). We assessed the performance of all algorithms by comparison to single nucleus RNAseq data. We identified consensus CI-DEGs that are common to multiple brain regions. Despite significant overlap between consensus CI-DEGs and bulk-DEGs, many CI-DEGs were absent from bulk-DEGs. Consensus CI-DEGs and their enriched GO terms include genes and pathways previously implicated in AD or neurodegeneration, as well as novel ones. We demonstrated that the detection of CI-DEGs through computational deconvolution methods is promising and highlight remaining challenges. These findings provide novel insights into cell-intrinsic transcriptional changes of individual cell types in AD and may refine discovery and modeling of molecular targets that drive this complex disease.
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Affiliation(s)
- Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA.
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Shaoyu Li
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary S Quicksall
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Troy P Carnwath
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Sarah J Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Thuy T Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA.
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Allen M, Reddy JS, Carrasquillo MM, Wang X, Lincoln SJ, Nguyen T, Malphrus KG, Asmann YW, Murray ME, Bu G, Dickson DW, Ertekin-Taner N. O5‐02‐04: INTEGRATIVE GENOMIC PROFILING TO IDENTIFY GENES AND PATHWAYS ASSOCIATED WITH VASCULAR RISK IN AD. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.4843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Allen M, Wang X, Serie DJ, Strickland SL, Burgess JD, Koga S, Younkin CS, Nguyen TT, Malphrus KG, Lincoln SJ, Alamprese M, Zhu K, Chang R, Carrasquillo MM, Kouri N, Murray ME, Reddy JS, Funk C, Price ND, Golde TE, Younkin SG, Asmann YW, Crook JE, Dickson DW, Ertekin-Taner N. Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy. Acta Neuropathol 2018; 136:709-727. [PMID: 30136084 PMCID: PMC6208732 DOI: 10.1007/s00401-018-1900-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 12/25/2022]
Abstract
Progressive supranuclear palsy (PSP) is a neurodegenerative parkinsonian disorder characterized by tau pathology in neurons and glial cells. Transcriptional regulation has been implicated as a potential mechanism in conferring disease risk and neuropathology for some PSP genetic risk variants. However, the role of transcriptional changes as potential drivers of distinct cell-specific tau lesions has not been explored. In this study, we integrated brain gene expression measurements, quantitative neuropathology traits and genome-wide genotypes from 268 autopsy-confirmed PSP patients to identify transcriptional associations with unique cell-specific tau pathologies. We provide individual transcript and transcriptional network associations for quantitative oligodendroglial (coiled bodies = CB), neuronal (neurofibrillary tangles = NFT), astrocytic (tufted astrocytes = TA) tau pathology, and tau threads and genomic annotations of these findings. We identified divergent patterns of transcriptional associations for the distinct tau lesions, with the neuronal and astrocytic neuropathologies being the most different. We determined that NFT are positively associated with a brain co-expression network enriched for synaptic and PSP candidate risk genes, whereas TA are positively associated with a microglial gene-enriched immune network. In contrast, TA is negatively associated with synaptic and NFT with immune system transcripts. Our findings have implications for the diverse molecular mechanisms that underlie cell-specific vulnerability and disease risk in PSP.
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Affiliation(s)
- Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Daniel J Serie
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Jeremy D Burgess
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Curtis S Younkin
- Division of Information Technology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Thuy T Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Sarah J Lincoln
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Kuixi Zhu
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Rui Chang
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, 85721, USA
- Department of Neurology, University of Arizona, Tucson, AZ, 85721, USA
| | | | - Naomi Kouri
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Cory Funk
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| | - Nathan D Price
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA, 98109, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL, 32224, USA.
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12
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Conway OJ, Carrasquillo MM, Wang X, Bredenberg JM, Reddy JS, Strickland SL, Younkin CS, Burgess JD, Allen M, Lincoln SJ, Nguyen T, Malphrus KG, Soto AI, Walton RL, Boeve BF, Petersen RC, Lucas JA, Ferman TJ, Cheshire WP, van Gerpen JA, Uitti RJ, Wszolek ZK, Ross OA, Dickson DW, Graff-Radford NR, Ertekin-Taner N. ABI3 and PLCG2 missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans. Mol Neurodegener 2018; 13:53. [PMID: 30326945 PMCID: PMC6190665 DOI: 10.1186/s13024-018-0289-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/04/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Rare coding variants ABI3_rs616338-T and PLCG2_rs72824905-G were identified as risk or protective factors, respectively, for Alzheimer's disease (AD). METHODS We tested the association of these variants with five neurodegenerative diseases in Caucasian case-control cohorts: 2742 AD, 231 progressive supranuclear palsy (PSP), 838 Parkinson's disease (PD), 306 dementia with Lewy bodies (DLB) and 150 multiple system atrophy (MSA) vs. 3351 controls; and in an African-American AD case-control cohort (181 AD, 331 controls). 1479 AD and 1491 controls were non-overlapping with a prior report. RESULTS Using Fisher's exact test, there was significant association of both ABI3_rs616338-T (OR = 1.41, p = 0.044) and PLCG2_rs72824905-G (OR = 0.56, p = 0.008) with AD. These OR estimates were maintained in the non-overlapping replication AD-control analysis, albeit at reduced significance (ABI3_rs616338-T OR = 1.44, p = 0.12; PLCG2_rs72824905-G OR = 0.66, p = 0.19). None of the other cohorts showed significant associations that were concordant with those for AD, although the DLB cohort had suggestive findings (Fisher's test: ABI3_rs616338-T OR = 1.79, p = 0.097; PLCG2_rs72824905-G OR = 0.32, p = 0.124). PLCG2_rs72824905-G showed suggestive association with pathologically-confirmed MSA (OR = 2.39, p = 0.050) and PSP (OR = 1.97, p = 0.061), although in the opposite direction of that for AD. We assessed RNA sequencing data from 238 temporal cortex (TCX) and 224 cerebellum (CER) samples from AD, PSP and control patients and identified co-expression networks, enriched in microglial genes and immune response GO terms, and which harbor PLCG2 and/or ABI3. These networks had higher expression in AD, but not in PSP TCX, compared to controls. This expression association did not survive adjustment for brain cell type population changes. CONCLUSIONS We validated the associations previously reported with ABI3_rs616338-T and PLCG2_rs72824905-G in a Caucasian AD case-control cohort, and observed a similar direction of effect in DLB. Conversely, PLCG2_rs72824905-G showed suggestive associations with PSP and MSA in the opposite direction. We identified microglial gene-enriched co-expression networks with significantly higher levels in AD TCX, but not in PSP, a primary tauopathy. This co-expression network association appears to be driven by microglial cell population changes in a brain region affected by AD pathology. Although these findings require replication in larger cohorts, they suggest distinct effects of the microglial genes, ABI3 and PLCG2 in neurodegenerative diseases that harbor significant vs. low/no amyloid ß pathology.
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Affiliation(s)
- Olivia J Conway
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | | | - Xue Wang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Jenny M Bredenberg
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Joseph S Reddy
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | | | - Curtis S Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Jeremy D Burgess
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Sarah J Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Kimberly G Malphrus
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Alexandra I Soto
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Ronald L Walton
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Bradley F Boeve
- Department of Neurology, Mayo Clinic Minnesota, Rochester, MN, 55905, USA
| | - Ronald C Petersen
- Department of Neurology, Mayo Clinic Minnesota, Rochester, MN, 55905, USA
| | - John A Lucas
- Department of Psychiatry and Psychology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Tanis J Ferman
- Department of Psychiatry and Psychology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - William P Cheshire
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Jay A van Gerpen
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Ryan J Uitti
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Zbigniew K Wszolek
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA. .,Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA.
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Allen M, Bredenberg JM, Reddy JS, Sarangi V, Carrasquillo MM, Wang X, Lincoln SJ, Nguyen T, Malphrus KG, Dickson DW, Asmann YW, Ertekin-Taner N. P3‐129: MAPPING FUNCTIONAL REGULATORY VARIANTS AT ALZHEIMER'S DISEASE RISK LOCI. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.1486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Carrasquillo MM, Reddy JS, Allen M, Reyes DA, McDonnell SK, Graff-Radford J, Kosel ML, Gregory JD, Nguyen T, Lincoln SJ, Malphrus KG, Crook JE, Jack CR, Lowe VJ, Knopman DS, Petersen RC, Kantarci K, Bu G, Ertekin-Taner N. P3‐132: GENOME‐WIDE ASSOCIATION STUDY OF CEREBRAL MICROBLEEDS AND INFARCTION IDENTIFIES CANDIDATE GENES FOR VASCULAR RISK IN DEMENTIA. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.06.1489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Allen M, Wang X, Burgess JD, Watzlawik J, Serie DJ, Younkin CS, Nguyen T, Malphrus KG, Lincoln S, Carrasquillo MM, Ho C, Chakrabarty P, Strickland S, Murray ME, Swarup V, Geschwind DH, Seyfried NT, Dammer EB, Lah JJ, Levey AI, Golde TE, Funk C, Li H, Price ND, Petersen RC, Graff-Radford NR, Younkin SG, Dickson DW, Crook JR, Asmann YW, Ertekin-Taner N. Conserved brain myelination networks are altered in Alzheimer's and other neurodegenerative diseases. Alzheimers Dement 2017; 14:352-366. [PMID: 29107053 DOI: 10.1016/j.jalz.2017.09.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/13/2017] [Accepted: 09/20/2017] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Comparative transcriptome analyses in Alzheimer's disease (AD) and other neurodegenerative proteinopathies can uncover both shared and distinct disease pathways. METHODS We analyzed 940 brain transcriptomes including patients with AD, progressive supranuclear palsy (PSP; a primary tauopathy), and control subjects. RESULTS We identified transcriptional coexpression networks implicated in myelination, which were lower in PSP temporal cortex (TCX) compared with AD. Some of these associations were retained even after adjustments for brain cell population changes. These TCX myelination network structures were preserved in cerebellum but they were not differentially expressed in cerebellum between AD and PSP. Myelination networks were downregulated in both AD and PSP, when compared with control TCX samples. DISCUSSION Downregulation of myelination networks may underlie both PSP and AD pathophysiology, but may be more pronounced in PSP. These data also highlight conservation of transcriptional networks across brain regions and the influence of cell type changes on these networks.
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Affiliation(s)
- Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | | | - Jens Watzlawik
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Daniel J Serie
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Curtis S Younkin
- Division of Information Technology, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Sarah Lincoln
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Charlotte Ho
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | | | | | - Vivek Swarup
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, USA
| | - Hongdong Li
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | | | - Julia R Crook
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
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Allen M, Wang X, Reddy JS, Carrasquillo MM, Younkin CS, Funk C, Burgess JD, Nguyen T, Lincoln SJ, Malphrus KG, Asmann YW, Younkin SG, Price ND, Golde TE, Dickson DW, Ertekin‐Taner N. [O2–13–03]: USING TISSUE‐BASED TRANSCRIPTOMICS TO PROFILE CELL TYPE VARIABILITY IN THE BRAIN. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.07.218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mariet Allen
- Mayo ClinicJacksonvilleFLUSA
- Institute for Systems BiologySeattleWAUSA
- University of FloridaGainesvilleFLUSA
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17
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Allen M, Wang X, Younkin CS, Serie D, Burgess JD, Nguyen T, Lincoln SJ, Malphrus KG, Carrasquillo MM, Kouri N, Murray ME, Schellenberg GD, Younkin SG, Crook JE, Asmann YW, Dickson DW, Ertekin‐Taner N. [P4–074]: INTEGRATIVE SYSTEMS BIOLOGY APPROACH TO IDENTIFY NOVEL RISK FACTORS FOR PSP. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.06.1939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Carrasquillo MM, Ho CC, Nsongo A, Wang X, Burgess JD, Nguyen T, Ma L, Bisceglio GD, Lincoln SJ, Malphrus KG, Asmann YW, Younkin SG, Duara R, Greig Custo MT, Graff‐Radford NR, Ertekin‐Taner N. [P3–096]: NOVEL CANDIDATE AD‐RISK LOCI IDENTIFIED THROUGH WHOLE EXOME SEQUENCING IN AFRICAN‐AMERICANS. Alzheimers Dement 2017. [DOI: 10.1016/j.jalz.2017.06.1306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | | | | | | | | | | | - Li Ma
- Mayo ClinicJacksonvilleFLUSA
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19
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Carrasquillo MM, Allen M, Burgess JD, Wang X, Strickland SL, Aryal S, Siuda J, Kachadoorian ML, Medway C, Younkin CS, Nair A, Wang C, Chanana P, Serie D, Nguyen T, Lincoln S, Malphrus KG, Morgan K, Golde TE, Price ND, White CC, De Jager PL, Bennett DA, Asmann YW, Crook JE, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression. Alzheimers Dement 2016; 13:663-673. [PMID: 27939925 DOI: 10.1016/j.jalz.2016.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 10/15/2016] [Accepted: 10/23/2016] [Indexed: 10/20/2022]
Abstract
INTRODUCTION We hypothesized that common Alzheimer's disease (AD)-associated variants within the triggering receptor expressed on myeloid (TREM) gene cluster influence disease through gene expression. METHODS Expression microarrays on temporal cortex and cerebellum from ∼400 neuropathologically diagnosed subjects and two independent RNAseq replication cohorts were used for expression quantitative trait locus analysis. RESULTS A variant within a DNase hypersensitive site 5' of TREM2, rs9357347-C, associates with reduced AD risk and increased TREML1 and TREM2 levels (uncorrected P = 6.3 × 10-3 and 4.6 × 10-2, respectively). Meta-analysis on expression quantitative trait locus results from three independent data sets (n = 1006) confirmed these associations (uncorrected P = 3.4 × 10-2 and 3.5 × 10-3, Bonferroni-corrected P = 6.7 × 10-2 and 7.1 × 10-3, respectively). DISCUSSION Our findings point to rs9357347 as a functional regulatory variant that contributes to a protective effect observed at the TREM locus in the International Genomics of Alzheimer's Project genome-wide association study meta-analysis and suggest concomitant increase in TREML1 and TREM2 brain levels as a potential mechanism for protection from AD.
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Affiliation(s)
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Jeremy D Burgess
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Shivani Aryal
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Joanna Siuda
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Christopher Medway
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA; Human Genetics Group, University of Nottingham, Nottingham, UK
| | - Curtis S Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic Rochester, MN, USA
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic Rochester, MN, USA
| | - Pritha Chanana
- Department of Health Sciences Research, Mayo Clinic Rochester, MN, USA
| | - Daniel Serie
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Sarah Lincoln
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | - Kevin Morgan
- Human Genetics Group, University of Nottingham, Nottingham, UK
| | - Todd E Golde
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | | | - Charles C White
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Philip L De Jager
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL, USA
| | | | | | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA; Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA.
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Allen M, Wang X, Burgess JD, Nguyen T, Malphrus KG, Nho K, Serie D, Strickland SL, Lincoln S, Carrasquillo MM, Crook JE, Schellenberg GD, Knopman DS, Saykin AJ, Lowe VJ, Jack CR, Younkin SG, Asmann YW, Petersen RC, Ertekin-Taner N. P1‐117: Blood Gene Expression Changes Implicated in Alzheimer’s Disease. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | | | | | - Kwangsik Nho
- Indiana University School of MedicineIndianapolisIN USA
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Golde TE, Ertekin-Taner N, Chakrabarty P, Allen M, Carrasquillo MM, Dickson DW, Younkin SG, Levites Y, Price ND, Funk C, Heavner BD, Logsdon B, Mangravite LM, Li HD, Burgess JD, Younkin CS, Petersen RC, Cruz PE, Ceballos-Diaz C, Rosario AM, Adamson J, Giasson BI, Graff-Radford NR, Yachnis T, Zou F, Eddy J, Crook JE, Wang X, Chai HS, Serie D, Wang C, Nguyen T, Lincoln S, Malphrus KG, Bisceglio G, Ma L, Asmann YW. F2‐01‐04: From Systems Level Transcriptomics to new Immune Targets for Alzheimer’s Disease. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Corey Funk
- Institute for Systems BiologySeattleWA USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - James Eddy
- Institute For Systems BiologySeattleWA USA
| | | | | | | | | | | | | | | | | | | | - Li Ma
- Mayo ClinicJacksonvilleFL USA
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Carrasquillo MM, Allen M, Burgess JD, Strickland SL, Aryal S, Siuda J, Kachadoorian M, Medway C, Younkin CS, Nair A, Chanana P, Wang X, Serie D, Nguyen T, Lincoln S, Malphrus KG, Morgan K, Golde TE, Price ND, White C, Jager P, Bennett DA, Asmann YW, Crook JE, Dickson DW, Younkin SG, Ertekin-Taner N. O2‐10‐04: A Regulatory Variant at the
TREM
Gene Cluster Associates with Decreased Alzheimer’s Disease Risk and Increased
TREML1
and
TREM2
Brain Gene Expression. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Christopher Medway
- Mayo Clinic JacksonvilleFL USA
- University of NottinghamNottingham United Kingdom
| | | | - Asha Nair
- Mayo Clinic Minnesota RochesterMN USA
| | | | | | | | | | | | | | - Kevin Morgan
- University of NottinghamNottingham United Kingdom
| | | | | | | | - Philip Jager
- Brigham and Women’s HospitalBostonMA USA
- Broad InstituteCambridgeMA USA
- Harvard Medical SchoolBostonMA USA
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Allen M, Wang X, Younkin CS, Burgess JD, Ballard T, Serie D, Wang C, Sun Z, Baheti S, Carrasquillo MM, Nguyen T, Malphrus KG, Lincoln S, Zou F, Chai HS, Schellenberg GD, Younkin SG, Crook J, Ordog T, Asmann YW, Dickson DW, Taner N. P2‐025: Genetic and epigenetic influences on brain gene expression in psp. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.06.561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tamas Ordog
- Mayo Clinic Center for Individualized MedicineRochesterMNUSA
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Burgess JD, Allen M, Kachadoorian M, Nguyen T, Malphrus KG, Lincoln S, Carrasquillo MM, Schellenberg GD, Knopman DS, Lowe VJ, Jack CR, Younkin SG, Dickson DW, Petersen RC, Taner N. P2‐015: Exploring alternative splicing and gene expression of load candidate genes in blood. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.06.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Allen M, Wang X, Serie D, Strickland SL, Burgess JD, Nguyen T, Malphrus KG, Lincoln S, Carrasquillo MM, Crook J, Schellenberg GD, Knopman DS, Lowe VJ, Jack CR, Younkin SG, Asmann YW, Petersen RC, Taner N. P1‐049: Exploiting blood transcriptome for gene and pathway identification in Alzheimer's disease. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.06.245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Carrasquillo MM, Crook JE, Pedraza O, Thomas CS, Pankratz VS, Allen M, Nguyen T, Malphrus KG, Ma L, Bisceglio GD, Roberts RO, Lucas JA, Smith GE, Ivnik RJ, Machulda MM, Graff-Radford NR, Petersen RC, Younkin SG, Ertekin-Taner N. Late-onset Alzheimer's risk variants in memory decline, incident mild cognitive impairment, and Alzheimer's disease. Neurobiol Aging 2014; 36:60-7. [PMID: 25189118 DOI: 10.1016/j.neurobiolaging.2014.07.042] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/04/2014] [Accepted: 07/28/2014] [Indexed: 11/19/2022]
Abstract
We tested association of nine late-onset Alzheimer's disease (LOAD) risk variants from genome-wide association studies (GWAS) with memory and progression to mild cognitive impairment (MCI) or LOAD (MCI/LOAD) in older Caucasians, cognitively normal at baseline and longitudinally evaluated at Mayo Clinic Rochester and Jacksonville (n>2000). Each variant was tested both individually and collectively using a weighted risk score. APOE-e4 associated with worse baseline memory and increased decline with highly significant overall effect on memory. CLU-rs11136000-G associated with worse baseline memory and incident MCI/LOAD. MS4A6A-rs610932-C associated with increased incident MCI/LOAD and suggestively with lower baseline memory. ABCA7-rs3764650-C and EPHA1-rs11767557-A associated with increased rates of memory decline in subjects with a final diagnosis of MCI/LOAD. PICALM-rs3851179-G had an unexpected protective effect on incident MCI/LOAD. Only APOE-inclusive risk scores associated with worse memory and incident MCI/LOAD. The collective influence of the nine top LOAD GWAS variants on memory decline and progression to MCI/LOAD appears limited. Discovery of biologically functional variants at these loci may uncover stronger effects on memory and incident disease.
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Affiliation(s)
| | - Julia E Crook
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - Otto Pedraza
- Department of Psychiatry and Psychology, Mayo Clinic, Jacksonville, FL, USA
| | - Colleen S Thomas
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - V Shane Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Li Ma
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Rosebud O Roberts
- Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA; Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - John A Lucas
- Department of Psychiatry and Psychology, Mayo Clinic, Jacksonville, FL, USA
| | - Glenn E Smith
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Robert J Ivnik
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Mary M Machulda
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
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Allen M, Zou F, Chai HS, Younkin CS, Crook J, Pankratz VS, Carrasquillo MM, Rowley CN, Nair AA, Middha S, Maharjan S, Nguyen T, Ma L, Malphrus KG, Palusak R, Lincoln S, Bisceglio G, Georgescu C, Schultz D, Rakhshan F, Kolbert CP, Jen J, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N, Apostolova LG, Arnold SE, Baldwin CT, Barber R, Barmada MM, Beach T, Beecham GW, Beekly D, Bennett DA, Bigio EH, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Burke JR, Buros J, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carney RM, Carroll SL, Chui HC, Clark DG, Corneveaux J, Cotman CW, Crane PK, Cruchaga C, Cummings JL, De Jager PL, DeCarli C, DeKosky ST, Demirci FY, Diaz-Arrastia R, Dick M, Dombroski BA, Duara R, Ellis WD, Evans D, Faber KM, Fallon KB, Farlow MR, Ferris S, Foroud TM, Frosch M, Galasko DR, Gallins PJ, Ganguli M, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Gilman S, Giordani B, Glass JD, Goate AM, Green RC, Growdon JH, Hakonarson H, Hamilton RL, Hardy J, Harrell LE, Head E, Honig LS, Huentelman MJ, Hulette CM, Hyman BT, Jarvik GP, Jicha GA, Jin LW, Jun G, Kamboh MI, Karlawish J, Karydas A, Kauwe JSK, Kaye JA, Kennedy N, Kim R, Koo EH, Kowall NW, Kramer P, Kukull WA, Lah JJ, Larson EB, Levey AI, Lieberman AP, Lopez OL, Lunetta KL, Mack WJ, Marson DC, Martin ER, Martiniuk F, Mash DC, Masliah E, McCormick WC, McCurry SM, McDavid AN, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Morris JC, Myers AJ, Naj AC, Nowotny P, Parisi JE, Perl DP, Peskind E, Poon WW, Potter H, Quinn JF, Raj A, Rajbhandary RA, Raskind M, Reiman EM, Reisberg B, Reitz C, Ringman JM, Roberson ED, Rogaeva E, Rosenberg RN, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley W, Shelanski ML, Slifer MA, Smith CD, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Tanzi RE, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, Vardarajan BN, Vinters HV, Vonsattel JP, Wang LS, Weintraub S, Welsh-Bohmer KA, Williamson J, Woltjer RL. Novel late-onset Alzheimer disease loci variants associate with brain gene expression. Neurology 2012; 79:221-8. [PMID: 22722634 DOI: 10.1212/wnl.0b013e3182605801] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE Recent genome-wide association studies (GWAS) of late-onset Alzheimer disease (LOAD) identified 9 novel risk loci. Discovery of functional variants within genes at these loci is required to confirm their role in Alzheimer disease (AD). Single nucleotide polymorphisms that influence gene expression (eSNPs) constitute an important class of functional variants. We therefore investigated the influence of the novel LOAD risk loci on human brain gene expression. METHODS We measured gene expression levels in the cerebellum and temporal cortex of autopsied AD subjects and those with other brain pathologies (∼400 total subjects). To determine whether any of the novel LOAD risk variants are eSNPs, we tested their cis-association with expression of 6 nearby LOAD candidate genes detectable in human brain (ABCA7, BIN1, CLU, MS4A4A, MS4A6A, PICALM) and an additional 13 genes ±100 kb of these SNPs. To identify additional eSNPs that influence brain gene expression levels of the novel candidate LOAD genes, we identified SNPs ±100 kb of their location and tested for cis-associations. RESULTS CLU rs11136000 (p = 7.81 × 10(-4)) and MS4A4A rs2304933/rs2304935 (p = 1.48 × 10(-4)-1.86 × 10(-4)) significantly influence temporal cortex expression levels of these genes. The LOAD-protective CLU and risky MS4A4A locus alleles associate with higher brain levels of these genes. There are other cis-variants that significantly influence brain expression of CLU and ABCA7 (p = 4.01 × 10(-5)-9.09 × 10(-9)), some of which also associate with AD risk (p = 2.64 × 10(-2)-6.25 × 10(-5)). CONCLUSIONS CLU and MS4A4A eSNPs may at least partly explain the LOAD risk association at these loci. CLU and ABCA7 may harbor additional strong eSNPs. These results have implications in the search for functional variants at the novel LOAD risk loci.
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Affiliation(s)
- Mariet Allen
- Department of Neuroscience, Biostatistics Unit, Mayo Clinic Florida, Jacksonville, FL, USA
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Zou F, Chai HS, Younkin CS, Allen M, Crook J, Pankratz VS, Carrasquillo MM, Rowley CN, Nair AA, Middha S, Maharjan S, Nguyen T, Ma L, Malphrus KG, Palusak R, Lincoln S, Bisceglio G, Georgescu C, Kouri N, Kolbert CP, Jen J, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. PLoS Genet 2012; 8:e1002707. [PMID: 22685416 PMCID: PMC3369937 DOI: 10.1371/journal.pgen.1002707] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 03/27/2012] [Indexed: 02/06/2023] Open
Abstract
Genetic variants that modify brain gene expression may also influence risk for human diseases. We measured expression levels of 24,526 transcripts in brain samples from the cerebellum and temporal cortex of autopsied subjects with Alzheimer's disease (AD, cerebellar n = 197, temporal cortex n = 202) and with other brain pathologies (non–AD, cerebellar n = 177, temporal cortex n = 197). We conducted an expression genome-wide association study (eGWAS) using 213,528 cisSNPs within ±100 kb of the tested transcripts. We identified 2,980 cerebellar cisSNP/transcript level associations (2,596 unique cisSNPs) significant in both ADs and non–ADs (q<0.05, p = 7.70×10−5–1.67×10−82). Of these, 2,089 were also significant in the temporal cortex (p = 1.85×10−5–1.70×10−141). The top cerebellar cisSNPs had 2.4-fold enrichment for human disease-associated variants (p<10−6). We identified novel cisSNP/transcript associations for human disease-associated variants, including progressive supranuclear palsy SLCO1A2/rs11568563, Parkinson's disease (PD) MMRN1/rs6532197, Paget's disease OPTN/rs1561570; and we confirmed others, including PD MAPT/rs242557, systemic lupus erythematosus and ulcerative colitis IRF5/rs4728142, and type 1 diabetes mellitus RPS26/rs1701704. In our eGWAS, there was 2.9–3.3 fold enrichment (p<10−6) of significant cisSNPs with suggestive AD–risk association (p<10−3) in the Alzheimer's Disease Genetics Consortium GWAS. These results demonstrate the significant contributions of genetic factors to human brain gene expression, which are reliably detected across different brain regions and pathologies. The significant enrichment of brain cisSNPs among disease-associated variants advocates gene expression changes as a mechanism for many central nervous system (CNS) and non–CNS diseases. Combined assessment of expression and disease GWAS may provide complementary information in discovery of human disease variants with functional implications. Our findings have implications for the design and interpretation of eGWAS in general and the use of brain expression quantitative trait loci in the study of human disease genetics. Genetic variants that regulate gene expression levels can also influence human disease risk. Discovery of genomic loci that alter brain gene expression levels (brain expression quantitative trait loci = eQTLs) can be instrumental in the identification of genetic risk underlying both central nervous system (CNS) and non–CNS diseases. To systematically assess the role of brain eQTLs in human disease and to evaluate the influence of brain region and pathology in eQTL mapping, we performed an expression genome-wide association study (eGWAS) in 773 brain samples from the cerebellum and temporal cortex of ∼200 autopsied subjects with Alzheimer's disease (AD) and ∼200 with other brain pathologies (non–AD). We identified ∼3,000 significant associations between cisSNPs near ∼700 genes and their cerebellar transcript levels, which replicate in ADs and non–ADs. More than 2,000 of these associations were reproducible in the temporal cortex. The top cisSNPs are enriched for both CNS and non–CNS disease-associated variants. We identified novel and confirmed previous cisSNP/transcript associations for many disease loci, suggesting gene expression regulation as their mechanism of action. These findings demonstrate the reproducibility of the eQTL approach across different brain regions and pathologies, and advocate the combined use of gene expression and disease GWAS for identification and functional characterization of human disease-associated variants.
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Affiliation(s)
- Fanggeng Zou
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - High Seng Chai
- Department of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Curtis S. Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Julia Crook
- Department of Biostatistics, Mayo Clinic, Jacksonville, Florida, United States of America
| | - V. Shane Pankratz
- Department of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Christopher N. Rowley
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Asha A. Nair
- Department of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sumit Middha
- Department of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sooraj Maharjan
- Department of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Li Ma
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Kimberly G. Malphrus
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Ryan Palusak
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Sarah Lincoln
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Gina Bisceglio
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Constantin Georgescu
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Naomi Kouri
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | | | - Jin Jen
- Microarray Core, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics and Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Richard Mayeux
- Gertrude H. Sergievsky Center, Department of Neurology, and Taub Institute on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, United States of America
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, United States of America
| | - Lindsay A. Farrer
- Departments of Biostatistics, Medicine (Genetics Program), Ophthalmology, Neurology, and Epidemiology, Boston University, Boston, Massachusetts, United States of America
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Ronald C. Petersen
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Steven G. Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, United States of America
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, United States of America
- * E-mail:
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Allen M, Zou F, Chai HS, Younkin CS, Miles R, Nair AA, Crook JE, Pankratz VS, Carrasquillo MM, Rowley CN, Nguyen T, Ma L, Malphrus KG, Bisceglio G, Ortolaza AI, Palusak R, Middha S, Maharjan S, Georgescu C, Schultz D, Rakhshan F, Kolbert CP, Jen J, Sando SB, Aasly JO, Barcikowska M, Uitti RJ, Wszolek ZK, Ross OA, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N. Glutathione S-transferase omega genes in Alzheimer and Parkinson disease risk, age-at-diagnosis and brain gene expression: an association study with mechanistic implications. Mol Neurodegener 2012; 7:13. [PMID: 22494505 PMCID: PMC3393625 DOI: 10.1186/1750-1326-7-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 04/11/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Glutathione S-transferase omega-1 and 2 genes (GSTO1, GSTO2), residing within an Alzheimer and Parkinson disease (AD and PD) linkage region, have diverse functions including mitigation of oxidative stress and may underlie the pathophysiology of both diseases. GSTO polymorphisms were previously reported to associate with risk and age-at-onset of these diseases, although inconsistent follow-up study designs make interpretation of results difficult. We assessed two previously reported SNPs, GSTO1 rs4925 and GSTO2 rs156697, in AD (3,493 ADs vs. 4,617 controls) and PD (678 PDs vs. 712 controls) for association with disease risk (case-controls), age-at-diagnosis (cases) and brain gene expression levels (autopsied subjects). RESULTS We found that rs156697 minor allele associates with significantly increased risk (odds ratio = 1.14, p = 0.038) in the older ADs with age-at-diagnosis > 80 years. The minor allele of GSTO1 rs4925 associates with decreased risk in familial PD (odds ratio = 0.78, p = 0.034). There was no other association with disease risk or age-at-diagnosis. The minor alleles of both GSTO SNPs associate with lower brain levels of GSTO2 (p = 4.7 × 10-11-1.9 × 10-27), but not GSTO1. Pathway analysis of significant genes in our brain expression GWAS, identified significant enrichment for glutathione metabolism genes (p = 0.003). CONCLUSION These results suggest that GSTO locus variants may lower brain GSTO2 levels and consequently confer AD risk in older age. Other glutathione metabolism genes should be assessed for their effects on AD and other chronic, neurologic diseases.
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Affiliation(s)
- Mariet Allen
- Mayo Clinic Florida, Department of Neuroscience, Jacksonville, FL, USA
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