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Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including MS4A4A and PICALM. Our approach is available in the Bioconductor package regionalpcs, opening avenues for research and facilitating a deeper understanding of the epigenetic landscape in complex diseases.
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Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
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2
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Fang W, Yin B, Fang Z, Tian M, Ke L, Ma X, Di Q. Heat stroke-induced cerebral cortex nerve injury by mitochondrial dysfunction: A comprehensive multi-omics profiling analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170869. [PMID: 38342446 DOI: 10.1016/j.scitotenv.2024.170869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/20/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
In recent years, global warming has led to frequent instances of extremely high temperatures during summer, arousing significant concern about the adverse effects of high temperature. Among these, heat stroke is the most serious, which has detrimental effects on the all organs of human body, especially on brain. However, the comprehensive pathogenesis leading to brain damage remains unclear. In this study, we constructed a mouse model of heat stroke and conducted multi-omics profiling to identify relevant pathogenesis induced by heat stroke. The mice were placed in a constant temperature chamber at 42 °C with a humidity of 50 %, and the criteria for success in modeling were that the rectal temperature reached 42 °C and that the mice were trembling. Then the mice were immediately taken out for further experiments. Firstly, we conducted cFos protein localization and identified the cerebral cortex, especially the anterior cingulate cortex as the region exhibiting the most pronounced damage. Secondly, we performed metabolomics, transcriptomics, and proteomics analysis on cerebral cortex. This multi-omics investigation unveiled noteworthy alterations in proteins and metabolites within pathways associated with neurotransmitter systems, heatstroke-induced mitochondrial dysfunction, encompassing histidine and pentose phosphate metabolic pathways, as well as oxidative stress. In addition, the cerebral cortex exhibited pronounced Reactive Oxygen Species (ROS) production, alongside significant downregulation of the mitochondrial outer membrane protein Tomm40 and mitochondrial permeability transition pore, implicating cerebral cortex mitochondrial dysfunction as the primary instigator of neural impairment. This study marks a significant milestone as the first to employ multi-omics analysis in exploring the molecular mechanisms underlying heat stroke-induced damage in cerebral cortex neurons. It comprehensively identifies all potentially impacted pathways by heat stroke, laying a solid foundation for ensuing research endeavors. Consequently, this study introduces a fresh angle to clinical approaches in heatstroke prevention and treatment, as well as establishes an innovative groundwork for shaping future-forward environmental policies.
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Affiliation(s)
- Wen Fang
- Division of Sports Science& Physical Education, Tsinghua University, Beijing, China; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Bo Yin
- School of Medicine, Tsinghua University, Beijing, China
| | - Zijian Fang
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Mengyi Tian
- School of Medicine, Tsinghua University, Beijing, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Limei Ke
- School of Medicine, Tsinghua University, Beijing, China
| | - Xindong Ma
- Division of Sports Science& Physical Education, Tsinghua University, Beijing, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
| | - Qian Di
- Vanke School of Public Health, Tsinghua University, Beijing, China; Institute for Healthy China, Tsinghua University, Beijing, China.
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3
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Panitch R, Sahelijo N, Hu J, Nho K, Bennett DA, Lunetta KL, Au R, Stein TD, Farrer LA, Jun GR. APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response. Transl Psychiatry 2024; 14:129. [PMID: 38424036 PMCID: PMC10904829 DOI: 10.1038/s41398-024-02834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The joint effects of APOE genotype and DNA methylation on Alzheimer disease (AD) risk is relatively unknown. We conducted genome-wide methylation analyses using 2,021 samples in blood (91 AD cases, 329 mild cognitive impairment, 1,391 controls) and 697 samples in brain (417 AD cases, 280 controls). We identified differentially methylated levels in AD compared to controls in an APOE genotype-specific manner at 25 cytosine-phosphate-guanine (CpG) sites in brain and 36 CpG sites in blood. Additionally, we identified seven CpG sites in the APOE region containing TOMM40, APOE, and APOC1 genes with P < 5 × 10-8 between APOE ε4 carriers and non-carriers in brain or blood. In brain, the most significant CpG site hypomethylated in ε4 carriers compared to non-carriers was from the TOMM40 in the total sample, while most of the evidence was derived from AD cases. However, the CpG site was not significantly modulating expression of these three genes in brain. Three CpG sites from the APOE were hypermethylated in APOE ε4 carriers in brain or blood compared in ε4 non-carriers and nominally significant with APOE expression in brain. Three CpG sites from the APOC1 were hypermethylated in blood, which one of the 3 CpG sites significantly lowered APOC1 expression in blood using all subjects or ε4 non-carriers. Co-methylation network analysis in blood and brain detected eight methylation networks associated with AD and APOE ε4 status. Five of the eight networks included genes containing network CpGs that were significantly enriched for estradiol perturbation, where four of the five networks were enriched for the estrogen response pathway. Our findings provide further evidence of the role of APOE genotype on methylation levels associated with AD, especially linked to estrogen response pathway.
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Affiliation(s)
- Rebecca Panitch
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Nathan Sahelijo
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Junming Hu
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences and Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison Street, Suite 1000, Chicago, IL, 60612, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Rhoda Au
- Department of Anatomy & Neurobiology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA
- VA Bedford Healthcare System, Bedford, MA, 01730, USA
- VA Boston Healthcare Center, Boston, MA, 02130, USA
| | - Lindsay A Farrer
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Epidemiology, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
| | - Gyungah R Jun
- Biomedical Genetics Section, Department of Medicine, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
- Department of Biostatistics, Boston University School of Public Health, 715 Albany Street, Boston, MA, 02118, USA.
- Department of Ophthalmology, Boston University Chobanian and Avedisian School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
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Honea RA, Hunt S, Lepping RJ, Vidoni ED, Morris JK, Watts A, Michaelis E, Burns JM, Swerdlow RH. Alzheimer's disease cortical morphological phenotypes are associated with TOMM40'523-APOE haplotypes. Neurobiol Aging 2023; 132:131-144. [PMID: 37804609 PMCID: PMC10763175 DOI: 10.1016/j.neurobiolaging.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 10/09/2023]
Abstract
Both the APOE ε4 and TOMM40 rs10524523 ("523") genes have been associated with risk for Alzheimer's disease (AD) and neuroimaging biomarkers of AD. No studies have investigated the relationship of TOMM40'523-APOE ε4 on the structural complexity of the brain in AD individuals. We quantified brain morphology and multiple cortical attributes in individuals with mild cognitive impairment (MCI) and AD, then tested whether APOE ε4 or TOMM40 poly-T genotypes were related to AD morphological biomarkers in cognitively unimpaired (CU) and MCI/AD individuals. We identified several AD-specific phenotypes in brain morphology and found that TOMM40 poly-T short alleles are associated with early, AD-specific brain morphological differences in healthy aging. We observed decreased cortical thickness, sulcal depth, and fractal dimension in CU individuals with the poly-T short alleles. Moreover, in MCI/AD participants, the APOE ε4 (TOMM40 L) individuals had a higher rate of gene-related morphological markers indicative of AD. Our data suggest that TOMM40'523 is associated with early brain structure variations in the precuneus, temporal, and limbic cortices.
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Affiliation(s)
- Robyn A Honea
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Neurology, University of Kansas School of Medicine, Kansas City, KS, USA.
| | - Suzanne Hunt
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Rebecca J Lepping
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Hoglund Biomedical Imaging Center, University of Kansas Medical Center, Kansas City, KS, USA; Department of Neurology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Eric D Vidoni
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Neurology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Jill K Morris
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Neurology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Amber Watts
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Psychology, University of Kansas, Lawrence, KS, USA
| | - Elias Michaelis
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA
| | - Jeffrey M Burns
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Neurology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Russell H Swerdlow
- University of Kansas Alzheimer's Disease Center, University of Kansas School of Medicine, Kansas City, KS, USA; Department of Neurology, University of Kansas School of Medicine, Kansas City, KS, USA
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Reed AL, Mitchell W, Alexandrescu AT, Alder NN. Interactions of amyloidogenic proteins with mitochondrial protein import machinery in aging-related neurodegenerative diseases. Front Physiol 2023; 14:1263420. [PMID: 38028797 PMCID: PMC10652799 DOI: 10.3389/fphys.2023.1263420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Most mitochondrial proteins are targeted to the organelle by N-terminal mitochondrial targeting sequences (MTSs, or "presequences") that are recognized by the import machinery and subsequently cleaved to yield the mature protein. MTSs do not have conserved amino acid compositions, but share common physicochemical properties, including the ability to form amphipathic α-helical structures enriched with basic and hydrophobic residues on alternating faces. The lack of strict sequence conservation implies that some polypeptides can be mistargeted to mitochondria, especially under cellular stress. The pathogenic accumulation of proteins within mitochondria is implicated in many aging-related neurodegenerative diseases, including Alzheimer's, Parkinson's, and Huntington's diseases. Mechanistically, these diseases may originate in part from mitochondrial interactions with amyloid-β precursor protein (APP) or its cleavage product amyloid-β (Aβ), α-synuclein (α-syn), and mutant forms of huntingtin (mHtt), respectively, that are mediated in part through their associations with the mitochondrial protein import machinery. Emerging evidence suggests that these amyloidogenic proteins may present cryptic targeting signals that act as MTS mimetics and can be recognized by mitochondrial import receptors and transported into different mitochondrial compartments. Accumulation of these mistargeted proteins could overwhelm the import machinery and its associated quality control mechanisms, thereby contributing to neurological disease progression. Alternatively, the uptake of amyloidogenic proteins into mitochondria may be part of a protein quality control mechanism for clearance of cytotoxic proteins. Here we review the pathomechanisms of these diseases as they relate to mitochondrial protein import and effects on mitochondrial function, what features of APP/Aβ, α-syn and mHtt make them suitable substrates for the import machinery, and how this information can be leveraged for the development of therapeutic interventions.
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Affiliation(s)
- Ashley L. Reed
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Wayne Mitchell
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Andrei T. Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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6
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Lutz MW, Chiba-Falek O. Bioinformatics pipeline to guide post-GWAS studies in Alzheimer's: A new catalogue of disease candidate short structural variants. Alzheimers Dement 2023; 19:4094-4109. [PMID: 37253165 PMCID: PMC10524333 DOI: 10.1002/alz.13168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Short structural variants (SSVs), including insertions/deletions (indels), are common in the human genome and impact disease risk. The role of SSVs in late-onset Alzheimer's disease (LOAD) has been understudied. In this study, we developed a bioinformatics pipeline of SSVs within LOAD-genome-wide association study (GWAS) regions to prioritize regulatory SSVs based on the strength of their predicted effect on transcription factor (TF) binding sites. METHODS The pipeline utilized publicly available functional genomics data sources including candidate cis-regulatory elements (cCREs) from ENCODE and single-nucleus (sn)RNA-seq data from LOAD patient samples. RESULTS We catalogued 1581 SSVs in candidate cCREs in LOAD GWAS regions that disrupted 737 TF sites. That included SSVs that disrupted the binding of RUNX3, SPI1, and SMAD3, within the APOE-TOMM40, SPI1, and MS4A6A LOAD regions. CONCLUSIONS The pipeline developed here prioritized non-coding SSVs in cCREs and characterized their putative effects on TF binding. The approach integrates multiomics datasets for validation experiments using disease models.
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Affiliation(s)
- Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
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7
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Overmeyer C, Jorgensen K, Vohra BPS. The Translocase of the Outer Mitochondrial Membrane (TOM40) is required for mitochondrial dynamics and neuronal integrity in Dorsal Root Ganglion Neurons. Mol Cell Neurosci 2023; 125:103853. [PMID: 37100265 DOI: 10.1016/j.mcn.2023.103853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Polymorphisms and altered expression of the Translocase of the Outer Mitochondrial Membrane - 40 kD (Tom40) are observed in neurodegenerative disease subjects. We utilized in vitro cultured dorsal root ganglion (DRG) neurons to investigate the association of TOM40 depletion to neurodegeneration, and to unravel the mechanism of neurodegeneration induced by decreased levels of TOM40 protein. We provide evidence that severity of neurodegeneration induced in the TOM40 depleted neurons increases with the increase in the depletion of TOM40 and is exacerbated by an increase in the duration of TOM40 depletion. We also demonstrate that TOM40 depletion causes a surge in neuronal calcium levels, decreases mitochondrial motility, increases mitochondrial fission, and decreases neuronal ATP levels. We observed that alterations in the neuronal calcium homeostasis and mitochondrial dynamics precede BCL-xl and NMNAT1 dependent neurodegenerative pathways in the TOM40 depleted neurons. This data also suggests that manipulation of BCL-xl and NMNAT1 may be of therapeutic value in TOM40 associated neurodegenerative disorders.
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Affiliation(s)
| | - Kylie Jorgensen
- Department of Biology, William Jewell College Liberty, MO 64068
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TOMM40 Genetic Variants Cause Neuroinflammation in Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24044085. [PMID: 36835494 PMCID: PMC9962462 DOI: 10.3390/ijms24044085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Translocase of outer mitochondrial membrane 40 (TOMM40) is located in the outer membrane of mitochondria. TOMM40 is essential for protein import into mitochondria. TOMM40 genetic variants are believed to increase the risk of Alzheimer's disease (AD) in different populations. In this study, three exonic variants (rs772262361, rs157581, and rs11556505) and three intronic variants (rs157582, rs184017, and rs2075650) of the TOMM40 gene were identified from Taiwanese AD patients using next-generation sequencing. Associations between the three TOMM40 exonic variants and AD susceptibility were further evaluated in another AD cohort. Our results showed that rs157581 (c.339T > C, p.Phe113Leu, F113L) and rs11556505 (c.393C > T, p.Phe131Leu, F131L) were associated with an increased risk of AD. We further utilized cell models to examine the role of TOMM40 variation in mitochondrial dysfunction that causes microglial activation and neuroinflammation. When expressed in BV2 microglial cells, the AD-associated mutant (F113L) or (F131L) TOMM40 induced mitochondrial dysfunction and oxidative stress-induced activation of microglia and NLRP3 inflammasome. Pro-inflammatory TNF-α, IL-1β, and IL-6 released by mutant (F113L) or (F131L) TOMM40-activated BV2 microglial cells caused cell death of hippocampal neurons. Taiwanese AD patients carrying TOMM40 missense (F113L) or (F131L) variants displayed an increased plasma level of inflammatory cytokines IL-6, IL-18, IL-33, and COX-2. Our results provide evidence that TOMM40 exonic variants, including rs157581 (F113L) and rs11556505 (F131L), increase the AD risk of the Taiwanese population. Further studies suggest that AD-associated mutant (F113L) or (F131L) TOMM40 cause the neurotoxicity of hippocampal neurons by inducing the activation of microglia and NLRP3 inflammasome and the release of pro-inflammatory cytokines.
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Pang S, Li S, Cheng H, Luo Z, Qi X, Guan F, Dong W, Gao S, Liu N, Gao X, Pan S, Zhang X, Zhang L, Yang Y, Zhang L. Discovery of an evodiamine derivative for PI3K/AKT/GSK3β pathway activation and AD pathology improvement in mouse models. Front Mol Neurosci 2023; 15:1025066. [PMID: 36698780 PMCID: PMC9868638 DOI: 10.3389/fnmol.2022.1025066] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive neurodegeneration and cognitive decline. Evodiamine, a main component in Chinese medicine, was found to improve cognitive impairment in AD model mice based on several intensive studies. However, evodiamine has high cytotoxicity and poor bioactivity. In this study, several evodiamine derivatives were synthesized via heterocyclic substitution and amide introduction and screened for cytotoxicity and antioxidant capacity. Under the same concentrations, compound 4c was found to exhibit lower cytotoxicity and higher activity against H2O2 and amyloid β oligomers (AβOs) than evodiamine in vitro and significantly improve the working memory and spatial memory of 3 x Tg and APP/PS1 AD mice. Subsequent RNA sequencing and pathway enrichment analysis showed that 4c affected AD-related genes and the AMPK and insulin signaling pathways. Furthermore, we confirmed that 4c recovered PI3K/AKT/GSK3β/Tau dysfunction in vivo and in vitro. In conclusion, 4c represents a potential lead compound for AD therapy based on the recovery of PI3K/AKT/GSK3β pathway dysfunction.
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Affiliation(s)
- Shuo Pang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China,Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Li
- Beijing Key Laboratory of Active Substance Discovery and Drug Ability Evaluation, Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hanzeng Cheng
- Beijing Key Laboratory of Active Substance Discovery and Drug Ability Evaluation, Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuohui Luo
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China,Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaolong Qi
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China,Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Feifei Guan
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China,Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Dong
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Gao
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ning Liu
- Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiang Gao
- Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuo Pan
- Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xu Zhang
- Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Li Zhang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China,Beijing Engineering Research Center for Experimental Animal Models of Human Diseases, Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yajun Yang
- Beijing Key Laboratory of Active Substance Discovery and Drug Ability Evaluation, Institute of Material Medical, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,*Correspondence: Yajun Yang ✉
| | - Lianfeng Zhang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China,Lianfeng Zhang ✉
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10
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Watts A, Haneline S, Welsh-Bohmer KA, Wu J, Alexander R, Swerdlow RH, Burns DK, Saunders AM. TOMM40 '523 Genotype Distinguishes Patterns of Cognitive Improvement for Executive Function in APOEɛ3 Homozygotes. J Alzheimers Dis 2023; 95:1697-1707. [PMID: 37718796 PMCID: PMC10578241 DOI: 10.3233/jad-230066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2023] [Indexed: 09/19/2023]
Abstract
BACKGROUND TOMM40 '523 has been associated with cognitive performance and risk for developing Alzheimer's disease independent of the effect of APOE genotype. Few studies have considered the longitudinal effect of this genotype on change in cognition over time. OBJECTIVE Our objective was to evaluate the relationship between TOMM40 genotype status and change in cognitive performance in the TOMMORROW study, which was designed to prospectively evaluate an algorithm that includes TOMM40 '523 for genetic risk for conversion to mild cognitive impairment. METHODS We used latent growth curve models to estimate the effect of TOMM40 allele carrier (short, very long) status on the intercept and slope of change in cognitive performance in four broad cognitive domains (attention, memory, executive function, and language) and a combined overall cognitive score over 30 months. RESULTS TOMM40 very long allele carriers had significantly lower baseline performance for the combined overall cognitive function score (B = -0.088, p = 0.034) and for the executive function domain score (B = -0.143, p = 0.013). Slopes for TOMM40 very long carriers had significantly greater increases over time for the executive function domain score only. In sensitivity analyses, the results for executive function were observed in participants who remained clinically stable, but not in those who progressed clinically over the study duration. CONCLUSIONS Our results add to the growing body of evidence that TOMM40, in the absence of APOEɛ4, may contribute to cognitive changes with aging and dementia and support the view that mitochondrial function is an important contributor to Alzheimer's disease risk.
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Affiliation(s)
- Amber Watts
- University of Kansas, Alzheimer’s Disease Research Center, Fairway, KS, USA
| | - Stephen Haneline
- Zinfandel Pharmaceuticals, Research Triangle Park, Chapel Hill, NC, USA
| | | | - Jingtao Wu
- Takeda Development Center Americas, Cambridge, MA, USA
| | | | | | - Daniel K. Burns
- Zinfandel Pharmaceuticals, Research Triangle Park, Chapel Hill, NC, USA
| | - Ann M. Saunders
- Zinfandel Pharmaceuticals, Research Triangle Park, Chapel Hill, NC, USA
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11
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Zou H, Luo S, Liu H, Lutz MW, Bennett DA, Plassman BL, Welsh-Bohmer KA. Genotypic Effects of the TOMM40'523 Variant and APOE on Longitudinal Cognitive Change over 4 Years: The TOMMORROW Study. J Prev Alzheimers Dis 2023; 10:886-894. [PMID: 37874111 PMCID: PMC10734664 DOI: 10.14283/jpad.2023.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
BACKGROUND The 523 poly-T length polymorphism (rs10524523) in TOMM40 has been reported to influence longitudinal cognitive test performance within APOE ε3/3 carriers. The results from prior studies are inconsistent. It is also unclear whether specific APOE and TOMM40 genotypes contribute to heterogeneity in longitudinal cognitive performance during the preclinical stages of AD. OBJECTIVES To determine the effects of these genes on longitudinal cognitive change in early preclinical stages of AD, we used the clinical trial data from the recently concluded TOMMORROW study to examine the effects of APOE and TOMM40 genotypes on neuropsychological test performance. DESIGN A phase 3, double-blind, placebo-controlled, randomized clinical trial. SETTING Academic affiliated and private research clinics in Australia, Germany, Switzerland, the UK, and the USA. PARTICIPANTS Cognitively normal older adults aged 65 to 83. INTERVENTION Pioglitazone tablet. MEASUREMENTS Participants from the TOMMORROW trial were stratified based on APOE genotype (APOE ε3/3, APOE ε3/4, APOE ε4/4). APOE ε3/3 carriers were further stratified by TOMM40'523 genotype. The final analysis dataset consists of 1,330 APOE ε3/3 carriers and 7,001 visits. Linear mixed models were used to compare the rates of decline in cognition across APOE groups and the APOE ε3/3 carriers with different TOMM40'523 genotypes. RESULTS APOE ε3/4 and APOE ε4/4 genotypes compared with the APOE ε3/3 genotype were associated with worse performance on measures of global cognition, episodic memory, and expressive language. Further, over the four years of observation, the APOE ε3/3 carriers with the TOMM40'523-S/S genotype showed better global cognition and accelerated rates of cognitive decline on tests of global cognition, executive function, and attentional processing compared to APOE ε3/3 carriers with TOMM40'523-S/VL and VL/VL genotypes and compared to the APOE ε3/4 and APOE ε4/4 carriers. CONCLUSIONS We suggest that both APOE and TOMM40 genotypes may independently contribute to cognitive heterogeneity in the pre-MCI stages of AD. Controlling for this genetic variability will be important in clinical trials designed to slow the rate of cognitive decline and/or prevent symptom onset in preclinical AD.
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Affiliation(s)
- H Zou
- Sheng Luo, PhD, Dept of Biostatistics and Bioinformatics, 2424 Erwin Rd, Suite 11082, Durham, NC, USA, 27705, Tel: 919-668-8038, Fax: 919-668-7059,
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12
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Tanguturi P, Streicher JM. The role of opioid receptors in modulating Alzheimer's Disease. Front Pharmacol 2023; 14:1056402. [PMID: 36937877 PMCID: PMC10014470 DOI: 10.3389/fphar.2023.1056402] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Alzheimer's disease (AD) is a complex neurological disorder characterized by accumulation of amyloid plaques and neurofibrillary tangles. Long term investigation of AD pathogenesis suggests that β-site amyloid precursor protein [APP] cleaving enzyme 1 (BACE1) and γ-secretase enzymes promote the amyloidogenic pathway and produce toxic Aβ peptides that are predisposed to aggregate in the brain. Hence, the targeted inhibition of BACE1/γ-secretase expression and function is a promising approach for AD therapy. Several reports have suggested that the opioid family of G-protein coupled receptors modulate the etiology of AD progression. It has also been found that changes in the signaling pathways of opioid receptors increased the expression of BACE1 and γ-secretase, and is strongly correlated with abnormal production of Aβ and pathogenesis of AD. Thus, the opioid receptor family is a promising candidate for targeted drug development to treat AD. In this review, we outline the involvement and mechanisms of opioid receptor signaling modulation in Alzheimer's Disease progression.
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Affiliation(s)
- Parthasaradhireddy Tanguturi
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Comprehensive Pain and Addiction Center, University of Arizona, Tucson, AZ, United States
| | - John M. Streicher
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States
- Comprehensive Pain and Addiction Center, University of Arizona, Tucson, AZ, United States
- *Correspondence: John M. Streicher,
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13
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Morozova A, Zorkina Y, Abramova O, Pavlova O, Pavlov K, Soloveva K, Volkova M, Alekseeva P, Andryshchenko A, Kostyuk G, Gurina O, Chekhonin V. Neurobiological Highlights of Cognitive Impairment in Psychiatric Disorders. Int J Mol Sci 2022; 23:1217. [PMID: 35163141 PMCID: PMC8835608 DOI: 10.3390/ijms23031217] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
This review is focused on several psychiatric disorders in which cognitive impairment is a major component of the disease, influencing life quality. There are plenty of data proving that cognitive impairment accompanies and even underlies some psychiatric disorders. In addition, sources provide information on the biological background of cognitive problems associated with mental illness. This scientific review aims to summarize the current knowledge about neurobiological mechanisms of cognitive impairment in people with schizophrenia, depression, mild cognitive impairment and dementia (including Alzheimer's disease).The review provides data about the prevalence of cognitive impairment in people with mental illness and associated biological markers.
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Affiliation(s)
- Anna Morozova
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Yana Zorkina
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Olga Abramova
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Olga Pavlova
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Konstantin Pavlov
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Kristina Soloveva
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Maria Volkova
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Polina Alekseeva
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Alisa Andryshchenko
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Georgiy Kostyuk
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Olga Gurina
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Vladimir Chekhonin
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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14
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Lee J, Howard RS, Schneider LS. The Current Landscape of Prevention Trials in Dementia. Neurotherapeutics 2022; 19:228-247. [PMID: 35587314 PMCID: PMC9130372 DOI: 10.1007/s13311-022-01236-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2022] [Indexed: 01/03/2023] Open
Abstract
As the prevalence of dementia and Alzheimer's disease (AD) increases worldwide, it is imperative to reflect on the major clinical trials in the prevention of dementia and the challenges that surround them. The pharmaceutical industry has focused on developing drugs that primarily affect the Aβ cascade and tau proteinopathy, while academics have focused on repurposed therapeutics and multi-domain interventions for prevention studies. This paper highlights significant primary, secondary, and tertiary prevention trials for dementia and AD, overall design, methods, and systematic issues to better understand the current landscape of prevention trials. We included 32 pharmacologic intervention trials and 9 multi-domain trials. Fourteen could be considered primary prevention, and 18 secondary or tertiary prevention trials. Major categories were Aβ vaccines, Aβ antibodies, tau antibodies, anti-inflammatories, sex hormones, and Ginkgo biloba extract. The 9 multi-domain studies mainly focused on lifestyle modifications such as blood pressure management, socialization, and physical activity. The lack of validated drug targets, and the complexity of the diagnostic frameworks, eligibility criteria, and outcome measurements for trials, make it difficult to show efficacy for both pharmacological and multi-domain interventions. We hope that this summative analysis of trials will stimulate discussion for scientists and clinicians interested in reviewing and developing preventative interventions for AD.
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Affiliation(s)
- Jonathan Lee
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, USA
| | - Rebecca Sitra Howard
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, USA
| | - Lon S Schneider
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, USA.
- Department of Neurology, Keck School of Medicine of the University of Southern California, Los Angeles, USA.
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15
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Rabaneda-Bueno R, Mena-Montes B, Torres-Castro S, Torres-Carrillo N, Torres-Carrillo NM. Advances in Genetics and Epigenetic Alterations in Alzheimer's Disease: A Notion for Therapeutic Treatment. Genes (Basel) 2021; 12:1959. [PMID: 34946908 PMCID: PMC8700838 DOI: 10.3390/genes12121959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is a disabling neurodegenerative disorder that leads to long-term functional and cognitive impairment and greatly reduces life expectancy. Early genetic studies focused on tracking variations in genome-wide DNA sequences discovered several polymorphisms and novel susceptibility genes associated with AD. However, despite the numerous risk factors already identified, there is still no fully satisfactory explanation for the mechanisms underlying the onset of the disease. Also, as with other complex human diseases, the causes of low heritability are unclear. Epigenetic mechanisms, in which changes in gene expression do not depend on changes in genotype, have attracted considerable attention in recent years and are key to understanding the processes that influence age-related changes and various neurological diseases. With the recent use of massive sequencing techniques, methods for studying epigenome variations in AD have also evolved tremendously, allowing the discovery of differentially expressed disease traits under different conditions and experimental settings. This is important for understanding disease development and for unlocking new potential AD therapies. In this work, we outline the genomic and epigenomic components involved in the initiation and development of AD and identify potentially effective therapeutic targets for disease control.
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Affiliation(s)
- Rubén Rabaneda-Bueno
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic
- School of Biological Sciences, James Clerk Maxwell Building, The King’s Buildings Campus, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Beatriz Mena-Montes
- Laboratorio de Biología del Envejecimiento, Departamento de Investigación Básica, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Sara Torres-Castro
- Departamento de Epidemiología Demográfica y Determinantes Sociales, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
| | - Nora Magdalena Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
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16
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Kulminski AM, Philipp I, Loika Y, He L, Culminskaya I. Protective association of the ε2/ε3 heterozygote with Alzheimer's disease is strengthened by TOMM40-APOE variants in men. Alzheimers Dement 2021; 17:1779-1787. [PMID: 34310032 DOI: 10.1002/alz.12413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/07/2021] [Accepted: 05/25/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Despite advances, understanding the protective role of the apolipoprotein E (APOE) ε2 allele in Alzheimer's disease (AD) remains elusive. METHODS We examined associations of variants comprised of the TOMM40 rs8106922 and APOE rs405509, rs440446, and ε2-encoding rs7412 polymorphisms with AD in a sample of 2862 AD-affected and 169,516 AD-unaffected non-carriers of the ε4 allele. RESULTS Association of the ε2/ε3 heterozygote of men with AD is 38% (P = 1.65 × 10-2 ) more beneficial when it is accompanied by rs8106922 major allele homozygote and rs405509 and rs440446 heterozygotes than by rs8106922 heterozygote and rs405509 and rs440446 major allele homozygotes. No difference in the beneficial associations of these two most common ε2/ε3-bearing variants with AD was identified in women. The role of ε2/ε3 heterozygote may be affected by different immunomodulation functions of rs8106922, rs405509, and rs440446 variants in a sex-specific manner. DISCUSSION Combination of TOMM40 and APOE variants defines a more homogeneous AD-protective ε2/ε3-bearing profile in men.
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Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Ian Philipp
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, North Carolina, USA
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17
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Brabec JL, Lara MK, Tyler AL, Mahoney JM. System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. Front Genet 2021; 12:625246. [PMID: 33889174 PMCID: PMC8056044 DOI: 10.3389/fgene.2021.625246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is a debilitating neurodegenerative disorder. Since the advent of the genome-wide association study (GWAS) we have come to understand much about the genes involved in AD heritability and pathophysiology. Large case-control meta-GWAS studies have increased our ability to prioritize weaker effect alleles, while the recent development of network-based functional prediction has provided a mechanism by which we can use machine learning to reprioritize GWAS hits in the functional context of relevant brain tissues like the hippocampus and amygdala. In parallel with these developments, groups like the Alzheimer’s Disease Neuroimaging Initiative (ADNI) have compiled rich compendia of AD patient data including genotype and biomarker information, including derived volume measures for relevant structures like the hippocampus and the amygdala. In this study we wanted to identify genes involved in AD-related atrophy of these two structures, which are often critically impaired over the course of the disease. To do this we developed a combined score prioritization method which uses the cumulative distribution function of a gene’s functional and positional score, to prioritize top genes that not only segregate with disease status, but also with hippocampal and amygdalar atrophy. Our method identified a mix of genes that had previously been identified in AD GWAS including APOE, TOMM40, and NECTIN2(PVRL2) and several others that have not been identified in AD genetic studies, but play integral roles in AD-effected functional pathways including IQSEC1, PFN1, and PAK2. Our findings support the viability of our novel combined score as a method for prioritizing region- and even cell-specific AD risk genes.
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Affiliation(s)
- Jeffrey L Brabec
- Department of Neurological Sciences, University of Vermont, Burlington, VT, United States
| | - Montana Kay Lara
- Department of Neurological Sciences, University of Vermont, Burlington, VT, United States
| | - Anna L Tyler
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - J Matthew Mahoney
- Department of Neurological Sciences, University of Vermont, Burlington, VT, United States.,The Jackson Laboratory, Bar Harbor, ME, United States
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18
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Tang S, Buchman AS, De Jager PL, Bennett DA, Epstein MP, Yang J. Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer's dementia. PLoS Genet 2021; 17:e1009482. [PMID: 33798195 PMCID: PMC8046351 DOI: 10.1371/journal.pgen.1009482] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 04/14/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Transcriptome-wide association studies (TWAS) have been widely used to integrate transcriptomic and genetic data to study complex human diseases. Within a test dataset lacking transcriptomic data, traditional two-stage TWAS methods first impute gene expression by creating a weighted sum that aggregates SNPs with their corresponding cis-eQTL effects on reference transcriptome. Traditional TWAS methods then employ a linear regression model to assess the association between imputed gene expression and test phenotype, thereby assuming the effect of a cis-eQTL SNP on test phenotype is a linear function of the eQTL's estimated effect on reference transcriptome. To increase TWAS robustness to this assumption, we propose a novel Variance-Component TWAS procedure (VC-TWAS) that assumes the effects of cis-eQTL SNPs on phenotype are random (with variance proportional to corresponding reference cis-eQTL effects) rather than fixed. VC-TWAS is applicable to both continuous and dichotomous phenotypes, as well as individual-level and summary-level GWAS data. Using simulated data, we show VC-TWAS is more powerful than traditional TWAS methods based on a two-stage Burden test, especially when eQTL genetic effects on test phenotype are no longer a linear function of their eQTL genetic effects on reference transcriptome. We further applied VC-TWAS to both individual-level (N = ~3.4K) and summary-level (N = ~54K) GWAS data to study Alzheimer's dementia (AD). With the individual-level data, we detected 13 significant risk genes including 6 known GWAS risk genes such as TOMM40 that were missed by traditional TWAS methods. With the summary-level data, we detected 57 significant risk genes considering only cis-SNPs and 71 significant genes considering both cis- and trans- SNPs, which also validated our findings with the individual-level GWAS data. Our VC-TWAS method is implemented in the TIGAR tool for public use.
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Affiliation(s)
- Shizhen Tang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Michael P. Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
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Bakeberg MC, Hoes ME, Gorecki AM, Theunissen F, Pfaff AL, Kenna JE, Plunkett K, Kõks S, Akkari PA, Mastaglia FL, Anderton RS. The TOMM40 '523' polymorphism in disease risk and age of symptom onset in two independent cohorts of Parkinson's disease. Sci Rep 2021; 11:6363. [PMID: 33737565 PMCID: PMC7973542 DOI: 10.1038/s41598-021-85510-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
Abnormal mitochondrial function is a key process in the pathogenesis of Parkinson's disease (PD). The central pore-forming protein TOM40 of the mitochondria is encoded by the translocase of outer mitochondrial membrane 40 homologue gene (TOMM40). The highly variant '523' poly-T repeat is associated with age-related cognitive decline and age of onset in Alzheimer's disease, but whether it plays a role in modifying the risk or clinical course of PD it yet to be elucidated. The TOMM40 '523' allele length was determined in 634 people with PD and 422 healthy controls from an Australian cohort and the Parkinson's Progression Markers Initiative (PPMI) cohort, using polymerase chain reaction or whole genome sequencing analysis. Genotype and allele frequencies of TOMM40 '523' and APOE ε did not differ significantly between the cohorts. Analyses revealed TOMM40 '523' allele groups were not associated with disease risk, while considering APOE ε genotype. Regression analyses revealed the TOMM40 S/S genotype was associated with a significantly later age of symptom onset in the PPMI PD cohort, but not after correction for covariates, or in the Australian cohort. Whilst variation in the TOMM40 '523' polymorphism was not associated with PD risk, the possibility that it may be a modifying factor for age of symptom onset warrants further investigation in other PD populations.
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Affiliation(s)
- Megan C Bakeberg
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Madison E Hoes
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Anastazja M Gorecki
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- The Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- The Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Jade E Kenna
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
| | - Kai Plunkett
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- The Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - P Anthony Akkari
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
- The Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia
- The Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Ryan S Anderton
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.
- Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, WA, Australia.
- Institute for Health Research and School of Health Sciences, University of Notre Dame Australia, 19 Mouat Street, Fremantle, WA, 6959, Australia.
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20
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Transcript Variants of Genes Involved in Neurodegeneration Are Differentially Regulated by the APOE and MAPT Haplotypes. Genes (Basel) 2021; 12:genes12030423. [PMID: 33804213 PMCID: PMC7999745 DOI: 10.3390/genes12030423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/01/2021] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic variations at the Apolipoprotein E (ApoE) and microtubule-associated protein tau (MAPT) loci have been implicated in multiple neurogenerative diseases, but their exact molecular mechanisms are unclear. In this study, we performed transcript level linear modelling using the blood whole transcriptome data and genotypes of the 570 subjects in the Parkinson’s Progression Markers Initiative (PPMI) cohort. ApoE, MAPT haplotypes and two SNPs at the SNCA locus (rs356181, rs3910105) were used to detect expression quantitative trait loci eQTLs associated with the transcriptome and differential usage of transcript isoforms. As a result, we identified 151 genes associated with the genotypic variations, 29 cis and 122 trans eQTL positions. Profound effect with genome-wide significance of ApoE e4 haplotype on the expression of TOMM40 transcripts was identified. This finding potentially explains in part the frequently established genetic association with the APOE e4 haplotypes in neurodegenerative diseases. Moreover, MAPT haplotypes had significant differential impact on 23 transcripts from the 17q21.31 and 17q24.1 loci. MAPT haplotypes had also the largest up-regulating (256) and the largest down-regulating (−178) effect sizes measured as β values on two different transcripts from the same gene (LRRC37A2). Intronic SNP in the SNCA gene, rs3910105, differentially induced expression of three SNCA isoforms. In conclusion, this study established clear association between well-known haplotypic variance and transcript specific regulation in the blood. APOE e4 and MAPT H1/H2 haplotypic variants are associated with the expression of several genes related to the neurodegeneration.
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Curtis D. Analysis of whole genome sequenced cases and controls shows that the association of variants in TOMM40, BCAM, NECTIN2 and APOC1 with late onset Alzheimer's disease is driven by linkage disequilibrium with APOE ε2/ε3/ε4 alleles. J Neurogenet 2021; 35:59-66. [PMID: 33970751 DOI: 10.1080/01677063.2020.1866569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/16/2020] [Indexed: 10/21/2022]
Abstract
Variants in APOE are associated with risk of late onset Alzheimer's disease (LOAD) but the magnitude of the effect has been reported to vary across ancestries. Also, other variants in the region have been reported to show association though it has been unclear whether this was secondary to their linkage disequilibrium with the APOE variants rs429358 and rs7412. Previous analyses of exome-sequenced samples have identified other genes in which rare variants impact risk of disease. In this study 2000 whole genome sequenced cases and controls with different ancestries were subjected to gene-based weighted burden analysis to identify risk genes. Additionally, individual variants in the APOE region were tested for association with LOAD. When using the APOE variants as covariates no individual genes showed statistically significant evidence for association after Bonferroni correction for multiple testing, which may well be a consequence of the modest sample size. Likewise, for those variants initially showing evidence of association with LOAD incorporating the APOE variants as covariates dramatically reduced the strength of association. These results demonstrate that the differential association of APOE across ancestries does not appear to be driven by another variant in the region. It seems likely that no other genes in the region have a direct effect on LOAD risk.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, UK
- Centre for Psychiatry, Queen Mary University of London, London, UK
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22
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Deters KD, Mormino EC, Yu L, Lutz MW, Bennett DA, Barnes LL. TOMM40-APOE haplotypes are associated with cognitive decline in non-demented Blacks. Alzheimers Dement 2021; 17:1287-1296. [PMID: 33580752 DOI: 10.1002/alz.12295] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/16/2020] [Accepted: 12/18/2020] [Indexed: 11/08/2022]
Abstract
INTRODUCTION The goal was to investigate effects of APOE-TOMM40-'523 haplotypes on cognitive decline in non-demented non-Hispanic Blacks (NHB), and determine whether effects differ from non-Hispanic Whites (NHW). METHODS The impact of zero to two copies of the '523-Short variant (S; poly-T alleles < 20) within apolipoprotein E (APOE) genotype on a composite measure of global cognition and five domains was examined. RESULTS In NHB with ε3/ε3 (N = 294), '523-S/S was associated with faster decline in global cognition (β = -0.048, P = 0.017), episodic memory (β = -0.05, P = 0.031), and visuospatial ability (β = -0.037, P = 0.034) relative to those without '523-S. For NHB ε4+ (N = 182), '523-S/S had slower decline in global cognition (β = 0.047, P = 0.042) and visuospatial ability (β = 0.07, P = 0.0005) relative to '523-S non-carriers. NHB ε4+ with '523-S also had a slower rate of decline than NHWs ε4+ with '523-S. DISCUSSION '523-S/S has a different effect on cognitive decline among NHB dependent on APOE allele. Differences in the effect of ε4-'523-S in NHB may explain prior mixed findings on ε4 and decline in this population.
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Affiliation(s)
- Kacie D Deters
- Stanford University School of Medicine, Department of Neurology and Neurological Sciences, Stanford, California, USA
| | - Elizabeth C Mormino
- Stanford University School of Medicine, Department of Neurology and Neurological Sciences, Stanford, California, USA
| | - Lei Yu
- Rush University Medical Center, Department of Neurological Sciences, Rush Alzheimer's Disease Center, Chicago, Illinois, USA
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, North Carolina, USA
| | - David A Bennett
- Rush University Medical Center, Department of Neurological Sciences, Rush Alzheimer's Disease Center, Chicago, Illinois, USA
| | - Lisa L Barnes
- Rush University Medical Center, Department of Neurological Sciences, Rush Alzheimer's Disease Center, Chicago, Illinois, USA
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23
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Novel PET Biomarkers to Disentangle Molecular Pathways across Age-Related Neurodegenerative Diseases. Cells 2020; 9:cells9122581. [PMID: 33276490 PMCID: PMC7761606 DOI: 10.3390/cells9122581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022] Open
Abstract
There is a need to disentangle the etiological puzzle of age-related neurodegenerative diseases, whose clinical phenotypes arise from known, and as yet unknown, pathways that can act distinctly or in concert. Enhanced sub-phenotyping and the identification of in vivo biomarker-driven signature profiles could improve the stratification of patients into clinical trials and, potentially, help to drive the treatment landscape towards the precision medicine paradigm. The rapidly growing field of neuroimaging offers valuable tools to investigate disease pathophysiology and molecular pathways in humans, with the potential to capture the whole disease course starting from preclinical stages. Positron emission tomography (PET) combines the advantages of a versatile imaging technique with the ability to quantify, to nanomolar sensitivity, molecular targets in vivo. This review will discuss current research and available imaging biomarkers evaluating dysregulation of the main molecular pathways across age-related neurodegenerative diseases. The molecular pathways focused on in this review involve mitochondrial dysfunction and energy dysregulation; neuroinflammation; protein misfolding; aggregation and the concepts of pathobiology, synaptic dysfunction, neurotransmitter dysregulation and dysfunction of the glymphatic system. The use of PET imaging to dissect these molecular pathways and the potential to aid sub-phenotyping will be discussed, with a focus on novel PET biomarkers.
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24
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Cardoso R, Lemos C, Oliveiros B, Almeida MR, Baldeiras I, Pereira CF, Santos A, Duro D, Vieira D, Santana I, Oliveira CR. APOEɛ4-TOMM40L Haplotype Increases the Risk of Mild Cognitive Impairment Conversion to Alzheimer's Disease. J Alzheimers Dis 2020; 78:587-601. [PMID: 33016906 DOI: 10.3233/jad-200556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Mild cognitive impairment (MCI) has been considered as a pre-dementia stage, although the factors leading to Alzheimer's disease (AD) conversion remain controversial. OBJECTIVE Evaluate whether TOMM40 poly-T (TOMM40' 523) polymorphism is associated with the risk and conversion time from MCI to AD and secondly with AD cerebrospinal fluid (CSF) biomarkers, disentangling the APOE genotype. METHODS 147 AD patients, 102 MCI patients, and 105 cognitively normal controls were genotyped for poly-T polymorphism. MCI patients were subdivided into two groups, the group of patients that converted to AD (MCI-AD) and the group of those that remained stable (MCI-S). RESULTS TOMM40' 523 L allele was significantly more frequent in the MCI-AD group and having at least one L allele significantly increased the risk of conversion from MCI to AD (OR = 8.346, p < 0.001, 95% CI: 2.830 to 24.617). However, when adjusted for the presence of APOEɛ4 allele, both the L allele and ɛ4 allele lost significance in the model (p > 0.05). We then analyzed the APOEɛ4-TOMM40' 523 L haplotype and observed that patients carrying this haplotype had significantly higher risk (OR = 5.83; 95% CI = 2.30-14.83) and mean lower times of conversion to AD (p = 0.003). This haplotype was also significantly associated with a biomarker profile compatible with AD (p = 0.007). CONCLUSION This study shows that the APOEɛ4-TOMM40' 523 L haplotype is associated with a higher risk and shorter times of conversion from MCI to AD, possibly driven by CSF biomarkers and mitochondrial dysfunction.
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Affiliation(s)
- Remy Cardoso
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal
| | - Carolina Lemos
- UnIGENe, IBMC -Institute for Molecular and Cell Biology, Porto, Portugal.,i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Bárbara Oliveiros
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maria Rosário Almeida
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Neurochemistry Laboratory, Neurology Department, Coimbra University Hospital (CHUC), Coimbra, Portugal
| | - Cláudia Fragão Pereira
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Santos
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal
| | - Diana Duro
- Neurology Department, Coimbra University Hospital (CHUC), Coimbra, Portugal
| | - Daniela Vieira
- Neurology Department, Coimbra University Hospital (CHUC), Coimbra, Portugal
| | - Isabel Santana
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Neurology Department, Coimbra University Hospital (CHUC), Coimbra, Portugal
| | - Catarina Resende Oliveira
- Center for Neuroscience and Cell Biology, CNC-CIBB, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra, Coimbra, Portugal
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25
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Swerdlow RH, Hui D, Chalise P, Sharma P, Wang X, Andrews SJ, Pa J, Mahnken JD, Morris J, Wilkins HM, Burns JM, Michaelis ML, Michaelis EK. Exploratory analysis of mtDNA haplogroups in two Alzheimer's longitudinal cohorts. Alzheimers Dement 2020; 16:1164-1172. [PMID: 32543785 PMCID: PMC9847473 DOI: 10.1002/alz.12119] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/06/2020] [Accepted: 04/29/2020] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Inherited mitochondrial DNA (mtDNA) variants may influence Alzheimer's disease (AD) risk. METHODS We sequenced mtDNA from 146 AD and 265 cognitively normal (CN) subjects from the University of Kansas AD Center (KUADC) and assigned haplogroups. We further considered 244 AD and 242 CN AD Neuroimaging Initiative (ADNI) subjects with equivalent data. RESULTS Without applying multiple comparisons corrections, KUADC haplogroup J AD and CN frequencies were 16.4% versus 7.6% (P = .007), and haplogroup K AD and CN frequencies were 4.8% versus 10.2% (P = .063). ADNI haplogroup J AD and CN frequencies were 10.7% versus 7.0% (P = .20), and haplogroup K frequencies were 4.9% versus 8.7% (P = .11). For the combined 390 AD and 507 CN cases haplogroup J frequencies were 12.8% versus 7.3% (P = .006), odds ratio (OR) = 1.87, and haplogroup K frequencies were 4.9% versus 9.5% (P = .010), OR = 0.49. Associations remained significant after adjusting for apolipoprotein E, age, and sex. CONCLUSION This exploratory analysis suggests inherited mtDNA variants influence AD risk.
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Affiliation(s)
- Russell H. Swerdlow
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Dongwei Hui
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Prabhakar Chalise
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Palash Sharma
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Xinkun Wang
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Shea J. Andrews
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy Pa
- Alzheimer’s Disease Research Center, Mark and Mary Stevens Neuroimaging and Informatics InstituteUniversity of Southern California, Los Angeles, California, USA
| | - Jonathan D. Mahnken
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jill Morris
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Heather M. Wilkins
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jeffrey M. Burns
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Mary L. Michaelis
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Elias K. Michaelis
- Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
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Squillario M, Abate G, Tomasi F, Tozzo V, Barla A, Uberti D. A telescope GWAS analysis strategy, based on SNPs-genes-pathways ensamble and on multivariate algorithms, to characterize late onset Alzheimer's disease. Sci Rep 2020; 10:12063. [PMID: 32694537 PMCID: PMC7374579 DOI: 10.1038/s41598-020-67699-8] [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: 10/04/2019] [Accepted: 06/10/2020] [Indexed: 12/18/2022] Open
Abstract
Genome–wide association studies (GWAS) have revealed a plethora of putative susceptibility genes for Alzheimer’s disease (AD), with the sole exception of APOE gene unequivocally validated in independent study. Considering that the etiology of complex diseases like AD could depend on functional multiple genes interaction network, here we proposed an alternative GWAS analysis strategy based on (i) multivariate methods and on a (ii) telescope approach, in order to guarantee the identification of correlated variables, and reveal their connections at three biological connected levels. Specifically as multivariate methods, we employed two machine learning algorithms and a genetic association test and we considered SNPs, Genes and Pathways features in the analysis of two public GWAS dataset (ADNI-1 and ADNI-2). For each dataset and for each feature we addressed two binary classifications tasks: cases vs. controls and the low vs. high risk of developing AD considering the allelic status of APOEe4. This complex strategy allowed the identification of SNPs, genes and pathways lists statistically robust and meaningful from the biological viewpoint. Among the results, we confirm the involvement of TOMM40 gene in AD and we propose GRM7 as a novel gene significantly associated with AD.
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Affiliation(s)
| | - Giulia Abate
- Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | | | | | | | - Daniela Uberti
- Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
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27
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Roda AR, Montoliu-Gaya L, Villegas S. The Role of Apolipoprotein E Isoforms in Alzheimer's Disease. J Alzheimers Dis 2020; 68:459-471. [PMID: 30775980 DOI: 10.3233/jad-180740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD), the most common type of dementia worldwide, is characterized by high levels of amyloid-β (Aβ) peptide and hyperphosphorylated tau protein. Genetically, the ɛ4 allele of apolipoprotein E (ApoE) has been established as the major risk factor for developing late-onset AD (LOAD), the most common form of the disease. Although the role ApoE plays in AD is still not completely understood, a differential role of its isoforms has long been known. The current review compiles the involvement of ApoE isoforms in amyloid-β protein precursor transcription, Aβ aggregation and clearance, synaptic plasticity, neuroinflammation, lipid metabolism, mitochondrial function, and tau hyperphosphorylation. Due to the complexity of LOAD, an accurate description of the interdependence among all the related molecular mechanisms involved in the disease is needed for developing successful therapies.
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Affiliation(s)
- Alejandro R Roda
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Laia Montoliu-Gaya
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Villegas
- Protein Design and Immunotherapy Group, Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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28
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Strickland SL, Reddy JS, Allen M, N'songo A, Burgess JD, Corda MM, Ballard T, Wang X, Carrasquillo MM, Biernacka JM, Jenkins GD, Mukherjee S, Boehme K, Crane P, Kauwe JS, Ertekin‐Taner N. MAPT haplotype-stratified GWAS reveals differential association for AD risk variants. Alzheimers Dement 2020; 16:983-1002. [PMID: 32400971 PMCID: PMC7983911 DOI: 10.1002/alz.12099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/26/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION MAPT H1 haplotype is implicated as a risk factor for neurodegenerative diseases including Alzheimer's disease (AD). METHODS Using Alzheimer's Disease Genetics Consortium (ADGC) genome-wide association study (GWAS) data (n = 18,841), we conducted a MAPT H1/H2 haplotype-stratified association to discover MAPT haplotype-specific AD risk loci. RESULTS We identified 11 loci-5 in H2-non-carriers and 6 in H2-carriers-although none of the MAPT haplotype-specific associations achieved genome-wide significance. The most significant H2 non-carrier-specific association was with a NECTIN2 intronic (P = 1.33E-07) variant, and that for H2 carriers was near NKX6-1 (P = 1.99E-06). The GABRG2 locus had the strongest epistasis with MAPT H1/H2 variant rs8070723 (P = 3.91E-06). Eight of the 12 genes at these loci had transcriptome-wide significant differential expression in AD versus control temporal cortex (q < 0.05). Six genes were members of the brain transcriptional co-expression network implicated in "synaptic transmission" (P = 9.85E-59), which is also enriched for neuronal genes (P = 1.0E-164), including MAPT. DISCUSSION This stratified GWAS identified loci that may confer AD risk in a MAPT haplotype-specific manner. This approach may preferentially enrich for neuronal genes implicated in synaptic transmission.
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Affiliation(s)
| | - Joseph S. Reddy
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | - Travis Ballard
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
| | - Xue Wang
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFloridaUSA
| | | | | | | | | | | | - Paul Crane
- University of WashingtonSeattleWashingtonUSA
| | | | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo ClinicJacksonvilleFloridaUSA
- Department of NeurologyMayo ClinicJacksonvilleFloridaUSA
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29
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Wang W, Zhao F, Ma X, Perry G, Zhu X. Mitochondria dysfunction in the pathogenesis of Alzheimer's disease: recent advances. Mol Neurodegener 2020; 15:30. [PMID: 32471464 PMCID: PMC7257174 DOI: 10.1186/s13024-020-00376-6] [Citation(s) in RCA: 490] [Impact Index Per Article: 122.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases, characterized by impaired cognitive function due to progressive loss of neurons in the brain. Under the microscope, neuronal accumulation of abnormal tau proteins and amyloid plaques are two pathological hallmarks in affected brain regions. Although the detailed mechanism of the pathogenesis of AD is still elusive, a large body of evidence suggests that damaged mitochondria likely play fundamental roles in the pathogenesis of AD. It is believed that a healthy pool of mitochondria not only supports neuronal activity by providing enough energy supply and other related mitochondrial functions to neurons, but also guards neurons by minimizing mitochondrial related oxidative damage. In this regard, exploration of the multitude of mitochondrial mechanisms altered in the pathogenesis of AD constitutes novel promising therapeutic targets for the disease. In this review, we will summarize recent progress that underscores the essential role of mitochondria dysfunction in the pathogenesis of AD and discuss mechanisms underlying mitochondrial dysfunction with a focus on the loss of mitochondrial structural and functional integrity in AD including mitochondrial biogenesis and dynamics, axonal transport, ER-mitochondria interaction, mitophagy and mitochondrial proteostasis.
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Affiliation(s)
- Wenzhang Wang
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA.
| | - Fanpeng Zhao
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - Xiaopin Ma
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA.
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30
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Wang X, Wen Y. A U-statistics for integrative analysis of multilayer omics data. Bioinformatics 2020; 36:2365-2374. [PMID: 31913435 DOI: 10.1093/bioinformatics/btaa004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/09/2019] [Accepted: 01/02/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The emerging multilayer omics data provide unprecedented opportunities for detecting biomarkers that are associated with complex diseases at various molecular levels. However, the high-dimensionality of multiomics data and the complex disease etiologies have brought tremendous analytical challenges. RESULTS We developed a U-statistics-based non-parametric framework for the association analysis of multilayer omics data, where consensus and permutation-based weighting schemes are developed to account for various types of disease models. Our proposed method is flexible for analyzing different types of outcomes as it makes no assumptions about their distributions. Moreover, it explicitly accounts for various types of underlying disease models through weighting schemes and thus provides robust performance against them. Through extensive simulations and the application to dataset obtained from the Alzheimer's Disease Neuroimaging Initiatives, we demonstrated that our method outperformed the commonly used kernel regression-based methods. AVAILABILITY AND IMPLEMENTATION The R-package is available at https://github.com/YaluWen/Uomic. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaqiong Wang
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Yalu Wen
- Department of Statistics, University of Auckland, Auckland, New Zealand
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31
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Bussies PL, Rajabli F, Griswold A, Dorfsman DA, Whitehead P, Adams LD, Mena PR, Cuccaro M, Haines JL, Byrd GS, Beecham GW, Pericak-Vance MA, Young JI, Vance JM. Use of local genetic ancestry to assess TOMM40-523' and risk for Alzheimer disease. Neurol Genet 2020; 6:e404. [PMID: 32337333 PMCID: PMC7164968 DOI: 10.1212/nxg.0000000000000404] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/14/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Here, we re-examine TOMM40-523' as a race/ethnicity-specific risk modifier for late-onset Alzheimer disease (LOAD) with adjustment for local genomic ancestry (LGA) in Apolipoprotein E (APOE) ε4 haplotypes. METHODS The TOMM40-523' size was determined by fragment analysis and whole genome sequencing in homozygous APOE ε3 and APOE ε4 haplotypes of African (AF) or European (EUR) ancestry. The risk for LOAD was assessed within groups by allele size. RESULTS The TOMM40-523' length did not modify risk for LOAD in APOE ε4 haplotypes with EUR or AF LGA. Increasing length of TOMM40-523' was associated with a significantly reduced risk for LOAD in EUR APOE ε3 haplotypes. CONCLUSIONS Adjustment for LGA confirms that TOMM40-523' cannot explain the strong differential risk for LOAD between APOE ε4 with EUR and AF LGA. Our study does confirm previous reports that increasing allele length of the TOMM40-523' repeat is associated with decreased risk for LOAD in carriers of homozygous APOE ε3 alleles and demonstrates that this effect is occurring in those individuals with the EUR LGA APOE ε3 allele haplotype.
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Affiliation(s)
- Parker L Bussies
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Anthony Griswold
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Daniel A Dorfsman
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Pedro R Mena
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Michael Cuccaro
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Jonathan L Haines
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Goldie S Byrd
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Juan I Young
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (P.L.B., F.R., A.G., D.A.D., P.W., L.D.A., P.R.M., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Dr. John T. MacDonald Foundation Department of Human Genetics (A.G., M.C., G.W.B., M.A.P.-V., J.I.Y., J.M.V.), Miller School of Medicine, University of Miami; Department of Population and Quantitative Health Sciences (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH; and Wake Forest School of Medicine (G.S.B.), Bowman Gray Center for Medical Education, Winston-Salem, NC
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Andrews SJ, Fulton-Howard B, Patterson C, McFall GP, Gross A, Michaelis EK, Goate A, Swerdlow RH, Pa J. Mitonuclear interactions influence Alzheimer's disease risk. Neurobiol Aging 2020; 87:138.e7-138.e14. [PMID: 31784277 PMCID: PMC7205324 DOI: 10.1016/j.neurobiolaging.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/24/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
We examined the associations between mitochondrial DNA haplogroups (MT-hgs; mitochondrial haplotype groups defined by a specific combination of single nucleotide polymorphisms labeled as letters running from A to Z) and their interactions with a polygenic risk score composed of nuclear-encoded mitochondrial genes (nMT-PRS) with risk of dementia and age of onset (AOO) of dementia. MT-hg K (Odds ratio [OR]: 2.03 [95% CI: 1.04, 3.97]) and a 1 SD larger nMT-PRS (OR: 2.2 [95% CI: 1.68, 2.86]) were associated with elevated odds of dementia. Significant antagonistic interactions between the nMT-PRS and MT-hg K (OR: 0.45 [95% CI: 0.22, 0.9]) and MT-hg T (OR: 0.22 [95% CI: 0.1, 0.49]) were observed. Individual MT-hgs were not associated with AOO; however, a significant antagonistic interactions was observed between the nMT-PRS and MT-hg T (Hazard ratio: 0.62 [95% CI: 0.42, 0.91]) and a synergistic interaction between the nMT-PRS and MT-hg V (Hazard ratio: 2.28 [95% CI: 1.19, 4.35]). These results suggest that MT-hgs influence dementia risk and that variants in the nuclear and mitochondrial genome interact to influence the AOO of dementia.
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Affiliation(s)
- Shea J Andrews
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher Patterson
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Neurology, Alzheimer's Disease Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - G Peggy McFall
- Department of Psychology, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Alden Gross
- Department of Epidemiology, JHSPH Center on Aging and Health, Baltimore, MD, USA
| | - Elias K Michaelis
- Higuchi Biosciences Center and Alzheimer's Disease Center, University of Kansas, Lawrence, KS, USA
| | - Alison Goate
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Russell H Swerdlow
- Department of Neurology, Alzheimer's Disease Center, University of Kansas Medical Center, Fairway, KS, USA
| | - Judy Pa
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Neurology, Alzheimer's Disease Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Alzheimer's disease pathology explains association between dementia with Lewy bodies and APOE-ε4/TOMM40 long poly-T repeat allele variants. ALZHEIMERS & DEMENTIA-TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2019; 5:814-824. [PMID: 31788537 PMCID: PMC6880091 DOI: 10.1016/j.trci.2019.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Introduction The role of TOMM40-APOE 19q13.3 region variants is well documented in Alzheimer's disease (AD) but remains contentious in dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD). Methods We dissected genetic profiles within the TOMM40-APOE region in 451 individuals from four European brain banks, including DLB and PDD cases with/without neuropathological evidence of AD-related pathology and healthy controls. Results TOMM40-L/APOE-ε4 alleles were associated with DLB (ORTOMM40-L = 3.61; P value = 3.23 × 10−9; ORAPOE-ε4 = 3.75; P value = 4.90 × 10−10) and earlier age at onset of DLB (HRTOMM40-L = 1.33, P value = .031; HRAPOE-ε4 = 1.46, P value = .004), but not with PDD. The TOMM40-L/APOE-ε4 effect was most pronounced in DLB individuals with concomitant AD pathology (ORTOMM40-L = 4.40, P value = 1.15 × 10−6; ORAPOE-ε4 = 5.65, P value = 2.97 × 10−8) but was not significant in DLB without AD. Meta-analyses combining all APOE-ε4 data in DLB confirmed our findings (ORDLB = 2.93, P value = 3.78 × 10−99; ORDLB+AD = 5.36, P value = 1.56 × 10−47). Discussion APOE-ε4/TOMM40-L alleles increase susceptibility and risk of earlier DLB onset, an effect explained by concomitant AD-related pathology. These findings have important implications in future drug discovery and development efforts in DLB.
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Wang X, Wang S, Liu W, Wang T, Wang J, Gao X, Duan R, Li Y, Pu L, Deng B, Chen Z. Epigenetic upregulation of miR-126 induced by heat stress contributes to apoptosis of rat cardiomyocytes by promoting Tomm40 transcription. J Mol Cell Cardiol 2019; 129:39-48. [DOI: 10.1016/j.yjmcc.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/22/2018] [Accepted: 10/04/2018] [Indexed: 10/28/2022]
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Lutz MW, Casanova R, Saldana S, Kuchibhatla M, Plassman BL, Hayden KM. Analysis of pleiotropic genetic effects on cognitive impairment, systemic inflammation, and plasma lipids in the Health and Retirement Study. Neurobiol Aging 2019; 80:173-186. [PMID: 31201950 DOI: 10.1016/j.neurobiolaging.2018.10.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/11/2018] [Accepted: 10/29/2018] [Indexed: 01/31/2023]
Abstract
Variants associated with modulation of c-reactive protein (CRP) and plasma lipids have been investigated for polygenic overlap with Alzheimer's disease risk variants. We examined pleiotropic genetic effects on cognitive impairment conditioned on genetic variants (SNPs) associated with systemic inflammation as measured by CRP and with plasma lipids using data from the Health and Retirement Study. SNP enrichment was observed for cognitive impairment conditioned on the secondary phenotypes of plasma CRP and lipids. Fold enrichment of 100%-800% was observed for increasingly stringent p-value thresholds for SNPs associated with cognitive impairment conditional on plasma CRP, 80%-800% for low-density lipoprotein, and 80%-600% for total cholesterol. Significant associations (false discovery rate Q ≤ 0.05) between cognitive impairment, conditional with either CRP, low-density lipoprotein, or total cholesterol, were found for the locus on chromosome 19 that contains the APOE, TOMM40, APOC1, and PVRL2 genes. Relative numbers of significant SNPs in each of the genes differed by the conditional associations with the secondary phenotypes. Biological interpretation of both the genetic pleiotropy results and the individual genome-wide association results showed that the variants and proximal genes identified are involved in multiple pathological processes including cholesterol metabolism, inflammation, and mitochondrial transport. These findings are potentially important for Alzheimer's disease risk prediction and development of novel therapeutic approaches.
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Affiliation(s)
- Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA.
| | - Ramon Casanova
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Santiago Saldana
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Maragatha Kuchibhatla
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Winston-Salem, NC, USA
| | - Brenda L Plassman
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Kathleen M Hayden
- Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC, USA
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Abstract
PURPOSE OF REVIEW Over the last decade over 40 loci have been associated with risk of Alzheimer's disease (AD). However, most studies have either focused on identifying risk loci or performing unbiased screens without a focus on protective variation in AD. Here, we provide a review of known protective variants in AD and their putative mechanisms of action. Additionally, we recommend strategies for finding new protective variants. RECENT FINDINGS Recent Genome-Wide Association Studies have identified both common and rare protective variants associated with AD. These include variants in or near APP, APOE, PLCG2, MS4A, MAPT-KANSL1, RAB10, ABCA1, CCL11, SORL1, NOCT, SCL24A4-RIN3, CASS4, EPHA1, SPPL2A, and NFIC. SUMMARY There are very few protective variants with functional evidence and a derived allele with a frequency below 20%. Additional fine mapping and multi-omic studies are needed to further validate and characterize known variants as well as specialized genome-wide scans to identify novel variants.
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Affiliation(s)
- Shea J Andrews
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Equal first author
| | - Brian Fulton-Howard
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Equal first author
| | - Alison Goate
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Watts A, Wilkins HM, Michaelis E, Swerdlow RH. TOMM40 '523 Associations with Baseline and Longitudinal Cognition in APOE ɛ3 Homozygotes. J Alzheimers Dis 2019; 70:1059-1068. [PMID: 31322569 PMCID: PMC7206989 DOI: 10.3233/jad-190293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
TOMM40 '523 is associated with Alzheimer's disease (AD), but APOE linkage disequilibrium confounds this association. In 170 APOE ɛ3 homozygotes, we evaluated relationships between short and very long TOMM40 alleles and longitudinal declines in three cognitive domains (attention, verbal memory, and executive function). We used factor analysis to create composite scores from 10 individual cognitive tests, and latent growth curve modeling adjusting for clinical status (normal, amnestic mild cognitive impairment, or AD) to summarize initial performance and change over three years. Relative to individuals with two very long TOMM40 alleles, APOEɛ3 homozygotes with one or two short alleles showed lower baseline cognitive performance regardless of clinical status. The number of short or very long TOMM40 alleles was not associated with longitudinal cognitive changes. In APOEɛ3 homozygotes from the University of Kansas Alzheimer's Disease Center cohort, an association between TOMM40 '523 and cognition is consistent with the possibility that TOMM40 influences cognition independent of APOE.
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Affiliation(s)
- Amber Watts
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Psychology, University of Kansas, Lawrence, KS, USA
| | | | - Elias Michaelis
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Pharmacology and Toxicology, University of Kansas, Lawrence, KS, USA
| | - Russell H. Swerdlow
- University of Kansas Alzheimer’s Disease Center, Kansas City, KS, USA
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
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Prendecki M, Florczak-Wyspianska J, Kowalska M, Ilkowski J, Grzelak T, Bialas K, Wiszniewska M, Kozubski W, Dorszewska J. Biothiols and oxidative stress markers and polymorphisms of TOMM40 and APOC1 genes in Alzheimer's disease patients. Oncotarget 2018; 9:35207-35225. [PMID: 30443289 PMCID: PMC6219666 DOI: 10.18632/oncotarget.26184] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/01/2018] [Indexed: 12/16/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive disease, with frequently observed improper biothiols turnover, homocysteine (Hcy) and glutathione (GSH). GSH protects cells from oxidative stress and may be determined by 8-oxo-2’-deoxyguanosine (8-oxo2dG) level and its repair enzyme 8-oxoguanine DNA glycosylase (OGG1). The presence of unfavorable alleles, e.g., in APOE cluster, TOMM40 or APOC1 is known to facilitate the dementia onset under oxidative stress. The aim of the study was to analyze rs1052452, rs2075650 TOMM40 polymorphisms, rs4420638 APOC1, and their correlation with Hcy, GSH, 8-oxo2dG, OGG1 levels in plasma of AD patients and controls. We recruited 230 individuals: 88 AD, 80 controls without (UC), 62 controls with (RC) positive family history of AD. The TOMM40 genotype was determined by HRM and capillary electrophoresis, while APOC1 by HRM. The concentrations of OGG1, 8-oxo2dG were determined by ELISA, whereas Hcy, GSH by HPLC/EC. We showed that over 60% of AD patients had increased Hcy levels (p<0.01 vs. UC, p<0.001 vs. RC), while GSH (p<0.01 vs. UC), 8-oxo2dG (p<0.01 vs. UC, p<0.001 vs. RC) were reduced. Minor variants: rs10524523-L, rs4420638-G, rs2075650-G were significantly overrepresented in AD. For rs4420638-G, rs2075650-G variants, the association remained significant in APOE E4 non-carriers. The misbalance of analyzed biothiols, and 8-oxo2dG, OGG1 were more pronounced in carriers of major variants: rs10524523-S/VL, rs4420638-A, rs2075650-A. We showed, for the first time, that APOC1 and TOMM40 rs2075650 polymorphisms may be independent risk factors of developing AD, whose major variants are accompanied by disruption of biothiols metabolism and inefficient removal of DNA oxidation.
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Affiliation(s)
- Michal Prendecki
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Marta Kowalska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jan Ilkowski
- Department of Emergency Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Teresa Grzelak
- Division of Biology of Civilization-Linked Diseases, Department of Chemistry and Clinical Biochemistry, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Bialas
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Malgorzata Wiszniewska
- Faculty of Health Care, Stanislaw Staszic University of Applied Sciences in Pila, Pila, Poland.,Department of Neurology, Specialistic Hospital in Pila, Pila, Poland
| | - Wojciech Kozubski
- Chair and Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jolanta Dorszewska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
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