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Gamache J, Gingerich D, Shwab EK, Barrera J, Garrett ME, Hume C, Crawford GE, Ashley-Koch AE, Chiba-Falek O. Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains. Cell Biosci 2023; 13:185. [PMID: 37789374 PMCID: PMC10546724 DOI: 10.1186/s13578-023-01120-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The genetic underpinnings of late-onset Alzheimer's disease (LOAD) are yet to be fully elucidated. Although numerous LOAD-associated loci have been discovered, the causal variants and their target genes remain largely unknown. Since the brain is composed of heterogenous cell subtypes, it is imperative to study the brain on a cell subtype specific level to explore the biological processes underlying LOAD. METHODS Here, we present the largest parallel single-nucleus (sn) multi-omics study to simultaneously profile gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) to date, using nuclei from 12 normal and 12 LOAD brains. We identified cell subtype clusters based on gene expression and chromatin accessibility profiles and characterized cell subtype-specific LOAD-associated differentially expressed genes (DEGs), differentially accessible peaks (DAPs) and cis co-accessibility networks (CCANs). RESULTS Integrative analysis defined disease-relevant CCANs in multiple cell subtypes and discovered LOAD-associated cell subtype-specific candidate cis regulatory elements (cCREs), their candidate target genes, and trans-interacting transcription factors (TFs), some of which, including ELK1, JUN, and SMAD4 in excitatory neurons, were also LOAD-DEGs. Finally, we focused on a subset of cell subtype-specific CCANs that overlap known LOAD-GWAS regions and catalogued putative functional SNPs changing the affinities of TF motifs within LOAD-cCREs linked to LOAD-DEGs, including APOE and MYO1E in a specific subtype of microglia and BIN1 in a subpopulation of oligodendrocytes. CONCLUSIONS To our knowledge, this study represents the most comprehensive systematic interrogation to date of regulatory networks and the impact of genetic variants on gene dysregulation in LOAD at a cell subtype resolution. Our findings reveal crosstalk between epigenetic, genomic, and transcriptomic determinants of LOAD pathogenesis and define catalogues of candidate genes, cCREs, and variants involved in LOAD genetic etiology and the cell subtypes in which they act to exert their pathogenic effects. Overall, these results suggest that cell subtype-specific cis-trans interactions between regulatory elements and TFs, and the genes dysregulated by these networks contribute to the development of LOAD.
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Affiliation(s)
- Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA
| | - Cordelia Hume
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC Box 3382, Durham, NC, 27708, USA.
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
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Lee EG, Leong L, Chen S, Tulloch J, Yu CE. APOE Locus-Associated Mitochondrial Function and Its Implication in Alzheimer's Disease and Aging. Int J Mol Sci 2023; 24:10440. [PMID: 37445616 PMCID: PMC10341489 DOI: 10.3390/ijms241310440] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
The Apolipoprotein E (APOE) locus has garnered significant clinical interest because of its association with Alzheimer's disease (AD) and longevity. This genetic association appears across multiple genes in the APOE locus. Despite the apparent differences between AD and longevity, both conditions share a commonality of aging-related changes in mitochondrial function. This commonality is likely due to accumulative biological effects partly exerted by the APOE locus. In this study, we investigated changes in mitochondrial structure/function-related markers using oxidative stress-induced human cellular models and postmortem brains (PMBs) from individuals with AD and normal controls. Our results reveal a range of expressional alterations, either upregulated or downregulated, in these genes in response to oxidative stress. In contrast, we consistently observed an upregulation of multiple APOE locus genes in all cellular models and AD PMBs. Additionally, the effects of AD status on mitochondrial DNA copy number (mtDNA CN) varied depending on APOE genotype. Our findings imply a potential coregulation of APOE locus genes possibly occurring within the same topologically associating domain (TAD) of the 3D chromosome conformation. The coordinated expression of APOE locus genes could impact mitochondrial function, contributing to the development of AD or longevity. Our study underscores the significant role of the APOE locus in modulating mitochondrial function and provides valuable insights into the underlying mechanisms of AD and aging, emphasizing the importance of this locus in clinical research.
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Affiliation(s)
- Eun-Gyung Lee
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Lesley Leong
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Sunny Chen
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Jessica Tulloch
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
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Chen YC, Chang SC, Lee YS, Ho WM, Huang YH, Wu YY, Chu YC, Wu KH, Wei LS, Wang HL, Chiu CC. TOMM40 Genetic Variants Cause Neuroinflammation in Alzheimer's Disease. Int J Mol Sci 2023; 24. [PMID: 36835494 DOI: 10.3390/ijms24044085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Gottschalk WK, Mahon S, Hodgson D, Barrera J, Hill D, Wei A, Kumar M, Dai K, Anderson L, Mihovilovic M, Lutz MW, Chiba-Falek O. The APOE-TOMM40 Humanized Mouse Model: Characterization of Age, Sex, and PolyT Variant Effects on Gene Expression. J Alzheimers Dis 2023; 94:1563-1576. [PMID: 37458041 PMCID: PMC10733864 DOI: 10.3233/jad-230451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
BACKGROUND The human chromosome 19q13.32 is a gene rich region and has been associated with multiple phenotypes, including late onset Alzheimer's disease (LOAD) and other age-related conditions. OBJECTIVE Here we developed the first humanized mouse model that contains the entire TOMM40 and APOE genes with all intronic and intergenic sequences including the upstream and downstream regions. Thus, the mouse model carries the human TOMM40 and APOE genes and their intact regulatory sequences. METHODS We generated the APOE-TOMM40 humanized mouse model in which the entire mouse region was replaced with the human (h)APOE-TOMM40 loci including their upstream and downstream flanking regulatory sequences using recombineering technologies. We then measured the expression of the human TOMM40 and APOE genes in the mice brain, liver, and spleen tissues using TaqMan based mRNA expression assays. RESULTS We investigated the effects of the '523' polyT genotype (S/S or VL/VL), sex, and age on the human TOMM40- and APOE-mRNAs expression levels using our new humanized mouse model. The analysis revealed tissue specific and shared effects of the '523' polyT genotype, sex, and age on the regulation of the human TOMM40 and APOE genes. Noteworthy, the regulatory effect of the '523' polyT genotype was observed for all studied organs. CONCLUSION The model offers new opportunities for basic science, translational, and preclinical drug discovery studies focused on the APOE genomic region in relation to LOAD and other conditions in adulthood.
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Affiliation(s)
- William K. Gottschalk
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Scott Mahon
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Dellila Hodgson
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Delaney Hill
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Angela Wei
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Manish Kumar
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Kathy Dai
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Lauren Anderson
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Mirta Mihovilovic
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Michael W. Lutz
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 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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7
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Kulminski AM, Feng F, Loiko E, Nazarian A, Loika Y, Culminskaya I. Prevailing Antagonistic Risks in Pleiotropic Associations with Alzheimer's Disease and Diabetes. J Alzheimers Dis 2023; 94:1121-1132. [PMID: 37355909 PMCID: PMC10666173 DOI: 10.3233/jad-230397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
BACKGROUND The lack of efficient preventive interventions against Alzheimer's disease (AD) calls for identifying efficient modifiable risk factors for AD. As diabetes shares many pathological processes with AD, including accumulation of amyloid plaques and neurofibrillary tangles, insulin resistance, and impaired glucose metabolism, diabetes is thought to be a potentially modifiable risk factor for AD. Mounting evidence suggests that links between AD and diabetes may be more complex than previously believed. OBJECTIVE To examine the pleiotropic architecture of AD and diabetes mellitus (DM). METHODS Univariate and pleiotropic analyses were performed following the discovery-replication strategy using individual-level data from 10 large-scale studies. RESULTS We report a potentially novel pleiotropic NOTCH2 gene, with a minor allele of rs5025718 associated with increased risks of both AD and DM. We confirm previously identified antagonistic associations of the same variants with the risks of AD and DM in the HLA and APOE gene clusters. We show multiple antagonistic associations of the same variants with AD and DM in the HLA cluster, which were not explained by the lead SNP in this cluster. Although the ɛ2 and ɛ4 alleles played a major role in the antagonistic associations with AD and DM in the APOE cluster, we identified non-overlapping SNPs in this cluster, which were adversely and beneficially associated with AD and DM independently of the ɛ2 and ɛ4 alleles. CONCLUSION This study emphasizes differences and similarities in the heterogeneous genetic architectures of AD and DM, which may differentiate the pathogenic mechanisms of these diseases.
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Affiliation(s)
- Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27705, USA
| | - Fan Feng
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27705, USA
| | - Elena Loiko
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27705, USA
| | - Alireza Nazarian
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27705, USA
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27705, USA
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, 27705, USA
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Periasamy A, Mitchell N, Zaytseva O, Chahal AS, Zhao J, Colman PM, Quinn LM, Gulbis JM. An increase in mitochondrial TOM activates apoptosis to drive retinal neurodegeneration. Sci Rep 2022; 12:21634. [PMID: 36517509 DOI: 10.1038/s41598-022-23280-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022] Open
Abstract
Intronic polymorphic TOMM40 variants increasing TOMM40 mRNA expression are strongly correlated to late onset Alzheimer's Disease. The gene product, hTomm40, encoded in the APOE gene cluster, is a core component of TOM, the translocase that imports nascent proteins across the mitochondrial outer membrane. We used Drosophila melanogaster eyes as an in vivo model to investigate the relationship between elevated Tom40 (the Drosophila homologue of hTomm40) expression and neurodegeneration. Here we provide evidence that an overabundance of Tom40 in mitochondria invokes caspase-dependent cell death in a dose-dependent manner, leading to degeneration of the primarily neuronal eye tissue. Degeneration is contingent on the availability of co-assembling TOM components, indicating that an increase in assembled TOM is the factor that triggers apoptosis and degeneration in a neural setting. Eye death is not contingent on inner membrane translocase components, suggesting it is unlikely to be a direct consequence of impaired import. Another effect of heightened Tom40 expression is upregulation and co-association of a mitochondrial oxidative stress biomarker, DmHsp22, implicated in extension of lifespan, providing new insight into the balance between cell survival and death. Activation of regulated death pathways, culminating in eye degeneration, suggests a possible causal route from TOMM40 polymorphisms to neurodegenerative disease.
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Kulminski AM, Jain‐Washburn E, Philipp I, He L, Loika Y, Loiko E, Bagley O, Ukraintseva S, Yashin A, Arbeev K, Stallard E, Feitosa MF, Schupf N, Christensen K, Culminskaya I. APOE ɛ4 allele and TOMM40-APOC1 variants jointly contribute to survival to older ages. Aging Cell 2022; 21:e13730. [PMID: 36330582 PMCID: PMC9741507 DOI: 10.1111/acel.13730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 09/23/2022] [Accepted: 03/10/2022] [Indexed: 11/06/2022] Open
Abstract
Age-related diseases characteristic of post-reproductive life, aging, and life span are the examples of polygenic non-Mendelian traits with intricate genetic architectures. Polygenicity of these traits implies that multiple variants can impact their risks independently or jointly as combinations of specific variants. Here, we examined chances to live to older ages, 85 years and older, for carriers of compound genotypes comprised of combinations of genotypes of rs429358 (APOE ɛ4 encoding polymorphism), rs2075650 (TOMM40), and rs12721046 (APOC1) polymorphisms using data from four human studies. The choice of these polymorphisms was motivated by our prior results showing that the ɛ4 carriers having minor alleles of the other two polymorphisms were at exceptionally high risk of Alzheimer's disease (AD), compared with non-carriers of the minor alleles. Consistent with our prior findings for AD, we show here that the adverse effect of the ɛ4 allele on survival to older ages is significantly higher in carriers of minor alleles of rs2075650 and/or rs12721046 polymorphisms compared with their non-carriers. The exclusion of AD cases made this effect stronger. Our results provide compelling evidence that AD does not mediate the associations of the same compound genotypes with chances to survive until older ages, indicating the existence of genetically heterogeneous mechanisms. The survival chances can be mainly associated with lipid- and immunity-related mechanisms, whereas the AD risk, can be driven by the AD-biomarker-related mechanism, among others. Targeting heterogeneous polygenic profiles of individuals at high risks of complex traits is promising for the translation of genetic discoveries to health care.
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Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Ethan Jain‐Washburn
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Ian Philipp
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Liang He
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Elena Loiko
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Olivia Bagley
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Svetlana Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Anatoliy Yashin
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Konstantin Arbeev
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Eric Stallard
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of GeneticsWashington University School of MedicineSt LouisMissouriUSA
| | - Nicole Schupf
- Gertrude H. Sergievsky CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public HealthSouthern Denmark UniversityOdenseDenmark
| | - Irina Culminskaya
- Biodemography of Aging Research Unit, Social Science Research InstituteDuke UniversityDurhamNorth CarolinaUSA
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10
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Ye F, Funk Q, Rockers E, Shulman JM, Masdeu JC, Pascual B. In Alzheimer-prone brain regions, metabolism and risk-gene expression are strongly correlated. Brain Commun 2022; 4:fcac216. [PMID: 36092303 PMCID: PMC9453434 DOI: 10.1093/braincomms/fcac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/20/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Neuroimaging in the preclinical phase of Alzheimer’s disease provides information crucial to early intervention, particularly in people with a high genetic risk. Metabolic network modularity, recently applied to the study of dementia, is increased in Alzheimer’s disease patients compared with controls, but network modularity in cognitively unimpaired elderly with various risks of developing Alzheimer’s disease needs to be determined. Based on their 5-year cognitive progression, we stratified 117 cognitively normal participants (78.3 ± 4.0 years of age, 52 women) into three age-matched groups, each with a different level of risk for Alzheimer’s disease. From their fluorodeoxyglucose PET we constructed metabolic networks, evaluated their modular structures using the Louvain algorithm, and compared them between risk groups. As the risk for Alzheimer’s disease increased, the metabolic connections among brain regions weakened and became more modular, indicating network fragmentation and functional impairment of the brain. We then set out to determine the correlation between regional brain metabolism, particularly in the modules derived from the previous analysis, and the regional expression of Alzheimer-risk genes in the brain, obtained from the Allen Human Brain Atlas. In all risk groups of this elderly population, the regional brain expression of most Alzheimer-risk genes showed a strong correlation with brain metabolism, particularly in the module that corresponded to regions of the brain that are affected earliest and most severely in Alzheimer’s disease. Among the genes, APOE and CD33 showed the strongest negative correlation and SORL1 showed the strongest positive correlation with brain metabolism. The Pearson correlation coefficients remained significant when contrasted against a null-hypothesis distribution of correlation coefficients across the whole transcriptome of 20 736 genes (SORL1: P = 0.0130; CD33, P = 0.0136; APOE: P = 0.0093). The strong regional correlation between Alzheimer-related gene expression in the brain and brain metabolism in older adults highlights the role of brain metabolism in the genesis of dementia.
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Affiliation(s)
- Fengdan Ye
- Department of Physics and Astronomy, Rice University , Houston, TX 77005 , USA
- Center for Theoretical Biological Physics, Rice University , Houston, TX 77005 , USA
- Nantz National Alzheimer Center, Houston Methodist Neurological and Research Institute, Houston Methodist Hospital, Weill Cornell Medicine , Houston, TX 77030 , USA
| | - Quentin Funk
- Nantz National Alzheimer Center, Houston Methodist Neurological and Research Institute, Houston Methodist Hospital, Weill Cornell Medicine , Houston, TX 77030 , USA
| | - Elijah Rockers
- Nantz National Alzheimer Center, Houston Methodist Neurological and Research Institute, Houston Methodist Hospital, Weill Cornell Medicine , Houston, TX 77030 , USA
| | - Joshua M Shulman
- Department of Neurology, Baylor College of Medicine , Houston, TX 77030 , USA
- Department of Neuroscience, Baylor College of Medicine , Houston, TX 77030 , USA
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Joseph C Masdeu
- Nantz National Alzheimer Center, Houston Methodist Neurological and Research Institute, Houston Methodist Hospital, Weill Cornell Medicine , Houston, TX 77030 , USA
| | - Belen Pascual
- Nantz National Alzheimer Center, Houston Methodist Neurological and Research Institute, Houston Methodist Hospital, Weill Cornell Medicine , Houston, TX 77030 , USA
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11
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Chen S, Sarasua SM, Davis NJ, DeLuca JM, Boccuto L, Thielke SM, Yu CE. TOMM40 genetic variants associated with healthy aging and longevity: a systematic review. BMC Geriatr 2022; 22:667. [PMID: 35964003 PMCID: PMC9375314 DOI: 10.1186/s12877-022-03337-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Healthy aging relies on mitochondrial functioning because this organelle provides energy and diminishes oxidative stress. Single nucleotide polymorphisms (SNPs) in TOMM40, a critical gene that produces the outer membrane protein TOM40 of mitochondria, have been associated with mitochondrial dysfunction and neurodegenerative processes. Yet it is not clear whether or how the mitochondria may impact human longevity. We conducted this review to ascertain which SNPs have been associated with markers of healthy aging. Methods Using the PRISMA methodology, we conducted a systematic review on PubMed and Embase databases to identify associations between TOMM40 SNPs and measures of longevity and healthy aging. Results Twenty-four articles were selected. The TOMM40 SNPs rs2075650 and rs10524523 were the two most commonly identified and studied SNPs associated with longevity. The outcomes associated with the TOMM40 SNPs were changes in BMI, brain integrity, cognitive functions, altered inflammatory network, vulnerability to vascular risk factors, and longevity. Discussions Our systematic review identified multiple TOMM40 SNPs potentially associated with healthy aging. Additional research can help to understand mechanisms in aging, including resilience, prevention of disease, and adaptation to the environment.
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Affiliation(s)
- Sunny Chen
- Geriatric Research, Education, and Clinical Center, Puget Sound VA Medical Center, VA Puget Sound Healthcare System, 1660 S Columbian Way, Seattle, WA, 98108, USA. .,Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA.
| | - Sara M Sarasua
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Nicole J Davis
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Jane M DeLuca
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC, USA
| | - Stephen M Thielke
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, Puget Sound VA Medical Center, VA Puget Sound Healthcare System, 1660 S Columbian Way, Seattle, WA, 98108, USA.,Department of Medicine, Division of Gerontology and Geriatric Medicine, University of Washington, Seattle, WA, USA
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12
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Chung J, Das A, Sun X, Sobreira DR, Leung YY, Igartua C, Mozaffari S, Chou YF, Thiagalingam S, Mez J, Zhang X, Jun GR, Stein TD, Kunkle BW, Martin ER, Pericak-Vance MA, Mayeux R, Haines JL, Schellenberg GD, Nobrega MA, Lunetta KL, Pinto JM, Wang LS, Ober C, Farrer LA. Genome-wide association and multi-omics studies identify MGMT as a novel risk gene for Alzheimer's disease among women. Alzheimers Dement 2022; 19:10.1002/alz.12719. [PMID: 35770850 PMCID: PMC9800643 DOI: 10.1002/alz.12719] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Variants in the tau gene (MAPT) region are associated with breast cancer in women and Alzheimer's disease (AD) among persons lacking apolipoprotein E ε4 (ε4-). METHODS To identify novel genes associated with tau-related pathology, we conducted two genome-wide association studies (GWAS) for AD, one among 10,340 ε4- women in the Alzheimer's Disease Genetics Consortium (ADGC) and another in 31 members (22 women) of a consanguineous Hutterite kindred. RESULTS We identified novel associations of AD with MGMT variants in the ADGC (rs12775171, odds ratio [OR] = 1.4, P = 4.9 × 10-8 ) and Hutterite (rs12256016 and rs2803456, OR = 2.0, P = 1.9 × 10-14 ) datasets. Multi-omics analyses showed that the most significant and largest number of associations among the single nucleotide polymorphisms (SNPs), DNA-methylated CpGs, MGMT expression, and AD-related neuropathological traits were observed among women. Furthermore, promoter capture Hi-C analyses revealed long-range interactions of the MGMT promoter with MGMT SNPs and CpG sites. DISCUSSION These findings suggest that epigenetically regulated MGMT expression is involved in AD pathogenesis, especially in women.
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Affiliation(s)
- Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Anjali Das
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Xinyu Sun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Débora R Sobreira
- Department of Surgery/Section of Otolaryngology-Head and Neck Surgery, The University of Chicago, Chicago, Illinois, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Catherine Igartua
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Sahar Mozaffari
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Yi-Fan Chou
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jesse Mez
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Gyungah R Jun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Brian W Kunkle
- Dr. John T. Macdonald Foundation of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Eden R Martin
- Dr. John T. Macdonald Foundation of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Margaret A Pericak-Vance
- Dr. John T. Macdonald Foundation of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University, New York City, New York, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Marcelo A Nobrega
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Jayant M Pinto
- Department of Surgery/Section of Otolaryngology-Head and Neck Surgery, The University of Chicago, Chicago, Illinois, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
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13
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Kelley CM, Ginsberg SD, Liang WS, Counts SE, Mufson EJ. Posterior cingulate cortex reveals an expression profile of resilience in cognitively intact elders. Brain Commun 2022; 4:fcac162. [PMID: 35813880 PMCID: PMC9263888 DOI: 10.1093/braincomms/fcac162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 12/20/2022] Open
Abstract
The posterior cingulate cortex, a key hub of the default mode network, underlies autobiographical memory retrieval and displays hypometabolic changes early in Alzheimer disease. To obtain an unbiased understanding of the molecular pathobiology of the aged posterior cingulate cortex, we performed RNA sequencing (RNA-seq) on tissue obtained from 26 participants of the Rush Religious Orders Study (11 males/15 females; aged 76-96 years) with a pre-mortem clinical diagnosis of no cognitive impairment and post-mortem neurofibrillary tangle Braak Stages I/II, III, and IV. Transcriptomic data were gathered using next-generation sequencing of RNA extracted from posterior cingulate cortex generating an average of 60 million paired reads per subject. Normalized expression of RNA-seq data was calculated using a global gene annotation and a microRNA profile. Differential expression (DESeq2, edgeR) using Braak staging as the comparison structure isolated genes for dimensional scaling, associative network building and functional clustering. Curated genes were correlated with the Mini-Mental State Examination and semantic, working and episodic memory, visuospatial ability, and a composite Global Cognitive Score. Regulatory mechanisms were determined by co-expression networks with microRNAs and an overlap of transcription factor binding sites. Analysis revealed 750 genes and 12 microRNAs significantly differentially expressed between Braak Stages I/II and III/IV and an associated six groups of transcription factor binding sites. Inputting significantly different gene/network data into a functional annotation clustering model revealed elevated presynaptic, postsynaptic and ATP-related expression in Braak Stages III and IV compared with Stages I/II, suggesting these pathways are integral for cognitive resilience seen in unimpaired elderly subjects. Principal component analysis and Kruskal-Wallis testing did not associate Braak stage with cognitive function. However, Spearman correlations between genes and cognitive test scores followed by network analysis revealed upregulation of classes of synaptic genes positively associated with performance on the visuospatial perceptual orientation domain. Upregulation of key synaptic genes suggests a role for these transcripts and associated synaptic pathways in cognitive resilience seen in elders despite Alzheimer disease pathology and dementia.
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Affiliation(s)
- Christy M Kelley
- Department of Translational Neuroscience, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
- Department of Neurology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Scott E Counts
- Department of Translational Neuroscience, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
- Department of Family Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Elliott J Mufson
- Department of Translational Neuroscience, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
- Department of Neurology, Barrow Neurological Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA
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14
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Kulminski AM, Philipp I, Shu L, Culminskaya I. Definitive roles of TOMM40-APOE-APOC1 variants in the Alzheimer's risk. Neurobiol Aging 2022; 110:122-131. [PMID: 34625307 PMCID: PMC8758518 DOI: 10.1016/j.neurobiolaging.2021.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 02/03/2023]
Abstract
Despite advances, the roles of genetic variants from the APOE-harboring 19q13.32 region in Alzheimer's disease (AD) remain controversial. We leverage a comprehensive approach to gain insights into a more homogeneous genetic architecture of AD in this region. We use a sample of 2,673 AD-affected and 16,246 unaffected subjects from 4 studies and validate our main findings in the landmark Alzheimer's Disease Genetics Consortium cohort (3,662 AD-cases and 1,541 controls). We report the remarkably high excesses of the AD risk for carriers of the ε4 allele who also carry minor alleles of rs2075650 (TOMM40) and rs12721046 (APOC1) polymorphisms compared to carriers of their major alleles. The exceptionally high 4.37-fold (p=1.34 × 10-3) excess was particularly identified for the minor allele homozygotes. The beneficial and adverse variants were significantly depleted and enriched, respectively, in the AD-affected families. This study provides compelling evidence for the definitive roles of the APOE-TOMM40-APOC1 variants in the AD risk.
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Affiliation(s)
- Alexander M. Kulminski
- Corresponding Author: Alexander M. Kulminski, Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA,
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15
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Lutz MW, Chiba‐Falek O. Bioinformatics pipeline to guide late‐onset Alzheimer's disease (LOAD) post‐GWAS studies: Prioritizing transcription regulatory variants within LOAD‐associated regions. A&D Transl Res & Clin Interv 2022; 8:e12244. [PMID: 35229021 PMCID: PMC8864953 DOI: 10.1002/trc2.12244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Introduction As new late‐onset Alzheimer's disease (LOAD) genetic risk loci are identified and brain cell–type specific omics data becomes available, there is an unmet need for a bioinformatics framework to prioritize genes and variants for testing in single‐cell molecular profiling experiments and validation using disease models and gene editing technologies. Prior work has characterized and prioritized active enhancers located in LOAD‐genome‐wide association study (GWAS) regions and their potential interactions with candidate genes. The current study extends this work by focusing on single nucleotide polymorphisms (SNPs) within these LOAD enhancers and their impact on altering transcription factor (TF) binding. The proposed bioinformatics pipeline progresses from SNPs located in LOAD‐GWAS regions to a filtered set of candidate regulatory SNPs that have a predicted strong effect on TF binding. Methods Active enhancers within LOAD‐associated regions were identified and SNPs located in the enhancers were catalogued. SNPs that disrupt TF binding sites were prioritized and the respective TFs were filtered to include only those that were expressed in brain tissues relevant to LOAD. The TFs binding to the corresponding sequence was further confirmed by ChIP‐seq signals. Finally, the high‐priority candidate SNPs were evaluated as expression quantitative trait loci (eQTLs) in disease‐relevant tissues. Results We catalogued 61 strong enhancers in LOAD‐GWAS regions encompassing 326 SNPs and 104 TF binding sites. Seventy‐seven and 78 of the TFs were expressed in brain and monocytes, respectively, out of which 19 TF‐binding sites showed ChIP‐seq signals. Eleven SNPs were found to interrupt with TF binding out of which three SNPs were also significant eQTL. Discussion This study provides a framework to catalogue noncoding variations in enhancers located in LOAD‐GWAS loci and characterize their likelihood to perturb TF binding. The approach integrates multiple data types to characterize and prioritize SNPs for putative regulatory function using single‐cell multi‐omics assays and gene editing.
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Affiliation(s)
- Michael W. Lutz
- Division of Translational Brain Sciences Department of Neurology Duke University Medical Center Durham North Carolina USA
| | - Ornit Chiba‐Falek
- Division of Translational Brain Sciences Department of Neurology Duke University Medical Center Durham North Carolina USA
- Center for Genomic and Computational Biology Duke University Medical Center Durham North Carolina USA
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16
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Wei Y, de Lange SC, Pijnenburg R, Scholtens LH, Ardesch DJ, Watanabe K, Posthuma D, van den Heuvel MP. Statistical testing in transcriptomic-neuroimaging studies: A how-to and evaluation of methods assessing spatial and gene specificity. Hum Brain Mapp 2021; 43:885-901. [PMID: 34862695 PMCID: PMC8764473 DOI: 10.1002/hbm.25711] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 11/14/2022] Open
Abstract
Multiscale integration of gene transcriptomic and neuroimaging data is becoming a widely used approach for exploring the molecular underpinnings of large‐scale brain organization in health and disease. Proper statistical evaluation of determined associations between imaging‐based phenotypic and transcriptomic data is key in these explorations, in particular to establish whether observed associations exceed “chance level” of random, nonspecific effects. Recent approaches have shown the importance of statistical models that can correct for spatial autocorrelation effects in the data to avoid inflation of reported statistics. Here, we discuss the need for examination of a second category of statistical models in transcriptomic‐neuroimaging analyses, namely those that can provide “gene specificity.” By means of a couple of simple examples of commonly performed transcriptomic‐neuroimaging analyses, we illustrate some of the potentials and challenges of transcriptomic‐imaging analyses, showing that providing gene specificity on observed transcriptomic‐neuroimaging effects is of high importance to avoid reports of nonspecific effects. Through means of simulations we show that the rate of reported nonspecific effects (i.e., effects that cannot be specifically linked to a specific gene or gene‐set) can run as high as 60%, with only less than 5% of transcriptomic‐neuroimaging associations observed through ordinary linear regression analyses showing both spatial and gene specificity. We provide a discussion, a tutorial, and an easy‐to‐use toolbox for the different options of null models in transcriptomic‐neuroimaging analyses.
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Affiliation(s)
- Yongbin Wei
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Siemon C de Lange
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Sleep and Cognition, Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Rory Pijnenburg
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lianne H Scholtens
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dirk Jan Ardesch
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Child and Adolescent Psychiatry and Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
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17
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Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gordân R, Ashley-Koch AE, Crawford GE, Chiba-Falek O. Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. Mol Neurodegener 2021; 16:58. [PMID: 34429139 PMCID: PMC8383438 DOI: 10.1186/s13024-021-00481-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the post-GWAS era, there is an unmet need to decode the underpinning genetic etiologies of late-onset Alzheimer's disease (LOAD) and translate the associations to causation. METHODS We conducted ATAC-seq profiling using NeuN sorted-nuclei from 40 frozen brain tissues to determine LOAD-specific changes in chromatin accessibility landscape in a cell-type specific manner. RESULTS We identified 211 LOAD-specific differential chromatin accessibility sites in neuronal-nuclei, four of which overlapped with LOAD-GWAS regions (±100 kb of SNP). While the non-neuronal nuclei did not show LOAD-specific differences, stratification by sex identified 842 LOAD-specific chromatin accessibility sites in females. Seven of these sex-dependent sites in the non-neuronal samples overlapped LOAD-GWAS regions including APOE. LOAD loci were functionally validated using single-nuclei RNA-seq datasets. CONCLUSIONS Using brain sorted-nuclei enabled the identification of sex-dependent cell type-specific LOAD alterations in chromatin structure. These findings enhance the interpretation of LOAD-GWAS discoveries, provide potential pathomechanisms, and suggest novel LOAD-loci.
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Affiliation(s)
- Julio Barrera
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Julia E. Gamache
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Young Yun
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Ivana Premasinghe
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Daniel Sprague
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Danielle Chipman
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Jeffrey Li
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Hélène Fradin
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Karen Soldano
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27705 USA
- Department of Computer Science, Duke University, Durham, NC 27705 USA
| | - Allison E. Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
- Department of Medicine, Duke University Medical Center, DUMC, Box 104775, Durham, NC 27708 USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC, Box 3382, Durham, NC 27708 USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC 27708 USA
| | - Ornit Chiba-Falek
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Lee EG, Chen S, Leong L, Tulloch J, Yu CE. TOMM40 RNA Transcription in Alzheimer's Disease Brain and Its Implication in Mitochondrial Dysfunction. Genes (Basel) 2021; 12:871. [PMID: 34204109 DOI: 10.3390/genes12060871] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/24/2022] Open
Abstract
Increasing evidence suggests that the Translocase of Outer Mitochondria Membrane 40 (TOMM40) gene may contribute to the risk of Alzheimer’s disease (AD). Currently, there is no consensus as to whether TOMM40 expression is up- or down-regulated in AD brains, hindering a clear interpretation of TOMM40’s role in this disease. The aim of this study was to determine if TOMM40 RNA levels differ between AD and control brains. We applied RT-qPCR to study TOMM40 transcription in human postmortem brain (PMB) and assessed associations of these RNA levels with genetic variants in APOE and TOMM40. We also compared TOMM40 RNA levels with mitochondrial functions in human cell lines. Initially, we found that the human genome carries multiple TOMM40 pseudogenes capable of producing highly homologous RNAs that can obscure precise TOMM40 RNA measurements. To circumvent this obstacle, we developed a novel RNA expression assay targeting the primary transcript of TOMM40. Using this assay, we showed that TOMM40 RNA was upregulated in AD PMB. Additionally, elevated TOMM40 RNA levels were associated with decreases in mitochondrial DNA copy number and mitochondrial membrane potential in oxidative stress-challenged cells. Overall, differential transcription of TOMM40 RNA in the brain is associated with AD and could be an indicator of mitochondrial dysfunction.
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20
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Bryan J, Mandan A, Kamat G, Gottschalk WK, Badea A, Adams KJ, Thompson JW, Colton CA, Mukherjee S, Lutz MW. Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. Alzheimers Dement 2021; 17:561-573. [PMID: 33480182 PMCID: PMC8044005 DOI: 10.1002/alz.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such as age or sex. Evaluation of AD biological pathways in the context of interactions with these covariates is critical to the understanding of AD as well as the development of model systems used to study the disease. METHODS Gene set enrichment methods are powerful tools used to interpret gene-level statistics at the level of biological pathways. We introduce a method for quantifying gene set enrichment using likelihood ratio-derived test statistics (gsLRT), which accounts for sample covariates like age and sex. We then use our method to test for age and sex interactions with protein expression levels in AD and to compare the pathway results between human and mouse species. RESULTS Our method, based on nested logistic regressions is competitive with the existing standard for gene set testing in the context of linear models and complex experimental design. The gene sets we identify as having a significant association with AD-both with and without additional covariate interactions-are validated by previous studies. Differences between gsLRT results on mouse and human datasets are observed. DISCUSSION Characterizing biological pathways involved in AD builds on the important work involving single gene drivers. Our gene set enrichment method finds pathways that are significantly related to AD while accounting for covariates that may be relevant to disease development. The method highlights commonalities and differences between human AD and mouse models, which may inform the development of higher fidelity models for the study of AD.
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Affiliation(s)
- Jordan Bryan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Arpita Mandan
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | - Gauri Kamat
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
| | | | - Alexandra Badea
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Kendra J. Adams
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | | | - Carol A. Colton
- Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Departments of Mathematics, Computer Science, and Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Michael W. Lutz
- Department of Neurology, Duke University, Durham, NC 27708, USA
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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22
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Koks S, Pfaff AL, Bubb VJ, Quinn JP. Transcript Variants of Genes Involved in Neurodegeneration Are Differentially Regulated by the APOE and MAPT Haplotypes. Genes (Basel) 2021; 12:423. [PMID: 33804213 DOI: 10.3390/genes12030423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Yang A, Kantor B, Chiba-Falek O. APOE: The New Frontier in the Development of a Therapeutic Target towards Precision Medicine in Late-Onset Alzheimer's. Int J Mol Sci 2021; 22:1244. [PMID: 33513969 PMCID: PMC7865856 DOI: 10.3390/ijms22031244] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) has a critical unmet medical need. The consensus around the amyloid cascade hypothesis has been guiding pre-clinical and clinical research to focus mainly on targeting beta-amyloid for treating AD. Nevertheless, the vast majority of the clinical trials have repeatedly failed, prompting the urgent need to refocus on other targets and shifting the paradigm of AD drug development towards precision medicine. One such emerging target is apolipoprotein E (APOE), identified nearly 30 years ago as one of the strongest and most reproduceable genetic risk factor for late-onset Alzheimer's disease (LOAD). An exploration of APOE as a new therapeutic culprit has produced some very encouraging results, proving that the protein holds promise in the context of LOAD therapies. Here, we review the strategies to target APOE based on state-of-the-art technologies such as antisense oligonucleotides, monoclonal antibodies, and gene/base editing. We discuss the potential of these initiatives in advancing the development of novel precision medicine therapies to LOAD.
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Affiliation(s)
- Anna Yang
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Boris Kantor
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA;
- Viral Vector Core, Duke University Medical Center, Durham, NC 27710, USA
- Duke Center for Advanced Genomic Technologies, Durham, NC 27708, 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 27708, USA
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24
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Chadha S, Behl T, Sehgal A, Kumar A, Bungau S. Exploring the role of mitochondrial proteins as molecular target in Alzheimer's disease. Mitochondrion 2020; 56:62-72. [PMID: 33221353 DOI: 10.1016/j.mito.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Brain is a fully differentiated organ and is sensitive towards oxidative damage of various compounds including lipids, proteins, and DNA that occurs during process of normal aging and is mainly due to its high energy metabolism and reduced activity of anti-oxidative defense mechanism. Mitochondria are dynamic ATP-generating organelles which constitutes cellular functions such as regulation of intracellular calcium, bio-energetic processes, and reduction-oxidation of cells. Such functioning is negatively affected due to the presence of amyloid β peptide (Aβ) which is involved in pathogenesis of Alzheimer disease (AD). Aβ interacts with mitochondria and leads to mitochondrial dysfunction. Mitochondrial dysfunction, abnormal interactions, oxidative stress, and mis-folding of synaptic proteins inside nervous system are explored and regarded as primary or initial features in insurgence of pathology (AD and other neurological disease). The major histopathological hallmarks of AD are characterized by presence of these hallmarks intracellularly, its further progression and exacerbation which leads to excessive accumulation of oligomeric as well as fibrillar-β-amyloid peptides (present extracellularly) and accumulation of neurofibrillary tangles intracellularly. The current review will focus on alterations and variation in mitochondria/mitochondrial DNA (mtDNA) and the rationale for involvement of related abnormalities in pathogenesis of AD.
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Affiliation(s)
- Swati Chadha
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Arun Kumar
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Simona Bungau
- Department of Pharmacy, Faculty of Pharmacy, University of Oradea, Romania
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Kotha S, B S, Kulkarni VM, S RS, B HK, R H. An in-silico approach: identification of PPAR-γ agonists from seaweeds for the management of Alzheimer's Disease. J Biomol Struct Dyn 2020; 39:2210-2229. [PMID: 32216605 DOI: 10.1080/07391102.2020.1747543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Alzheimer's Disease is a complex progressive neurodegenerative disorder characterized by neurofibrillary tangles and senile plaques in various parts of the brain particularly cerebral cortex affecting memory and cognition. Nuclear receptors such as Peroxisome proliferator-activated receptor γ [PPAR-γ] is reported to have a role in lipid and glucose homeostasis in the brain, reduces the synthesis of Aβ (beta-amyloid plaques) and also regulates mitochondrial biogenesis and inhibit the neuro-inflammation, which contributes for the improvement in the cognitive function in AD. Hence PPAR-γ is one of the newer targets for the researchers to understand the pathology of AD and to evolve the novel strategy to retard/reverse the progression of AD. PPAR-γ agonists such as Rosiglitazone and Pioglitazone have shown promising results in AD by decreasing neuro-inflammation and restoring glucose dysmetabolism leading to a reduction in neuronal deterioration. These agonists possess poor blood-brain permeability and are poor candidates for clinical use in AD. Therefore, search, design, and development for new PPAR- γ agonists with improved BBB penetration ability are imperative. The present work deals with the use of computational tools and techniques such as molecular docking, molecular dynamics to discover PPAR-γ agonists from the unexplored Seaweed Metabolite Database and predicts it's toxicological and physiochemical profile, thereby saving time and resources. Out of 1,110 seaweed compounds, the hit molecule BS052 displayed a strong binding affinity towards PPAR-γ, which possessed better lipid solubility indicating the potential to be considered as a PPAR-γ agonist, which may be useful in the management of AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Satvik Kotha
- Department of Pharmacology, Government College of Pharmacy, Bengaluru, India
| | - Swapna B
- Department of Pharmacology, Government College of Pharmacy, Bengaluru, India
| | - Vithal M Kulkarni
- Department of Chemistry, Bharati Vidyapeeth Deemed University, Poona College of Pharmacy, Pune, India
| | - Ramachandra Setty S
- Department of Pharmacology, Government College of Pharmacy, Bengaluru, India
| | - Harish Kumar B
- Department of Pharmacology, Government College of Pharmacy, Bengaluru, India
| | - Harisha R
- Department of Pharmacology, Government College of Pharmacy, Bengaluru, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pytte J, Anderton RS, Flynn LL, Theunissen F, Jiang L, Pitout I, James I, Mastaglia FL, Saunders AM, Bedlack R, Siddique T, Siddique N, Akkari PA. Association of a structural variant within the SQSTM1 gene with amyotrophic lateral sclerosis. Neurol Genet 2020; 6:e406. [PMID: 32185242 PMCID: PMC7061286 DOI: 10.1212/nxg.0000000000000406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/23/2020] [Indexed: 11/15/2022]
Abstract
Objective As structural variations may underpin susceptibility to complex neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), the objective of this study was to investigate a structural variant (SV) within sequestosome 1 (SQSTM1). Methods A candidate insertion/deletion variant within intron 5 of the SQSTM1 gene was identified using a previously established SV evaluation algorithm and chosen according to its subsequent theoretical effect on gene expression. The variant was systematically assessed through PCR, polyacrylamide gel fractionation, Sanger sequencing, and reverse transcriptase PCR. Results A reliable and robust assay confirmed the polymorphic nature of this variant and that the variant may influence SQSTM1 transcript levels. In a North American cohort of patients with familial ALS (fALS) and sporadic ALS (sALS) (n = 403) and age-matched healthy controls (n = 562), we subsequently showed that the SQSTM1 variant is associated with fALS (p = 0.0036), particularly in familial superoxide dismutase 1 mutation positive patients (p = 0.0005), but not with patients with sALS (p = 0.97). Conclusions This disease association highlights the importance and implications of further investigation into SVs that may provide new targets for cohort stratification and therapeutic development.
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Affiliation(s)
- Julia Pytte
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ryan S Anderton
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Loren L Flynn
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Frances Theunissen
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Leanne Jiang
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ianthe Pitout
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ian James
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Frank L Mastaglia
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Ann M Saunders
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Richard Bedlack
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Teepu Siddique
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - Nailah Siddique
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
| | - P Anthony Akkari
- University of Western Australia (J.P., R.S.A., L.L.F., F.T., L.J., F.L.M., P.A.A.), Centre for Neuromuscular and Neurological Disorders, Crawley; Perron Institute for Neurological and Translational Science (J.P., R.S.A., L.L.F., F.T., L.J., I.P., F.L.M., P.A.A.), Nedlands; University of Notre Dame Australia (R.S.A.), School of Health Sciences; University of Notre Dame Australia (R.S.A.), Institute for Health Research, Fremantle; Murdoch University (L.L.F., I.P., P.A.A.), Centre for Molecular Medicine and Innovative Therapeutics; Murdoch University, Institute for Immunology and Infectious Diseases (I.J.), Western Australia, Australia; Department of Neurology (R.B.), Duke University School of Medicine, Durham, NC; Zinfandel Pharmaceuticals (A.M.S.), Inc.; Duke University (R.B.), ALS Clinic, Durham, NC; and Departments of Neurology, Pathology and Cell and Molecular Biology (T.S., N.S.), Northwestern University Feinberg School of Medicine, the Les Turner ALS Center and the Northwestern University Interdepartmental Neuroscience Program, Chicago, IL
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29
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Lee EG, Tulloch J, Chen S, Leong L, Saxton AD, Kraemer B, Darvas M, Keene CD, Shutes-David A, Todd K, Millard S, Yu CE. Redefining transcriptional regulation of the APOE gene and its association with Alzheimer's disease. PLoS One 2020; 15:e0227667. [PMID: 31978088 PMCID: PMC6980611 DOI: 10.1371/journal.pone.0227667] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/24/2019] [Indexed: 01/09/2023] Open
Abstract
The apolipoprotein E gene (APOE) is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), yet the expression of APOE is not clearly understood. For example, it is unclear whether AD patients have elevated or decreased APOE expression or why the correlation levels of APOE RNA and the ApoE protein differ across studies. Likewise, APOE has a single CpG island (CGI) that overlaps with its 3'-exon, and this CGI's effect is unknown. We previously reported that the APOE CGI is highly methylated in human postmortem brain (PMB) and that this methylation is altered in AD frontal lobe. In this study, we comprehensively characterized APOE RNA transcripts and correlated levels of RNA expression with DNA methylation levels across the APOE CGI. We discovered the presence of APOE circular RNA (circRNA) and found that circRNA and full-length mRNA each constitute approximately one third of the total APOE RNA, with truncated mRNAs likely constituting some of the missing fraction. All APOE RNA species demonstrated significantly higher expression in AD frontal lobe than in control frontal lobe. Furthermore, we observed a negative correlation between the levels of total APOE RNA and DNA methylation at the APOE CGI in the frontal lobe. When stratified by disease status, this correlation was strengthened in controls but not in AD. Our findings suggest a possible modified mechanism of gene action for APOE in AD that involves not only the protein isoforms but also an epigenetically regulated transcriptional program driven by DNA methylation in the APOE CGI.
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Affiliation(s)
- Eun-Gyung Lee
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Jessica Tulloch
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Sunny Chen
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Lesley Leong
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Aleen D. Saxton
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Brian Kraemer
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Martin Darvas
- Department of Pathology, University of Washington, Seattle, WA, United States of America
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, United States of America
| | - Andrew Shutes-David
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Kaitlin Todd
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Steve Millard
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
| | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, United States of America
- Department of Medicine, University of Washington, Seattle, WA, United States of America
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Abstract
Alzheimer disease (AD) is a progressive and deleterious neurodegenerative disorder that affects mostly the elderly population. At the moment, no effective treatments are available in the market, making the whole situation a compelling challenge for societies worldwide. Recently, novel mechanisms have been proposed to explain the etiology of this disease leading to the new concept that AD is a multifactor pathology. Among others, the function of mitochondria has been considered as one of the intracellular processes severely compromised in AD since the early stages and likely represents a common feature of many neurodegenerative diseases. Many mitochondrial parameters decline already during the aging, reaching an extensive functional failure concomitant with the onset of neurodegenerative conditions, although the exact timeline of these events is still unclear. Thereby, it is not surprising that mitochondria have been already considered as therapeutic targets in neurodegenerative diseases including AD. Together with an overview of the role of mitochondrial dysfunction, this review examines the pros and cons of the tested therapeutic approaches targeting mitochondria in the context of AD. Since mitochondrial therapies in AD have shown different degrees of progress, it is imperative to perform a detailed analysis of the significance of mitochondrial deterioration in AD and of a pharmacological treatment at this level. This step would be very important for the field, as an effective drug treatment in AD is still missing and new therapeutic concepts are urgently needed.
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Affiliation(s)
- Giovanna Cenini
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wolfgang Voos
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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Lutz MW, Sprague D, Chiba-Falek O. Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. Alzheimers Dement 2019; 15:1048-1058. [PMID: 31262699 PMCID: PMC6699885 DOI: 10.1016/j.jalz.2019.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/20/2019] [Accepted: 04/17/2019] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Genome-wide association studies (GWAS) discovered multiple late-onset Alzheimer's disease (LOAD)-associated SNPs and inferred the genes based on proximity; however, the actual causal genes are yet to be identified. METHODS We defined LOAD-GWAS regions by the most significantly associated SNP ±0.5 Mb and developed a bioinformatics pipeline that uses and integrates chromatin state segmentation track to map active enhancers and virtual 4C software to visualize interactions between active enhancers and gene promoters. We augmented our pipeline with biomedical and functional information. RESULTS We applied the bioinformatics pipeline using three ∼1 Mb LOAD-GWAS loci: BIN1, PICALM, CELF1. These loci contain 10-24 genes, an average of 106 active enhancers and 80 CTCF sites. Our strategy identified all genes corresponding to the promoters that interact with the active enhancer that is closest to the LOAD-GWAS-SNP and generated a shorter list of prioritized candidate LOAD genes (5-14/loci), feasible for post-GWAS investigations of causality. DISCUSSION Interpretation of LOAD-GWAS discoveries requires the integration of brain-specific functional genomic data sets and information related to regulatory activity.
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Affiliation(s)
- Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Daniel Sprague
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA.
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Cacabelos R, Carril JC, Cacabelos N, Kazantsev AG, Vostrov AV, Corzo L, Cacabelos P, Goldgaber D. Sirtuins in Alzheimer's Disease: SIRT2-Related GenoPhenotypes and Implications for PharmacoEpiGenetics. Int J Mol Sci 2019; 20:ijms20051249. [PMID: 30871086 PMCID: PMC6429449 DOI: 10.3390/ijms20051249] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 12/11/2022] Open
Abstract
Sirtuins (SIRT1-7) are NAD+-dependent protein deacetylases/ADP ribosyltransferases with important roles in chromatin silencing, cell cycle regulation, cellular differentiation, cellular stress response, metabolism and aging. Sirtuins are components of the epigenetic machinery, which is disturbed in Alzheimer’s disease (AD), contributing to AD pathogenesis. There is an association between the SIRT2-C/T genotype (rs10410544) (50.92%) and AD susceptibility in the APOEε4-negative population (SIRT2-C/C, 34.72%; SIRT2-T/T 14.36%). The integration of SIRT2 and APOE variants in bigenic clusters yields 18 haplotypes. The 5 most frequent bigenic genotypes in AD are 33CT (27.81%), 33CC (21.36%), 34CT (15.29%), 34CC (9.76%) and 33TT (7.18%). There is an accumulation of APOE-3/4 and APOE-4/4 carriers in SIRT2-T/T > SIRT2-C/T > SIRT2-C/C carriers, and also of SIRT2-T/T and SIRT2-C/T carriers in patients who harbor the APOE-4/4 genotype. SIRT2 variants influence biochemical, hematological, metabolic and cardiovascular phenotypes, and modestly affect the pharmacoepigenetic outcome in AD. SIRT2-C/T carriers are the best responders, SIRT2-T/T carriers show an intermediate pattern, and SIRT2-C/C carriers are the worst responders to a multifactorial treatment. In APOE-SIRT2 bigenic clusters, 33CC carriers respond better than 33TT and 34CT carriers, whereas 24CC and 44CC carriers behave as the worst responders. CYP2D6 extensive metabolizers (EM) are the best responders, poor metabolizers (PM) are the worst responders, and ultra-rapid metabolizers (UM) tend to be better responders that intermediate metabolizers (IM). In association with CYP2D6 genophenotypes, SIRT2-C/T-EMs are the best responders. Some Sirtuin modulators might be potential candidates for AD treatment.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Juan C Carril
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Natalia Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Aleksey G Kazantsev
- Department of Psychiatry and Behavioral Science, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Alex V Vostrov
- Department of Psychiatry and Behavioral Science, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Lola Corzo
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Pablo Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165 Bergondo, Corunna, Spain.
| | - Dmitry Goldgaber
- Department of Psychiatry and Behavioral Science, Stony Brook University, Stony Brook, NY 11794, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chai YL, Xing H, Chong JR, Francis PT, Ballard CG, Chen CP, Lai MKP. Mitochondrial Translocase of the Outer Membrane Alterations May Underlie Dysfunctional Oxidative Phosphorylation in Alzheimer's Disease. J Alzheimers Dis 2019; 61:793-801. [PMID: 29254089 DOI: 10.3233/jad-170613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The translocase of the outer membrane (TOM) is a vital mitochondrial transport system facilitating the importation of nuclear encoded proteins into the organelle. While mitochondrial dysfunction, including perturbation of oxidative phosphorylation (OXPHOS) complex, is evident in Alzheimer's disease (AD), it remains unclear whether the observed OXPHOS deficits may be associated with TOM alterations. OBJECTIVES To correlate TOM subunits with OXPHOS complex proteins in AD. METHODS Postmortem neocortex (BA40) from AD and age-matched controls were processed to obtain mitochondrial enriched homogenates for the measurement of Tom20, Tom22, Tom40, and Tom70 as well as components of OXPHOS complex I-V by immunoblotting. RESULTS Tom20 and Tom70 immunoreactivities were significantly reduced in AD, as were components of OXPHOS complex I and III. Both Tom20 and Tom70 positively correlated with complex III and V, while Tom20 also correlated withcomplex IV. CONCLUSION Reductions in certain TOM subunits and their correlations with specific OXPHOS complex proteins suggest that an impaired mitochondrial transportation system may contribute to previously observed oxidative phosphorylation deficits in AD. Follow-up studies are needed to corroborate the present correlative study.
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Affiliation(s)
- Yuek Ling Chai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Huayang Xing
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joyce R Chong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul T Francis
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Clive G Ballard
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK.,University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Wolfson Centre for Age-Related Diseases, King's College London, London, UK
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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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36
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Heinemeyer T, Stemmet M, Bardien S, Neethling A. Underappreciated Roles of the Translocase of the Outer and Inner Mitochondrial Membrane Protein Complexes in Human Disease. DNA Cell Biol 2018; 38:23-40. [PMID: 30481057 DOI: 10.1089/dna.2018.4292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are critical for cellular survival, and for their proper functioning, translocation of ∼1500 proteins across the mitochondrial membranes is required. The translocase of the outer (TOMM) and inner mitochondrial membrane (TIMM) complexes are major components of this translocation machinery. Through specific processes, preproteins and other molecules are imported, translocated, and directed to specific mitochondrial compartments for their function. In this study, we review the association of subunits of these complexes with human disease. Pathogenic mutations have been identified in the TIMM8A (DDP) and DNAJC19 (TIMM14) genes and are linked to Mohr-Tranebjærg syndrome and dilated cardiomyopathy syndrome (with and without ataxia), respectively. Polymorphisms in TOMM40 have been associated with Alzheimer's disease, frontotemporal lobar degeneration, Parkinson's disease with dementia, dementia with Lewy bodies, nonpathological cognitive aging, and various cardiovascular-related traits. Furthermore, reduced protein expression levels of several complex subunits have been associated with Parkinson's disease, Meniere's disease, and cardiovascular disorders. However, increased mRNA and protein levels of complex subunits are found in cancers. This review highlights the importance of the mitochondrial import machinery in human disease and stresses the need for further studies. Ultimately, this knowledge may prove to be critical for the development of therapeutic modalities for these conditions.
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Affiliation(s)
- Thea Heinemeyer
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Monique Stemmet
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
| | - Annika Neethling
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town, South Africa
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Govindarajulu M, Pinky PD, Bloemer J, Ghanei N, Suppiramaniam V, Amin R. Signaling Mechanisms of Selective PPAR γ Modulators in Alzheimer's Disease. PPAR Res 2018; 2018:2010675. [PMID: 30420872 PMCID: PMC6215547 DOI: 10.1155/2018/2010675] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/31/2018] [Accepted: 09/13/2018] [Indexed: 01/22/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by abnormal protein accumulation, synaptic dysfunction, and cognitive impairment. The continuous increase in the incidence of AD with the aged population and mortality rate indicates the urgent need for establishing novel molecular targets for therapeutic potential. Peroxisome proliferator-activated receptor gamma (PPARγ) agonists such as rosiglitazone and pioglitazone reduce amyloid and tau pathologies, inhibit neuroinflammation, and improve memory impairments in several rodent models and in humans with mild-to-moderate AD. However, these agonists display poor blood brain barrier permeability resulting in inadequate bioavailability in the brain and thus requiring high dosing with chronic time frames. Furthermore, these dosing levels are associated with several adverse effects including increased incidence of weight gain, liver abnormalities, and heart failure. Therefore, there is a need for identifying novel compounds which target PPARγ more selectively in the brain and could provide therapeutic benefits without a high incidence of adverse effects. This review focuses on how PPARγ agonists influence various pathologies in AD with emphasis on development of novel selective PPARγ modulators.
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Affiliation(s)
- Manoj Govindarajulu
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Priyanka D. Pinky
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Jenna Bloemer
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Nila Ghanei
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Vishnu Suppiramaniam
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
- Center for Neuroscience, Auburn University, Auburn, AL, USA
| | - Rajesh Amin
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
- Center for Neuroscience, Auburn University, Auburn, AL, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Motivation Despite recent advances of modern GWAS methods, it is still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. Results We developed an R package rqt, which offers gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone. We applied this tool to the analysis of Alzheimer's disease data from three datasets CHS, FHS and LOADFS. Test results from meta-analysis of three Alzheimer studies show its applicability for association testing. Availability and implementation The package rqt is freely available under the following link: https://github.com/izhbannikov/rqt. Contact ilya.zhbannikov@duke.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ilya Y Zhbannikov
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Konstantin G Arbeev
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Anatoliy I Yashin
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
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40
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Mise A, Yoshino Y, Yamazaki K, Ozaki Y, Sao T, Yoshida T, Mori T, Mori Y, Ochi S, Iga JI, Ueno SI. TOMM40 and APOE Gene Expression and Cognitive Decline in Japanese Alzheimer's Disease Subjects. J Alzheimers Dis 2018; 60:1107-1117. [PMID: 28984592 DOI: 10.3233/jad-170361] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND TOMM40 is located on chromosome 19, is in linkage disequilibrium with apolipoprotein E (APOE), andis reported in several genome-wide association studies to be associated with Alzheimer's disease (AD). OBJECTIVE Assess APOE and TOM40 and mitochondrial genes as blood biomarkers for AD. METHODS We examined TOMM40, PTEN-induced putative kinase 1 (PINK1), Parkin RBR E3 ubiquitin protein ligase (PARK2), and APOE mRNA expression in relation to the methylation rates of CpG sites in the upstream region of TOMM40exon 1 in peripheral leukocytes and TOMM40523 polyT genotypes in 60 AD and age- and sex-matched control subjects. RESULTS TOMM40 mRNA expression was significantly lower in AD subjects (0.87±0.18 versus 1.0±0.23, p = 0.005), and PINK1 mRNA expression was higher in AD subjects (1.5±0.61 versus 1.0±0.52, p < 0.001). TOMM40 mRNA expression was significantly correlated with the Mini-Mental State Examination total score (r = 0.290, p = 0.027). There was no expressional change in peripheral APOE mRNA in either AD or control subjects (p = 0.32). Methylation rates in the upstream region of TOMM40exon 1 were not different between AD and control subjects (average rate: 1.37±0.99 versus 1.39±1.20, p = 0.885), and TOMM40523 polyT genotypes were also not different between AD and control subjects (p = 0.67). CONCLUSION TOMM40 mRNA expression was lower in AD subjects and was correlated with cognitive decline. Significant changes in both TOMM40 and PINK1 mRNA may be related to mitochondrial dysfunction.
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Affiliation(s)
- Ayano Mise
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
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Afek A, Tagliafierro L, Glenn OC, Lukatsky DB, Gordan R, Chiba-Falek O. Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene. Neurogenetics 2018; 19:135-144. [PMID: 29730780 DOI: 10.1007/s10048-018-0546-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/25/2018] [Indexed: 12/01/2022]
Abstract
Short structural variants-variants other than single nucleotide polymorphisms-are hypothesized to contribute to many complex diseases, possibly by modulating gene expression. However, the molecular mechanisms by which noncoding short structural variants exert their effects on gene regulation have not been discovered. Here, we study simple sequence repeats (SSRs), a common class of short structural variants. Previously, we showed that repetitive sequences can directly influence the binding of transcription factors to their proximate recognition sites, a mechanism we termed non-consensus binding. In this study, we focus on the SSR termed Rep1, which was associated with Parkinson's disease (PD) and has been implicated in the cis-regulation of the PD-risk SNCA gene. We show that Rep1 acts via the non-consensus binding mechanism to affect the binding of transcription factors from the GATA and ELK families to their specific sites located right next to the Rep1 repeat. Next, we performed an expression analysis to further our understanding regarding the GATA and ELK family members that are potentially relevant for SNCA transcriptional regulation in health and disease. Our analysis indicates a potential role for GATA2, consistent with previous reports. Our study proposes non-consensus transcription factor binding as a potential mechanism through which noncoding repeat variants could exert their pathogenic effects by regulating gene expression.
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Affiliation(s)
- A Afek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, 27710, USA.,Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - L Tagliafierro
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Neurology, Duke University Medical Center, Durham, NC, 27710, USA
| | - O C Glenn
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA.,Department of Neurology, Duke University Medical Center, Durham, NC, 27710, USA
| | - D B Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, 8410501, Beersheba, Israel
| | - R Gordan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, 27710, USA. .,Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA. .,Department of Computer Science, Duke University, Durham, NC, 27708, USA.
| | - O Chiba-Falek
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27710, USA. .,Department of Neurology, Duke University Medical Center, Durham, NC, 27710, USA.
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Barrera J, Subramanian S, Chiba-Falek O. Probing the role of PPARγ in the regulation of late-onset Alzheimer's disease-associated genes. PLoS One 2018; 13:e0196943. [PMID: 29723294 PMCID: PMC5933777 DOI: 10.1371/journal.pone.0196943] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
Peroxisome proliferator-activated receptor-γ (PPARγ), is a transcription factor that governs pathways, such as lipid metabolism and immune response, that have been implicated in the etiology of LOAD. Previously, we established HepG2-derived cell-lines with stable knockdown of PPARγ gene, and showed an increase in mRNA levels of genes mapped in the APOE linkage disequilibrium (LD) region on chromosome 19q13.32, with the greatest effect observed for APOE-mRNA. Here, we extended the analysis using our PPARγ knockdown model system and investigated the broader effect on expression changes of genes implicated in LOAD via genome wide association studies (GWAS). We applied the nCounter gene expression assay (NanoString) using a panel of twenty-four LOAD-associated genes inferred by proximity to the top significantly associated SNPs. Two independent PPARγ knockdown cell-lines showed changes in mRNA levels of a total of seven genes compared to a control HepG2 cell-line; six of which, ABCA7, APOE, CASS4, CELF1, PTK2B, and ZCWPW1, were upregulated and one, DSG2, was downregulated upon PPARγ knockdown. Our results propose that PPARγ may act as a master regulator of the transcription of several genes involved in LOAD pathogenesis. Our study provided the premise for further analyses including a larger set of genes positioned within a wider range of linkage disequilibrium (LD) regions tagged by all LOAD significantly associated SNPs.
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Affiliation(s)
- Julio Barrera
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shobana Subramanian
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Abstract
The TOMM40 poly-T is a polymorphism in intron 6 of the TOMM40 gene, which is adjacent to and in linkage disequilibrium with APOE. Roses et al. identified the association between the length of TOMM40 poly-T with the risk and age of onset of late-onset Alzheimer's disease (LOAD). Following the original discovery, additional studies found associations between the TOMM40 poly-T and LOAD-related phenotypes independent of APOE genotypes, while others did not replicate these associations. Furthermore, the identity of the TOMM40 poly-T risk allele has been controversial between different LOAD-related phenotypes. Here, we propose a framework to address the conflicting findings with respect to the TOMM40 poly-T allele associations with LOAD phenotypes and their functional effects. The framework is used to interpret previous studies as means to gain insights regarding the nature of the risk allele, very long versus short. We suggest that the identity of the TOMM40 poly-T risk allele depends on the phenotype being evaluated, the ages of the study subjects at the time of assessment, and the context of the APOE genotypes. In concluding remarks, we outline future studies that will inform the mechanistic interpretation of the genetic data.
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Affiliation(s)
- Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA.
| | | | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
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Yu L, Lutz MW, Farfel JM, Wilson RS, Burns DK, Saunders AM, De Jager PL, Barnes LL, Schneider JA, Bennett DA. Neuropathologic features of TOMM40 '523 variant on late-life cognitive decline. Alzheimers Dement 2017; 13:1380-8. [PMID: 28624335 DOI: 10.1016/j.jalz.2017.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/03/2017] [Indexed: 11/22/2022]
Abstract
INTRODUCTION The study investigated the role of neuropathologies in the relationship between TOMM40 '523 genotype and late-life cognitive decline. METHODS Participants were community-dwelling older persons who had annual cognitive assessments and brain autopsies after death. Genotyping used DNA from peripheral blood or postmortem brain tissue. Linear mixed models assessed the extent to which the association of '523 genotype with cognitive decline is attributable to neuropathologies. RESULTS Relative to ε3/ε3 homozygotes with '523-S/VL or '523-VL/VL genotype, both '523-L carriers and ε3/ε3 homozygotes with '523-S/S genotype had faster cognitive decline. The association of '523-L with cognitive decline was attenuated and no longer significant after controlling for Alzheimer's and other neuropathologies. By contrast, the association of '523-S/S was unchanged. DISCUSSION There are two distinct TOMM40 '523 signals in relation to late-life cognitive decline. One signal primarily acts through AD and other common neuropathologies, whereas the other operates through a different mechanism.
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Zeitlow K, Charlambous L, Ng I, Gagrani S, Mihovilovic M, Luo S, Rock DL, Saunders A, Roses AD, Gottschalk WK. The biological foundation of the genetic association of TOMM40 with late-onset Alzheimer's disease. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2973-86. [PMID: 28768149 DOI: 10.1016/j.bbadis.2017.07.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/13/2017] [Accepted: 07/28/2017] [Indexed: 02/06/2023]
Abstract
A variable-length poly-T variant in intron 6 of the TOMM40 gene, rs10524523, is associated with risk and age-of-onset of sporadic (late-onset) Alzheimer's disease. In Caucasians, the three predominant alleles at this locus are Short (S), Long (L) or Very long (VL). On an APOE ε3/3 background, the S/VL and VL/VL genotypes are more protective than S/S. The '523 poly-T has regulatory properties, in that the VL poly-T results in higher expression than the S poly-T in luciferase expression systems. The aim of the current work was to identify effects on cellular bioenergetics of increased TOM40 protein expression. MitoTracker Green fluorescence and autophagic vesicle staining was the same in control and over-expressing cells, but TOM40 over-expression was associated with increased expression of TOM20, a preprotein receptor of the TOM complex, the mitochondrial chaperone HSPA9, and PDHE1a, and increased activities of the oxidative phosphorylation complexes I and IV and of the TCA member α-ketoglutaric acid dehydrogenase. Consistent with the complex I findings, respiration was more sensitive to inhibition by rotenone in control cells than in the TOM40 over-expressing cells. In the absence of inhibitors, total cellular ATP, the mitochondrial membrane potential, and respiration were elevated in the over-expressing cells. Spare respiratory capacity was greater in the TOM40 over-expressing cells than in the controls. TOM40 over-expression blocked Ab-elicited decreases in the mitochondrial membrane potential, cellular ATP levels, and cellular viability in the control cells. These data suggest elevated expression of TOM40 may be protective of mitochondrial function.
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Yu L, Lutz MW, Wilson RS, Burns DK, Roses AD, Saunders AM, Yang J, Gaiteri C, De Jager PL, Barnes LL, Bennett DA. APOE ε4-TOMM40 '523 haplotypes and the risk of Alzheimer's disease in older Caucasian and African Americans. PLoS One 2017; 12:e0180356. [PMID: 28672022 PMCID: PMC5495438 DOI: 10.1371/journal.pone.0180356] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/14/2017] [Indexed: 11/23/2022] Open
Abstract
Patterns of linkage between the ε4 allele of Apolipoprotein E (APOE) and '523 poly-T alleles in the adjacent gene, TOMM40, differ between Caucasian and African Americans. The extent to which this difference affects the risk of Alzheimer's disease (AD) is unclear. We compared the APOE ε4-TOMM40 '523 haplotypes between older Caucasian and African Americans, and examined their relationship with AD dementia. Data came from three community based cohort studies of diverse participants. APOE genotypes were determined by polymorphisms of rs429358 and rs7412. TOMM40 '523 genotypes were defined by the poly-T repeat length of rs10524523 (short ['523-S]: poly-T ≤ 19, long ['523-L]: 20 ≤ poly-T ≤ 29, and very long ['523-VL]: poly-T ≥ 30). Cox proportional hazards models examined the effect of haplotype variation on the risk of incident AD dementia. A total of 1,848 Caucasian and 540 African American individuals were included in the study. In Caucasians, nearly none (0.8%) of the non-ε4 carriers and almost all (94.2%) of the ε4 carriers had '523-L. The classification was highly concordant. Each ε4 allele doubled the risk for AD dementia and the dose effect was evident. Almost identical effect size and effect pattern were observed for TOMM40 '523-L. In African Americans, nearly none (1.1%) of the non-ε4 carriers had '523-L, but only 47.8% of the ε4 carriers had '523-L. The concordance was weaker compared with Caucasians. The effect patterns on incident AD dementia differed distinctively between ε4 and '523-L carriers. Further, both genotypic and allelic data support that among African Americans the ε4-'523-L haplotype had stronger effect on risk of AD dementia than other ε4-'523 haplotypes.
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Affiliation(s)
- Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Michael W. Lutz
- Department of Neurology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Robert S. Wilson
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Daniel K. Burns
- Zinfandel Pharmaceuticals, Inc., Research Triangle Park, North Carolina, United States of America
| | - Allen D. Roses
- Department of Neurology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Zinfandel Pharmaceuticals, Inc., Research Triangle Park, North Carolina, United States of America
| | - Ann M. Saunders
- Zinfandel Pharmaceuticals, Inc., Research Triangle Park, North Carolina, United States of America
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, New York, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Lisa L. Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - David A. Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
- * E-mail:
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Völgyi K, Gulyássy P, Todorov MI, Puska G, Badics K, Hlatky D, Kékesi KA, Nyitrai G, Czurkó A, Drahos L, Dobolyi A. Chronic Cerebral Hypoperfusion Induced Synaptic Proteome Changes in the rat Cerebral Cortex. Mol Neurobiol 2017; 55:4253-4266. [PMID: 28620701 DOI: 10.1007/s12035-017-0641-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/29/2017] [Indexed: 12/23/2022]
Abstract
Chronic cerebral hypoperfusion (CCH) evokes mild cognitive impairment (MCI) and contributes to the progression of vascular dementia and Alzheimer's disease (AD). How CCH induces these neurodegenerative processes that may spread along the synaptic network and whether they are detectable at the synaptic proteome level of the cerebral cortex remains to be established. In the present study, we report the synaptic protein changes in the cerebral cortex after stepwise bilateral common carotid artery occlusion (BCCAO) induced CCH in the rat. The occlusions were confirmed with magnetic resonance angiography 5 weeks after the surgery. Synaptosome fractions were prepared using sucrose gradient centrifugation from cerebral cortex dissected 7 weeks after the occlusion. The synaptic protein differences between the sham operated and CCH groups were analyzed with label-free nanoUHPLC-MS/MS. We identified 46 proteins showing altered abundance due to CCH. In particular, synaptic protein and lipid metabolism, as well as GABA shunt-related proteins showed increased while neurotransmission and synaptic assembly-related proteins showed decreased protein level changes in CCH rats. Protein network analysis of CCH-induced protein alterations suggested the importance of increased synaptic apolipoprotein E (APOE) level as a consequence of CCH. Therefore, the change in APOE level was confirmed with Western blotting. The identified synaptic protein changes would precede the onset of dementia-like symptoms in the CCH model, suggesting their importance in the development of vascular dementia.
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Affiliation(s)
- Katalin Völgyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary.
| | - Péter Gulyássy
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Mihail Ivilinov Todorov
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary.,Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gina Puska
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Kata Badics
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Hlatky
- Preclinical Imaging and Biomarker Laboratory, Pharmacology and Drug Safety Research, Richter Gedeon Plc, Budapest, Hungary
| | - Katalin Adrienna Kékesi
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - Gabriella Nyitrai
- Preclinical Imaging and Biomarker Laboratory, Pharmacology and Drug Safety Research, Richter Gedeon Plc, Budapest, Hungary
| | - András Czurkó
- Preclinical Imaging and Biomarker Laboratory, Pharmacology and Drug Safety Research, Richter Gedeon Plc, Budapest, Hungary
| | - László Drahos
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Arpád Dobolyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary
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Wilkins HM, Koppel SJ, Bothwell R, Mahnken J, Burns JM, Swerdlow RH. Platelet cytochrome oxidase and citrate synthase activities in APOE ε4 carrier and non-carrier Alzheimer's disease patients. Redox Biol 2017; 12:828-832. [PMID: 28448944 PMCID: PMC5406545 DOI: 10.1016/j.redox.2017.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 11/12/2022] Open
Abstract
A degradation product of APOE ε4-encoded apolipoprotein E protein targets mitochondria and inhibits cytochrome oxidase (COX), and autopsy brains from young adult APOE ε4 carriers show reduced COX activity. To further explore relationships between APOE alleles and COX, we measured platelet mitochondria COX activity in AD subjects with (n=8) and without (n=7) an APOE ε4 allele and found the mean COX activity, when normalized to sample total protein, was lower in the APOE ε4 carriers (p<0.05). Normalizing COX activity to citrate synthase (CS) activity eliminated this difference, but notably the mean CS activity was itself lower in the APOE ε4 carriers (p<0.05). COX and CS protein levels did not appear to cause the lower APOE ε4 carrier COX and CS Vmax activities. If confirmed in larger studies, these data could suggest mitochondria at least partly mediate the well-recognized association between APOE alleles and AD risk. Platelet mitochondria from APOE ε4 carrier AD subjects have lower COX activity. Platelet mitochondria from APOE ε4 carrier AD subjects have lower CS activity. CS and COX protein expression were equivalent between groups.
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Affiliation(s)
- Heather M Wilkins
- Department of Neurology University of Kansas Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Scott J Koppel
- Department of Neurology University of Kansas Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Rebecca Bothwell
- University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Jonathan Mahnken
- University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Jeffrey M Burns
- Department of Neurology University of Kansas Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Russell H Swerdlow
- Department of Neurology University of Kansas Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease 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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49
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Larsen PA, Lutz MW, Hunnicutt KE, Mihovilovic M, Saunders AM, Yoder AD, Roses AD. The Alu neurodegeneration hypothesis: A primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease. Alzheimers Dement 2017; 13:828-838. [PMID: 28242298 PMCID: PMC6647845 DOI: 10.1016/j.jalz.2017.01.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/12/2017] [Accepted: 01/24/2017] [Indexed: 01/13/2023]
Abstract
It is hypothesized that retrotransposons have played a fundamental role in primate evolution and that enhanced neurologic retrotransposon activity in humans may underlie the origin of higher cognitive function. As a potential consequence of this enhanced activity, it is likely that neurons are susceptible to deleterious retrotransposon pathways that can disrupt mitochondrial function. An example is observed in the TOMM40 gene, encoding a β-barrel protein critical for mitochondrial preprotein transport. Primate-specific Alu retrotransposons have repeatedly inserted into TOMM40 introns, and at least one variant associated with late-onset Alzheimer’s disease originated from an Alu insertion event. We provide evidence of enriched Alu content in mitochondrial genes and postulate that Alus can disrupt mitochondrial populations in neurons, thereby setting the stage for progressive neurologic dysfunction. This Alu neurodegeneration hypothesis is compatible with decades of research and offers a plausible mechanism for the disruption of neuronal mitochondrial homeostasis, ultimately cascading into neurodegenerative disease.
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Affiliation(s)
- Peter A Larsen
- Department of Biology, Duke University, Durham, NC, USA.
| | - Michael W Lutz
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | | | - Mirta Mihovilovic
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Ann M Saunders
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA; Duke Lemur Center, Duke University, Durham, NC, USA
| | - Allen D Roses
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA; Zinfandel Pharmaceuticals, Inc, Durham, NC, USA
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50
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Chiba-Falek O, Lutz MW. Towards precision medicine in Alzheimer's disease: deciphering genetic data to establish informative biomarkers. Expert Rev Precis Med Drug Dev 2017; 2:47-55. [PMID: 28944295 DOI: 10.1080/23808993.2017.1286227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Developing biomarker tools for identification of individuals at high-risk for late-onset Alzheimer's disease (LOAD) is important for prognosis and early treatment. This review focuses on genetic factors and their potential role for precision medicine in LOAD. AREAS COVERED APOEe4 is the strongest genetic risk factor for non-Mendelian LOAD, and the APOE-linkage disequilibrium (LD) region has produced the most significant association signal in multi-center genome-wide-association-studies (GWAS). Consideration of extended haplotypes in the APOE-LD region and specifically, non-coding variants in putative enhancer elements, such as the TOMM40-polyT, in-addition to the coding variants that comprise the APOE-genotypes, may be useful for predicting subjects at high-risk of developing LOAD and estimating age-of-onset of early disease-stage symptoms. A genetic-biomarker based on APOE-TOMM40-polyT haplotypes, and age is currently applied in a clinical trial for prevention/delay of LOAD onset. Additionally, we discuss LOAD-GWAS discoveries and the development of new genetic risk scores based on LOAD-GWAS findings other than the APOE-LD region. EXPERT COMMENTARY Deciphering the precise causal genetic-variants within LOAD-GWAS regions will advance the development of genetic-biomarkers to complement and refine the APOE-LD region based prediction model. Collectively, the genetic-biomarkers will be translational for early diagnosis and enrichment of clinical trials with subjects at high-risk.
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Affiliation(s)
- Ornit Chiba-Falek
- 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
| | - Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
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