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de Ávila C, Suazo C, Nolz J, Nicholas Cochran J, Wang Q, Velazquez R, Dammer E, Readhead B, Mastroeni D. Reduced PIN1 expression in neocortical and limbic brain regions in female Alzheimer's patients correlates with cognitive and neuropathological phenotypes. Neurobiol Aging 2024; 141:160-170. [PMID: 38964013 DOI: 10.1016/j.neurobiolaging.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 06/19/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Women have a higher incidence of Alzheimer's disease (AD), even after adjusting for increased longevity. Thus, there is an urgent need to identify genes that underpin sex-associated risk of AD. PIN1 is a key regulator of the tau phosphorylation signaling pathway; however, potential differences in PIN1 expression, in males and females, are still unknown. We analyzed brain transcriptomic datasets focusing on sex differences in PIN1 mRNA levels in an aging and AD cohort, which revealed reduced PIN1 levels primarily within females. We validated this observation in an independent dataset (ROS/MAP), which also revealed that PIN1 is negatively correlated with multiregional neurofibrillary tangle density and global cognitive function in females only. Additional analysis revealed a decrease in PIN1 in subjects with mild cognitive impairment (MCI) compared with aged individuals, again driven predominantly by female subjects. Histochemical analysis of PIN1 in AD and control male and female neocortex revealed an overall decrease in axonal PIN1 protein levels in females. These findings emphasize the importance of considering sex differences in AD research.
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Affiliation(s)
- Camila de Ávila
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Crystal Suazo
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jennifer Nolz
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Ramon Velazquez
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Eric Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Benjamin Readhead
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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Rezaie N, Rebboah E, Williams BA, Liang HY, Reese F, Balderrama-Gutierrez G, Dionne LA, Reinholdt L, Trout D, Wold BJ, Mortazavi A. Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582178. [PMID: 38464087 PMCID: PMC10925135 DOI: 10.1101/2024.02.26.582178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each cell that can be altered by disease progression as well as genetic background. The identification of these active cellular programs is an open challenge in the analysis of single-cell RNA-seq data. Latent Dirichlet Allocation (LDA) is a generative method used to identify recurring patterns in counts data, commonly referred to as topics that can be used to interpret the state of each cell. However, LDA's interpretability is hindered by several key factors including the hyperparameter selection of the number of topics as well as the variability in topic definitions due to random initialization. We developed Topyfic, a Reproducible LDA (rLDA) package, to accurately infer the identity and activity of cellular programs in single-cell data, providing insights into the relative contributions of each program in individual cells. We apply Topyfic to brain single-cell and single-nucleus datasets of two 5xFAD mouse models of Alzheimer's disease crossed with C57BL6/J or CAST/EiJ mice to identify distinct cell types and states in different cell types such as microglia. We find that 8-month 5xFAD/Cast F1 males show higher level of microglial activation than matching 5xFAD/BL6 F1 males, whereas female mice show similar levels of microglial activation. We show that regulatory genes such as TFs, microRNA host genes, and chromatin regulatory genes alone capture cell types and cell states. Our study highlights how topic modeling with a limited vocabulary of regulatory genes can identify gene expression programs in single-cell data in order to quantify similar and divergent cell states in distinct genotypes.
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Affiliation(s)
- Narges Rezaie
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Elisabeth Rebboah
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Brian A Williams
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Heidi Yahan Liang
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | | | | | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
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Mehmood A, Song S, Du X, Yan H, Wang X, Guo L, Li B. mRNA expression profile reveals differentially expressed genes in splenocytes of experimental autoimmune encephalomyelitis model. Int J Exp Pathol 2023; 104:247-257. [PMID: 37427716 PMCID: PMC10500171 DOI: 10.1111/iep.12488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/04/2023] [Accepted: 06/18/2023] [Indexed: 07/11/2023] Open
Abstract
Experimental autoimmune encephalomyelitis (EAE) is a mouse model that can be used to investigate aetiology, pathogenesis, and treatment approaches for multiple sclerosis (MS). A novel integrated bioinformatics approach was used to understand the involvement of differentially expressed genes (DEGs) in the spleen of EAE mice through data mining of existing microarray and RNA-seq datasets. We screened differentially expressed mRNAs using mRNA expression profile data of EAE spleens taken from Gene Expression Omnibus (GEO). Functional and pathway enrichment analyses of DEGs were performed by Database for Annotation, Visualization, and Integrated Discovery (DAVID). Subsequently, the DEGs-encoded protein-protein interaction (PPI) network was constructed. The 784 DEGs in GSE99300 A.SW PP-EAE mice spleen mRNA profiles, 859 DEGs in GSE151701 EAE mice spleen mRNA profiles, and 646 DEGs in GSE99300 SJL/J PP-EAE mice spleen mRNA profiles were explored. Functional enrichment of 55 common DEGs among 3 sub-datasets revealed several immune-related terms, such as neutrophil extravasation, leucocyte migration, antimicrobial humoral immune response mediated by an antimicrobial peptide, toll-like receptor 4 bindings, IL-17 signalling pathway, and TGF-beta signalling pathway. In the screening of 10 hub genes, including MPO, ELANE, CTSG, LTF, LCN2, SELP, CAMP, S100A9, ITGA2B, and PRTN3, and in choosing and validating the 5 DEGs, including ANK1, MBOAT2, SLC25A21, SLC43A1, and SOX6, the results showed that SLC43A1 and SOX6 were significantly decreased in EAE mice spleen. Thus this study offers a list of genes expressed in the spleen that might play a key role in the pathogenesis of EAE.
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Affiliation(s)
- Arshad Mehmood
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Shuang Song
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Xiaochen Du
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Hongjing Yan
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Xuan Wang
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Li Guo
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
| | - Bin Li
- Department of NeurologyThe Second Hospital of Hebei Medical UniversityShijiazhuangHebeiChina
- Key Laboratory of Neurology of Hebei ProvinceShijiazhuangHebeiChina
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4
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de Ávila C, Suazo C, Nolz J, Cochran JN, Wang Q, Velazquez R, Dammer E, Readhead B, Mastroeni D. Reduced PIN1 gene expression in neocortical and limbic brain regions in female Alzheimer's patients correlates with cognitive and neuropathological phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553279. [PMID: 37645898 PMCID: PMC10462057 DOI: 10.1101/2023.08.14.553279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Women have a higher incidence of Alzheimer's disease (AD), even after adjusting for increased longevity. Thus, there is an urgent need to identify the molecular networks that underpin the sex-associated risk of AD. Recent efforts have identified PIN1 as a key regulator of tau phosphorylation signaling pathway. Pin1 is the only gene, to date, that when deleted can cause both tau and Aβ-related pathologies in an age-dependent manner. We analyzed multiple brain transcriptomic datasets focusing on sex differences in PIN1 mRNA levels, in an aging and AD cohort, which revealed reduced PIN1 levels driven by females. Then, we validated this observation in an independent dataset (ROS/MAP) which also revealed that PIN1 is negatively correlated with multiregional neurofibrillary tangle density and global cognitive function, in females only. Additional analysis revealed a decrease in PIN1 in subjects with mild cognitive impairment (MCI) compared with aged individuals, again, driven predominantly by female subjects. Our results show that while both male and female AD patients show decreased PIN1 expression, changes occur before the onset of clinical symptoms of AD in females and correlate to early events associated with AD risk (e.g., synaptic dysfunction). These changes are specific to neurons, and may be a potential prognostic marker to assess AD risk in the aging population and even more so in AD females with increased risk of AD.
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Affiliation(s)
- Camila de Ávila
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Crystal Suazo
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Jennifer Nolz
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - J. Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Ramon Velazquez
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Eric Dammer
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Benjamin Readhead
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
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Piras IS, Brokaw D, Kong Y, Weisenberger DJ, Krate J, Delvaux E, Mahurkar S, Blattler A, Siegmund KD, Sue L, Serrano GE, Beach TG, Laird PW, Huentelman MJ, Coleman PD. Integrated DNA Methylation/RNA Profiling in Middle Temporal Gyrus of Alzheimer's Disease. Cell Mol Neurobiol 2023:10.1007/s10571-022-01307-3. [PMID: 36596913 DOI: 10.1007/s10571-022-01307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/08/2022] [Indexed: 01/05/2023]
Abstract
Alzheimer's disease is a neurodegenerative disorder clinically defined by gradual cognitive impairment and alteration in executive function. We conducted an epigenome-wide association study (EWAS) of a clinically and neuropathologically characterized cohort of 296 brains, including Alzheimer's disease (AD) and non-demented controls (ND), exploring the relationship with the RNA expression from matched donors. We detected 5246 CpGs and 832 regions differentially methylated, finding overlap with previous EWAS but also new associations. CpGs previously identified in ANK1, MYOC, and RHBDF2 were differentially methylated, and one of our top hits (GPR56) was not previously detected. ANK1 was differentially methylated at the region level, along with APOE and RHBDF2. Only a small number of genes showed a correlation between DNA methylation and RNA expression statistically significant. Multiblock partial least-squares discriminant analysis showed several CpG sites and RNAs discriminating AD and ND (AUC = 0.908) and strongly correlated with each other. Furthermore, the CpG site cg25038311 was negatively correlated with the expression of 22 genes. Finally, with the functional epigenetic module analysis, we identified a protein-protein network characterized by inverse RNA/DNA methylation correlation and enriched for "Regulation of insulin-like growth factor transport", with IGF1 as the hub gene. Our results confirm and extend the previous EWAS, providing new information about a brain region not previously explored in AD DNA methylation studies. The relationship between DNA methylation and gene expression is not significant for most of the genes in our sample, consistently with the complexities in the gene expression regulation.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Danielle Brokaw
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Yinfei Kong
- Department of Information Systems and Decision Sciences, California State University Fullerton, Fullerton, CA, 92831, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Biology, University of South California, Los Angeles, CA, 90033, USA
| | - Jonida Krate
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
- UnityPoint Clinic, Waterloo, IA, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Swapna Mahurkar
- UCLA Division of Digestive Diseases, University of California, Los Angeles, CA, 90024, USA
| | - Adam Blattler
- Department of Biochemistry and Molecular Biology, University of South California, Los Angeles, CA, 90033, USA
- Genetics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Kimberly D Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089-9175, USA
| | - Lucia Sue
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Geidy E Serrano
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Paul D Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287, USA.
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6
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Polanco JC, Akimov Y, Fernandes A, Briner A, Hand GR, van Roijen M, Balistreri G, Götz J. CRISPRi screening reveals regulators of tau pathology shared between exosomal and vesicle-free tau. Life Sci Alliance 2023; 6:6/1/e202201689. [PMID: 36316035 PMCID: PMC9622425 DOI: 10.26508/lsa.202201689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
The aggregation of the microtubule-associated protein tau is a defining feature of Alzheimer's disease and other tauopathies. Tau pathology is believed to be driven by free tau aggregates and tau carried within exosome-like extracellular vesicles, both of which propagate trans-synaptically and induce tau pathology in recipient neurons by a corrupting process of seeding. Here, we performed a genome-wide CRISPRi screen in tau biosensor cells and identified cellular regulators shared by both mechanisms of tau seeding. We identified ANKLE2, BANF1, NUSAP1, EIF1AD, and VPS18 as the top validated regulators that restrict tau aggregation initiated by both exosomal and vesicle-free tau seeds. None of our validated hits affected the uptake of either form of tau seeds, supporting the notion that they operate through a cell-autonomous mechanism downstream of the seed uptake. Lastly, validation studies with human brain tissue also revealed that several of the identified protein hits are down-regulated in the brains of Alzheimer's patients, suggesting that their decreased activity may be required for the emergence or progression of tau pathology in the human brain.
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Affiliation(s)
- Juan Carlos Polanco
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Avinash Fernandes
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Adam Briner
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Gabriel Rhys Hand
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | - Giuseppe Balistreri
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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7
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Wu CH, Tsai HP, Su YF, Tsai CY, Lu YY, Lin CL. 2-PMAP Ameliorates Cerebral Vasospasm and Brain Injury after Subarachnoid Hemorrhage by Regulating Neuro-Inflammation in Rats. Cells 2022; 11:242. [PMID: 35053358 PMCID: PMC8773560 DOI: 10.3390/cells11020242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
A subarachnoid hemorrhage (SAH), leading to severe disability and high fatality in survivors, is a devastating disease. Neuro-inflammation, a critical mechanism of cerebral vasospasm and brain injury from SAH, is tightly related to prognoses. Interestingly, studies indicate that 2-[(pyridine-2-ylmethyl)-amino]-phenol (2-PMAP) crosses the blood-brain barrier easily. Here, we investigated whether the vasodilatory and neuroprotective roles of 2-PMAP were observed in SAH rats. Rats were assigned to three groups: sham, SAH and SAH+2-PMAP. SAHs were induced by a cisterna magna injection. In the SAH+2-PMAP group, 5 mg/kg 2-PMAP was injected into the subarachnoid space before SAH induction. The administration of 2-PMAP markedly ameliorated cerebral vasospasm and decreased endothelial apoptosis 48 h after SAH. Meanwhile, 2-PMAP decreased the severity of neurological impairments and neuronal apoptosis after SAH. Furthermore, 2-PMAP decreased the activation of microglia and astrocytes, expressions of TLR-4 and p-NF-κB, inflammatory markers (TNF-α, IL-1β and IL-6) and reactive oxygen species. This study is the first to confirm that 2-PMAP has vasodilatory and neuroprotective effects in a rat model of SAH. Taken together, the experimental results indicate that 2-PMAP treatment attenuates neuro-inflammation, oxidative stress and cerebral vasospasm, in addition to ameliorating neurological deficits, and that these attenuating and ameliorating effects are conferred through the TLR-4/NF-κB pathway.
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Affiliation(s)
- Chieh-Hsin Wu
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; (C.-H.W.); (H.-P.T.); (Y.-F.S.); (C.-Y.T.)
- Department of Surgery, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Hung-Pei Tsai
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; (C.-H.W.); (H.-P.T.); (Y.-F.S.); (C.-Y.T.)
| | - Yu-Feng Su
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; (C.-H.W.); (H.-P.T.); (Y.-F.S.); (C.-Y.T.)
- Department of Surgery, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Cheng-Yu Tsai
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; (C.-H.W.); (H.-P.T.); (Y.-F.S.); (C.-Y.T.)
- Department of Surgery, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Ying-Yi Lu
- Department of Dermatology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Department of Health and Beauty, Shu-Zen Junior College of Medicine and Management, Kaohsiung 821, Taiwan
| | - Chih-Lung Lin
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan; (C.-H.W.); (H.-P.T.); (Y.-F.S.); (C.-Y.T.)
- Department of Surgery, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
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8
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Iatrou A, Clark EM, Wang Y. Nuclear dynamics and stress responses in Alzheimer's disease. Mol Neurodegener 2021; 16:65. [PMID: 34535174 PMCID: PMC8447732 DOI: 10.1186/s13024-021-00489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
In response to extracellular and intracellular stressors, the nucleus and nuclear compartments undergo distinct molecular changes to maintain cell homeostasis. In the context of Alzheimer’s disease, misfolded proteins and various cellular stressors lead to profound structural and molecular changes at the nucleus. This review summarizes recent research on nuclear alterations in AD development, from the nuclear envelope changes to chromatin and epigenetic regulation and then to common nuclear stress responses. Finally, we provide our thoughts on the importance of understanding cell-type-specific changes and identifying upstream causal events in AD pathogenesis and highlight novel sequencing and gene perturbation technologies to address those challenges.
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Affiliation(s)
- Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA
| | - Eric M Clark
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA.
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9
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Yuen SC, Liang X, Zhu H, Jia Y, Leung SW. Prediction of differentially expressed microRNAs in blood as potential biomarkers for Alzheimer's disease by meta-analysis and adaptive boosting ensemble learning. Alzheimers Res Ther 2021; 13:126. [PMID: 34243793 PMCID: PMC8272278 DOI: 10.1186/s13195-021-00862-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 06/17/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Blood circulating microRNAs that are specific for Alzheimer's disease (AD) can be identified from differentially expressed microRNAs (DEmiRNAs). However, non-reproducible and inconsistent reports of DEmiRNAs hinder biomarker development. The most reliable DEmiRNAs can be identified by meta-analysis. To enrich the pool of DEmiRNAs for potential AD biomarkers, we used a machine learning method called adaptive boosting for miRNA disease association (ABMDA) to identify eligible candidates that share similar characteristics with the DEmiRNAs identified from meta-analysis. This study aimed to identify blood circulating DEmiRNAs as potential AD biomarkers by augmenting meta-analysis with the ABMDA ensemble learning method. METHODS Studies on DEmiRNAs and their dysregulation states were corroborated with one another by meta-analysis based on a random-effects model. DEmiRNAs identified by meta-analysis were collected as positive examples of miRNA-AD pairs for ABMDA ensemble learning. ABMDA identified similar DEmiRNAs according to a set of predefined criteria. The biological significance of all resulting DEmiRNAs was determined by their target genes according to pathway enrichment analyses. The target genes common to both meta-analysis- and ABMDA-identified DEmiRNAs were collected to construct a network to investigate their biological functions. RESULTS A systematic database search found 7841 studies for an extensive meta-analysis, covering 54 independent comparisons of 47 differential miRNA expression studies, and identified 18 reliable DEmiRNAs. ABMDA ensemble learning was conducted based on the meta-analysis results and the Human MicroRNA Disease Database, which identified 10 additional AD-related DEmiRNAs. These 28 DEmiRNAs and their dysregulated pathways were related to neuroinflammation. The dysregulated pathway related to neuronal cell cycle re-entry (CCR) was the only statistically significant pathway of the ABMDA-identified DEmiRNAs. In the biological network constructed from 1865 common target genes of the identified DEmiRNAs, the multiple core ubiquitin-proteasome system, that is involved in neuroinflammation and CCR, was highly connected. CONCLUSION This study identified 28 DEmiRNAs as potential AD biomarkers in blood, by meta-analysis and ABMDA ensemble learning in tandem. The DEmiRNAs identified by meta-analysis and ABMDA were significantly related to neuroinflammation, and the ABMDA-identified DEmiRNAs were related to neuronal CCR.
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Affiliation(s)
- Sze Chung Yuen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Xiaonan Liang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Hongmei Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
| | - Yongliang Jia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078 Macao China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan China
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Siu-wai Leung
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, China
- Edinburgh Bayes Centre for AI Research in Shenzhen, College of Science and Engineering, University of Edinburgh, Edinburgh, Scotland, UK
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10
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Pellegrini C, Pirazzini C, Sala C, Sambati L, Yusipov I, Kalyakulina A, Ravaioli F, Kwiatkowska KM, Durso DF, Ivanchenko M, Monti D, Lodi R, Franceschi C, Cortelli P, Garagnani P, Bacalini MG. A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration. Front Aging Neurosci 2021; 13:639428. [PMID: 33790779 PMCID: PMC8006465 DOI: 10.3389/fnagi.2021.639428] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.
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Affiliation(s)
- Camilla Pellegrini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Katarzyna M. Kwiatkowska
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Danielle F. Durso
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Raffaele Lodi
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Applied Biomedical Research Center, Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy
- National Research Council of Italy Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” Unit of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Istituto di Ricovero e Cura a Carattere Scientifico Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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11
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Allegra A, Giarratana RM, Scola L, Balistreri CR. The close link between the fetal programming imprinting and neurodegeneration in adulthood: The key role of "hemogenic endothelium" programming. Mech Ageing Dev 2021; 195:111461. [PMID: 33600833 DOI: 10.1016/j.mad.2021.111461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
The research on neurodegenerative diseases (NeuroDegD) has been traditionally focused on later life stages. There is now an increasing evidence, that they may be programmed during early development. Here, we propose that NeuroDegD are the result of the complex process of imprinting on fetal hemogenic endothelium, from which the microglial cells make to origin. The central role of placenta and epigenetic mechanisms (methylation of DNA, histone modifications and regulation by non-coding RNAs) in mediating the short and long-term effects has been also described. Precisely, it reports their role in impacting plasticity and memory of microglial cells. In addition, we also underline the necessity of further studies for clearing all mechanisms involved and developing epigenetic methods for identifying potential targets as biomarkers, and for developing preventive measures. Such biomarkers might be used to identify individuals at risk to NeuroDegD. Finally, the sex dependence of fetal programming process has been discussed. It might justify the sex differences in the epidemiologic, imaging, biomarkers, and pathology studies of these pathologies. The discovery of related mechanisms might have important clinical implications in both the etiology of disorders and the management of pregnant women for encouraging healthy long-term outcomes for their children, and future generations. Impending research on the mechanisms related to transgenerational transmission of prenatal stress might consent the development and application of therapies and/or intervention strategies for these disorders in humans.
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Affiliation(s)
| | - Rosa Maria Giarratana
- Department of BioMedicine, Neuroscience, and Advanced Diagnostics (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Letizia Scola
- Department of BioMedicine, Neuroscience, and Advanced Diagnostics (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Carmela Rita Balistreri
- Department of BioMedicine, Neuroscience, and Advanced Diagnostics (Bi.N.D.), University of Palermo, Palermo, Italy.
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12
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Smith AR, Smith RG, Macdonald R, Marzi SJ, Burrage J, Troakes C, Al-Sarraj S, Mill J, Lunnon K. The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain. Future Sci OA 2021; 7:FSO665. [PMID: 33815817 PMCID: PMC8015672 DOI: 10.2144/fsoa-2020-0161] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/04/2020] [Indexed: 01/24/2023] Open
Abstract
Several epigenome-wide association studies of DNA methylation have highlighted altered DNA methylation in the ANK1 gene in Alzheimer's disease (AD) brain samples. However, no study has specifically examined ANK1 histone modifications in the disease. We use chromatin immunoprecipitation-qPCR to quantify tri-methylation at histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) in the ANK1 gene in entorhinal cortex from donors with high (n = 59) or low (n = 29) Alzheimer's disease pathology. We demonstrate decreased levels of H3K4me3, a marker of active gene transcription, with no change in H3K27me3, a marker of inactive genes. H3K4me3 is negatively correlated with DNA methylation in specific regions of the ANK1 gene. Our study suggests that the ANK1 gene shows altered epigenetic marks indicative of reduced gene activation in Alzheimer's disease.
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Affiliation(s)
- Adam R Smith
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Ruby Macdonald
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Sarah J Marzi
- The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
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13
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Lee S, Lee JH, Lee RH, Shin YP, Kim IW, Seo M, Kim MA, Hwang JS, Shin D, Lee HK. De novo assembly and functional annotation of the Red-striped golden stink bug (Poecilocoris lewisi) transcriptome. Gene 2020; 767:145188. [PMID: 33002574 DOI: 10.1016/j.gene.2020.145188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/25/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022]
Abstract
Insect antimicrobial peptides (AMPs) have a wide range of functions and potential applications, and have recently attracted attention as alternative foods and medicines for humans. Our study performed transcriptome analysis to explore the potential of the red-striped golden stink bug (Poecilocoris lewisi), and as a result, we have discovered new features of P. lewisi that have not been identified. Specifically, defensin found in P. lewisi is a well-known AMP and is expressed by various plants, animals and fungi for host defense. Moreover, the discovery of defensin in P. lewisi provides new research and important information. In this study, we identified AMP and related DEG in P. lewisi that are closely related to human disease and immune response. These findings will provide the basis and important information for future research on P. lewisi that has not yet been studied.
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Affiliation(s)
- Seokhyun Lee
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea.
| | - Joon Ha Lee
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea.
| | - Ra Ham Lee
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea.
| | - Yong Pyo Shin
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea.
| | - In-Woo Kim
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea.
| | - Minchul Seo
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea.
| | - Mi-Ae Kim
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea.
| | - Jae Sam Hwang
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea.
| | - Donghyun Shin
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Republic of Korea.
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14
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Brokaw DL, Piras IS, Mastroeni D, Weisenberger DJ, Nolz J, Delvaux E, Serrano GE, Beach TG, Huentelman MJ, Coleman PD. Cell death and survival pathways in Alzheimer's disease: an integrative hypothesis testing approach utilizing -omic data sets. Neurobiol Aging 2020; 95:15-25. [PMID: 32745806 DOI: 10.1016/j.neurobiolaging.2020.06.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/28/2020] [Accepted: 06/27/2020] [Indexed: 01/01/2023]
Abstract
Whether a cell lives or dies is controlled by an array of intercepting and dynamic molecular pathways. Although there is evidence of neuronal loss in Alzheimer's disease (AD) and multiple programmed cell death (PCD) pathways have been implicated in this process, there has been no comprehensive evaluation of the dominant pathway responsible for cell death in AD. Likewise, the relative dominance of survival and PCD pathways in AD remains unclear. Here, we present the results of hypothesis-driven bioinformatic analysis of PCD and survival pathway activation in paired methylation and expression data from the middle temporal gyrus (MTG) as well as expression from laser-captured cells from the MTG and hippocampus. The results not only indicate activation of cell death pathways in AD-of which apoptosis is responsible for the largest fraction of upregulated genes-but also of cell survival pathways. These results are indicative of a complex balance between survival and death pathways in AD that future studies should work to delineate at a single cell level.
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Affiliation(s)
- Danielle L Brokaw
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA.
| | - Ignazio S Piras
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ, USA
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | | | - Jennifer Nolz
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Elaine Delvaux
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Matthew J Huentelman
- Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ, USA
| | - Paul D Coleman
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
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15
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Piras IS, Bleul C, Talboom JS, De Both MD, Schrauwen I, Halliday G, Myers AJ, Serrano GE, Beach TG, Huentelman MJ. ESHRD: deconvolution of brain homogenate RNA expression data to identify cell-type-specific alterations in Alzheimer's disease. Aging (Albany NY) 2020; 12:4124-4162. [PMID: 32125278 PMCID: PMC7093163 DOI: 10.18632/aging.102840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022]
Abstract
Objective: We describe herein a bioinformatics approach that leverages gene expression data from brain homogenates to derive cell-type specific differential expression results. Results: We found that differentially expressed (DE) cell-specific genes were mostly identified as neuronal, microglial, or endothelial in origin. However, a large proportion (75.7%) was not attributable to specific cells due to the heterogeneity in expression among brain cell types. Neuronal DE genes were consistently downregulated and associated with synaptic and neuronal processes as described previously in the field thereby validating this approach. We detected several DE genes related to angiogenesis (endothelial cells) and proteoglycans (oligodendrocytes). Conclusions: We present a cost- and time-effective method exploiting brain homogenate DE data to obtain insights about cell-specific expression. Using this approach we identify novel findings in AD in endothelial cells and oligodendrocytes that were previously not reported. Methods: We derived an enrichment score for each gene using a publicly available RNA profiling database generated from seven different cell types isolated from mouse cerebral cortex. We then classified the differential expression results from 3 publicly accessible Late-Onset Alzheimer’s disease (AD) studies including seven different brain regions.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Christiane Bleul
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Joshua S Talboom
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Matthew D De Both
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Glenda Halliday
- The University of Sydney School of Medicine, Sydney, Camperdown NSW 2050, Australia
| | | | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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16
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Gris T, Laplante P, Thebault P, Cayrol R, Najjar A, Joannette-Pilon B, Brillant-Marquis F, Magro E, English SW, Lapointe R, Bojanowski M, Francoeur CL, Cailhier JF. Innate immunity activation in the early brain injury period following subarachnoid hemorrhage. J Neuroinflammation 2019; 16:253. [PMID: 31801576 PMCID: PMC6894125 DOI: 10.1186/s12974-019-1629-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/31/2019] [Indexed: 01/01/2023] Open
Abstract
Background Aneurysmal subarachnoid hemorrhage (SAH) is a catastrophic disease with devastating consequences, including a high mortality rate and severe disabilities among survivors. Inflammation is induced following SAH, but the exact role and phenotype of innate immune cells remain poorly characterized. We investigated the inflammatory components of the early brain injury in an animal model and in SAH patients. Method SAH was induced through injection of blood in the subarachnoid space of C57Bl/6 J wild-type mice. Prospective blood collections were obtained at 12 h, days 1, 2, and 7 to evaluate the systemic inflammatory consequences of SAH by flow cytometry and enzyme-linked immunosorbent-assay (ELISA). Brains were collected, enzymatically digested, or fixed to characterize infiltrating inflammatory cells and neuronal death using flow cytometry and immunofluorescence. Phenotypic evaluation was performed at day 7 using the holding time and footprint tests. We then compared the identified inflammatory proteins to the profiles obtained from the plasma of 13 human SAH patients. Results Following SAH, systemic IL-6 levels increased rapidly, whereas IL-10 levels were reduced. Neutrophils were increased both in the brain and in the blood reflecting local and peripheral inflammation following SAH. More intracerebral pro-inflammatory monocytes were found at early time points. Astrocyte and microglia activation were also increased, and mice had severe motor deficits, which were associated with an increase in the percentage of caspase-3-positive apoptotic neurons. Similarly, we found that IL-6 levels in patients were rapidly increased following SAH. ICAM-1, bFGF, IL-7, IL-12p40, and MCP-4 variations over time were different between SAH patients with good versus bad outcomes. Moreover, high levels of Flt-1 and VEGF at admission were associated with worse outcomes. Conclusion SAH induces an early intracerebral infiltration and peripheral activation of innate immune cells. Furthermore, microglia and astrocytic activation are present at later time points. Our human and mouse data illustrate that SAH is a systemic inflammatory disease and that immune cells represent potential therapeutic targets to help this population of patients in need of new treatments.
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Affiliation(s)
- Typhaine Gris
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada.,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Patrick Laplante
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada.,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Paméla Thebault
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada.,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Romain Cayrol
- Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 5e étage, 2900, Boulevard Édouard-Montpetit, Montreal, Quebec, Canada
| | - Ahmed Najjar
- Department of Surgery, Division of Neurosurgery, Centre Hospitalier de l'Université de Montréal (CHUM), 850 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Benjamin Joannette-Pilon
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada.,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Frédéric Brillant-Marquis
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada.,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Elsa Magro
- Neurosurgery Service of CHU Cavale Blanche, INSERM, Boulevard Tanguy Prigent, Finistère, 29200, Brest, Bretagne, France
| | - Shane W English
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Civic Campus, 1053 Carling Avenue, Ottawa, ON, K1Y 4E9, Canada.,Departments of Medicine (Critical Care) and School of Epidemiology and Public Health, Division of Critical Care, The Ottawa Hospital, University of Ottawa, Civic Campus, 1053 Carling Avenue, Ottawa, ON, K1Y 4E9, Canada
| | - Réjean Lapointe
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada.,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Michel Bojanowski
- Department of Surgery, Division of Neurosurgery, Centre Hospitalier de l'Université de Montréal (CHUM), 850 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada
| | - Charles L Francoeur
- Population Health and Optimal Health Practices Research Unit (Trauma-Emergency-Critical Care Medicine) and Department of Anesthesiology and Critical Care, CHU de Québec-Université Laval, (Hôpital de l'Enfant-Jésus), 1401, 18e rue, Room Z-204, Québec, G1J 1Z4, Canada
| | - Jean-François Cailhier
- Research Centre of Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada. .,CRCHUM and Montreal Cancer Institute, 900 rue St-Denis, Montreal, Quebec, H2X 0A9, Canada. .,Nephrology Division, CHUM and Department of Medicine, Université de Montréal, Montreal, Quebec, Canada.
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17
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Deng W, Xing C, David R, Mastroeni D, Ning M, Lo EH, Coleman PD. AmpliSeq Transcriptome of Laser Captured Neurons from Alzheimer Brain: Comparison of Single Cell Versus Neuron Pools. Aging Dis 2019; 10:1146-1158. [PMID: 31788328 PMCID: PMC6844587 DOI: 10.14336/ad.2019.0225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of dementia in older adults. However, the pathogenesis of AD remains to be fully understood and clinically effective treatments are lacking. Recent advances in single cell RNA sequencing offers an opportunity to characterize the heterogeneity of cell response and explore the molecular mechanism of complex diseases at a single cell level. Here, we present the application of the Ion AmpliSeq transcriptome approach to profile gene expression in single laser captured neurons as well as pooled 10 and 100 neurons from hippocampal CA1 of AD brains versus matching normal aged brains. Our results demonstrated the high sensitivity and high genome coverage of the AmpliSeq transcriptome in single cell sequencing. In addition to capturing the known changes related to AD, our data confirmed the diversity of neuronal profiles in AD brain, which allow the potential identification of single cell response that might be hidden in population analyses. Notably, we also revealed the extensive inhibition of olfactory signaling and confirmed the reduction of neurotransmitter receptors in AD hippocampus. We conclude that although single neuron data show more variance than data from 10 or 100 pooled neurons, single neuron data can be informative. These findings support the utility of the Ion AmpliSeq method for obtaining and analyzing gene expression data from single defined laser captured neurons.
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Affiliation(s)
- Wenjun Deng
- 1Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02192, USA.,2Clinical Proteomics Research Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Changhong Xing
- 1Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02192, USA.,3Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rob David
- 4Thermo-Fisher Scientific, Salem, MA 02114, USA
| | - Diego Mastroeni
- 5ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - MingMing Ning
- 1Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02192, USA.,2Clinical Proteomics Research Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Eng H Lo
- 1Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02192, USA
| | - Paul D Coleman
- 5ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
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18
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Higham JP, Malik BR, Buhl E, Dawson JM, Ogier AS, Lunnon K, Hodge JJL. Alzheimer's Disease Associated Genes Ankyrin and Tau Cause Shortened Lifespan and Memory Loss in Drosophila. Front Cell Neurosci 2019; 13:260. [PMID: 31244615 PMCID: PMC6581016 DOI: 10.3389/fncel.2019.00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia and is characterized by intracellular neurofibrillary tangles of hyperphosphorylated Tau, including the 0N4R isoform and accumulation of extracellular amyloid beta (Aβ) plaques. However, less than 5% of AD cases are familial, with many additional risk factors contributing to AD including aging, lifestyle, the environment and epigenetics. Recent epigenome-wide association studies (EWAS) of AD have identified a number of loci that are differentially methylated in the AD cortex. Indeed, hypermethylation and reduced expression of the Ankyrin 1 (ANK1) gene in AD has been reported in the cortex in numerous different post-mortem brain cohorts. Little is known about the normal function of ANK1 in the healthy brain, nor the role it may play in AD. We have generated Drosophila models to allow us to functionally characterize Drosophila Ank2, the ortholog of human ANK1 and to determine its interaction with human Tau and Aβ. We show expression of human Tau 0N4R or the oligomerizing Aβ 42 amino acid peptide caused shortened lifespan, degeneration, disrupted movement, memory loss, and decreased excitability of memory neurons with co-expression tending to make the pathology worse. We find that Drosophila with reduced neuronal Ank2 expression have shortened lifespan, reduced locomotion, reduced memory and reduced neuronal excitability similar to flies overexpressing either human Tau 0N4R or Aβ42. Therefore, we show that the mis-expression of Ank2 can drive disease relevant processes and phenocopy some features of AD. Therefore, we propose targeting human ANK1 may have therapeutic potential. This represents the first study to characterize an AD-relevant gene nominated from EWAS.
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Affiliation(s)
- James P. Higham
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Bilal R. Malik
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Edgar Buhl
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Jennifer M. Dawson
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Anna S. Ogier
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - James J. L. Hodge
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
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Semick SA, Bharadwaj RA, Collado-Torres L, Tao R, Shin JH, Deep-Soboslay A, Weiss JR, Weinberger DR, Hyde TM, Kleinman JE, Jaffe AE, Mattay VS. Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease. Acta Neuropathol 2019; 137:557-569. [PMID: 30712078 DOI: 10.1007/s00401-019-01966-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/09/2019] [Accepted: 01/22/2019] [Indexed: 12/14/2022]
Abstract
Late-onset Alzheimer's disease (AD) is a complex age-related neurodegenerative disorder that likely involves epigenetic factors. To better understand the epigenetic state associated with AD, we surveyed 420,852 DNA methylation (DNAm) sites from neurotypical controls (N = 49) and late-onset AD patients (N = 24) across four brain regions (hippocampus, entorhinal cortex, dorsolateral prefrontal cortex and cerebellum). We identified 858 sites with robust differential methylation collectively annotated to 772 possible genes (FDR < 5%, within 10 kb). These sites were overrepresented in AD genetic risk loci (p = 0.00655) and were enriched for changes during normal aging (p < 2.2 × 10-16), and nearby genes were enriched for processes related to cell-adhesion, immunity, and calcium homeostasis (FDR < 5%). To functionally validate these associations, we generated and analyzed corresponding transcriptome data to prioritize 130 genes within 10 kb of the differentially methylated sites. These 130 genes were differentially expressed between AD cases and controls and their expression was associated with nearby DNAm (p < 0.05). This integrated analysis implicates novel genes in Alzheimer's disease, such as ANKRD30B. These results highlight DNAm differences in Alzheimer's disease that have gene expression correlates, further implicating DNAm as an epigenetic mechanism underlying pathological molecular changes associated with AD. Furthermore, our framework illustrates the value of integrating epigenetic and transcriptomic data for understanding complex disease.
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Smith AR, Smith RG, Pishva E, Hannon E, Roubroeks JAY, Burrage J, Troakes C, Al-Sarraj S, Sloan C, Mill J, van den Hove DL, Lunnon K. Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer's disease. Clin Epigenetics 2019; 11:52. [PMID: 30898171 PMCID: PMC6429761 DOI: 10.1186/s13148-019-0636-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alzheimer's disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. Previous studies of DNA modifications in Alzheimer's disease have been unable to distinguish between DNA methylation and DNA hydroxymethylation. DNA hydroxymethylation has been shown to be enriched in the human brain, although its role in Alzheimer's disease has not yet been fully explored. Here, we utilize oxidative bisulfite conversion, in conjunction with the Illumina Infinium Human Methylation 450K microarray, to identify neuropathology-associated differential DNA methylation and DNA hydroxymethylation in the entorhinal cortex. RESULTS We identified one experiment-wide significant differentially methylated position residing in the WNT5B gene. Next, we investigated pathology-associated regions consisting of multiple adjacent loci. We identified one significant differentially hydroxymethylated region consisting of four probes spanning 104 bases in the FBXL16 gene. We also identified two significant differentially methylated regions: one consisting of two probes in a 93 base-pair region in the ANK1 gene and the other consisting of six probes in a 99-base pair region in the ARID5B gene. We also highlighted three regions that show alterations in unmodified cytosine: two probes in a 39-base pair region of ALLC, two probes in a 69-base pair region in JAG2, and the same six probes in ARID5B that were differentially methylated. Finally, we replicated significant ANK1 disease-associated hypermethylation and hypohydroxymethylation patterns across eight CpG sites in an extended 118-base pair region in an independent cohort using oxidative-bisulfite pyrosequencing. CONCLUSIONS Our study represents the first epigenome-wide association study of both DNA methylation and hydroxymethylation in Alzheimer's disease entorhinal cortex. We demonstrate that previous estimates of DNA hypermethylation in ANK1 in Alzheimer's disease were underestimates as it is confounded by hypohydroxymethylation.
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Affiliation(s)
- Adam R Smith
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Rebecca G Smith
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Ehsan Pishva
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Eilis Hannon
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Janou A Y Roubroeks
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Joe Burrage
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Claire Troakes
- Institute of Psychiatry, King's College London, London, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, King's College London, London, UK
| | - Carolyn Sloan
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
- Laboratory of Translational Neuroscience, Division of Molecular Psychiatry, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK.
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21
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Morris G, Berk M, Maes M, Puri BK. Could Alzheimer's Disease Originate in the Periphery and If So How So? Mol Neurobiol 2019; 56:406-434. [PMID: 29705945 PMCID: PMC6372984 DOI: 10.1007/s12035-018-1092-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022]
Abstract
The classical amyloid cascade model for Alzheimer's disease (AD) has been challenged by several findings. Here, an alternative molecular neurobiological model is proposed. It is shown that the presence of the APOE ε4 allele, altered miRNA expression and epigenetic dysregulation in the promoter region and exon 1 of TREM2, as well as ANK1 hypermethylation and altered levels of histone post-translational methylation leading to increased transcription of TNFA, could variously explain increased levels of peripheral and central inflammation found in AD. In particular, as a result of increased activity of triggering receptor expressed on myeloid cells 2 (TREM-2), the presence of the apolipoprotein E4 (ApoE4) isoform, and changes in ANK1 expression, with subsequent changes in miR-486 leading to altered levels of protein kinase B (Akt), mechanistic (previously mammalian) target of rapamycin (mTOR) and signal transducer and activator of transcription 3 (STAT3), all of which play major roles in microglial activation, proliferation and survival, there is activation of microglia, leading to the subsequent (further) production of cytokines, chemokines, nitric oxide, prostaglandins, reactive oxygen species, inducible nitric oxide synthase and cyclooxygenase-2, and other mediators of inflammation and neurotoxicity. These changes are associated with the development of amyloid and tau pathology, mitochondrial dysfunction (including impaired activity of the electron transport chain, depleted basal mitochondrial potential and oxidative damage to key tricarboxylic acid enzymes), synaptic dysfunction, altered glycogen synthase kinase-3 (GSK-3) activity, mTOR activation, impairment of autophagy, compromised ubiquitin-proteasome system, iron dyshomeostasis, changes in APP translation, amyloid plaque formation, tau hyperphosphorylation and neurofibrillary tangle formation.
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Affiliation(s)
- Gerwyn Morris
- IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Deakin University, P.O. Box 291, Geelong, Victoria, Australia
| | - Michael Berk
- IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Deakin University, P.O. Box 291, Geelong, Victoria, Australia
- Department of Psychiatry, Level 1 North, Main Block, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Florey Institute for Neuroscience and Mental Health, Kenneth Myer Building, University of Melbourne, 30 Royal Parade, Parkville, Victoria, Australia
- Orygen, The National Centre of Excellence in Youth Mental Health, 35 Poplar Rd, Parkville, Victoria, Australia
| | - Michael Maes
- IMPACT Strategic Research Centre, School of Medicine, Barwon Health, Deakin University, P.O. Box 291, Geelong, Victoria, Australia
- Department of Psychiatry, Chulalongkorn University, Bangkok, Thailand
| | - Basant K Puri
- Department of Medicine, Hammersmith Hospital, Imperial College London, London, UK.
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22
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Smith AR, Smith RG, Burrage J, Troakes C, Al-Sarraj S, Kalaria RN, Sloan C, Robinson AC, Mill J, Lunnon K. A cross-brain regions study of ANK1 DNA methylation in different neurodegenerative diseases. Neurobiol Aging 2018; 74:70-76. [PMID: 30439595 DOI: 10.1016/j.neurobiolaging.2018.09.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 07/11/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022]
Abstract
Recent epigenome-wide association studies in Alzheimer's disease have highlighted consistent robust neuropathology-associated DNA hypermethylation of the ankyrin 1 (ANK1) gene in the cortex. The extent to which altered ANK1 DNA methylation is also associated with other neurodegenerative diseases is not currently known. In the present study, we used bisulfite pyrosequencing to quantify DNA methylation across 8 CpG sites within a 118 bp region of the ANK1 gene across multiple brain regions in Alzheimer's disease, Vascular dementia, Dementia with Lewy bodies, Huntington's disease, and Parkinson's disease. We demonstrate disease-associated ANK1 hypermethylation in the entorhinal cortex in Alzheimer's disease, Huntington's disease, and Parkinson's disease, whereas in donors with Vascular dementia and Dementia with Lewy bodies, we observed elevated ANK1 DNA methylation only in individuals with coexisting Alzheimer's disease pathology. We did not observe any disease-associated differential ANK1 DNA methylation in the striatum in Huntington's disease or the substantia nigra in Parkinson's disease. Our data suggest that ANK1 is characterized by region and disease-specific differential DNA methylation in multiple neurodegenerative diseases.
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Affiliation(s)
- Adam R Smith
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | | | - Carolyn Sloan
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Andrew C Robinson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, University of Bristol, Exeter, UK.
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Kurochkina N, Bhaskar M, Yadav SP, Pant HC. Phosphorylation, Dephosphorylation, and Multiprotein Assemblies Regulate Dynamic Behavior of Neuronal Cytoskeleton: A Mini-Review. Front Mol Neurosci 2018; 11:373. [PMID: 30349458 PMCID: PMC6186834 DOI: 10.3389/fnmol.2018.00373] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/20/2018] [Indexed: 12/28/2022] Open
Abstract
Cellular localization, assembly and abnormal aggregation of neurofilaments depend on phosphorylation. Pathological processes associated with neurodegeneration exhibit aberrant accumulation of microtubule associated aggregated forms of hyperphosphorylated neuronal protein tau in cell bodies. These processes are critical for the disease progression in patients suffering from Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral Sclerosis. In healthy cells, tau is localized in axons. Topographic regulation suggests that whereas the sites of synthesis of kinases and neurofilaments are the cell bodies, and sites of their functional assemblies are axons, phosphorylation/dephosphorylation are the key processes that arrange the molecules at their precise locations. Phosphorylation sites in the dynamic developmental and degenerative processes differ. Not all these processes are well understood. New advancements identify epigenetic factors involved in AD which account for the influence of age-related environment/genome interactions leading to the disease. Progress in proteomics highlights previously found major proteins and adds more to the list of those involved in AD. New key elements of specificity provide determinants of molecular recognition important for the assembly of macromolecular complexes. In this review, we discuss aberrant spatial distribution of neuronal polypeptides observed in neuropathies: aggregation, association with proteins of the neuronal cytoskeleton, and phosphorylation dependent dynamics. Particularly, we emphasize recent advancements in understanding the function and determinants of specific association of molecules involved in Alzheimer's disease with respect to the topographic regulation of phosphorylation in neuronal cytoskeleton and implications for the design of new therapies. Further, we address the role of various filament systems in maintenance of the shape, rigidity and dynamics of the cytoskeleton.
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Affiliation(s)
- Natalya Kurochkina
- Department of Biophysics, The School of Theoretical Modeling, Washington, DC, United States
| | - Manju Bhaskar
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sharda Prasad Yadav
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Harish C. Pant
- Neuronal Cytoskeletal Protein Regulation Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex. Epigenetics Chromatin 2018; 11:41. [PMID: 30045751 PMCID: PMC6058387 DOI: 10.1186/s13072-018-0211-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Background Epigenome-wide association studies (EWAS) based on human brain samples allow a deep and direct understanding of epigenetic dysregulation in Alzheimer’s disease (AD). However, strong variation of cell-type proportions across brain tissue samples represents a significant source of data noise. Here, we report the first EWAS based on sorted neuronal and non-neuronal (mostly glia) nuclei from postmortem human brain tissues. Results We show that cell sorting strongly enhances the robust detection of disease-related DNA methylation changes even in a relatively small cohort. We identify numerous genes with cell-type-specific methylation signatures and document differential methylation dynamics associated with aging specifically in neurons such as CLU, SYNJ2 and NCOR2 or in glia RAI1,CXXC5 and INPP5A. Further, we found neuron or glia-specific associations with AD Braak stage progression at genes such as MCF2L, ANK1, MAP2, LRRC8B, STK32C and S100B. A comparison of our study with previous tissue-based EWAS validates multiple AD-associated DNA methylation signals and additionally specifies their origin to neuron, e.g., HOXA3 or glia (ANK1). In a meta-analysis, we reveal two novel previously unrecognized methylation changes at the key AD risk genes APP and ADAM17. Conclusions Our data highlight the complex interplay between disease, age and cell-type-specific methylation changes in AD risk genes thus offering new perspectives for the validation and interpretation of large EWAS results. Electronic supplementary material The online version of this article (10.1186/s13072-018-0211-3) contains supplementary material, which is available to authorized users.
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Lardenoije R, Pishva E, Lunnon K, van den Hove DL. Neuroepigenetics of Aging and Age-Related Neurodegenerative Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:49-82. [PMID: 30072060 DOI: 10.1016/bs.pmbts.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current state of play for epigenetic research into neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. We focus on the recent evidence for a potential role of DNA modifications, histone modifications and non-coding RNA in the etiology of these disorders. Finally, we discuss how new technological and bioinformatics advances in the field of epigenetics could further progress our understanding about the underlying mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Roy Lardenoije
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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26
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Upregulation of histone deacetylase 2 in laser capture nigral microglia in Parkinson's disease. Neurobiol Aging 2018; 68:134-141. [PMID: 29803514 DOI: 10.1016/j.neurobiolaging.2018.02.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/19/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Histone deacetylase (HDAC) inhibitors have been widely reported to have considerable therapeutic potential in a host of neurodegenerative diseases. However, HDAC inhibitor selectivity and specificity in specific cell classes have been a source of much debate. To address the role of HDAC2 in specific cell classes, and in disease, we examined glial protein and mRNA levels in the substantia nigra (SN) of Parkinson's disease (PD) and normal controls (NCs) by immunohistochemistry and laser captured microdissection followed by quantitative real time polymerase chain reaction. Differential expression analysis in immunohistochemically defined laser capture microglia revealed significant upregulation of HDAC2 in the PD SN compared to NC subjects. Complementary in vivo evidence reveals significant upregulation of HDAC2 protein levels in PD SN microglia compared to NC subjects. Correspondingly, human immortalized telencephalic/mesencephalic microglial cells reveal significant upregulation of HDAC2 in the presence of the potent microglial activator lipopolysaccharide. These data provide evidence that selective inhibition of HDAC2 in PD SN microglia could be a promising approach to treat microglial-initiated nigral dopaminergic neuronal cell loss in PD.
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27
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Mastroeni D, Nolz J, Khdour OM, Sekar S, Delvaux E, Cuyugan L, Liang WS, Hecht SM, Coleman PD. Oligomeric amyloid β preferentially targets neuronal and not glial mitochondrial-encoded mRNAs. Alzheimers Dement 2018; 14:775-786. [PMID: 29396107 DOI: 10.1016/j.jalz.2017.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/28/2017] [Accepted: 12/07/2017] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Our laboratories have demonstrated that accumulation of oligomeric amyloid β (OAβ) in neurons is an essential step leading to OAβ-mediated mitochondrial dysfunction. METHODS Alzheimer's disease (AD) and matching control hippocampal neurons, astrocytes, and microglia were isolated by laser-captured microdissection from the same subjects, followed by whole-transcriptome sequencing. Complementary in vitro work was performed in OAβ-treated differentiated SH-SY5Y, followed by the use of a novel CoQ10 analogue for protection. This compound is believed to be effective both in suppressing reactive oxygen species and also functioning in mitochondrial electron transport. RESULTS We report decreases in the same mitochondrial-encoded mRNAs in Alzheimer's disease laser-captured CA1 neurons and in OAβ-treated SH-SY5Y cells, but not in laser-captured microglia and astrocytes. Pretreatment with a novel CoQ10 analogue, protects neuronal mitochondria from OAβ-induced mitochondrial changes. DISCUSSION Similarity of expression changes in neurons from Alzheimer's disease brain and neuronal cells treated with OAβ, and the effect of a CoQ10 analogue on the latter, suggests a pretreatment option to prevent OAβ toxicity, long before the damage is apparent.
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Affiliation(s)
- Diego Mastroeni
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ.
| | - Jennifer Nolz
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ
| | - Omar M Khdour
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ
| | | | - Elaine Delvaux
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ
| | | | | | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, AZ
| | - Paul D Coleman
- ASU-Banner Biodesign Neurodegenerative Disease Research Center, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ
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28
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Correction: ANK1 is up-regulated in laser captured microglia in Alzheimer's brain; the importance of addressing cellular heterogeneity. PLoS One 2018; 13:e0191382. [PMID: 29324907 PMCID: PMC5764407 DOI: 10.1371/journal.pone.0191382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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29
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Lardenoije R, van den Hove DLA, Havermans M, van Casteren A, Le KX, Palmour R, Lemere CA, Rutten BPF. Age-related epigenetic changes in hippocampal subregions of four animal models of Alzheimer's disease. Mol Cell Neurosci 2018; 86:1-15. [PMID: 29113959 PMCID: PMC6863355 DOI: 10.1016/j.mcn.2017.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 10/18/2017] [Accepted: 11/02/2017] [Indexed: 12/20/2022] Open
Abstract
Both aging and Alzheimer's disease (AD) are associated with widespread epigenetic changes, with most evidence suggesting global hypomethylation in AD. It is, however, unclear how these age-related epigenetic changes are linked to molecular aberrations as expressed in animal models of AD. Here, we investigated age-related changes of epigenetic markers of DNA methylation and hydroxymethylation in a range of animal models of AD, and their correlations with amyloid plaque load. Three transgenic mouse models, including the J20, APP/PS1dE9 and 3xTg-AD models, as well as Caribbean vervets (a non-transgenic non-human primate model of AD) were investigated. In the J20 mouse model, an age-related decrease in DNA methylation was found in the dentate gyrus (DG) and a decrease in the ratio between DNA methylation and hydroxymethylation was found in the DG and cornu ammonis (CA) 3. In the 3xTg-AD mice, an age-related increase in DNA methylation was found in the DG and CA1-2. No significant age-related alterations were found in the APP/PS1dE9 mice and non-human primate model. In the J20 model, hippocampal plaque load showed a significant negative correlation with DNA methylation in the DG, and with the ratio a negative correlation in the DG and CA3. For the APP/PS1dE9 model a negative correlation between the ratio and plaque load was observed in the CA3, as well as a negative correlation between DNA methyltransferase 3A (DNMT3A) levels and plaque load in the DG and CA3. Thus, only the J20 model showed an age-related reduction in global DNA methylation, while DNA hypermethylation was observed in the 3xTg-AD model. Given these differences between animal models, future studies are needed to further elucidate the contribution of different AD-related genetic variation to age-related epigenetic changes.
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Affiliation(s)
- Roy Lardenoije
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, USA; School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, The Netherlands
| | - Daniël L A van den Hove
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, The Netherlands; Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Germany
| | - Monique Havermans
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, The Netherlands
| | - Anne van Casteren
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, The Netherlands
| | - Kevin X Le
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, USA
| | - Roberta Palmour
- Behavioral Science Foundation, Eastern Caribbean, Saint Kitts and Nevis; McGill University Faculty of Medicine, Montreal, Quebec, Canada
| | - Cynthia A Lemere
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, USA
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, The Netherlands.
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Mastroeni D, Nolz J, Sekar S, Delvaux E, Serrano G, Cuyugan L, Liang WS, Beach TG, Rogers J, Coleman PD. Laser-captured microglia in the Alzheimer's and Parkinson's brain reveal unique regional expression profiles and suggest a potential role for hepatitis B in the Alzheimer's brain. Neurobiol Aging 2017; 63:12-21. [PMID: 29207277 DOI: 10.1016/j.neurobiolaging.2017.10.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/02/2017] [Accepted: 10/22/2017] [Indexed: 01/24/2023]
Abstract
Expression array data from dozens of laboratories, including our own, show significant changes in expression of many genes in Alzheimer's disease (AD) patients compared with normal controls. These data typically rely on brain homogenates, and information about transcripts specific to microglia and other central nervous system (CNS) cell types, which far outnumber microglia-specific transcripts, is lost. We therefore used single-cell laser capture methods to assess the full range of microglia-specific expression changes that occur in different brain regions (substantia nigra and hippocampus CA1) and disease states (AD, Parkinson's disease, and normal controls). Two novel pathways, neuronal repair and viral processing were identified. Based on KEGG analysis (Kyoto Encyclopedia of Genes and Genomes, a collection of biological pathways), one of the most significant viruses was hepatitis B virus (HBV) (false discovery rate < 0.00000001). Immunohistochemical analysis using HBV-core antibody in HBV-positive control, amnestic mild cognitive impairment, and HBV-positive AD cases show increased HBV immunoreactivity as disease pathology increases. These results are the first, to our knowledge, to show regional differences in human microglia. In addition, these data reveal new functions for microglia and suggest a novel risk factor for AD.
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Affiliation(s)
- Diego Mastroeni
- Biodesign, ASU-Banner Biodesign Neurodegenerative Disease Research Center, School of Life Sciences, Arizona State University, Tempe, AZ, USA; Banner Sun Health Research Institute, Sun City, AZ, USA.
| | - Jennifer Nolz
- Biodesign, ASU-Banner Biodesign Neurodegenerative Disease Research Center, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Shobana Sekar
- Translational Genomics Institute, Phoenix, Arizona, USA
| | - Elaine Delvaux
- Biodesign, ASU-Banner Biodesign Neurodegenerative Disease Research Center, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Geidy Serrano
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Lori Cuyugan
- Translational Genomics Institute, Phoenix, Arizona, USA
| | | | | | | | - Paul D Coleman
- Biodesign, ASU-Banner Biodesign Neurodegenerative Disease Research Center, School of Life Sciences, Arizona State University, Tempe, AZ, USA; Banner Sun Health Research Institute, Sun City, AZ, USA
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