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Diany R, Gagliano Taliun SA. Systematic Review and Phenome-Wide Scans of Genetic Associations with Vascular Cognitive Impairment. Adv Biol (Weinh) 2024:e2300692. [PMID: 38935518 DOI: 10.1002/adbi.202300692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/12/2024] [Indexed: 06/29/2024]
Abstract
Vascular cognitive impairment (VCI) is a heterogenous form of cognitive impairment that results from cerebrovascular disease. It is a result of both genetic and non-genetic factors. Although much research has been conducted on the genetic contributors to other forms of cognitive impairment (e.g. Alzheimer's disease), knowledge is lacking on the genetic factors associated with VCI. A better understanding of the genetics of VCI will be critical for prevention and treatment. To begin to fill this gap, the genetic contributors are reviewed with VCI from the literature. Phenome-wide scans of the identified genes are conducted and genetic variants identified in the review in large-scale resources displaying genetic variant-trait association information. Gene set are also carried out enrichment analysis using the genes identified from the review. Thirty one articles are identified meeting the search criteria and filters, from which 107 unique protein-coding genes are noted related to VCI. The phenome-wide scans and gene set enrichment analysis identify pathways associated with a diverse set of biological systems. This results indicate that genes with evidence of involvement in VCI are involved in a diverse set of biological functions. This information can facilitate downstream research to better dissect possible shared biological mechanisms for future therapies.
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Affiliation(s)
- Rime Diany
- Faculty of Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3C 3J7, Canada
| | - Sarah A Gagliano Taliun
- Department of Medicine & Department of Neurosciences, Faculty of Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec, H3C 3J7, Canada
- Montreal Heart Institute, 5000 rue Bélanger, Montréal, Québec, H1T 1C8, Canada
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2
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Eysert F, Kinoshita PF, Lagarde J, Lacas-Gervais S, Xicota L, Dorothée G, Bottlaender M, Checler F, Potier MC, Sarazin M, Chami M. Mitochondrial alterations in fibroblasts from sporadic Alzheimer's disease (AD) patients correlate with AD-related clinical hallmarks. Acta Neuropathol Commun 2024; 12:90. [PMID: 38851733 PMCID: PMC11161956 DOI: 10.1186/s40478-024-01807-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
Mitochondrial dysfunctions are key features of Alzheimer's disease (AD). The occurrence of these disturbances in the peripheral cells of AD patients and their potential correlation with disease progression are underinvestigated. We studied mitochondrial structure, function and mitophagy in fibroblasts from healthy volunteers and AD patients at the prodromal (AD-MCI) or demented (AD-D) stages. We carried out correlation studies with clinical cognitive scores, namely, (i) Mini-Mental State Examination (MMSE) and (ii) Dementia Rating-Scale Sum of Boxes (CDR-SOB), and with (iii) amyloid beta (Aβ) plaque burden (PiB-PET imaging) and (iv) the accumulation of peripheral amyloid precursor protein C-terminal fragments (APP-CTFs). We revealed alterations in mitochondrial structure as well as specific mitochondrial dysfunction signatures in AD-MCI and AD-D fibroblasts and revealed that defective mitophagy and autophagy are linked to impaired lysosomal activity in AD-D fibroblasts. We reported significant correlations of a subset of these dysfunctions with cognitive decline, AD-related clinical hallmarks and peripheral APP-CTFs accumulation. This study emphasizes the potential use of peripheral cells for investigating AD pathophysiology.
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Affiliation(s)
- Fanny Eysert
- INSERM, CNRS, Institute of Molecular and Cellular Pharmacology, Laboratory of Excellence DistALZ, Université Côte d'Azur, 660 Route des Lucioles, 06560, Sophia-Antipolis, Valbonne, France
| | - Paula-Fernanda Kinoshita
- INSERM, CNRS, Institute of Molecular and Cellular Pharmacology, Laboratory of Excellence DistALZ, Université Côte d'Azur, 660 Route des Lucioles, 06560, Sophia-Antipolis, Valbonne, France
| | - Julien Lagarde
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, 75014, Paris, France
- Université Paris-Cité, 75006, Paris, France
- BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, Université Paris-Saclay, 91401, Orsay, France
| | - Sandra Lacas-Gervais
- Centre Commun de Microscopie Appliquée, Université de Nice Côte d'Azur, 06108, Nice, France
| | - Laura Xicota
- UPMC University Paris 06, UMRS 1127, Sorbonne Universités, Paris, France
- ICM Research Center, CNRS UMR 7225, Paris, France
| | - Guillaume Dorothée
- Inserm, Centre de Recherche Saint-Antoine, CRSA, Immune System and Neuroinflammation Laboratory, Hôpital Saint-Antoine, Sorbonne Université, 75012, Paris, France
| | - Michel Bottlaender
- BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, Université Paris-Saclay, 91401, Orsay, France
- UNIACT, Neurospin, Joliot Institute, CEA, Université Paris-Saclay, 91140, Gif sur Yvette, France
| | - Frédéric Checler
- INSERM, CNRS, Institute of Molecular and Cellular Pharmacology, Laboratory of Excellence DistALZ, Université Côte d'Azur, 660 Route des Lucioles, 06560, Sophia-Antipolis, Valbonne, France
| | - Marie-Claude Potier
- UPMC University Paris 06, UMRS 1127, Sorbonne Universités, Paris, France
- ICM Research Center, CNRS UMR 7225, Paris, France
| | - Marie Sarazin
- Department of Neurology of Memory and Language, GHU Paris Psychiatrie & Neurosciences, Hôpital Sainte Anne, 75014, Paris, France
- Université Paris-Cité, 75006, Paris, France
- BioMaps, Service Hospitalier Frédéric Joliot CEA, CNRS, Inserm, Université Paris-Saclay, 91401, Orsay, France
| | - Mounia Chami
- INSERM, CNRS, Institute of Molecular and Cellular Pharmacology, Laboratory of Excellence DistALZ, Université Côte d'Azur, 660 Route des Lucioles, 06560, Sophia-Antipolis, Valbonne, France.
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Huang YH, Chen YC, Ho WM, Lee RG, Chung RH, Liu YL, Chang PY, Chang SC, Wang CW, Chung WH, Tsai SJ, Kuo PH, Lee YS, Hsiao CC. Classifying Alzheimer's disease and normal subjects using machine learning techniques and genetic-environmental features. J Formos Med Assoc 2024; 123:701-709. [PMID: 38044212 DOI: 10.1016/j.jfma.2023.10.021] [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: 06/01/2023] [Revised: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is complicated by multiple environmental and polygenetic factors. The accuracy of artificial neural networks (ANNs) incorporating the common factors for identifying AD has not been evaluated. METHODS A total of 184 probable AD patients and 3773 healthy individuals aged 65 and over were enrolled. AD-related genes (51 SNPs) and 8 environmental factors were selected as features for multilayer ANN modeling. Random Forest (RF) and Support Vector Machine with RBF kernel (SVM) were also employed for comparison. Model results were verified using traditional statistics. RESULTS The ANN achieved high accuracy (0.98), sensitivity (0.95), and specificity (0.96) in the intrinsic test for AD classification. Excluding age and genetic data still yielded favorable results (accuracy: 0.97, sensitivity: 0.94, specificity: 0.96). The assigned weights to ANN features highlighted the importance of mental evaluation, years of education, and specific genetic variations (CASS4 rs7274581, PICALM rs3851179, and TOMM40 rs2075650) for AD classification. Receiver operating characteristic analysis revealed AUC values of 0.99 (intrinsic test), 0.60 (TWB-GWA), and 0.72 (CG-WGS), with slightly lower AUC values (0.96, 0.80, 0.52) when excluding age in ANN. The performance of the ANN model in AD classification was comparable to RF, SVM (linear kernel), and SVM (RBF kernel). CONCLUSION The ANN model demonstrated good sensitivity, specificity, and accuracy in AD classification. The top-weighted SNPs for AD prediction were CASS4 rs7274581, PICALM rs3851179, and TOMM40 rs2075650. The ANN model performed similarly to RF and SVM, indicating its capability to handle the complexity of AD as a disease entity.
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Affiliation(s)
- Yu-Hua Huang
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Yi-Chun Chen
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Wei-Min Ho
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Ren-Guey Lee
- Department of Electronics Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Chaung-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan; Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
| | - Chun-Chieh Hsiao
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan; Department of Computer Information and Network Engineering, Lunghwa University of Science and Technology, Taoyuan, Taiwan.
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4
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Seo H, Brand L, Wang H. Learning semi-supervised enrichment of longitudinal imaging-genetic data for improved prediction of cognitive decline. BMC Med Inform Decis Mak 2024; 24:61. [PMID: 38807132 PMCID: PMC11134626 DOI: 10.1186/s12911-024-02455-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/05/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Alzheimer's Disease (AD) is a progressive memory disorder that causes irreversible cognitive decline. Given that there is currently no cure, it is critical to detect AD in its early stage during the disease progression. Recently, many statistical learning methods have been presented to identify cognitive decline with temporal data, but few of these methods integrate heterogeneous phenotype and genetic information together to improve the accuracy of prediction. In addition, many of these models are often unable to handle incomplete temporal data; this often manifests itself in the removal of records to ensure consistency in the number of records across participants. RESULTS To address these issues, in this work we propose a novel approach to integrate the genetic data and the longitudinal phenotype data to learn a fixed-length "enriched" biomarker representation derived from the temporal heterogeneous neuroimaging records. Armed with this enriched representation, as a fixed-length vector per participant, conventional machine learning models can be used to predict clinical outcomes associated with AD. CONCLUSION The proposed method shows improved prediction performance when applied to data derived from Alzheimer's Disease Neruoimaging Initiative cohort. In addition, our approach can be easily interpreted to allow for the identification and validation of biomarkers associated with cognitive decline.
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Affiliation(s)
- Hoon Seo
- Department of Computer Science, Colorado School of Mines, Golden, Colorado, 80401, USA
| | - Lodewijk Brand
- Department of Computer Science, Colorado School of Mines, Golden, Colorado, 80401, USA
| | - Hua Wang
- Department of Computer Science, Colorado School of Mines, Golden, Colorado, 80401, USA.
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5
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Dilliott AA, Costanzo MC, Burtt NP, Bandres-Ciga S, Blauwendraat C, Casey B, Hoang Q, Iwaki H, Jang D, Kim JJ, Leonard HL, Levine KS, Makarious M, Nguyen TT, Rouleau GA, Singleton AB, Smadbeck P, Solle J, Vitale D, Nalls MA, Flannick J, Farhan SM. The Neurodegenerative Disease Knowledge Portal: Propelling Discovery Through the Sharing of Neurodegenerative Disease Genomic Resources. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.27.24307990. [PMID: 38853922 PMCID: PMC11160810 DOI: 10.1101/2024.05.27.24307990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Although large-scale genetic association studies have proven opportunistic for the delineation of neurodegenerative disease processes, we still lack a full understanding of the pathological mechanisms of these diseases, resulting in few appropriate treatment options and diagnostic challenges. To mitigate these gaps, the Neurodegenerative Disease Knowledge Portal (NDKP) was created as an open-science initiative with the aim to aggregate, enable analysis, and display all available genomic datasets of neurodegenerative disease, while protecting the integrity and confidentiality of the underlying datasets. The portal contains 218 genomic datasets, including genotyping and sequencing studies, of individuals across ten different phenotypic groups, including neurological conditions such as Alzheimer's disease, amyotrophic lateral sclerosis, Lewy body dementia, and Parkinson's disease. In addition to securely hosting large genomic datasets, the NDKP provides accessible workflows and tools to effectively utilize the datasets and assist in the facilitation of customized genomic analyses. Here, we summarize the genomic datasets currently included within the portal, the bioinformatics processing of the datasets, and the variety of phenotypes captured. We also present example use-cases of the various user interfaces and integrated analytic tools to demonstrate their extensive utility in enabling the extraction of high-quality results at the source, for both genomics experts and those in other disciplines. Overall, the NDKP promotes open-science and collaboration, maximizing the potential for discovery from the large-scale datasets researchers and consortia are expending immense resources to produce and resulting in reproducible conclusions to improve diagnostic and therapeutic care for neurodegenerative disease patients.
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Affiliation(s)
- Allison A. Dilliott
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Maria C. Costanzo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noël P. Burtt
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- Laboratory of Neurogenetics, NIH, Bethesda, MD, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- Laboratory of Neurogenetics, NIH, Bethesda, MD, USA
| | - Bradford Casey
- Michael J. Fox Foundation for Parkinson’s Research, NY, NY USA
| | - Quy Hoang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- DataTecnica LLC, Washington, DC, USA
| | - Dongkeun Jang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonggeol Jeffrey Kim
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- Laboratory of Neurogenetics, NIH, Bethesda, MD, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- DataTecnica LLC, Washington, DC, USA
| | - Kristin S. Levine
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- DataTecnica LLC, Washington, DC, USA
| | - Mary Makarious
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- Laboratory of Neurogenetics, NIH, Bethesda, MD, USA
| | - Trang T. Nguyen
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guy A. Rouleau
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- Laboratory of Neurogenetics, NIH, Bethesda, MD, USA
| | - Patrick Smadbeck
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J Solle
- Michael J. Fox Foundation for Parkinson’s Research, NY, NY USA
| | - Dan Vitale
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- DataTecnica LLC, Washington, DC, USA
| | - Mike A. Nalls
- Center for Alzheimer’s and Related Dementias, NIH, Bethesda, MD USA
- Laboratory of Neurogenetics, NIH, Bethesda, MD, USA
- DataTecnica LLC, Washington, DC, USA
| | - Jason Flannick
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sali M.K. Farhan
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
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Rahimzadeh N, Srinivasan SS, Zhang J, Swarup V. Gene networks and systems biology in Alzheimer's disease: Insights from multi-omics approaches. Alzheimers Dement 2024; 20:3587-3605. [PMID: 38534018 PMCID: PMC11095483 DOI: 10.1002/alz.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Despite numerous studies in the field of dementia and Alzheimer's disease (AD), a comprehensive understanding of this devastating disease remains elusive. Bulk transcriptomics have provided insights into the underlying genetic factors at a high level. Subsequent technological advancements have focused on single-cell omics, encompassing techniques such as single-cell RNA sequencing and epigenomics, enabling the capture of RNA transcripts and chromatin states at a single cell or nucleus resolution. Furthermore, the emergence of spatial omics has allowed the study of gene responses in the vicinity of amyloid beta plaques or across various brain regions. With the vast amount of data generated, utilizing gene regulatory networks to comprehensively study this disease has become essential. This review delves into some techniques employed in the field of AD, explores the discoveries made using these techniques, and provides insights into the future of the field.
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Affiliation(s)
- Negin Rahimzadeh
- Mathematical, Computational, and Systems Biology (MCSB) ProgramUniversity of California IrvineIrvineCaliforniaUSA
| | - Shushrruth Sai Srinivasan
- Mathematical, Computational, and Systems Biology (MCSB) ProgramUniversity of California IrvineIrvineCaliforniaUSA
| | - Jing Zhang
- Department of Computer ScienceUniversity of CaliforniaIrvineCaliforniaUSA
| | - Vivek Swarup
- Department of Neurobiology and BehaviorUniversity of California IrvineIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders (MIND)University of California IrvineIrvineCaliforniaUSA
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7
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Peng KY, Liemisa B, Pasato J, D'Acunzo P, Pawlik M, Heguy A, Penikalapati SC, Labuza A, Pidikiti H, Alldred MJ, Ginsberg SD, Levy E, Mathews PM. Apolipoprotein E2 Expression Alters Endosomal Pathways in a Mouse Model With Increased Brain Exosome Levels During Aging. Traffic 2024; 25:e12937. [PMID: 38777335 PMCID: PMC11141728 DOI: 10.1111/tra.12937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
The polymorphic APOE gene is the greatest genetic determinant of sporadic Alzheimer's disease risk: the APOE4 allele increases risk, while the APOE2 allele is neuroprotective compared with the risk-neutral APOE3 allele. The neuronal endosomal system is inherently vulnerable during aging, and APOE4 exacerbates this vulnerability by driving an enlargement of early endosomes and reducing exosome release in the brain of humans and mice. We hypothesized that the protective effects of APOE2 are, in part, mediated through the endosomal pathway. Messenger RNA analyses showed that APOE2 leads to an enrichment of endosomal pathways in the brain when compared with both APOE3 and APOE4. Moreover, we show age-dependent alterations in the recruitment of key endosomal regulatory proteins to vesicle compartments when comparing APOE2 to APOE3. In contrast to the early endosome enlargement previously shown in Alzheimer's disease and APOE4 models, we detected similar morphology and abundance of early endosomes and retromer-associated vesicles within cortical neurons of aged APOE2 targeted-replacement mice compared with APOE3. Additionally, we observed increased brain extracellular levels of endosome-derived exosomes in APOE2 compared with APOE3 mice during aging, consistent with enhanced endosomal cargo clearance by exosomes to the extracellular space. Our findings thus demonstrate that APOE2 enhances an endosomal clearance pathway, which has been shown to be impaired by APOE4 and which may be protective due to APOE2 expression during brain aging.
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Affiliation(s)
- Katherine Y Peng
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Braison Liemisa
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Jonathan Pasato
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Pasquale D'Acunzo
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Monika Pawlik
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Adriana Heguy
- Genome Technology Center, New York University Grossman School of Medicine, New York, New York, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Sai C Penikalapati
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Amanda Labuza
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Harshitha Pidikiti
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Melissa J Alldred
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
| | - Stephen D Ginsberg
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Efrat Levy
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, New York, USA
- Department of Biochemistry & Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Paul M Mathews
- Department of Psychiatry, New York University Grossman School of Medicine, New York, New York, USA
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, New York, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, New York, USA
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8
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Lee S, Hecker J, Hahn G, Mullin K, Lutz SM, Tanzi RE, Lange C, Prokopenko D. On the effect heterogeneity of established disease susceptibility loci for Alzheimer's disease across different genetic ancestries. Alzheimers Dement 2024; 20:3397-3405. [PMID: 38563508 PMCID: PMC11095441 DOI: 10.1002/alz.13796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Genome-wide association studies have identified numerous disease susceptibility loci (DSLs) for Alzheimer's disease (AD). However, only a limited number of studies have investigated the dependence of the genetic effect size of established DSLs on genetic ancestry. METHODS We utilized the whole genome sequencing data from the Alzheimer's Disease Sequencing Project (ADSP) including 35,569 participants. A total of 25,459 subjects in four distinct populations (African ancestry, non-Hispanic White, admixed Hispanic, and Asian) were analyzed. RESULTS We found that nine DSLs showed significant heterogeneity across populations. Single nucleotide polymorphism (SNP) rs2075650 in translocase of outer mitochondrial membrane 40 (TOMM40) showed the largest heterogeneity (Cochran's Q = 0.00, I2 = 90.08), followed by other SNPs in apolipoprotein C1 (APOC1) and apolipoprotein E (APOE). Two additional loci, signal-induced proliferation-associated 1 like 2 (SIPA1L2) and solute carrier 24 member 4 (SLC24A4), showed significant heterogeneity across populations. DISCUSSION We observed substantial heterogeneity for the APOE-harboring 19q13.32 region with TOMM40/APOE/APOC1 genes. The largest risk effect was seen among African Americans, while Asians showed a surprisingly small risk effect.
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Affiliation(s)
- Sanghun Lee
- Department of Medical ConsilienceDivision of MedicineGraduate schoolDankook UniversityYongin‐siGyeonggi‐doSouth Korea
- Channing Division of Network MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Julian Hecker
- Channing Division of Network MedicineBrigham and Women's HospitalBostonMassachusettsUSA
| | - Georg Hahn
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Kristina Mullin
- Genetics and Aging Unit and McCance Center for Brain HealthDepartment of NeurologyMassachusetts General HospitalCharlestownMassachusettsUSA
| | | | - Sharon M. Lutz
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
- Department of Population MedicineHarvard Medical School and Harvard Pilgrim Healthcare InstituteBostonMassachusettsUSA
| | - Rudolph E. Tanzi
- Genetics and Aging Unit and McCance Center for Brain HealthDepartment of NeurologyMassachusetts General HospitalCharlestownMassachusettsUSA
| | - Christoph Lange
- Channing Division of Network MedicineBrigham and Women's HospitalBostonMassachusettsUSA
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain HealthDepartment of NeurologyMassachusetts General HospitalCharlestownMassachusettsUSA
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Cheek CL, Lindner P, Grigorenko EL. Statistical and Machine Learning Analysis in Brain-Imaging Genetics: A Review of Methods. Behav Genet 2024; 54:233-251. [PMID: 38336922 DOI: 10.1007/s10519-024-10177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
Brain-imaging-genetic analysis is an emerging field of research that aims at aggregating data from neuroimaging modalities, which characterize brain structure or function, and genetic data, which capture the structure and function of the genome, to explain or predict normal (or abnormal) brain performance. Brain-imaging-genetic studies offer great potential for understanding complex brain-related diseases/disorders of genetic etiology. Still, a combined brain-wide genome-wide analysis is difficult to perform as typical datasets fuse multiple modalities, each with high dimensionality, unique correlational landscapes, and often low statistical signal-to-noise ratios. In this review, we outline the progress in brain-imaging-genetic methodologies starting from early massive univariate to current deep learning approaches, highlighting each approach's strengths and weaknesses and elongating it with the field's development. We conclude by discussing selected remaining challenges and prospects for the field.
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Affiliation(s)
- Connor L Cheek
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA.
- Department of Physics, University of Houston, Houston, TX, USA.
| | - Peggy Lindner
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA
- Department of Information Science Technology, University of Houston, Houston, TX, USA
| | - Elena L Grigorenko
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA
- Department of Psychology, University of Houston, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
- Sirius University of Science and Technology, Sochi, Russia
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10
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Ma J, Li J, Chen Y, Yang Z, He Y. Poor statistical power in population-based association study of gene interaction. BMC Med Genomics 2024; 17:111. [PMID: 38678264 PMCID: PMC11055307 DOI: 10.1186/s12920-024-01884-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Statistical epistasis, or "gene-gene interaction" in genetic association studies, means the nonadditive effects between the polymorphic sites on two different genes affecting the same phenotype. In the genetic association analysis of complex traits, nevertheless, the researchers haven't found enough clues of statistical epistasis so far. METHODS We developed a statistical model where the statistical epistasis was presented as an extra linkage disequilibrium between the polymorphic sites of different risk genes. The power of statistical test for identifying the gene-gene interaction was calculated and then compared in different hypothesis scenarios. RESULTS Our results show the statistical power increases with the increasing of interaction coefficient, relative risk, and linkage disequilibrium with genetic markers. However, the power of interaction discovery is much lower than that of regular single-site association test. When rigorous criteria were employed in statistical tests, the identification of gene-gene interaction became a very difficult task. Since the criterion of significance was given to be p-value ≤ 5.0 × 10-8, the same as that of many genome-wide association studies, there is little chance to identify the gene-gene interaction in all kind of circumstances. CONCLUSIONS The lack of epistasis tends to be an inevitable result caused by the statistical principles of methods in the genetic association studies and therefore is the inherent characteristic of the research itself.
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Affiliation(s)
- Jiarui Ma
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jian Li
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuqi Chen
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Yungang He
- Shanghai Fifth People's Hospital, Intelligent Medicine Institute, Fudan University, Shanghai, 200032, PR China.
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11
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Ramakrishnan A, Piehl N, Simonton B, Parikh M, Zhang Z, Teregulova V, van Olst L, Gate D. Epigenetic dysregulation in Alzheimer's disease peripheral immunity. Neuron 2024; 112:1235-1248.e5. [PMID: 38340719 PMCID: PMC11031321 DOI: 10.1016/j.neuron.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/10/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
The peripheral immune system in Alzheimer's disease (AD) has not been thoroughly studied with modern sequencing methods. To investigate epigenetic and transcriptional alterations to the AD peripheral immune system, we used single-cell sequencing strategies, including assay for transposase-accessible chromatin and RNA sequencing. We reveal a striking amount of open chromatin in peripheral immune cells in AD. In CD8 T cells, we uncover a cis-regulatory DNA element co-accessible with the CXC motif chemokine receptor 3 gene promoter. In monocytes, we identify a novel AD-specific RELA transcription factor binding site adjacent to an open chromatin region in the nuclear factor kappa B subunit 2 gene. We also demonstrate apolipoprotein E genotype-dependent epigenetic changes in monocytes. Surprisingly, we also identify differentially accessible chromatin regions in genes associated with sporadic AD risk. Our findings provide novel insights into the complex relationship between epigenetics and genetic risk factors in AD peripheral immunity.
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Affiliation(s)
- Abhirami Ramakrishnan
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Natalie Piehl
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Brooke Simonton
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Milan Parikh
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ziyang Zhang
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Victoria Teregulova
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lynn van Olst
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Gate
- The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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12
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Yao X, Ouyang S, Lian Y, Peng Q, Zhou X, Huang F, Hu X, Shi F, Xia J. PheSeq, a Bayesian deep learning model to enhance and interpret the gene-disease association studies. Genome Med 2024; 16:56. [PMID: 38627848 PMCID: PMC11020195 DOI: 10.1186/s13073-024-01330-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Despite the abundance of genotype-phenotype association studies, the resulting association outcomes often lack robustness and interpretations. To address these challenges, we introduce PheSeq, a Bayesian deep learning model that enhances and interprets association studies through the integration and perception of phenotype descriptions. By implementing the PheSeq model in three case studies on Alzheimer's disease, breast cancer, and lung cancer, we identify 1024 priority genes for Alzheimer's disease and 818 and 566 genes for breast cancer and lung cancer, respectively. Benefiting from data fusion, these findings represent moderate positive rates, high recall rates, and interpretation in gene-disease association studies.
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Affiliation(s)
- Xinzhi Yao
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Sizhuo Ouyang
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Yulong Lian
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Qianqian Peng
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Xionghui Zhou
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Feier Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuehai Hu
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Feng Shi
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Jingbo Xia
- College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China.
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13
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Rubinski A, Dewenter A, Zheng L, Franzmeier N, Stephenson H, Deming Y, Duering M, Gesierich B, Denecke J, Pham AV, Bendlin B, Ewers M. Florbetapir PET-assessed demyelination is associated with faster tau accumulation in an APOE ε4-dependent manner. Eur J Nucl Med Mol Imaging 2024; 51:1035-1049. [PMID: 38049659 PMCID: PMC10881623 DOI: 10.1007/s00259-023-06530-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023]
Abstract
PURPOSE The main objectives were to test whether (1) a decrease in myelin is associated with enhanced rate of fibrillar tau accumulation and cognitive decline in Alzheimer's disease, and (2) whether apolipoprotein E (APOE) ε4 genotype is associated with worse myelin decrease and thus tau accumulation. METHODS To address our objectives, we repurposed florbetapir-PET as a marker of myelin in the white matter (WM) based on previous validation studies showing that beta-amyloid (Aβ) PET tracers bind to WM myelin. We assessed 43 Aβ-biomarker negative (Aβ-) cognitively normal participants and 108 Aβ+ participants within the AD spectrum with florbetapir-PET at baseline and longitudinal flortaucipir-PET as a measure of fibrillar tau (tau-PET) over ~ 2 years. In linear regression analyses, we tested florbetapir-PET in the whole WM and major fiber tracts as predictors of tau-PET accumulation in a priori defined regions of interest (ROIs) and fiber-tract projection areas. In mediation analyses we tested whether tau-PET accumulation mediates the effect of florbetapir-PET in the whole WM on cognition. Finally, we assessed the role of myelin alteration on the association between APOE and tau-PET accumulation. RESULTS Lower florbetapir-PET in the whole WM or at a given fiber tract was predictive of faster tau-PET accumulation in Braak stages or the connected grey matter areas in Aβ+ participants. Faster tau-PET accumulation in higher cortical brain areas mediated the association between a decrease in florbetapir-PET in the WM and a faster rate of decline in global cognition and episodic memory. APOE ε4 genotype was associated with a worse decrease in the whole WM florbetapir-PET and thus enhanced tau-PET accumulation. CONCLUSION Myelin alterations are associated in an APOE ε4 dependent manner with faster tau progression and cognitive decline, and may therefore play a role in the etiology of AD.
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Affiliation(s)
- Anna Rubinski
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Anna Dewenter
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Lukai Zheng
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Nicolai Franzmeier
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - Henry Stephenson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin- Madison, Madison, WI, USA
| | - Yuetiva Deming
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin- Madison, Madison, WI, USA
| | - Marco Duering
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
- Medical Image Analysis Center (MIAC) and Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - Benno Gesierich
- Medical Image Analysis Center (MIAC) and Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - Jannis Denecke
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
| | - An-Vi Pham
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany
- Department of Neuroradiology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Barbara Bendlin
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin- Madison, Madison, WI, USA
| | - Michael Ewers
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilian-University Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
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14
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Zhang Z, Liu X, Zhang S, Song Z, Lu K, Yang W. A review and analysis of key biomarkers in Alzheimer's disease. Front Neurosci 2024; 18:1358998. [PMID: 38445255 PMCID: PMC10912539 DOI: 10.3389/fnins.2024.1358998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects over 50 million elderly individuals worldwide. Although the pathogenesis of AD is not fully understood, based on current research, researchers are able to identify potential biomarker genes and proteins that may serve as effective targets against AD. This article aims to present a comprehensive overview of recent advances in AD biomarker identification, with highlights on the use of various algorithms, the exploration of relevant biological processes, and the investigation of shared biomarkers with co-occurring diseases. Additionally, this article includes a statistical analysis of key genes reported in the research literature, and identifies the intersection with AD-related gene sets from databases such as AlzGen, GeneCard, and DisGeNet. For these gene sets, besides enrichment analysis, protein-protein interaction (PPI) networks utilized to identify central genes among the overlapping genes. Enrichment analysis, protein interaction network analysis, and tissue-specific connectedness analysis based on GTEx database performed on multiple groups of overlapping genes. Our work has laid the foundation for a better understanding of the molecular mechanisms of AD and more accurate identification of key AD markers.
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Affiliation(s)
- Zhihao Zhang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Xiangtao Liu
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Suixia Zhang
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Zhixin Song
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Ke Lu
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
| | - Wenzhong Yang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
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15
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Firdaus Z, Li X. Unraveling the Genetic Landscape of Neurological Disorders: Insights into Pathogenesis, Techniques for Variant Identification, and Therapeutic Approaches. Int J Mol Sci 2024; 25:2320. [PMID: 38396996 PMCID: PMC10889342 DOI: 10.3390/ijms25042320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic abnormalities play a crucial role in the development of neurodegenerative disorders (NDDs). Genetic exploration has indeed contributed to unraveling the molecular complexities responsible for the etiology and progression of various NDDs. The intricate nature of rare and common variants in NDDs contributes to a limited understanding of the genetic risk factors associated with them. Advancements in next-generation sequencing have made whole-genome sequencing and whole-exome sequencing possible, allowing the identification of rare variants with substantial effects, and improving the understanding of both Mendelian and complex neurological conditions. The resurgence of gene therapy holds the promise of targeting the etiology of diseases and ensuring a sustained correction. This approach is particularly enticing for neurodegenerative diseases, where traditional pharmacological methods have fallen short. In the context of our exploration of the genetic epidemiology of the three most prevalent NDDs-amyotrophic lateral sclerosis, Alzheimer's disease, and Parkinson's disease, our primary goal is to underscore the progress made in the development of next-generation sequencing. This progress aims to enhance our understanding of the disease mechanisms and explore gene-based therapies for NDDs. Throughout this review, we focus on genetic variations, methodologies for their identification, the associated pathophysiology, and the promising potential of gene therapy. Ultimately, our objective is to provide a comprehensive and forward-looking perspective on the emerging research arena of NDDs.
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Affiliation(s)
- Zeba Firdaus
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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16
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Wang H, Chang TS, Dombroski BA, Cheng PL, Patil V, Valiente-Banuet L, Farrell K, Mclean C, Molina-Porcel L, Rajput A, De Deyn PP, Bastard NL, Gearing M, Kaat LD, Swieten JCV, Dopper E, Ghetti BF, Newell KL, Troakes C, de Yébenes JG, Rábano-Gutierrez A, Meller T, Oertel WH, Respondek G, Stamelou M, Arzberger T, Roeber S, Müller U, Hopfner F, Pastor P, Brice A, Durr A, Ber IL, Beach TG, Serrano GE, Hazrati LN, Litvan I, Rademakers R, Ross OA, Galasko D, Boxer AL, Miller BL, Seeley WW, Deerlin VMV, Lee EB, White CL, Morris H, de Silva R, Crary JF, Goate AM, Friedman JS, Leung YY, Coppola G, Naj AC, Wang LS, Dickson DW, Höglinger GU, Schellenberg GD, Geschwind DH, Lee WP. Whole-Genome Sequencing Analysis Reveals New Susceptibility Loci and Structural Variants Associated with Progressive Supranuclear Palsy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.12.28.23300612. [PMID: 38234807 PMCID: PMC10793533 DOI: 10.1101/2023.12.28.23300612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease characterized by the accumulation of aggregated tau proteins in astrocytes, neurons, and oligodendrocytes. Previous genome-wide association studies for PSP were based on genotype array, therefore, were inadequate for the analysis of rare variants as well as larger mutations, such as small insertions/deletions (indels) and structural variants (SVs). Method In this study, we performed whole genome sequencing (WGS) and conducted association analysis for single nucleotide variants (SNVs), indels, and SVs, in a cohort of 1,718 cases and 2,944 controls of European ancestry. Of the 1,718 PSP individuals, 1,441 were autopsy-confirmed and 277 were clinically diagnosed. Results Our analysis of common SNVs and indels confirmed known genetic loci at MAPT, MOBP, STX6, SLCO1A2, DUSP10, and SP1, and further uncovered novel signals in APOE, FCHO1/MAP1S, KIF13A, TRIM24, TNXB, and ELOVL1. Notably, in contrast to Alzheimer's disease (AD), we observed the APOE ε2 allele to be the risk allele in PSP. Analysis of rare SNVs and indels identified significant association in ZNF592 and further gene network analysis identified a module of neuronal genes dysregulated in PSP. Moreover, seven common SVs associated with PSP were observed in the H1/H2 haplotype region (17q21.31) and other loci, including IGH, PCMT1, CYP2A13, and SMCP. In the H1/H2 haplotype region, there is a burden of rare deletions and duplications (P = 6.73×10-3) in PSP. Conclusions Through WGS, we significantly enhanced our understanding of the genetic basis of PSP, providing new targets for exploring disease mechanisms and therapeutic interventions.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy S Chang
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vishakha Patil
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Leopoldo Valiente-Banuet
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kurt Farrell
- Department of Pathology, Department of Artificial Intelligence & Human Health, Nash Family, Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain, Institute, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catriona Mclean
- Victorian Brain Bank, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Laura Molina-Porcel
- Alzheimer's disease and other cognitive disorders unit. Neurology Service, Hospital Clínic, Fundació Recerca Clínic Barcelona (FRCB). Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Neurological Tissue Bank of the Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Alex Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Peter Paul De Deyn
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, University of Antwerp, Wilrijk (Antwerp), Belgium
- Department of Neurology, University Medical Center Groningen, NL-9713 AV Groningen, Netherlands
| | | | - Marla Gearing
- Department of Pathology and Laboratory Medicine and Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Elise Dopper
- Netherlands Brain Bank and Erasmus University, Netherlands
| | - Bernardino F Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | | | - Alberto Rábano-Gutierrez
- Fundación CIEN (Centro de Investigación de Enfermedades Neurológicas) - Centro Alzheimer Fundación Reina Sofía, Madrid, Spain
| | - Tina Meller
- Department of Neurology, Philipps-Universität, Marburg, Germany
| | | | - Gesine Respondek
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Maria Stamelou
- Parkinson's disease and Movement Disorders Department, HYGEIA Hospital, Athens, Greece
- European University of Cyprus, Nicosia, Cyprus
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, University Hospital Munich, Ludwig-Maximilians-University Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Germany
| | | | | | - Franziska Hopfner
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pau Pastor
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- Neurosciences, The Germans Trias i Pujol Research Institute (IGTP) Badalona, Badalona, Spain
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Isabelle Le Ber
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, APHP - Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | | | - Irene Litvan
- Department of Neuroscience, University of California, San Diego, CA, USA
| | - Rosa Rademakers
- VIB Center for Molecular Neurology, University of Antwerp, Belgium
- Department of Neuroscience, Mayo Clinic Jacksonville, FL, USA
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic Jacksonville, FL, USA
| | - Douglas Galasko
- Department of Neuroscience, University of California, San Diego, CA, USA
| | - Adam L Boxer
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Bruce L Miller
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Willian W Seeley
- Memory and Aging Center, University of California, San Francisco, CA, USA
| | - Vivanna M Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles L White
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huw Morris
- Departmento of Clinical and Movement Neuroscience, University College of London, London, UK
| | - Rohan de Silva
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - John F Crary
- Department of Pathology, Department of Artificial Intelligence & Human Health, Nash Family, Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain, Institute, Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey S Friedman
- Friedman Bioventure, Inc., Del Mar, CA, USA; Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giovanni Coppola
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Günter U Höglinger
- Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) München; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel H Geschwind
- Movement Disorders Programs, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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17
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Zhang R, Liu S, Mousavi SM. Cognitive Dysfunction and Exercise: From Epigenetic to Genetic Molecular Mechanisms. Mol Neurobiol 2024:10.1007/s12035-024-03970-7. [PMID: 38286967 DOI: 10.1007/s12035-024-03970-7] [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: 11/16/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024]
Abstract
Maintaining good health is crucial, and exercise plays a vital role in achieving this goal. It offers a range of positive benefits for cognitive function, regardless of age. However, as our population ages and life expectancy increases, cognitive impairment has become a prevalent issue, often coexisting with age-related neurodegenerative conditions. This can result in devastating consequences such as memory loss, difficulty speaking, and confusion, greatly hindering one's ability to lead an ordinary life. In addition, the decrease in mental capacity has a significant effect on an individual's physical and emotional well-being, greatly reducing their overall level of contentment and causing a significant financial burden for communities. While most current approaches aim to slow the decline of cognition, exercise offers a non-pharmacological, safe, and accessible solution. Its effects on cognition are intricate and involve changes in the brain's neural plasticity, mitochondrial stability, and energy metabolism. Moreover, exercise triggers the release of cytokines, playing a significant role in the body-brain connection and its impact on cognition. Additionally, exercise can influence gene expression through epigenetic mechanisms, leading to lasting improvements in brain function and behavior. Herein, we summarized various genetic and epigenetic mechanisms that can be modulated by exercise in cognitive dysfunction.
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Affiliation(s)
- Runhong Zhang
- Department of Physical Education, Luliang University, Lishi, 033000, Shanxi, China.
| | - Shangwu Liu
- Department of Physical Education, Luliang University, Lishi, 033000, Shanxi, China
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18
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Ma M, Yu Q, Delafield DG, Cui Y, Li Z, Li M, Wu W, Shi X, Westmark PR, Gutierrez A, Ma G, Gao A, Xu M, Xu W, Westmark CJ, Li L. On-Tissue Spatial Proteomics Integrating MALDI-MS Imaging with Shotgun Proteomics Reveals Soy Consumption-Induced Protein Changes in a Fragile X Syndrome Mouse Model. ACS Chem Neurosci 2024; 15:119-133. [PMID: 38109073 PMCID: PMC11127747 DOI: 10.1021/acschemneuro.3c00497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Fragile X syndrome (FXS), the leading cause of inherited intellectual disability and autism, is caused by the transcriptional silencing of the FMR1 gene, which encodes the fragile X messenger ribonucleoprotein (FMRP). FMRP interacts with numerous brain mRNAs that are involved in synaptic plasticity and implicated in autism spectrum disorders. Our published studies indicate that single-source, soy-based diets are associated with increased seizures and autism. Thus, there is an acute need for an unbiased protein marker identification in FXS in response to soy consumption. Herein, we present a spatial proteomics approach integrating mass spectrometry imaging with label-free proteomics in the FXS mouse model to map the spatial distribution and quantify levels of proteins in the hippocampus and hypothalamus brain regions. In total, 1250 unique peptides were spatially resolved, demonstrating the diverse array of peptidomes present in the tissue slices and the broad coverage of the strategy. A group of proteins that are known to be involved in glycolysis, synaptic transmission, and coexpression network analysis suggest a significant association between soy proteins and metabolic and synaptic processes in the Fmr1KO brain. Ultimately, this spatial proteomics work represents a crucial step toward identifying potential candidate protein markers and novel therapeutic targets for FXS.
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Affiliation(s)
- Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Daniel G. Delafield
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Pamela R. Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Alejandra Gutierrez
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Molecular Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Gui Ma
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Ang Gao
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Meng Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Cara J. Westmark
- Department of Neurology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Molecular Environmental Toxicology Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53705, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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19
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Sun X, Jia X, Lu Z, Tang J, Li M. Drug repositioning with adaptive graph convolutional networks. Bioinformatics 2024; 40:btad748. [PMID: 38070161 PMCID: PMC10761094 DOI: 10.1093/bioinformatics/btad748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 01/04/2024] Open
Abstract
MOTIVATION Drug repositioning is an effective strategy to identify new indications for existing drugs, providing the quickest possible transition from bench to bedside. With the rapid development of deep learning, graph convolutional networks (GCNs) have been widely adopted for drug repositioning tasks. However, prior GCNs based methods exist limitations in deeply integrating node features and topological structures, which may hinder the capability of GCNs. RESULTS In this study, we propose an adaptive GCNs approach, termed AdaDR, for drug repositioning by deeply integrating node features and topological structures. Distinct from conventional graph convolution networks, AdaDR models interactive information between them with adaptive graph convolution operation, which enhances the expression of model. Concretely, AdaDR simultaneously extracts embeddings from node features and topological structures and then uses the attention mechanism to learn adaptive importance weights of the embeddings. Experimental results show that AdaDR achieves better performance than multiple baselines for drug repositioning. Moreover, in the case study, exploratory analyses are offered for finding novel drug-disease associations. AVAILABILITY AND IMPLEMENTATION The soure code of AdaDR is available at: https://github.com/xinliangSun/AdaDR.
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Affiliation(s)
- Xinliang Sun
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Xiao Jia
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Zhangli Lu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, FI00014 Helsinki, Finland
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
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20
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Asiamah EA, Feng B, Guo R, Yaxing X, Du X, Liu X, Zhang J, Cui H, Ma J. The Contributions of the Endolysosomal Compartment and Autophagy to APOEɛ4 Allele-Mediated Increase in Alzheimer's Disease Risk. J Alzheimers Dis 2024; 97:1007-1031. [PMID: 38306054 DOI: 10.3233/jad-230658] [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] [Indexed: 02/03/2024]
Abstract
Apolipoprotein E4 (APOE4), although yet-to-be fully understood, increases the risk and lowers the age of onset of Alzheimer's disease (AD), which is the major cause of dementia among elderly individuals. The endosome-lysosome and autophagy pathways, which are necessary for homeostasis in both neurons and glia, are dysregulated even in early AD. Nonetheless, the contributory roles of these pathways to developing AD-related pathologies in APOE4 individuals and models are unclear. Therefore, this review summarizes the dysregulations in the endosome-lysosome and autophagy pathways in APOE4 individuals and non-human models, and how these anomalies contribute to developing AD-relevant pathologies. The available literature suggests that APOE4 causes endosomal enlargement, increases endosomal acidification, impairs endosomal recycling, and downregulates exosome production. APOE4 impairs autophagy initiation and inhibits basal autophagy and autophagy flux. APOE4 promotes lysosome formation and trafficking and causes ApoE to accumulate in lysosomes. APOE4-mediated changes in the endosome, autophagosome and lysosome could promote AD-related features including Aβ accumulation, tau hyperphosphorylation, glial dysfunction, lipid dyshomeostasis, and synaptic defects. ApoE4 protein could mediate APOE4-mediated endosome-lysosome-autophagy changes. ApoE4 impairs vesicle recycling and endosome trafficking, impairs the synthesis of autophagy genes, resists being dissociated from its receptors and degradation, and forms a stable folding intermediate that could disrupt lysosome structure. Drugs such as molecular correctors that target ApoE4 molecular structure and enhance autophagy may ameliorate the endosome-lysosome-autophagy-mediated increase in AD risk in APOE4 individuals.
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Affiliation(s)
- Ernest Amponsah Asiamah
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Department of Biomedical Sciences, College of Health and Allied Sciences, University of Cape Coast, PMB UCC, Cape Coast, Ghana
| | - Baofeng Feng
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
- Hebei Technology Innovation Center for Stem Cell and Regenerative Medicine, Hebei, China
| | - Ruiyun Guo
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
| | - Xu Yaxing
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
| | - Xiaofeng Du
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
| | - Xin Liu
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
| | - Jinyu Zhang
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
| | - Huixian Cui
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
- Hebei Technology Innovation Center for Stem Cell and Regenerative Medicine, Hebei, China
| | - Jun Ma
- Hebei Medical University-Galway University of Ireland Stem Cell Research Center, Hebei Medical University, Hebei, China
- Hebei Research Center for Stem Cell Medical Translational Engineering, Hebei, China
- Hebei Technology Innovation Center for Stem Cell and Regenerative Medicine, Hebei, China
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21
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Wagemann O, Li Y, Hassenstab J, Aschenbrenner AJ, McKay NS, Gordon BA, Benzinger TLS, Xiong C, Cruchaga C, Renton AE, Perrin RJ, Berman SB, Chhatwal JP, Farlow MR, Day GS, Ikeuchi T, Jucker M, Lopera F, Mori H, Noble JM, Sánchez-Valle R, Schofield PR, Morris JC, Daniels A, Levin J, Bateman RJ, McDade E, Llibre-Guerra JJ. Investigation of sex differences in mutation carriers of the Dominantly Inherited Alzheimer Network. Alzheimers Dement 2024; 20:47-62. [PMID: 37740921 PMCID: PMC10841236 DOI: 10.1002/alz.13460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 09/25/2023]
Abstract
INTRODUCTION Studies suggest distinct differences in the development, presentation, progression, and response to treatment of Alzheimer's disease (AD) between females and males. We investigated sex differences in cognition, neuroimaging, and fluid biomarkers in dominantly inherited AD (DIAD). METHODS Three hundred twenty-five mutation carriers (55% female) and one hundred eighty-six non-carriers (58% female) of the Dominantly Inherited Alzheimer Network Observational Study were analyzed. Linear mixed models and Spearman's correlation explored cross-sectional sex differences in cognition, cerebrospinal fluid (CSF) biomarkers, Pittsburgh compound B positron emission tomography (11 C-PiB PET) and structural magnetic resonance imaging (MRI). RESULTS Female carriers performed better than males on delayed recall and processing speed despite similar hippocampal volumes. As the disease progressed, symptomatic females revealed higher increases in MRI markers of neurodegeneration and memory impairment. PiB PET and established CSF AD markers revealed no sex differences. DISCUSSION Our findings suggest an initial cognitive reserve in female carriers followed by a pronounced increase in neurodegeneration coupled with worse performance on delayed recall at later stages of DIAD.
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Affiliation(s)
- Olivia Wagemann
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yan Li
- Department of Biostatistics, Washington University St. Louis, St. Louis, Missouri, USA
| | - Jason Hassenstab
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
| | | | - Nicole S McKay
- Department of Radiology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Brian A Gordon
- Department of Radiology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Tammie L S Benzinger
- Department of Radiology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Chengjie Xiong
- Department of Biostatistics, Washington University St. Louis, St. Louis, Missouri, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University St. Louis, St. Louis, Missouri, USA
| | - Alan E Renton
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Richard J Perrin
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Sarah B Berman
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jasmeer P Chhatwal
- Department of Neurology, Massachusetts General and Brigham & Female's Hospitals, Harvard Medical School, Boston, Massachusetts, USA
| | - Martin R Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Gregory S Day
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Mathias Jucker
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Francisco Lopera
- Grupo de Neurociencias de Antioquia (GNA), Universidad de Antioquia, Medellin, Colombia
| | - Hiroshi Mori
- Department of Clinical Neuroscience, Osaka Metropolitan University Medical School, Nagaoka Sutoku University, Osaka, Japan
| | - James M Noble
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Raquel Sánchez-Valle
- Department of Neurology, Hospital Clínic de Barcelona (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Peter R Schofield
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - John C Morris
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Alisha Daniels
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Johannes Levin
- Department of Neurology, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Randall J Bateman
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
| | - Eric McDade
- Department of Neurology, Washington University St. Louis, St. Louis, Missouri, USA
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22
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Tournier BB, Sorce S, Marteyn A, Ghidoni R, Benussi L, Binetti G, Herrmann FR, Krause K, Zekry D. CCR5 deficiency: Decreased neuronal resilience to oxidative stress and increased risk of vascular dementia. Alzheimers Dement 2024; 20:124-135. [PMID: 37489764 PMCID: PMC10917026 DOI: 10.1002/alz.13392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
INTRODUCTION As the chemokine receptor5 (CCR5) may play a role in ischemia, we studied the links between CCR5 deficiency, the sensitivity of neurons to oxidative stress, and the development of dementia. METHODS Logistic regression models with CCR5/apolipoprotein E (ApoE) polymorphisms were applied on a sample of 205 cognitively normal individuals and 189 dementia patients from Geneva. The impact of oxidative stress on Ccr5 expression and cell death was assessed in mice neurons. RESULTS CCR5-Δ32 allele synergized with ApoEε4 as risk factor for dementia and specifically for dementia with a vascular component. We confirmed these results in an independent cohort from Italy (157 cognitively normal and 620 dementia). Carriers of the ApoEε4/CCR5-Δ32 genotype aged ≥80 years have an 11-fold greater risk of vascular-and-mixed dementia. Oxidative stress-induced cell death in Ccr5-/- mice neurons. DISCUSSION We propose the vulnerability of CCR5-deficient neurons in response to oxidative stress as possible mechanisms contributing to dementia.
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Affiliation(s)
- Benjamin B. Tournier
- Department of PsychiatryGeneva University Hospitals and University of GenevaGenevaSwitzerland
| | - Silvia Sorce
- Department of Pathology and ImmunologyFaculty of MedicineUniversity of GenevaGenevaSwitzerland
| | - Antoine Marteyn
- Department of Pathology and ImmunologyFaculty of MedicineUniversity of GenevaGenevaSwitzerland
- Division of GeriatricsDepartment of Rehabilitation and GeriatricsGeneva University HospitalsThônexSwitzerland
- Division of Internal Medicine for the AgedDepartment of Rehabilitation and GeriatricsGeneva University HospitalsThônexSwitzerland
| | - Roberta Ghidoni
- Molecular Markers LaboratoryIRCCS Istituto Centro San Giovanni di Dio FatebenefratelliBresciaItaly
| | - Luisa Benussi
- Molecular Markers LaboratoryIRCCS Istituto Centro San Giovanni di Dio FatebenefratelliBresciaItaly
| | - Giuliano Binetti
- MAC Memory Clinic and Molecular Markers LaboratoryIRCCS Istituto Centro San Giovanni di Dio FatebenefratelliBresciaItaly
| | - François R Herrmann
- Division of GeriatricsDepartment of Rehabilitation and GeriatricsGeneva University HospitalsThônexSwitzerland
| | - Karl‐Heinz Krause
- Department of Pathology and ImmunologyFaculty of MedicineUniversity of GenevaGenevaSwitzerland
| | - Dina Zekry
- Division of Internal Medicine for the AgedDepartment of Rehabilitation and GeriatricsGeneva University HospitalsThônexSwitzerland
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Paradela RS, Justo AFO, Paes VR, Leite REP, Pasqualucci CA, Grinberg LT, Naslavsky MS, Zatz M, Nitrini R, Jacob-Filho W, Suemoto CK. Association between APOE-ε4 allele and cognitive function is mediated by Alzheimer's disease pathology: a population-based autopsy study in an admixed sample. Acta Neuropathol Commun 2023; 11:205. [PMID: 38115150 PMCID: PMC10731799 DOI: 10.1186/s40478-023-01681-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Apolipoprotein E ε4 allele (APOE-ε4) is the main genetic risk factor for late-onset Alzheimer's disease (AD) and may impact cognitive function also via other neuropathological lesions. However, there is limited evidence available from diverse populations, as APOE associations with dementia seem to differ by race. Therefore, we aimed to evaluate the pathways linking APOE-ε4 to cognitive abilities through AD and non-AD neuropathology in an autopsy study with an admixed sample. METHODS Neuropathological lesions were evaluated following international criteria using immunohistochemistry. Participants were classified into APOE-ε4 carriers (at least one ε4 allele) and non-carriers. Cognitive abilities were evaluated by the Clinical Dementia Rating Scale sum of boxes. Mediation analyses were conducted to assess the indirect association of APOE-ε4 with cognition through AD-pathology, lacunar infarcts, hyaline arteriosclerosis, cerebral amyloid angiopathy (CAA), Lewy body disease (LBD), and TAR DNA-binding protein 43 (TDP-43). RESULTS We included 648 participants (mean age 75 ± 12 years old, mean education 4.4 ± 3.7 years, 52% women, 69% White, and 28% APOE-ε4 carriers). The association between APOE-ε4 and cognitive abilities was mediated by neurofibrillary tangles (β = 0.88, 95% CI = 0.45; 1.38, p < 0.001) and neuritic plaques (β = 1.36, 95% CI = 0.86; 1.96, p < 0.001). Lacunar infarcts, hyaline arteriosclerosis, CAA, LBD, and TDP-43 were not mediators in the pathway from APOE-ε4 to cognition. CONCLUSION The association between APOE-ε4 and cognitive abilities was partially mediated by AD-pathology. On the other hand, cerebrovascular lesions and other neurodegenerative diseases did not mediate the association between APOE-ε4 and cognition.
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Affiliation(s)
- Regina Silva Paradela
- Division of Geriatrics, University of São Paulo Medical School, 455 Doutor Arnaldo Avenue, room 1355, São Paulo, SP, Brazil.
| | | | - Vítor Ribeiro Paes
- Department of Pathology, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Renata E P Leite
- Department of Pathology, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Carlos A Pasqualucci
- Department of Pathology, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Lea T Grinberg
- Memory and Aging Center, University of California, San Francisco, USA
| | - Michel Satya Naslavsky
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Center, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Ricardo Nitrini
- Department of Neurology, University of São Paulo Medical School, São Paulo, Brazil
| | - Wilson Jacob-Filho
- Division of Geriatrics, University of São Paulo Medical School, 455 Doutor Arnaldo Avenue, room 1355, São Paulo, SP, Brazil
| | - Claudia Kimie Suemoto
- Division of Geriatrics, University of São Paulo Medical School, 455 Doutor Arnaldo Avenue, room 1355, São Paulo, SP, Brazil
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24
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Liu W, You J, Ge Y, Wu B, Zhang Y, Chen S, Zhang Y, Huang S, Ma L, Feng J, Cheng W, Yu J. Association of biological age with health outcomes and its modifiable factors. Aging Cell 2023; 22:e13995. [PMID: 37723992 PMCID: PMC10726867 DOI: 10.1111/acel.13995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
Identifying the clinical implications and modifiable and unmodifiable factors of aging requires the measurement of biological age (BA) and age gap. Leveraging the biomedical traits involved with physical measures, biochemical assays, genomic data, and cognitive functions from the healthy participants in the UK Biobank, we establish an integrative BA model consisting of multi-dimensional indicators. Accelerated aging (age gap >3.2 years) at baseline is associated incident circulatory diseases, related chronic disorders, all-cause, and cause-specific mortality. We identify 35 modifiable factors for age gap (p < 4.81 × 10-4 ), where pulmonary functions, body mass, hand grip strength, basal metabolic rate, estimated glomerular filtration rate, and C-reactive protein show the most significant associations. Genetic analyses replicate the possible associations between age gap and health-related outcomes and further identify CST3 as an essential gene for biological aging, which is highly expressed in the brain and is associated with immune and metabolic traits. Our study profiles the landscape of biological aging and provides insights into the preventive strategies and therapeutic targets for aging.
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Affiliation(s)
- Wei‐Shi Liu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Jia You
- Institute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
- Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence (Fudan University), Ministry of EducationShanghaiChina
| | - Yi‐Jun Ge
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Bang‐Sheng Wu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Yi Zhang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shi‐Dong Chen
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Ya‐Ru Zhang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shu‐Yi Huang
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
| | - Ling‐Zhi Ma
- Department of Neurology, Qingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Jian‐Feng Feng
- Institute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
- Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence (Fudan University), Ministry of EducationShanghaiChina
- Department of Computer ScienceUniversity of WarwickCoventryUK
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
- Institute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
- Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligence (Fudan University), Ministry of EducationShanghaiChina
- Fudan ISTBI—ZJNU Algorithm Centre for Brain‐Inspired IntelligenceZhejiang Normal UniversityJinhuaChina
- Shanghai Medical College and Zhongshan Hosptital Immunotherapy Technology Transfer CenterShanghaiChina
| | - Jin‐Tai Yu
- Department of Neurology and National Center for Neurological Diseases, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain ScienceShanghai Medical College, Fudan UniversityShanghaiChina
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Kaur I, Behl T, Sundararajan G, Panneerselvam P, Vijayakumar AR, Senthilkumar GP, Venkatachalam T, Jaglan D, Yadav S, Anwer K, Fuloria NK, Sehgal A, Gulati M, Chigurupati S. BIN1 in the Pursuit of Ousting the Alzheimer's Reign: Impact on Amyloid and Tau Neuropathology. Neurotox Res 2023; 41:698-707. [PMID: 37847429 DOI: 10.1007/s12640-023-00670-3] [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: 12/13/2022] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023]
Abstract
Alzheimer's disease contributes to 60-70% of all dementia cases in the general population. Belonging to the BIN1/amphiphysin/RVS167 (BAR) superfamily, the bridging integrator (BIN1) has been identified to impact two major pathological hallmarks in Alzheimer's disease (AD), i.e., amyloid beta (Aβ) and tau accumulation. Aβ accumulation is found to increase by BIN1 knockdown in cortical neurons in late-onset AD, due to BACE1 accumulation at enlarged early endosomes. Two BIN1 mutants, KR and PL, were identified to exhibit Aβ accumulation. Furthermore, BIN1 deficiency by BIN1-related polymorphisms impairs the interaction with tau, thus elevating tau phosphorylation, altering synapse structure and tau function. Even though the precise role of BIN1 in the neuronal tissue needs further investigation, the authors aim to throw light on the potential of BIN1 and unfold its implications on tau and Aβ pathology, to aid AD researchers across the globe to examine BIN1, as an appropriate target gene for disease management.
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Affiliation(s)
- Ishnoor Kaur
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Tapan Behl
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Bidholi, Dehradun, India.
| | - G Sundararajan
- Department of Pharmaceutics, Faculty of Pharmacy, Sree Balaji Medical College and Hospital, Chromepet, Chennai, Tamil Nadu, India
| | - P Panneerselvam
- Faculty of Pharmacy, Sree Balaji Medical College and Hospital Campus, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - A R Vijayakumar
- Faculty of Pharmacy, Sree Balaji Medical College and Hospital Campus, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - G P Senthilkumar
- Faculty of Pharmacy, Sree Balaji Medical College and Hospital Campus, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - T Venkatachalam
- Department of Pharmaceutical Chemistry, JKKMMRFs-Amnai JKK Sampoorani Ammal College of Pharmacy, Komarapalayam, Tamil Nadu, India
| | - Dharmender Jaglan
- Faculty of Pharmaceutical Sciences, DAV University, Jalandhar, Punjab, India
| | - Shivam Yadav
- School of Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Chhatrapti Shahu Ji Maharaj University, Uttar Pradesh, Kanpur, India
| | - Khalid Anwer
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Neeraj Kumar Fuloria
- Faculty of Pharmacy, AIMST University, Bedong, Kedah, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospital, Saveetha University, Chennai, Tamil Nadu, India
| | - Aayush Sehgal
- GHG Khalsa College of Pharmacy, Gurusar Sadhar, Punjab, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 1444411, India
- Faculty of Health, ARCCIM, University of Technology Sydney, Ultimo, NSW, 20227, Australia
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, 52571, Kingdom of Saudi Arabia.
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Saveetha Nagar, Thandalam, Chennai, Tamilnadu, 602105, India.
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Marzi SJ, Schilder BM, Nott A, Frigerio CS, Willaime-Morawek S, Bucholc M, Hanger DP, James C, Lewis PA, Lourida I, Noble W, Rodriguez-Algarra F, Sharif JA, Tsalenchuk M, Winchester LM, Yaman Ü, Yao Z, Ranson JM, Llewellyn DJ. Artificial intelligence for neurodegenerative experimental models. Alzheimers Dement 2023; 19:5970-5987. [PMID: 37768001 DOI: 10.1002/alz.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Experimental models are essential tools in neurodegenerative disease research. However, the translation of insights and drugs discovered in model systems has proven immensely challenging, marred by high failure rates in human clinical trials. METHODS Here we review the application of artificial intelligence (AI) and machine learning (ML) in experimental medicine for dementia research. RESULTS Considering the specific challenges of reproducibility and translation between other species or model systems and human biology in preclinical dementia research, we highlight best practices and resources that can be leveraged to quantify and evaluate translatability. We then evaluate how AI and ML approaches could be applied to enhance both cross-model reproducibility and translation to human biology, while sustaining biological interpretability. DISCUSSION AI and ML approaches in experimental medicine remain in their infancy. However, they have great potential to strengthen preclinical research and translation if based upon adequate, robust, and reproducible experimental data. HIGHLIGHTS There are increasing applications of AI in experimental medicine. We identified issues in reproducibility, cross-species translation, and data curation in the field. Our review highlights data resources and AI approaches as solutions. Multi-omics analysis with AI offers exciting future possibilities in drug discovery.
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Affiliation(s)
- Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Brian M Schilder
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Alexi Nott
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | | | - Magda Bucholc
- School of Computing, Engineering & Intelligent Systems, Ulster University, Derry, UK
| | - Diane P Hanger
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Patrick A Lewis
- Royal Veterinary College, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | - Wendy Noble
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | | | - Jalil-Ahmad Sharif
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Ümran Yaman
- UK Dementia Research Institute at UCL, London, UK
| | | | | | - David J Llewellyn
- University of Exeter Medical School, Exeter, UK
- Alan Turing Institute, London, UK
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Zhang J, Wang Y, Zhang Y, Yao J. Genome-wide association study in Alzheimer's disease: a bibliometric and visualization analysis. Front Aging Neurosci 2023; 15:1290657. [PMID: 38094504 PMCID: PMC10716290 DOI: 10.3389/fnagi.2023.1290657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/08/2023] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Thousands of research studies concerning genome-wide association studies (GWAS) in Alzheimer's disease (AD) have been published in the last decades. However, a comprehensive understanding of the current research status and future development trends of GWAS in AD have not been clearly shown. In this study, we tried to gain a systematic overview of GWAS in AD by bibliometric and visualization analysis. METHODS The literature search terms are: ("genome-wide analysis" or "genome-wide association study" or "whole-genome analysis") AND ("Alzheimer's Disease" or "Alzheimer Disease"). Relevant publications were extracted from the Web of Science Core Collection (WoSCC) database. Collected data were further analyzed using VOSviewer, CiteSpace and R package Bibliometrix. The countries, institutions, authors and scholar collaborations were investigated. The co-citation analysis of publications was visualized. In addition, research hotspots and fronts were examined. RESULTS A total of 1,350 publications with 59,818 citations were identified. The number of publications and citations presented a significant rising trend since 2013. The United States was the leading country with an overwhelming number of publications (775) and citations (42,237). The University of Washington and Harvard University were the most prolific institutions with 101 publications each. Bennett DA was the most influential researcher with the highest local H-index. Neurobiology of Aging was the journal with the highest number of publications. Aβ, tau, immunity, microglia and DNA methylation were research hotspots. Disease and causal variants were research fronts. CONCLUSION The most frequently studied AD pathogenesis and research hotspots are (1) Aβ and tau, (2) immunity and microglia, with TREM2 as a potential immunotherapy target, and (3) DNA methylation. The research fronts are (1) looking for genetic similarities between AD and other neurological diseases and syndromes, and (2) searching for causal variants of AD. These hotspots suggest noteworthy directions for future studies on AD pathogenesis and genetics, in which basic research regarding immunity is promising for clinical conversion. The current under-researched directions are (1) GWAS in AD biomarkers based on large sample sizes, (2) studies of causal variants of AD, and (3) GWAS in AD based on non-European populations, which need to be strengthened in the future.
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Affiliation(s)
- Junyao Zhang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinuo Wang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingying Zhang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junyan Yao
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anesthesiology and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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28
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Liemisa B, Newbury SF, Novy MJ, Pasato JA, Morales-Corraliza J, Peng KY, Mathews PM. Brain apolipoprotein E levels in mice challenged by a Western diet increase in an allele-dependent manner. AGING BRAIN 2023; 4:100102. [PMID: 38058491 PMCID: PMC10696459 DOI: 10.1016/j.nbas.2023.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Human apolipoprotein E (APOE) is the greatest determinant of genetic risk for memory deficits and Alzheimer's disease (AD). While APOE4 drives memory loss and high AD risk, APOE2 leads to healthy brain aging and reduced AD risk compared to the common APOE3 variant. We examined brain APOE protein levels in humanized mice homozygous for these alleles and found baseline levels to be age- and isoform-dependent: APOE2 levels were greater than APOE3, which were greater than APOE4. Despite the understanding that APOE lipoparticles do not traverse the blood-brain barrier, we show that brain APOE levels are responsive to dietary fat intake. Challenging mice for 6 months on a Western diet high in fat and cholesterol increased APOE protein levels in an allele-dependent fashion with a much greater increase within blood plasma than within the brain. In the brain, APOE2 levels responded most to the Western diet challenge, increasing by 20 % to 30 %. While increased lipoparticles are generally deleterious in the periphery, we propose that higher brain APOE2 levels may represent a readily available pool of beneficial lipid particles for neurons.
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Affiliation(s)
- Braison Liemisa
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Samantha F. Newbury
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Mariah J. Novy
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Jonathan A. Pasato
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Jose Morales-Corraliza
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Katherine Y. Peng
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Paul M. Mathews
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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29
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Hammers DB, Eloyan A, Taurone A, Thangarajah M, Beckett L, Gao S, Kirby K, Aisen P, Dage JL, Foroud T, Griffin P, Grinberg LT, Jack CR, Kramer J, Koeppe R, Kukull WA, Mundada NS, Joie RL, Soleimani-Meigooni DN, Iaccarino L, Murray ME, Nudelman K, Polsinelli AJ, Rumbaugh M, Toga A, Touroutoglou A, Vemuri P, Atri A, Day GS, Duara R, Graff-Radford NR, Honig LS, Jones DT, Masdeu J, Mendez MF, Womack K, Musiek E, Onyike CU, Riddle M, Rogalski E, Salloway S, Sha SJ, Turner RS, Wingo TS, Wolk DA, Carrillo MC, Dickerson BC, Rabinovici GD, Apostolova LG. Profiling baseline performance on the Longitudinal Early-Onset Alzheimer's Disease Study (LEADS) cohort near the midpoint of data collection. Alzheimers Dement 2023; 19 Suppl 9:S8-S18. [PMID: 37256497 PMCID: PMC10806768 DOI: 10.1002/alz.13160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE The Longitudinal Early-Onset Alzheimer's Disease Study (LEADS) seeks to provide comprehensive understanding of early-onset Alzheimer's disease (EOAD; onset <65 years), with the current study profiling baseline clinical, cognitive, biomarker, and genetic characteristics of the cohort nearing the data-collection mid-point. METHODS Data from 371 LEADS participants were compared based on diagnostic group classification (cognitively normal [n = 89], amyloid-positive EOAD [n = 212], and amyloid-negative early-onset non-Alzheimer's disease [EOnonAD; n = 70]). RESULTS Cognitive performance was worse for EOAD than other groups, and EOAD participants were apolipoprotein E (APOE) ε4 homozygotes at higher rates. An amnestic presentation was common among impaired participants (81%), with several clinical phenotypes present. LEADS participants generally consented at high rates to optional trial procedures. CONCLUSIONS We present the most comprehensive baseline characterization of sporadic EOAD in the United States to date. EOAD presents with widespread cognitive impairment within and across clinical phenotypes, with differences in APOE ε4 allele carrier status appearing to be relevant. HIGHLIGHTS Findings represent the most comprehensive baseline characterization of sporadic early-onset Alzheimer's disease (EOAD) to date. Cognitive impairment was widespread for EOAD participants and more severe than other groups. EOAD participants were homozygous apolipoprotein E (APOE) ε4 carriers at higher rates than the EOnonAD group. Amnestic presentation predominated in EOAD and EOnonAD participants, but other clinical phenotypes were present.
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Affiliation(s)
- Dustin B. Hammers
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ani Eloyan
- Department of Biostatistics, Center for Statistical Sciences, Brown University, Providence, Rhode Island, USA
| | - Alexander Taurone
- Department of Biostatistics, Center for Statistical Sciences, Brown University, Providence, Rhode Island, USA
| | - Maryanne Thangarajah
- Department of Biostatistics, Center for Statistical Sciences, Brown University, Providence, Rhode Island, USA
| | - Laurel Beckett
- Department of Public Health Sciences, University of California – Davis, Davis, California, USA
| | - Sujuan Gao
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kala Kirby
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Paul Aisen
- Alzheimer’s Therapeutic Research Institute, University of Southern California, San Diego, California, USA
| | - Jeffrey L. Dage
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Percy Griffin
- Medical & Scientific Relations Division, Alzheimer’s Association, Chicago, Illinois, USA
| | - Lea T. Grinberg
- Department of Pathology, University of California – San Francisco, San Francisco, California, USA
- Department of Neurology, University of California – San Francisco, San Francisco, California, USA
| | | | - Joel Kramer
- Department of Neurology, University of California – San Francisco, San Francisco, California, USA
| | - Robert Koeppe
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Walter A. Kukull
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Nidhi S Mundada
- Department of Neurology, University of California – San Francisco, San Francisco, California, USA
| | - Renaud La Joie
- Department of Neurology, University of California – San Francisco, San Francisco, California, USA
| | | | - Leonardo Iaccarino
- Department of Neurology, University of California – San Francisco, San Francisco, California, USA
| | | | - Kelly Nudelman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Angelina J. Polsinelli
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Malia Rumbaugh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Arthur Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Alexandra Touroutoglou
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Alireza Atri
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Gregory S. Day
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Ranjan Duara
- Wien Center for Alzheimer’s Disease and Memory Disorders, Mount Sinai Medical Center, Miami, Florida, USA
| | | | - Lawrence S. Honig
- Taub Institute and Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - David T. Jones
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph Masdeu
- Nantz National Alzheimer Center, Houston Methodist and Weill Cornell Medicine, Houston, Texas, USA
| | - Mario F. Mendez
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Kyle Womack
- Department of Neurology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Erik Musiek
- Department of Neurology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chiadi U. Onyike
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Meghan Riddle
- Department of Neurology, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Emily Rogalski
- Department of Psychiatry and Behavioral Sciences, Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Steven Salloway
- Department of Neurology, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Sharon J. Sha
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto, California, USA
| | | | - Thomas S. Wingo
- Department of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David A. Wolk
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria C. Carrillo
- Medical & Scientific Relations Division, Alzheimer’s Association, Chicago, Illinois, USA
| | - Bradford C. Dickerson
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gil D. Rabinovici
- Department of Neurology, University of California – San Francisco, San Francisco, California, USA
| | - Liana G. Apostolova
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine Indianapolis, Indianapolis, Indiana, USA
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Zenuni H, Bovenzi R, Bissacco J, Grillo P, Simonetta C, Mascioli D, Pieri M, Bernardini S, Sancesario GM, Stefani A, Mercuri NB, Schirinzi T. Clinical and neurochemical correlates of the APOE genotype in early-stage Parkinson's disease. Neurobiol Aging 2023; 131:24-28. [PMID: 37572524 DOI: 10.1016/j.neurobiolaging.2023.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 08/14/2023]
Abstract
Emerging evidence indicates that apolipoprotein E (APOE) genotype may influence Parkinson's disease (PD) course, although clinical and neurochemical correlates have not been completely established. This study aimed to determine the associations of APOE genotypes (ε4 vs. non-ε4) with cerebrospinal fluid (CSF) neurodegeneration biomarkers and clinical parameters in early-stage PD patients. One hundred and seventy-five PD patients and 89 non-neurodegenerative controls grouped in APOE-ε4 carriers (28 PD; 12 controls) and non-APOE-ε4 carriers (147 PD; 78 controls) were enrolled. CSF levels of amyloid-β-42, amyloid-β-40, total and 181-phosphorylated tau, and clinical scores were compared among groups adjusting for main covariates. APOE genotypes prevalence was similar in PD and controls. PD APOE-ε4 carriers had lower amyloid-β-42 CSF levels than PD non-APOE-ε4 carriers and controls, independently from age. PD APOE-ε4 carriers also had higher total and "item 5" (attention and memory) non-motor symptoms scale scores than PD non-APOE-ε4 carriers, independently from confounding factors. APOE-ε4 genotype might thus account for a more vulnerable PD subtype characterized by prominent amyloidopathy and a greater burden of non-motor symptoms in the early disease stages. DATA AVAILABILITY: Data are available upon reasonable request.
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Affiliation(s)
- Henri Zenuni
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Roberta Bovenzi
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Jacopo Bissacco
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Piergiorgio Grillo
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Clara Simonetta
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Davide Mascioli
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Massimo Pieri
- Clinical Biochemistry Unit, Department of Experimental Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Segio Bernardini
- Clinical Biochemistry Unit, Department of Experimental Medicine, University of Roma Tor Vergata, Rome, Italy
| | | | - Alessandro Stefani
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Nicola Biagio Mercuri
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy
| | - Tommaso Schirinzi
- Unit of Neurology, Department of Systems Medicine, University of Roma Tor Vergata, Rome, Italy.
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31
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Kashtanova DA, Mamchur AA, Dzhumaniyazova IH, Ivanov MV, Erema VV, Zelenova EA, Yakovchik AY, Gusakova MS, Rumyantseva AM, Terekhov MV, Matkava LR, Akopyan AA, Strazhesko ID, Yudin VS, Makarov VV, Kraevoy SA, Tkacheva ON, Yudin SM. Cognitive impairment in long-living adults: a genome-wide association study, polygenic risk score model and molecular modeling of the APOE protein. Front Aging Neurosci 2023; 15:1273825. [PMID: 37953886 PMCID: PMC10637623 DOI: 10.3389/fnagi.2023.1273825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Background Cognitive impairment is an irreversible, aging-associated condition that robs people of their independence. The purpose of this study was to investigate possible causes of this condition and propose preventive options. Methods We assessed cognitive status in long-living adults aged 90+ (n = 2,559) and performed a genome wide association study using two sets of variables: Mini-Mental State Examination scores as a continuous variable (linear regression) and cognitive status as a binary variable (> 24, no cognitive impairment; <10, impairment) (logistic regression). Results Both variations yielded the same polymorphisms, including a well-known marker of dementia, rs429358in the APOE gene. Molecular dynamics simulations showed that this polymorphism leads to changes in the structure of alpha helices and the mobility of the lipid-binding domain in the APOE protein. Conclusion These changes, along with higher LDL and total cholesterol levels, could be the mechanism underlying the development of cognitive impairment in older adults. However, this polymorphism is not the only determining factor in cognitive impairment. The polygenic risk score model included 45 polymorphisms (ROC AUC 69%), further confirming the multifactorial nature of this condition. Our findings, particularly the results of PRS modeling, could contribute to the development of early detection strategies for predisposition to cognitive impairment in older adults.
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Affiliation(s)
- D. A. Kashtanova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - A. A. Mamchur
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - I. H. Dzhumaniyazova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - M. V. Ivanov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - V. V. Erema
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - E. A. Zelenova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - A. Y. Yakovchik
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - M. S. Gusakova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - A. M. Rumyantseva
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - M. V. Terekhov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - L. R. Matkava
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - A. A. Akopyan
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - I. D. Strazhesko
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - V. S. Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - V. V. Makarov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - S. A. Kraevoy
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
| | - O. N. Tkacheva
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - S. M. Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, Federal Medical Biological Agency, Moscow, Russia
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Furman S, Green K, Lane TE. COVID-19 and the impact on Alzheimer's disease pathology. J Neurochem 2023:10.1111/jnc.15985. [PMID: 37850241 PMCID: PMC11024062 DOI: 10.1111/jnc.15985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has rapidly escalated into a global pandemic that primarily affects older and immunocompromised individuals due to underlying clinical conditions and suppressed immune responses. Furthermore, COVID-19 patients exhibit a spectrum of neurological symptoms, indicating that COVID-19 can affect the brain in a variety of manners. Many studies, past and recent, suggest a connection between viral infections and an increased risk of neurodegeneration, raising concerns about the neurological effects of COVID-19 and the possibility that it may contribute to Alzheimer's disease (AD) onset or worsen already existing AD pathology through inflammatory processes given that both COVID-19 and AD share pathological features and risk factors. This leads us to question whether COVID-19 is a risk factor for AD and how these two conditions might influence each other. Considering the extensive reach of the COVID-19 pandemic and the devastating impact of the ongoing AD pandemic, their combined effects could have significant public health consequences worldwide.
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Affiliation(s)
- Susana Furman
- Department of Neurobiology & Behavior, School of Biological Sciences, University of California, Irvine 92697
| | - Kim Green
- Department of Neurobiology & Behavior, School of Biological Sciences, University of California, Irvine 92697
| | - Thomas E. Lane
- Department of Neurobiology & Behavior, School of Biological Sciences, University of California, Irvine 92697
- Department of Molecular Biology & Biochemistry, School of Biological Sciences, University of California, Irvine 92697, USA
- Center for Virus Research, University of California, Irvine 92697, USA
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33
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Wood ME, Xiong LY, Wong YY, Buckley RF, Swardfager W, Masellis M, Lim ASP, Nichols E, Joie RL, Casaletto KB, Kumar RG, Dams-O'Connor K, Palta P, George KM, Satizabal CL, Barnes LL, Schneider JA, Binet AP, Villeneuve S, Pa J, Brickman AM, Black SE, Rabin JS. Sex differences in associations between APOE ε2 and longitudinal cognitive decline. Alzheimers Dement 2023; 19:4651-4661. [PMID: 36994910 PMCID: PMC10544702 DOI: 10.1002/alz.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 03/31/2023]
Abstract
INTRODUCTION We examined whether sex modifies the association between APOE ε2 and cognitive decline in two independent samples. METHODS We used observational data from cognitively unimpaired non-Hispanic White (NHW) and non-Hispanic Black (NHB) adults. Linear mixed models examined interactive associations of APOE genotype (ε2 or ε4 carrier vs. ε3/ε3) and sex on cognitive decline in NHW and NHB participants separately. RESULTS In both Sample 1 (N = 9766) and Sample 2 (N = 915), sex modified the association between APOE ε2 and cognitive decline in NHW participants. Specifically, relative to APOE ε3/ε3, APOE ε2 protected against cognitive decline in men but not women. Among APOE ε2 carriers, men had slower decline than women. Among APOE ε3/ε3 carriers, cognitive trajectories did not differ between sexes. There were no sex-specific associations of APOE ε2 with cognition in NHB participants (N = 2010). DISCUSSION In NHW adults, APOE ε2 may protect men but not women against cognitive decline. HIGHLIGHTS We studied sex-specific apolipoprotein E (APOE) ε2 effects on cognitive decline. In non-Hispanic White (NHW) adults, APOE ε2 selectively protects men against decline. Among men, APOE ε2 was more protective than APOE ε3/ε3. In women, APOE ε2 was no more protective than APOE ε3/ε3. Among APOE ε2 carriers, men had slower decline than women. There were no sex-specific APOE ε2 effects in non-Hispanic Black (NHB) adults.
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Affiliation(s)
- Madeline E Wood
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Rehabilitation Sciences Institute, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Y Xiong
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Yuen Yan Wong
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Rachel F Buckley
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Florey Institute, University of Melbourne, Parkville, Victoria, Australia
- Melbourne School of Psychological Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Walter Swardfager
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Mario Masellis
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Andrew S P Lim
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Emma Nichols
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Renaud La Joie
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, California, USA
| | - Kaitlin B Casaletto
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, California, USA
| | - Raj G Kumar
- Department of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristen Dams-O'Connor
- Department of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Priya Palta
- Departments of Medicine and Epidemiology, Columbia University Irving Medical Center, New York, New York, USA
| | - Kristen M George
- Department of Public Health Sciences, University of California Davis School of Medicine, Davis, California, USA
| | - Claudia L Satizabal
- Department of Population Health Science and Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, Texas, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Alexa Pichette Binet
- Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sylvia Villeneuve
- Centre for Studies on Prevention of Alzheimer's Disease (StoP-AD), Douglas Mental Health University Institute, Centre for Studies on the Prevention of Alzheimer's Disease (StoP-AD), Montreal, Quebec, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Quebec, Canada
| | - Judy Pa
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Department of Neurology, University of Southern California, Los Angeles, California, USA
| | - Adam M Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Sandra E Black
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer S Rabin
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Rehabilitation Sciences Institute, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
- Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
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Orobets KS, Karamyshev AL. Amyloid Precursor Protein and Alzheimer's Disease. Int J Mol Sci 2023; 24:14794. [PMID: 37834241 PMCID: PMC10573485 DOI: 10.3390/ijms241914794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative disorders associated with age or inherited mutations. It is characterized by severe dementia in the late stages that affect memory, cognitive functions, and daily life overall. AD progression is linked to the accumulation of cytotoxic amyloid beta (Aβ) and hyperphosphorylated tau protein combined with other pathological features such as synaptic loss, defective energy metabolism, imbalances in protein, and metal homeostasis. Several treatment options for AD are under investigation, including antibody-based therapy and stem cell transplantation. Amyloid precursor protein (APP) is a membrane protein considered to play a main role in AD pathology. It is known that APP in physiological conditions follows a non-amyloidogenic pathway; however, it can proceed to an amyloidogenic scenario, which leads to the generation of extracellular deleterious Aβ plaques. Not all steps of APP biogenesis are clear so far, and these questions should be addressed in future studies. AD is a complex chronic disease with many factors that contribute to disease progression.
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Affiliation(s)
| | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
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35
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Coleman C, Wang M, Wang E, Micallef C, Shao Z, Vicari JM, Li Y, Yu K, Cai D, Peng J, Haroutunian V, Fullard JF, Bendl J, Zhang B, Roussos P. Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease. Sci Data 2023; 10:602. [PMID: 37684260 PMCID: PMC10491684 DOI: 10.1038/s41597-023-02507-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia worldwide, with a projection of 151 million cases by 2050. Previous genetic studies have identified three main genes associated with early-onset familial Alzheimer's disease, however this subtype accounts for less than 5% of total cases. Next-generation sequencing has been well established and holds great promise to assist in the development of novel therapeutics as well as biomarkers to prevent or slow the progression of this devastating disease. Here we present a public resource of functional genomic data from the parahippocampal gyrus of 201 postmortem control, mild cognitively impaired (MCI) and AD individuals from the Mount Sinai brain bank, of which whole-genome sequencing (WGS), and bulk RNA sequencing (RNA-seq) were previously published. The genomic data include bulk proteomics and DNA methylation, as well as cell-type-specific RNA-seq and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) data. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource available on the Synapse platform at https://doi.org/10.7303/syn51180043.2 .
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Affiliation(s)
- Claire Coleman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Courtney Micallef
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhiping Shao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James M Vicari
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yuxin Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Dongming Cai
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA.
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36
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Lee WP, Choi SH, Shea MG, Cheng PL, Dombroski BA, Pitsillides AN, Heard-Costa NL, Wang H, Bulekova K, Kuzma AB, Leung YY, Farrell JJ, Lin H, Naj A, Blue EE, Nusetor F, Wang D, Boerwinkle E, Bush WS, Zhang X, De Jager PL, Dupuis J, Farrer LA, Fornage M, Martin E, Pericak-Vance M, Seshadri S, Wijsman EM, Wang LS, Schellenberg GD, Destefano AL, Haines JL, Peloso GM. Association of Common and Rare Variants with Alzheimer's Disease in over 13,000 Diverse Individuals with Whole-Genome Sequencing from the Alzheimer's Disease Sequencing Project. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.01.23294953. [PMID: 37693521 PMCID: PMC10491367 DOI: 10.1101/2023.09.01.23294953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Alzheimer's Disease (AD) is a common disorder of the elderly that is both highly heritable and genetically heterogeneous. Here, we investigated the association between AD and both common variants and aggregates of rare coding and noncoding variants in 13,371 individuals of diverse ancestry with whole genome sequence (WGS) data. Pooled-population analyses identified genetic variants in or near APOE, BIN1, and LINC00320 significantly associated with AD (p < 5×10-8). Population-specific analyses identified a haplotype on chromosome 14 including PSEN1 associated with AD in Hispanics, further supported by aggregate testing of rare coding and noncoding variants in this region. Finally, we observed suggestive associations (p < 5×10-5) of aggregates of rare coding rare variants in ABCA7 among non-Hispanic Whites (p=5.4×10-6), and rare noncoding variants in the promoter of TOMM40 distinct of APOE in pooled-population analyses (p=7.2×10-8). Complementary pooled-population and population-specific analyses offered unique insights into the genetic architecture of AD.
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Affiliation(s)
- Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Margaret G Shea
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Nancy L Heard-Costa
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katia Bulekova
- Research Computing Services, Information Services & Technology, Boston University, Boston, MA, USA
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Adam Naj
- Department of Biostatistics, Epidemiology, and Informatics, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth E Blue
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Frederick Nusetor
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Dongyu Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaoling Zhang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Lindsay A Farrer
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
- Department of Ophthalmology, Department of Medicine, Boston University Medical School, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eden Martin
- John P Hussman Institute for Human Genomics, Miami, FL, USA
- John T Macdonald Department of Human Genetics, Miami, FL, USA
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret Pericak-Vance
- John P Hussman Institute for Human Genomics, Miami, FL, USA
- John T Macdonald Department of Human Genetics, Miami, FL, USA
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ellen M Wijsman
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anita L Destefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
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37
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Mehta K, Mohebbi M, Pasco JA, Williams LJ, Sui SX, Walder K, Ng BL, Gupta VB. A plasma protein signature associated with cognitive function in men without severe cognitive impairment. Alzheimers Res Ther 2023; 15:148. [PMID: 37658429 PMCID: PMC10472730 DOI: 10.1186/s13195-023-01294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND A minimally invasive blood-based assessment of cognitive function could be a promising screening strategy to identify high-risk groups for the incidence of Alzheimer's disease. METHODS The study included 448 cognitively unimpaired men (mean age 64.1 years) drawn from the Geelong Osteoporosis Study. A targeted mass spectrometry-based proteomic assay was performed to measure the abundance levels of 269 plasma proteins followed by linear regression analyses adjusted for age and APOE ε4 carrier status to identify the biomarkers related to overall cognitive function. Furthermore, two-way interactions were conducted to see whether Alzheimer's disease-linked genetic variants or health conditions modify the association between biomarkers and cognitive function. RESULTS Ten plasma proteins showed an association with overall cognitive function. This association was modified by allelic variants in genes ABCA7, CLU, BDNF and MS4A6A that have been previously linked to Alzheimer's disease. Modifiable health conditions such as mood disorders and poor bone health, which are postulated to be risk factors for Alzheimer's disease, also impacted the relationship observed between protein marker levels and cognition. In addition to the univariate analyses, an 11-feature multianalyte model was created using the least absolute shrinkage and selection operator regression that identified 10 protein features and age associated with cognitive function. CONCLUSIONS Overall, the present study revealed plasma protein candidates that may contribute to the development of a blood-based screening test for identifying early cognitive changes. This study also highlights the importance of considering other risk factors in elucidating the relationship between biomarkers and cognition, an area that remains largely unexplored.
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Affiliation(s)
- Kanika Mehta
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mohammadreza Mohebbi
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Biostatistics Unit, Faculty of Health, Deakin University, Burwood, VIC, Australia
| | - Julie A Pasco
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Department of Medicine-Western Health, The University of Melbourne, St Albans, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Prahran, VIC, Australia
- Barwon Health, Geelong, VIC, Australia
| | - Lana J Williams
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
- Barwon Health, Geelong, VIC, Australia
| | - Sophia X Sui
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
| | - Ken Walder
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia
| | - Boon Lung Ng
- Department of Geriatric Medicine, Barwon Health, Geelong, VIC, Australia
| | - Veer Bala Gupta
- Deakin University, IMPACT - The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, VIC, 3216, Australia.
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Letko A, Brülisauer F, Häfliger IM, Corr E, Scholes S, Drögemüller C. Loss-of-function variant in the ovine TMCO6 gene in North Country Cheviot sheep with motor neuron disease. Genomics 2023; 115:110689. [PMID: 37488055 DOI: 10.1016/j.ygeno.2023.110689] [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: 05/03/2023] [Revised: 06/27/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
In North Country Cheviot lambs with early-onset progressive ataxia and motor neuron degeneration, whole-genome sequencing identified a homozygous loss-of-function variant in the ovine transmembrane and coiled-coil domains (TMCO6) gene. The familial recessive form of motor neuron disease in sheep is due to a pathogenic 4 bp deletion leading to a 50% protein truncation that is assumed to result in the absence of a functional TMCO6. This uncharacterised protein is proposed to interact with ubiquilin 1 which is associated with Alzheimer's disease, whereas sporadic forms of amyotrophic lateral sclerosis are caused by variants in UBQLN2. Our findings provide a first spontaneous animal model for TMCO6, which could have implications in the studies of other comparative neurodegenerative diseases. In addition, these results will allow the design of a genetic test to prevent the occurrence of this fatal disease in the affected sheep population.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
| | - Franz Brülisauer
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom.
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
| | - Eilidh Corr
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom.
| | - Sandra Scholes
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
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Naletova I, Schmalhausen E, Tomasello B, Pozdyshev D, Attanasio F, Muronetz V. The role of sperm-specific glyceraldehyde-3-phosphate dehydrogenase in the development of pathologies-from asthenozoospermia to carcinogenesis. Front Mol Biosci 2023; 10:1256963. [PMID: 37711387 PMCID: PMC10499166 DOI: 10.3389/fmolb.2023.1256963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
The review considers various aspects of the influence of the glycolytic enzyme, sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) on the energy metabolism of spermatozoa and on the occurrence of several pathologies both in spermatozoa and in other cells. GAPDS is a unique enzyme normally found only in mammalian spermatozoa. GAPDS provides movement of the sperm flagellum through the ATP formation in glycolytic reactions. Oxidation of cysteine residues in GAPDS results in inactivation of the enzyme and decreases sperm motility. In particular, reduced sperm motility in diabetes can be associated with GAPDS oxidation by superoxide anion produced during glycation reactions. Mutations in GAPDS gene lead in the loss of motility, and in some cases, disrupts the formation of the structural elements of the sperm flagellum, in which the enzyme incorporates during spermiogenesis. GAPDS activation can be used to increase the spermatozoa fertility, and inhibitors of this enzyme are being tried as contraceptives. A truncated GAPDS lacking the N-terminal fragment of 72 amino acids that attaches the enzyme to the sperm flagellum was found in melanoma cell lines and then in specimens of melanoma and other tumors. Simultaneous production of the somatic form of GAPDH and sperm-specific GAPDS in cancer cells leads to a reorganization of their energy metabolism, which is accompanied by a change in the efficiency of metastasis of certain forms of cancer. Issues related to the use of GAPDS for the diagnosis of cancer, as well as the possibility of regulating the activity of this enzyme to prevent metastasis, are discussed.
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Affiliation(s)
- Irina Naletova
- Institute of Crystallography, National Council of Research, Catania, Italy
| | - Elena Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Denis Pozdyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Butlerov Chemical Institute, Kazan Federal University, Kazan, Russia
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Chandy T. Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects. Dement Neuropsychol 2023; 17:e20220025. [PMID: 37577182 PMCID: PMC10417152 DOI: 10.1590/1980-5764-dn-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 08/15/2023] Open
Abstract
Clinical diagnosis of several neurodegenerative disorders based on clinical phenotype is challenging due to its heterogeneous nature and overlapping disease manifestations. Therefore, the identification of underlying genetic mechanisms is of paramount importance for better diagnosis and therapeutic regimens. With the emergence of next-generation sequencing, it becomes easier to identify all gene variants in the genome simultaneously, with a system-wide and unbiased approach. Presently various bioinformatics databases are maintained on discovered gene variants and phenotypic indications are available online. Since individuals are unique in their genome, evaluation based on their genetic makeup helps evolve the diagnosis, counselling, and treatment process at the personal level. This article aims to briefly summarize the utilization of next-generation sequencing in deciphering the genetic causes of Alzheimer's disease and address the limitations of whole genome and exome sequencing.
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Affiliation(s)
- Tijimol Chandy
- MedGenome Labs Pvt. Ltd., Bangalore-560100, Karnataka, India
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Quan M, Cao S, Wang Q, Wang S, Jia J. Genetic Phenotypes of Alzheimer's Disease: Mechanisms and Potential Therapy. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:333-349. [PMID: 37589021 PMCID: PMC10425323 DOI: 10.1007/s43657-023-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 08/18/2023]
Abstract
Years of intensive research has brought us extensive knowledge on the genetic and molecular factors involved in Alzheimer's disease (AD). In addition to the mutations in the three main causative genes of familial AD (FAD) including presenilins and amyloid precursor protein genes, studies have identified several genes as the most plausible genes for the onset and progression of FAD, such as triggering receptor expressed on myeloid cells 2, sortilin-related receptor 1, and adenosine triphosphate-binding cassette transporter subfamily A member 7. The apolipoprotein E ε4 allele is reported to be the strongest genetic risk factor for sporadic AD (SAD), and it also plays an important role in FAD. Here, we reviewed recent developments in genetic and molecular studies that contributed to the understanding of the genetic phenotypes of FAD and compared them with SAD. We further reviewed the advancements in AD gene therapy and discussed the future perspectives based on the genetic phenotypes.
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Affiliation(s)
- Meina Quan
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
- National Medical Center for Neurological Disorders and National Clinical Research Center for Geriatric Diseases, Beijing, 100053 China
| | - Shuman Cao
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
| | - Qi Wang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
- National Medical Center for Neurological Disorders and National Clinical Research Center for Geriatric Diseases, Beijing, 100053 China
| | - Shiyuan Wang
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
| | - Jianping Jia
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053 China
- National Medical Center for Neurological Disorders and National Clinical Research Center for Geriatric Diseases, Beijing, 100053 China
- Beijing Key Laboratory of Geriatric Cognitive Disorders, Beijing, 100053 China
- Clinical Center for Neurodegenerative Disease and Memory Impairment, Capital Medical University, Beijing, 100053 China
- Center of Alzheimer’s Disease, Collaborative Innovation Center for Brain Disorders, Beijing Institute of Brain Disorders, Capital Medical University, Beijing, 100053 China
- Key Laboratory of Neurodegenerative Diseases, Ministry of Education, Beijing, 100053 China
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Charisis S, Lin H, Ray R, Joehanes R, Beiser AS, Levy D, Seshadri S, Sargurupremraj M, Satizabal CL. Obesity impacts the expression of Alzheimer's disease-related genes: The Framingham Heart Study. Alzheimers Dement 2023; 19:3496-3505. [PMID: 36811231 PMCID: PMC10435662 DOI: 10.1002/alz.12954] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 02/24/2023]
Abstract
INTRODUCTION We investigated associations of obesity with the expression of Alzheimer's disease (AD)-related genes in a large community-based cohort. METHODS The sample consisted of 5619 participants from the Framingham Heart Study. Obesity metrics included body mass index (BMI) and waist-to-hip ratio (WHR). Gene expression was measured for a set of 74 AD-related genes, derived by integrating genome-wide association study results with functional genomics data. RESULTS Obesity metrics were associated with the expression of 21 AD-related genes. The strongest associations were observed with CLU, CD2AP, KLC3, and FCER1G. Unique associations were noted with TSPAN14, SLC24A4 for BMI, and ZSCAN21, BCKDK for WHR. After adjustment for cardiovascular risk factors, 13 associations remained significant for BMI and 8 for WHR. Dichotomous obesity metrics exhibited unique associations with EPHX2 for BMI, and with TSPAN14 for WHR. DISCUSSION Obesity was associated with AD-related gene expression; these findings shed light on the molecular pathways linking obesity to AD.
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Affiliation(s)
- Sokratis Charisis
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Honghuang Lin
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Roshni Ray
- Long School of Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Roby Joehanes
- The Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
| | - Alexa S Beiser
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA
| | - Daniel Levy
- The Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Muralidharan Sargurupremraj
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
- The Framingham Heart Study, Framingham, MA, USA
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Zhao X, Song L, Yang A, Zhang Z, Zhang J, Yang YT, Zhao XM. Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues. Genome Med 2023; 15:56. [PMID: 37488639 PMCID: PMC10364416 DOI: 10.1186/s13073-023-01210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Prioritizing genes that underlie complex brain disorders poses a considerable challenge. Despite previous studies have found that they shared symptoms and heterogeneity, it remained difficult to systematically identify the risk genes associated with them. METHODS By using the CAGE (Cap Analysis of Gene Expression) read alignment files for 439 human cell and tissue types (including primary cells, tissues and cell lines) from FANTOM5 project, we predicted enhancer-promoter interactions (EPIs) of 439 cell and tissue types in human, and examined their reliability. Then we evaluated the genetic heritability of 17 diverse brain disorders and behavioral-cognitive phenotypes in each neural cell type, brain region, and developmental stage. Furthermore, we prioritized genes associated with brain disorders and phenotypes by leveraging the EPIs in each neural cell and tissue type, and analyzed their pleiotropy and functionality for different categories of disorders and phenotypes. Finally, we characterized the spatiotemporal expression dynamics of these associated genes in cells and tissues. RESULTS We found that identified EPIs showed activity specificity and network aggregation in cell and tissue types, and enriched TF binding in neural cells played key roles in synaptic plasticity and nerve cell development, i.e., EGR1 and SOX family. We also discovered that most neurological disorders exhibit heritability enrichment in neural stem cells and astrocytes, while psychiatric disorders and behavioral-cognitive phenotypes exhibit enrichment in neurons. Furthermore, our identified genes recapitulated well-known risk genes, which exhibited widespread pleiotropy between psychiatric disorders and behavioral-cognitive phenotypes (i.e., FOXP2), and indicated expression specificity in neural cell types, brain regions, and developmental stages associated with disorders and phenotypes. Importantly, we showed the potential associations of brain disorders with brain regions and developmental stages that have not been well studied. CONCLUSIONS Overall, our study characterized the gene-enhancer regulatory networks and genetic mechanisms in the human neural cells and tissues, and illustrated the value of reanalysis of publicly available genomic datasets.
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Affiliation(s)
- Xingzhong Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Liting Song
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Anyi Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Zichao Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Jinglong Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
- Internatioal Human Phenome Institutes (Shanghai), Shanghai, 200433, China.
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Kim Y, Lee H. PINNet: a deep neural network with pathway prior knowledge for Alzheimer's disease. Front Aging Neurosci 2023; 15:1126156. [PMID: 37520124 PMCID: PMC10380929 DOI: 10.3389/fnagi.2023.1126156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Identification of Alzheimer's Disease (AD)-related transcriptomic signatures from blood is important for early diagnosis of the disease. Deep learning techniques are potent classifiers for AD diagnosis, but most have been unable to identify biomarkers because of their lack of interpretability. Methods To address these challenges, we propose a pathway information-based neural network (PINNet) to predict AD patients and analyze blood and brain transcriptomic signatures using an interpretable deep learning model. PINNet is a deep neural network (DNN) model with pathway prior knowledge from either the Gene Ontology or Kyoto Encyclopedia of Genes and Genomes databases. Then, a backpropagation-based model interpretation method was applied to reveal essential pathways and genes for predicting AD. Results The performance of PINNet was compared with a DNN model without a pathway. Performances of PINNet outperformed or were similar to those of DNN without a pathway using blood and brain gene expressions, respectively. Moreover, PINNet considers more AD-related genes as essential features than DNN without a pathway in the learning process. Pathway analysis of protein-protein interaction modules of highly contributed genes showed that AD-related genes in blood were enriched with cell migration, PI3K-Akt, MAPK signaling, and apoptosis in blood. The pathways enriched in the brain module included cell migration, PI3K-Akt, MAPK signaling, apoptosis, protein ubiquitination, and t-cell activation. Discussion By integrating prior knowledge about pathways, PINNet can reveal essential pathways related to AD. The source codes are available at https://github.com/DMCB-GIST/PINNet.
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Affiliation(s)
- Yeojin Kim
- Artificial Intelligence Graduate School, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Hyunju Lee
- Artificial Intelligence Graduate School, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
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Vasiljevic E, Koscik RL, Jonaitis E, Betthauser T, Johnson SC, Engelman CD. Cognitive trajectories diverge by genetic risk in a preclinical longitudinal cohort. Alzheimers Dement 2023; 19:3108-3118. [PMID: 36723444 PMCID: PMC10390653 DOI: 10.1002/alz.12920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 02/02/2023]
Abstract
INTRODUCTION We sought to characterize the timing of changes in cognitive trajectories related to genetic risk using the apolipoprotein E (APOE) score, a continuous measure of Alzheimer's disease (AD) risk. We also aimed to determine whether that timing was different when genetic risk was measured using an AD polygenic risk score (PRS) that contains APOE. METHODS We analyzed trajectories (N ≈1135) for four neuropsychological composite scores using mixed effects regression for longitudinal change across APOE scores and PRS of participants in the Wisconsin Registry for Alzheimer's Prevention, a longitudinal study of adults aged 40 to 70 at baseline, with a median participant follow-up time of 7.8 years. RESULTS We found a significant non-linear age-by-APOE score interaction in predicting cognitive decline. Cognitive trajectories diverged by APOE score at approximately 65 years of age. A 0.5 standard deviation difference in cognition between extreme percentiles of the PRS was predicted to occur 1 to 2 years before that of the APOE score. DISCUSSION Cognitive decline differs across time and APOE score. Estimates did not substantially shift with the AD PRS. HIGHLIGHTS The apolipoprotein E (APOE) score, a continuous measure, accounts for non-linear genetic risk of Alzheimer's disease. Non-linear age interacts with the APOE score to affect cognition. Cognitive decline starts to differ by APOE score levels at approximately age 65. Cognitive decline timing by polygenic risk (including APOE) is similar to APOE alone.
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Affiliation(s)
- Eva Vasiljevic
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, 610 Walnut Dr., Madison, WI 53726, USA
- Center for Demography of Health and Aging, University of Wisconsin-Madison, 1180 Observatory Drive Madison, WI 53706, USA
| | - Rebecca Langhough Koscik
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health, 610 Walnut Street, 9th Floor, Madison, WI 53726, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, MC 2420, Madison, Wisconsin 53792, USA
| | - Erin Jonaitis
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health, 610 Walnut Street, 9th Floor, Madison, WI 53726, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, MC 2420, Madison, Wisconsin 53792, USA
| | - Tobey Betthauser
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, MC 2420, Madison, Wisconsin 53792, USA
- Department of Medicine, University of Wisconsin-Madison, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Sterling C. Johnson
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health, 610 Walnut Street, 9th Floor, Madison, WI 53726, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, MC 2420, Madison, Wisconsin 53792, USA
- Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, 2500 Overlook Terrace, Madison, WI 53705, USA
| | - Corinne D. Engelman
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, 610 Walnut Dr., Madison, WI 53726, USA
- Wisconsin Alzheimer’s Institute, University of Wisconsin School of Medicine and Public Health, 610 Walnut Street, 9th Floor, Madison, WI 53726, USA
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, 600 Highland Avenue, MC 2420, Madison, Wisconsin 53792, USA
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Lambert JC, Ramirez A, Grenier-Boley B, Bellenguez C. Step by step: towards a better understanding of the genetic architecture of Alzheimer's disease. Mol Psychiatry 2023; 28:2716-2727. [PMID: 37131074 PMCID: PMC10615767 DOI: 10.1038/s41380-023-02076-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023]
Abstract
Alzheimer's disease (AD) is considered to have a large genetic component. Our knowledge of this component has progressed over the last 10 years, thanks notably to the advent of genome-wide association studies and the establishment of large consortia that make it possible to analyze hundreds of thousands of cases and controls. The characterization of dozens of chromosomal regions associated with the risk of developing AD and (in some loci) the causal genes responsible for the observed disease signal has confirmed the involvement of major pathophysiological pathways (such as amyloid precursor protein metabolism) and opened up new perspectives (such as the central role of microglia and inflammation). Furthermore, large-scale sequencing projects are starting to reveal the major impact of rare variants - even in genes like APOE - on the AD risk. This increasingly comprehensive knowledge is now being disseminated through translational research; in particular, the development of genetic risk/polygenic risk scores is helping to identify the subpopulations more at risk or less at risk of developing AD. Although it is difficult to assess the efforts still needed to comprehensively characterize the genetic component of AD, several lines of research can be improved or initiated. Ultimately, genetics (in combination with other biomarkers) might help to redefine the boundaries and relationships between various neurodegenerative diseases.
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Affiliation(s)
- Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Neurodegenerative diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- Department of Psychiatry & Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Benjamin Grenier-Boley
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Céline Bellenguez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
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Danziger R, Fuchs DT, Koronyo Y, Rentsendorj A, Sheyn J, Hayden EY, Teplow DB, Black KL, Fuchs S, Bernstein KE, Koronyo-Hamaoui M. The effects of enhancing angiotensin converting enzyme in myelomonocytes on ameliorating Alzheimer's-related disease and preserving cognition. Front Physiol 2023; 14:1179315. [PMID: 37427403 PMCID: PMC10326285 DOI: 10.3389/fphys.2023.1179315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
This review examines the role of angiotensin-converting enzyme (ACE) in the context of Alzheimer's disease (AD) and its potential therapeutic value. ACE is known to degrade the neurotoxic 42-residue long alloform of amyloid β-protein (Aβ42), a peptide strongly associated with AD. Previous studies in mice, demonstrated that targeted overexpression of ACE in CD115+ myelomonocytic cells (ACE10 models) improved their immune responses to effectively reduce viral and bacterial infection, tumor growth, and atherosclerotic plaque. We further demonstrated that introducing ACE10 myelomonocytes (microglia and peripheral monocytes) into the double transgenic APPSWE/PS1ΔE9 murine model of AD (AD+ mice), diminished neuropathology and enhanced the cognitive functions. These beneficial effects were dependent on ACE catalytic activity and vanished when ACE was pharmacologically blocked. Moreover, we revealed that the therapeutic effects in AD+ mice can be achieved by enhancing ACE expression in bone marrow (BM)-derived CD115+ monocytes alone, without targeting central nervous system (CNS) resident microglia. Following blood enrichment with CD115+ ACE10-monocytes versus wild-type (WT) monocytes, AD+ mice had reduced cerebral vascular and parenchymal Aβ burden, limited microgliosis and astrogliosis, as well as improved synaptic and cognitive preservation. CD115+ ACE10-versus WT-monocyte-derived macrophages (Mo/MΦ) were recruited in higher numbers to the brains of AD+ mice, homing to Aβ plaque lesions and exhibiting a highly Aβ-phagocytic and anti-inflammatory phenotype (reduced TNFα/iNOS and increased MMP-9/IGF-1). Moreover, BM-derived ACE10-Mo/MΦ cultures had enhanced capability to phagocytose Aβ42 fibrils, prion-rod-like, and soluble oligomeric forms that was associated with elongated cell morphology and expression of surface scavenger receptors (i.e., CD36, Scara-1). This review explores the emerging evidence behind the role of ACE in AD, the neuroprotective properties of monocytes overexpressing ACE and the therapeutic potential for exploiting this natural mechanism for ameliorating AD pathogenesis.
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Affiliation(s)
- Ron Danziger
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dieu-Trang Fuchs
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
| | - Yosef Koronyo
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
| | - Altan Rentsendorj
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
| | - Julia Sheyn
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
| | - Eric Y. Hayden
- Department of Neurology, David Geffen School of Medicine at UCLA, Mary S. Easton Center for Alzheimer’s Disease Research at UCLA, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, United States
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Mary S. Easton Center for Alzheimer’s Disease Research at UCLA, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, United States
| | - Keith L. Black
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
| | - Sebastien Fuchs
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Kenneth E. Bernstein
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Maya Koronyo-Hamaoui
- Department of Neurosurgery, Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical center, Los Angeles, CA, United States
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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48
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Guo L, Cao J, Hou J, Li Y, Huang M, Zhu L, Zhang L, Lee Y, Duarte ML, Zhou X, Wang M, Liu CC, Martens Y, Chao M, Goate A, Bu G, Haroutunian V, Cai D, Zhang B. Sex specific molecular networks and key drivers of Alzheimer's disease. Mol Neurodegener 2023; 18:39. [PMID: 37340466 PMCID: PMC10280841 DOI: 10.1186/s13024-023-00624-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 05/08/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a progressive and age-associated neurodegenerative disorder that affects women disproportionally. However, the underlying mechanisms are poorly characterized. Moreover, while the interplay between sex and ApoE genotype in AD has been investigated, multi-omics studies to understand this interaction are limited. Therefore, we applied systems biology approaches to investigate sex-specific molecular networks of AD. METHODS We integrated large-scale human postmortem brain transcriptomic data of AD from two cohorts (MSBB and ROSMAP) via multiscale network analysis and identified key drivers with sexually dimorphic expression patterns and/or different responses to APOE genotypes between sexes. The expression patterns and functional relevance of the top sex-specific network driver of AD were further investigated using postmortem human brain samples and gene perturbation experiments in AD mouse models. RESULTS Gene expression changes in AD versus control were identified for each sex. Gene co-expression networks were constructed for each sex to identify AD-associated co-expressed gene modules shared by males and females or specific to each sex. Key network regulators were further identified as potential drivers of sex differences in AD development. LRP10 was identified as a top driver of the sex differences in AD pathogenesis and manifestation. Changes of LRP10 expression at the mRNA and protein levels were further validated in human AD brain samples. Gene perturbation experiments in EFAD mouse models demonstrated that LRP10 differentially affected cognitive function and AD pathology in sex- and APOE genotype-specific manners. A comprehensive mapping of brain cells in LRP10 over-expressed (OE) female E4FAD mice suggested neurons and microglia as the most affected cell populations. The female-specific targets of LRP10 identified from the single cell RNA-sequencing (scRNA-seq) data of the LRP10 OE E4FAD mouse brains were significantly enriched in the LRP10-centered subnetworks in female AD subjects, validating LRP10 as a key network regulator of AD in females. Eight LRP10 binding partners were identified by the yeast two-hybrid system screening, and LRP10 over-expression reduced the association of LRP10 with one binding partner CD34. CONCLUSIONS These findings provide insights into key mechanisms mediating sex differences in AD pathogenesis and will facilitate the development of sex- and APOE genotype-specific therapies for AD.
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Affiliation(s)
- Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jiqing Cao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
| | - Jianwei Hou
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
| | - Yonghe Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Min Huang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
| | - Li Zhu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
| | - Larry Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
| | - Yeji Lee
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
| | - Mariana Lemos Duarte
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Yuka Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Michael Chao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alison Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Vahram Haroutunian
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA
- Alzheimer Disease Research Center Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J Peters VA Medical Center, MIRECC, Bronx, NY, 10468, USA
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J Peters VA Medical Center, Research & Development, Bronx, NY, 10468, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Alzheimer Disease Research Center Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Miao J, Ma H, Yang Y, Liao Y, Lin C, Zheng J, Yu M, Lan J. Microglia in Alzheimer's disease: pathogenesis, mechanisms, and therapeutic potentials. Front Aging Neurosci 2023; 15:1201982. [PMID: 37396657 PMCID: PMC10309009 DOI: 10.3389/fnagi.2023.1201982] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by protein aggregation in the brain. Recent studies have revealed the critical role of microglia in AD pathogenesis. This review provides a comprehensive summary of the current understanding of microglial involvement in AD, focusing on genetic determinants, phenotypic state, phagocytic capacity, neuroinflammatory response, and impact on synaptic plasticity and neuronal regulation. Furthermore, recent developments in drug discovery targeting microglia in AD are reviewed, highlighting potential avenues for therapeutic intervention. This review emphasizes the essential role of microglia in AD and provides insights into potential treatments.
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Affiliation(s)
- Jifei Miao
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Haixia Ma
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yang Yang
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yuanpin Liao
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Cui Lin
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Juanxia Zheng
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Muli Yu
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Jiao Lan
- Shenzhen Bao’an Traditional Chinese Medicine Hospital, Shenzhen, China
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50
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Trindade D, Cachide M, Soares Martins T, Guedes S, Rosa IM, da Cruz e Silva OA, Henriques AG. Monitoring clusterin and fibrillar structures in aging and dementia. AGING BRAIN 2023; 3:100080. [PMID: 37346145 PMCID: PMC10279921 DOI: 10.1016/j.nbas.2023.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Objective Clusterin is involved in a variety of physiological processes, including proteostasis. Several clusterin polymorphisms were associated with an increased risk of developing Alzheimer's disease, the world-leading cause of dementia. Herein, the effect of a clusterin polymorphism, aging and dementia in the levels of clusterin in human plasma were analysed in a primary care-based cohort, and the association of this chaperone with fibrillar structures discussed. Methods 64 individuals with dementia (CDR≥1) and 64 age- and sex-matched Controls from a Portuguese cohort were genotyped for CLU rs1136000 polymorphism, and the plasma levels of clusterin and fibrils were assessed. Results An increased prevalence of the CC genotype was observed for the dementia group, although no significant robustness was achieved. CLU rs11136000 SNP did not significantly change plasma clusterin levels in demented individuals. Instead, clusterin levels decreased with aging and even more in individuals with dementia. Importantly, plasma clusterin levels correlated with the presence of fibrillar structures in Control individuals, but not in those with dementia. Conclusion This study reveals a significant decrease in plasma clusterin in demented individuals with aging, which related to altered clusterin-fibrils dynamics. Potentially, plasma clusterin and its association with fibrillar structures can be used to monitor dementia progression along aging.
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Affiliation(s)
| | | | | | | | | | | | - Ana Gabriela Henriques
- Corresponding author at: Neuroscience and Signaling Group, Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal.
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