1
|
Yu M, Risacher SL, Nho KT, Wen Q, Oblak AL, Unverzagt FW, Apostolova LG, Farlow MR, Brosch JR, Clark DG, Wang S, Deardorff R, Wu YC, Gao S, Sporns O, Saykin AJ. Spatial transcriptomic patterns underlying amyloid-β and tau pathology are associated with cognitive dysfunction in Alzheimer's disease. Cell Rep 2024; 43:113691. [PMID: 38244198 PMCID: PMC10926093 DOI: 10.1016/j.celrep.2024.113691] [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: 07/13/2023] [Revised: 11/29/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
Amyloid-β (Aβ) and tau proteins accumulate within distinct neuronal systems in Alzheimer's disease (AD). Although it is not clear why certain brain regions are more vulnerable to Aβ and tau pathologies than others, gene expression may play a role. We study the association between brain-wide gene expression profiles and regional vulnerability to Aβ (gene-to-Aβ associations) and tau (gene-to-tau associations) pathologies by leveraging two large independent AD cohorts. We identify AD susceptibility genes and gene modules in a gene co-expression network with expression profiles specifically related to regional vulnerability to Aβ and tau pathologies in AD. In addition, we identify distinct biochemical pathways associated with the gene-to-Aβ and the gene-to-tau associations. These findings may explain the discordance between regional Aβ and tau pathologies. Finally, we propose an analytic framework, linking the identified gene-to-pathology associations to cognitive dysfunction in AD at the individual level, suggesting potential clinical implication of the gene-to-pathology associations.
Collapse
Affiliation(s)
- Meichen Yu
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Network Science Institute, Bloomington, IN, USA.
| | - Shannon L Risacher
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik T Nho
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Network Science Institute, Bloomington, IN, USA
| | - Qiuting Wen
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adrian L Oblak
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Frederick W Unverzagt
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liana G Apostolova
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Martin R Farlow
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jared R Brosch
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David G Clark
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sophia Wang
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rachael Deardorff
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yu-Chien Wu
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sujuan Gao
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Olaf Sporns
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Network Science Institute, Bloomington, IN, USA; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Andrew J Saykin
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA; Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Network Science Institute, Bloomington, IN, USA.
| |
Collapse
|
2
|
Yu M, Risacher SL, Nho KT, Wen Q, Oblak AL, Unverzagt FW, Apostolova LG, Farlow MR, Brosch JR, Clark DG, Wang S, Deardorff R, Wu YC, Gao S, Sporns O, Saykin AJ. Spatial transcriptomic patterns underlying regional vulnerability to amyloid-β and tau pathologies and their relationships to cognitive dysfunction in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.12.23294017. [PMID: 37645867 PMCID: PMC10462206 DOI: 10.1101/2023.08.12.23294017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Amyloid-β (Aβ) and tau proteins accumulate within distinct neuronal systems in Alzheimer's disease (AD). Although it is not clear why certain brain regions are more vulnerable to Aβ and tau pathologies than others, gene expression may play a role. We studied the association between brain-wide gene expression profiles and regional vulnerability to Aβ (gene-to-Aβ associations) and tau (gene-to-tau associations) pathologies leveraging two large independent cohorts (n = 715) of participants along the AD continuum. We identified several AD susceptibility genes and gene modules in a gene co-expression network with expression profiles related to regional vulnerability to Aβ and tau pathologies in AD. In particular, we found that the positive APOE -to-tau association was only seen in the AD cohort, whereas patients with AD and frontotemporal dementia shared similar positive MAPT -to-tau association. Some AD candidate genes showed sex-dependent negative gene-to-Aβ and gene-to-tau associations. In addition, we identified distinct biochemical pathways associated with the gene-to-Aβ and the gene-to-tau associations. Finally, we proposed a novel analytic framework, linking the identified gene-to-pathology associations to cognitive dysfunction in AD at the individual level, suggesting potential clinical implication of the gene-to-pathology associations. Taken together, our study identified distinct gene expression profiles and biochemical pathways that may explain the discordance between regional Aβ and tau pathologies, and filled the gap between gene-to-pathology associations and cognitive dysfunction in individual AD patients that may ultimately help identify novel personalized pathogenetic biomarkers and therapeutic targets. One Sentence Summary We identified replicable cognition-related associations between regional gene expression profiles and selectively regional vulnerability to amyloid-β and tau pathologies in AD.
Collapse
|
3
|
Chu YN, Akahori A, Takatori S, Tomita T. Pathological Roles of INPP5D in Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:289-301. [PMID: 37525057 DOI: 10.1007/978-3-031-31978-5_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Current hypothesis of Alzheimer's disease (AD) postulates that amyloid β (Aβ) deposition in the brain causes tau inclusion in neurons and leads to cognitive decline. The discovery of the genetic association between triggering receptor expressed on myeloid cells 2 (TREM2) with increased AD risk points to a causal link between microglia and AD pathogenesis, and revealed a crucial role of TREM2-dependent clustering of microglia around amyloid plaques that prevents Aβ toxicity to facilitate tau deposition near the plaques. Here we review the physiological and pathological roles of another AD risk gene expressed in microglia, inositol polyphosphate-5-polyphosphatase D (INPP5D), which encodes a phosphoinositide phosphatase. Evidence suggests that its risk polymorphisms alter the expression level and/or function of INPP5D, while concomitantly affecting tau levels in cerebrospinal fluids. In β-amyloidosis mice, INPP5D was upregulated upon Aβ deposition and negatively regulated the microglial clustering toward amyloid plaques. INPP5D seems to exert its function by acting antagonistically at downstream of the TREM2 signaling pathway, suggesting that it is a novel regulator of the protective barrier by microglia. Further studies to elucidate INPP5D's role in AD may help in developing new therapeutic targets for AD treatment.
Collapse
Affiliation(s)
- Yung Ning Chu
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Aika Akahori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sho Takatori
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Taisuke Tomita
- Laboratory of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
4
|
Chang HI, Chang YT, Huang CW, Huang KL, Hsu JL, Hsu SW, Tsai SJ, Chang WN, Lee CC, Huang SH, Chang CC. Structural Covariance Network as an Endophenotype in Alzheimer's Disease-Susceptible Single-Nucleotide Polymorphisms and the Correlations With Cognitive Outcomes. Front Aging Neurosci 2022; 13:721217. [PMID: 34975449 PMCID: PMC8719443 DOI: 10.3389/fnagi.2021.721217] [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: 06/06/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
The cognitive manifestations of Alzheimer’s disease (AD) are related to brain network degeneration, and genetic differences may mediate network degeneration. Several AD-susceptible loci have been reported to involve amyloid or tau cascades; however, their relationships with gray matter (GM) volume and cognitive outcomes have yet to be established. We hypothesized that single-nucleotide polymorphism genotype groups may interact with apolipoprotein E4 (ApoE4) status or independently exert an effect on cognitive outcomes. We also hypothesized that GM structural covariance networks (SCNs) may serve as an endophenotype of the genetic effect, which, in turn, may be related to neurobehavior test scores. Gray matter SCNs were constructed in 324 patients with AD using T1 magnetic resonance imaging with independent component analysis (ICA). We assessed the effects of 15 genetic loci (rs9349407, rs3865444, rs670139, rs744373, rs3851179, rs11136000, rs3764650, rs610932, rs6887649, rs7849530, rs4866650, rs3765728, rs34011, rs6656401, and rs597668) using additive, recessive, and dominant models on cognitive outcomes. Statistical analysis was performed to explore the independent role of each locus, interactions with ApoE4 status, and relationships to GM ICA network intensity score. For outcome measures, we used the Mini-Mental State Examination (MMSE), Cognitive Abilities Screening Instrument (CASI) total score, and short-term memory (STM) subscores, adjusted for the covariates of education, disease duration, and age. Clinically, the CD2AP G allele showed a protective role in MMSE, CASI total, and CASI-STM scores independently or via interactions with non-ApoE4 status, while the CR1 A genotype group was associated with lower STM subscores independent of ApoE4 status. Three loci showed synergic interactions with ApoE4: BIN 1, MS4A6A, and FTMT. Of the 15 meaningful ICA components, 5 SCNs (anterior and posterior hippocampus, right temporal, left thalamus, default mode network) showed relationships with general cognitive performance, in which only the ApoE4 and MS4A6A genotype groups were independently related to the hippocampus network. The genetic loci MS4A6A, BIN1, CLU, CR1, BIN1, PICALM, and FGF1 influenced the networks independently or in synergy. This study suggests that AD-susceptible loci may each exert clinical significance independently through interactions with ApoE4 status or through SCNs as an endophenotype and that this effect is associated with the cognitive outcomes.
Collapse
Affiliation(s)
- Hsin-I Chang
- Department of Neurology, Cognition and Aging Center, Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yu-Tzu Chang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Wei Huang
- Department of Neurology, Cognition and Aging Center, Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Lun Huang
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Neuroscience Research Center, Chang Gung University, Taoyuan City, Taiwan
| | - Jung-Lung Hsu
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Neuroscience Research Center, Chang Gung University, Taoyuan City, Taiwan.,Department of Neurology, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan.,Graduate Institute of Mind, Brain, and Consciousness, Taipei and Brain and Consciousness Research Center, TMU Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shih-Wei Hsu
- Department of Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shih-Jen Tsai
- Psychiatric Department of Taipei Veterans General Hospital, Taipei, Taiwan.,Psychiatric Division, School of Medicine, National Yang-Ming University, Taipei City, Taiwan
| | - Wen-Neng Chang
- Department of Neurology, Cognition and Aging Center, Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chen-Chang Lee
- Department of Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shu-Hua Huang
- Department of Nuclear Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chiung-Chih Chang
- Department of Neurology, Cognition and Aging Center, Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| |
Collapse
|
5
|
Camacho J, Rábano A, Marazuela P, Bonaterra‐Pastra A, Serna G, Moliné T, Ramón y Cajal S, Martínez‐Sáez E, Hernández‐Guillamon M. Association of CD2AP neuronal deposits with Braak neurofibrillary stage in Alzheimer's disease. Brain Pathol 2022; 32:e13016. [PMID: 34514662 PMCID: PMC8713526 DOI: 10.1111/bpa.13016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/25/2021] [Accepted: 07/29/2021] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies have described several genes as genetic susceptibility loci for Alzheimer's disease (AD). Among them, CD2AP encodes CD2-associated protein, a scaffold protein implicated in dynamic actin remodeling and membrane trafficking during endocytosis and cytokinesis. Although a clear link between CD2AP defects and glomerular pathology has been described, little is known about the function of CD2AP in the brain. The aim of this study was to analyze the distribution of CD2AP in the AD brain and its potential associations with tau aggregation and β-amyloid (Aβ) deposition. First, we performed immunohistochemical analysis of CD2AP expression in brain tissue from AD patients and controls (N = 60). Our results showed granular CD2AP immunoreactivity in the human brain endothelium in all samples. In AD cases, no CD2AP was found to be associated with Aβ deposits in vessels or parenchymal plaques. CD2AP neuronal inclusions similar to neurofibrillary tangles (NFT) and neuropil thread-like deposits were found only in AD samples. Moreover, immunofluorescence analysis revealed that CD2AP colocalized with pTau. Regarding CD2AP neuronal distribution, a hierarchical progression from the entorhinal to the temporal and occipital cortex was detected. We found that CD2AP immunodetection in neurons was strongly and positively associated with Braak neurofibrillary stage, independent of age and other pathological hallmarks. To further investigate the association between pTau and CD2AP, we included samples from cases of primary tauopathies (corticobasal degeneration [CBD], progressive supranuclear palsy [PSP], and Pick's disease [PiD]) in our study. Among these cases, CD2AP positivity was only found in PiD samples as neurofibrillary tangle-like and Pick body-like deposits, whereas no neuronal CD2AP deposits were detected in PSP or CBD samples, which suggested an association of CD2AP neuronal expression with 3R-Tau-diseases. In conclusion, our findings open a new road to investigate the complex cellular mechanism underlying the tangle conformation and tau pathology in the brain.
Collapse
Affiliation(s)
- Jessica Camacho
- Pathology DepartmentVall d’Hebron University HospitalBarcelonaSpain
- Morphological Science DepartmentUniversitat Autonoma de BarcelonaBarcelonaSpain
| | - Alberto Rábano
- Neuropathology DepartmentCIEN FoundationAlzheimer’s Centre Queen Sofía FoundationMadridSpain
| | - Paula Marazuela
- Neurovascular Research LaboratoryVall d’Hebron Research InstituteUniversitat Autonoma de BarcelonaBarcelonaSpain
| | - Anna Bonaterra‐Pastra
- Neurovascular Research LaboratoryVall d’Hebron Research InstituteUniversitat Autonoma de BarcelonaBarcelonaSpain
| | - Garazi Serna
- Morphological Science DepartmentUniversitat Autonoma de BarcelonaBarcelonaSpain
- Molecular Oncology GroupVall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Teresa Moliné
- Pathology DepartmentVall d’Hebron University HospitalBarcelonaSpain
| | - Santiago Ramón y Cajal
- Pathology DepartmentVall d’Hebron University HospitalBarcelonaSpain
- Morphological Science DepartmentUniversitat Autonoma de BarcelonaBarcelonaSpain
| | - Elena Martínez‐Sáez
- Pathology DepartmentVall d’Hebron University HospitalBarcelonaSpain
- Morphological Science DepartmentUniversitat Autonoma de BarcelonaBarcelonaSpain
| | - Mar Hernández‐Guillamon
- Neurovascular Research LaboratoryVall d’Hebron Research InstituteUniversitat Autonoma de BarcelonaBarcelonaSpain
| |
Collapse
|
6
|
Tan MS, Yang YX, Xu W, Wang HF, Tan L, Zuo CT, Dong Q, Tan L, Suckling J, Yu JT. Associations of Alzheimer's disease risk variants with gene expression, amyloidosis, tauopathy, and neurodegeneration. Alzheimers Res Ther 2021; 13:15. [PMID: 33419465 PMCID: PMC7792349 DOI: 10.1186/s13195-020-00755-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Genome-wide association studies have identified more than 30 Alzheimer's disease (AD) risk genes, although the detailed mechanism through which all these genes are associated with AD pathogenesis remains unknown. We comprehensively evaluate the roles of the variants in top 30 non-APOE AD risk genes, based on whether these variants were associated with altered mRNA transcript levels, as well as brain amyloidosis, tauopathy, and neurodegeneration. METHODS Human brain gene expression data were obtained from the UK Brain Expression Consortium (UKBEC), while other data used in our study were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. We examined the association of AD risk allele carrier status with the levels of gene expression in blood and brain regions and tested the association with brain amyloidosis, tauopathy, and neurodegeneration at baseline, using a multivariable linear regression model. Next, we analyzed the longitudinal effects of these variants on the change rates of pathology using a mixed effect model. RESULTS Altogether, 27 variants were detected to be associated with the altered expression of 21 nearby genes in blood and brain regions. Eleven variants (especially novel variants in ADAM10, IGHV1-68, and SLC24A4/RIN3) were associated with brain amyloidosis, 7 variants (especially in INPP5D, PTK2B) with brain tauopathy, and 8 variants (especially in ECHDC3, HS3ST1) with brain neurodegeneration. Variants in ADAMTS1, BZRAP1-AS1, CELF1, CD2AP, and SLC24A4/RIN3 participated in more than one cerebral pathological process. CONCLUSIONS Genetic variants might play functional roles and suggest potential mechanisms in AD pathogenesis, which opens doors to uncover novel targets for AD treatment.
Collapse
Affiliation(s)
- Meng-Shan Tan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Yu-Xiang Yang
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, 12th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Wei Xu
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Hui-Fu Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Lin Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Chuan-Tao Zuo
- PET Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, 12th Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - John Suckling
- Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, 12th Wulumuqi Zhong Road, Shanghai, 200040, China.
| |
Collapse
|
7
|
Manzali SB, Ravona-Springer R, Alkelai A, Yu E, Gan-Or Z, Ganmore I, Heymann A, Beeri MS, Greenbaum L. Association of the CD2AP locus with cognitive functioning among middle-aged individuals with a family history of Alzheimer's disease. Neurobiol Aging 2020; 101:50-56. [PMID: 33578194 DOI: 10.1016/j.neurobiolaging.2020.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/19/2022]
Abstract
First-degree family history is an established risk factor for Alzheimer's disease (AD). We investigated the association of late-onset AD risk loci with cognitive functioning among 315 offspring of AD patients. Participants were cognitively normal Jewish individuals, aged 40-65 years, from the Israel Registry for Alzheimer's Prevention (IRAP) study. Twenty-two single-nucleotide polymorphisms (SNPs) within these loci and the APOE E4 allele were included in the final analyses, and a polygenic risk score was also calculated. Using linear regression (assuming an additive genetic model), we found a significant association only for SNP rs9473117, located near the CD2-associated protein (CD2AP) gene, with global cognition. Controlling for demographic variables (age, sex, years of education, and ancestry), the late-onset AD risk allele C was associated with lower global cognitive functioning (p = 0.0005), and withstood correction for multiple testing. After adjusting for additional characteristics (APOE E4 status and then also for cardiovascular factors), the results remained essentially unchanged (p = 0.0003 and p = 0.0005, respectively). In secondary analyses examining specific cognitive domains, rs9473117 was similarly associated with episodic memory (p = 0.005), language (p = 0.009), and working memory/attention (p = 0.018) but not with executive functions (p = 0.27). Again, the results were similar after adjusting for APOE E4 status and cardiovascular factors. The polygenic risk score was not associated with global cognitive functioning or with any of the 4 domains. In conclusion, our findings suggest a contribution of the CD2AP locus to cognitive functioning in middle-aged individuals with a parental history of AD. Further validations, including in longitudinal studies, are required.
Collapse
Affiliation(s)
- Sigalit Batia Manzali
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ramit Ravona-Springer
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Eric Yu
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Ithamar Ganmore
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Memory Clinic, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anthony Heymann
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Maccabi Healthcare Services, Tel Aviv, Israel
| | - Michal Schnaider Beeri
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lior Greenbaum
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.
| |
Collapse
|
8
|
Avram S, Mernea M, Limban C, Borcan F, Chifiriuc C. Potential Therapeutic Approaches to Alzheimer's Disease By Bioinformatics, Cheminformatics And Predicted Adme-Tox Tools. Curr Neuropharmacol 2020; 18:696-719. [PMID: 31885353 PMCID: PMC7536829 DOI: 10.2174/1570159x18666191230120053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/24/2019] [Accepted: 12/28/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is considered a severe, irreversible and progressive neurodegenerative disorder. Currently, the pharmacological management of AD is based on a few clinically approved acethylcholinesterase (AChE) and N-methyl-D-aspartate (NMDA) receptor ligands, with unclear molecular mechanisms and severe side effects. METHODS Here, we reviewed the most recent bioinformatics, cheminformatics (SAR, drug design, molecular docking, friendly databases, ADME-Tox) and experimental data on relevant structurebiological activity relationships and molecular mechanisms of some natural and synthetic compounds with possible anti-AD effects (inhibitors of AChE, NMDA receptors, beta-secretase, amyloid beta (Aβ), redox metals) or acting on multiple AD targets at once. We considered: (i) in silico supported by experimental studies regarding the pharmacological potential of natural compounds as resveratrol, natural alkaloids, flavonoids isolated from various plants and donepezil, galantamine, rivastagmine and memantine derivatives, (ii) the most important pharmacokinetic descriptors of natural compounds in comparison with donepezil, memantine and galantamine. RESULTS In silico and experimental methods applied to synthetic compounds led to the identification of new AChE inhibitors, NMDA antagonists, multipotent hybrids targeting different AD processes and metal-organic compounds acting as Aβ inhibitors. Natural compounds appear as multipotent agents, acting on several AD pathways: cholinesterases, NMDA receptors, secretases or Aβ, but their efficiency in vivo and their correct dosage should be determined. CONCLUSION Bioinformatics, cheminformatics and ADME-Tox methods can be very helpful in the quest for an effective anti-AD treatment, allowing the identification of novel drugs, enhancing the druggability of molecular targets and providing a deeper understanding of AD pathological mechanisms.
Collapse
Affiliation(s)
| | - Maria Mernea
- Address correspondence to this author at the Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95th Spl. Independentei, Bucharest, Romania; Tel/Fax: ++4-021-318-1573; E-mail:
| | | | | | | |
Collapse
|
9
|
Van Acker ZP, Bretou M, Annaert W. Endo-lysosomal dysregulations and late-onset Alzheimer's disease: impact of genetic risk factors. Mol Neurodegener 2019; 14:20. [PMID: 31159836 PMCID: PMC6547588 DOI: 10.1186/s13024-019-0323-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/10/2019] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence supports that cellular dysregulations in the degradative routes contribute to the initiation and progression of neurodegenerative diseases, including Alzheimer's disease. Autophagy and endolysosomal homeostasis need to be maintained throughout life as they are major cellular mechanisms involved in both the production of toxic amyloid peptides and the clearance of misfolded or aggregated proteins. As such, alterations in endolysosomal and autophagic flux, as a measure of degradation activity in these routes or compartments, may directly impact as well on disease-related mechanisms such as amyloid-β clearance through the blood-brain-barrier and the interneuronal spreading of amyloid-β and/or Tau seeds, affecting synaptic function, plasticity and metabolism. The emerging of several genetic risk factors for late-onset Alzheimer's disease that are functionally related to endocytic transport regulation, including cholesterol metabolism and clearance, supports the notion that in particular the autophagy/lysosomal flux might become more vulnerable during ageing thereby contributing to disease onset. In this review we discuss our current knowledge of the risk genes APOE4, BIN1, CD2AP, PICALM, PLD3 and TREM2 and their impact on endolysosomal (dys)regulations in the light of late-onset Alzheimer's disease pathology.
Collapse
Affiliation(s)
- Zoë P. Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| |
Collapse
|
10
|
Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. Genes (Basel) 2018; 9:E593. [PMID: 30501127 PMCID: PMC6315915 DOI: 10.3390/genes9120593] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/28/2022] Open
Abstract
The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. Gene Ontology (GO, geneontology.org) is a major resource for gene enrichment analysis. The aim of this project, funded by the Alzheimer's Research United Kingdom (ARUK) foundation and led by the University College London (UCL) biocuration team, was to enhance the GO resource by developing new neurological GO terms, and use GO terms to annotate gene products associated with dementia. Specifically, proteins and protein complexes relevant to processes involving amyloid-beta and tau have been annotated and the resulting annotations are denoted in GO databases as 'ARUK-UCL'. Biological knowledge presented in the scientific literature was captured through the association of GO terms with dementia-relevant protein records; GO itself was revised, and new GO terms were added. This literature biocuration increased the number of Alzheimer's-relevant gene products that were being associated with neurological GO terms, such as 'amyloid-beta clearance' or 'learning or memory', as well as neuronal structures and their compartments. Of the total 2055 annotations that we contributed for the prioritised gene products, 526 have associated proteins and complexes with neurological GO terms. To ensure that these descriptive annotations could be provided for Alzheimer's-relevant gene products, over 70 new GO terms were created. Here, we describe how the improvements in ontology development and biocuration resulting from this initiative can benefit the scientific community and enhance the interpretation of dementia data.
Collapse
Affiliation(s)
- Barbara Kramarz
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| | - Paola Roncaglia
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Birgit H M Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Rachael P Huntley
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| | - Maria J Martin
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK.
| | - Rina Bandopadhyay
- UCL Queen Square Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, 1 Wakefield Street, London WC1N 1PJ, UK.
| | - Nigel M Hooper
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK.
| | - Ruth C Lovering
- UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK.
| |
Collapse
|