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Dabin LC, Kersey H, Kim B, Acri DJ, Sharify D, Lee-Gosselin A, Lasagna-Reeves CA, Oblak AL, Lamb BT, Kim J. Loss of Inpp5d has disease-relevant and sex-specific effects on glial transcriptomes. Alzheimers Dement 2024. [PMID: 38923164 DOI: 10.1002/alz.13901] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION Inpp5d is genetically associated with Alzheimer's disease risk. Loss of Inpp5d alters amyloid pathology in models of amyloidosis. Inpp5d is expressed predominantly in microglia but its function in brain is poorly understood. METHODS We performed single-cell RNA sequencing to study the effect of Inpp5d loss on wild-type mouse brain transcriptomes. RESULTS Loss of Inpp5d has sex-specific effects on the brain transcriptome. Affected genes are enriched for multiple neurodegeneration terms. Network analyses reveal a gene co-expression module centered around Inpp5d in female mice. Inpp5d loss alters Pleotrophin (PTN), Prosaposin (PSAP), and Vascular Endothelial Growth Factor A (VEGFA) signaling probability between cell types. DISCUSSION Our data suggest that the normal function of Inpp5d is entangled with mechanisms involved in neurodegeneration. We report the effect of Inpp5d loss without pathology and show that this has dramatic effects on gene expression. Our study provides a critical reference for researchers of neurodegeneration, allowing separation of disease-specific changes mediated by Inpp5d in disease from baseline effects of Inpp5d loss. HIGHLIGHTS Loss of Inpp5d has different effects in male and female mice. Genes dysregulated by Inpp5d loss relate to neurodegeneration. Total loss of Inpp5d in female mice collapses a conserved gene co-expression module. Loss of microglial Inpp5d affects the transcriptome of other cell types.
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Affiliation(s)
- Luke C Dabin
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Holly Kersey
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Byungwook Kim
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Dominic J Acri
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Daniel Sharify
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Audrey Lee-Gosselin
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Cristian A Lasagna-Reeves
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Adrian L Oblak
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Bruce T Lamb
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jungsu Kim
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Jiang S, Zhang CY, Tang L, Zhao LX, Chen HZ, Qiu Y. Integrated Genomic Analysis Revealed Associated Genes for Alzheimer's Disease in APOE4 Non-Carriers. Curr Alzheimer Res 2020; 16:753-763. [PMID: 31441725 DOI: 10.2174/1567205016666190823124724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 07/14/2019] [Accepted: 08/08/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND APOE4 is the strongest genetic risk factor for late-onset Alzheimer's disease (LOAD). LOAD patients carrying or not carrying APOE4 manifest distinct clinico-pathological characteristics. APOE4 has been shown to play a critical role in the pathogenesis of AD by affecting various aspects of pathological processes. However, the pathogenesis involved in LOAD not-carrying APOE4 remains elusive. OBJECTIVE We aimed to identify the associated genes involved in LOAD not-carrying APOE4. METHODS An integrated genomic analysis of datasets of genome-wide association study, genome-wide expression profiling and genome-wide linkage scan and protein-protein interaction network construction were applied to identify associated gene clusters in APOE4 non-carriers. The role of one of hub gene of an APOE4 non-carrier-associated gene cluster in tau phosphorylation was studied by knockdown and western blot. RESULTS We identified 12 gene clusters associated with AD APOE4 non-carriers. The hub genes associated with AD in these clusters were MAPK8, POU2F1, XRCC1, PRKCG, EXOC6, VAMP4, SIRT1, MME, NOS1, ABCA1 and LDLR. The associated genes for APOE4 non-carriers were enriched in hereditary disorder, neurological disease and psychological disorders. Moreover, knockdown of PRKCG to reduce the expression of protein kinase Cγ isoform enhanced tau phosphorylation at Thr181 and Thr231 and the expression of glycogen synthase kinase 3β and cyclin-dependent kinase 5 in the presence of APOE3 but not APOE4. CONCLUSION The study provides new insight into the mechanism of distinct pathogenesis of LOAD not carrying APOE4 and prompts the functional exploration of identified genes based on APOE genotypes.
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Affiliation(s)
- Shan Jiang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Chun-Yun Zhang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ling Tang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lan-Xue Zhao
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201210, China
| | - Yu Qiu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Cacabelos R. Pharmacogenetic considerations when prescribing cholinesterase inhibitors for the treatment of Alzheimer's disease. Expert Opin Drug Metab Toxicol 2020; 16:673-701. [PMID: 32520597 DOI: 10.1080/17425255.2020.1779700] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Cholinergic dysfunction, demonstrated in the late 1970s and early 1980s, led to the introduction of acetylcholinesterase inhibitors (AChEIs) in 1993 (Tacrine) to enhance cholinergic neurotransmission as the first line of treatment against Alzheimer's disease (AD). The new generation of AChEIs, represented by Donepezil (1996), Galantamine (2001) and Rivastigmine (2002), is the only treatment for AD to date, together with Memantine (2003). AChEIs are not devoid of side-effects and their cost-effectiveness is limited. An option to optimize the correct use of AChEIs is the implementation of pharmacogenetics (PGx) in the clinical practice. AREAS COVERED (i) The cholinergic system in AD, (ii) principles of AD PGx, (iii) PGx of Donepezil, Galantamine, Rivastigmine, Huperzine and other treatments, and (iv) practical recommendations. EXPERT OPINION The most relevant genes influencing AChEI efficacy and safety are APOE and CYPs. APOE-4 carriers are the worst responders to AChEIs. With the exception of Rivastigmine (UGT2B7, BCHE-K), the other AChEIs are primarily metabolized via CYP2D6, CYP3A4, and UGT enzymes, with involvement of ABC transporters and cholinergic genes (CHAT, ACHE, BCHE, SLC5A7, SLC18A3, CHRNA7) in most ethnic groups. Defective variants may affect the clinical response to AChEIs. PGx geno-phenotyping is highly recommended prior to treatment.
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Affiliation(s)
- Ramón Cacabelos
- Department of Genomic Medicine, EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine , Bergondo, Corunna, Spain
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Yao X, Risacher SL, Nho K, Saykin AJ, Wang Z, Shen L. Targeted genetic analysis of cerebral blood flow imaging phenotypes implicates the INPP5D gene. Neurobiol Aging 2019; 81:213-221. [PMID: 31319229 PMCID: PMC6732252 DOI: 10.1016/j.neurobiolaging.2019.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 12/22/2022]
Abstract
The vascular hypothesis of Alzheimer's disease (AD) has proposed the involvement of brain hypoperfusion in AD pathogenesis, where cognitive decline and dysfunction result from dwindling cerebral blood flow (CBF). Based on the vascular hypothesis of Alzheimer's disease, we focused on exploring how genetic factors influence AD pathogenesis via the cerebrovascular system. To investigate the role of CBF endophenotypes in AD pathogenesis, we performed a targeted genetic analysis of 258 subjects from the Alzheimer's Disease Neuroimaging Initiative cohort to examine associations between 4033 single-nucleotide polymorphisms of 24 AD genes and CBF measures in 4 brain regions. A novel association with CBF measure in the left angular gyrus was identified in an INPP5D single-nucleotide polymorphism (i.e., rs61068452; p = 1.48E-7; corrected p = 2.39E-3). The gene-based analysis discovered both INPP5D and CD2AP associated with the left angular gyrus CBF. Further analyses on nonoverlapping samples revealed that rs61068452-G was associated with lower CSF t-tau/Aβ1-42 ratio. Our findings suggest a protective role of rs61068452-G in an AD-relevant cerebrovascular endophenotype, which has the potential to provide novel insights for better mechanistic understanding of AD.
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Affiliation(s)
- Xiaohui Yao
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shannon L Risacher
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ze Wang
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Jiang S, Tang L, Zhao N, Yang W, Qiu Y, Chen HZ. A Systems View of the Differences between APOE ε4 Carriers and Non-carriers in Alzheimer's Disease. Front Aging Neurosci 2016; 8:171. [PMID: 27462267 PMCID: PMC4941795 DOI: 10.3389/fnagi.2016.00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/27/2016] [Indexed: 12/19/2022] Open
Abstract
APOE ε4 is the strongest genetic risk factor for late-onset Alzheimer's disease (AD) and accounts for 50-65% of late-onset AD. Late-onset AD patients carrying or not carrying APOE ε4 manifest many clinico-pathological distinctions. Thus, we applied a weighted gene co-expression network analysis to identify specific co-expression modules in AD based on APOE ε4 stratification. Two specific modules were identified in AD APOE ε4 carriers and one module was identified in non-carriers. The hub genes of one module of AD APOE ε4 carriers were ISOC1, ENO3, GDF10, GNB3, XPO4, ACLY and MATN2. The other module of AD APOE ε4 carriers consisted of 10 hub genes including ANO3, ARPP21, HPCA, RASD2, PCP4 and ADORA2A. The module of AD APOE ε4 non-carriers consisted of 16 hub genes including DUSP5, TNFRSF18, ZNF331, DNAJB5 and RIN1. The module of AD APOE ε4 carriers including ISOC1 and ENO3 and the module of non-carriers contained the most highly connected hub gene clusters. mRNA expression of the genes in the cluster of the ISOC1 and ENO3 module of carriers was shown to be correlated in a time-dependent manner under APOE ε4 treatment but not under APOE ε3 treatment. In contrast, mRNA expression of the genes in the cluster of non-carriers' module was correlated under APOE ε3 treatment but not under APOE ε4 treatment. The modules of carriers demonstrated genetic bases and were mainly enriched in hereditary disorders and neurological diseases, energy metabolism-associated signaling and G protein-coupled receptor-associated pathways. The module including ISOC1 and ENO3 harbored two conserved promoter motifs in its hub gene cluster that could be regulated by common transcription factors and miRNAs. The module of non-carriers was mainly enriched in neurological, immunological and cardiovascular diseases and was correlated with Parkinson's disease. These data demonstrate that AD in APOE ε4 carriers involves more genetic factors and particular biological processes, whereas AD in APOE ε4 non-carriers shares more common pathways with other types of diseases. The study reveals differential genetic bases and pathogenic and pathological processes between carriers and non-carriers, providing new insight into the mechanisms of the differences between APOE ε4 carriers and non-carriers in AD.
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Affiliation(s)
- Shan Jiang
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Ling Tang
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Na Zhao
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Hong Kong
| | - Yu Qiu
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai China
| | - Hong-Zhuan Chen
- Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai China
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