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Jaye S, Sandau US, Saugstad JA. Clathrin mediated endocytosis in Alzheimer's disease: cell type specific involvement in amyloid beta pathology. Front Aging Neurosci 2024; 16:1378576. [PMID: 38694257 PMCID: PMC11061891 DOI: 10.3389/fnagi.2024.1378576] [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: 01/29/2024] [Accepted: 04/03/2024] [Indexed: 05/04/2024] Open
Abstract
This review provides a comprehensive examination of the role of clathrin-mediated endocytosis (CME) in Alzheimer's disease (AD) pathogenesis, emphasizing its impact across various cellular contexts beyond neuronal dysfunction. In neurons, dysregulated CME contributes to synaptic dysfunction, amyloid beta (Aβ) processing, and Tau pathology, highlighting its involvement in early AD pathogenesis. Furthermore, CME alterations extend to non-neuronal cell types, including astrocytes and microglia, which play crucial roles in Aβ clearance and neuroinflammation. Dysregulated CME in these cells underscores its broader implications in AD pathophysiology. Despite significant progress, further research is needed to elucidate the precise mechanisms underlying CME dysregulation in AD and its therapeutic implications. Overall, understanding the complex interplay between CME and AD across diverse cell types holds promise for identifying novel therapeutic targets and interventions.
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Affiliation(s)
| | | | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, United States
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Asadie M, Miri A, Badri T, Hosseini Nejad J, Gharechahi J. Dysregulated AEBP1 and COLEC12 Genes in Late-Onset Alzheimer's Disease: Insights from Brain Cortex and Peripheral Blood Analysis. J Mol Neurosci 2024; 74:37. [PMID: 38568322 DOI: 10.1007/s12031-024-02212-8] [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: 01/29/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by memory and cognitive impairment, often accompanied by alterations in mood, confusion, and, ultimately, a state of acute mental disturbance. The cerebral cortex is considered a promising area for investigating the underlying causes of AD by analyzing transcriptional patterns, which could be complemented by investigating blood samples obtained from patients. We analyzed the RNA expression profiles of three distinct areas of the brain cortex, including the frontal cortex (FC), temporal cortex (TC), and entorhinal cortex (EC) in patients with AD. Functional enrichment analysis was performed on the differentially expressed genes (DEGs) across the three regions. The two genes with the most significant expression changes in the EC region were selected for assessing mRNA expression levels in the peripheral blood of late-onset AD patients using quantitative PCR (qPCR). We identified eight shared DEGs in these regions, including AEBP1 and COLEC12, which exhibited prominent changes in expression. Functional enrichment analysis uncovered a significant association of these DEGs with the transforming growth factor-β (TGF-β) signaling pathway and processes related to angiogenesis. Importantly, we established a robust connection between the up-regulation of AEBP1 and COLEC12 in both the brain and peripheral blood. Furthermore, we have demonstrated the potential of AEBP1 and COLEC12 genes as effective diagnostic tools for distinguishing between late-onset AD patients and healthy controls. This study unveils the intricate interplay between AEBP1 and COLEC12 in AD and underscores their potential as markers for disease detection and monitoring.
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Affiliation(s)
- Mohamadreza Asadie
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Miri
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Taleb Badri
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Hosseini Nejad
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Tatemoto P, Pértille F, Bernardino T, Zanella R, Guerrero-Bosagna C, Zanella AJ. An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets. Epigenetics 2023; 18:2196656. [PMID: 37192378 DOI: 10.1080/15592294.2023.2196656] [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: 03/09/2022] [Revised: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 05/18/2023] Open
Abstract
Epigenetic mechanisms are important modulators of neurodevelopmental outcomes in the offspring of animals challenged during pregnancy. Pregnant sows living in a confined environment are challenged with stress and lack of stimulation which may result in the expression of stereotypies (repetitive behaviours without an apparent function). Little attention has been devoted to the postnatal effects of maternal stereotypies in the offspring. We investigated how the environment and stereotypies of pregnant sows affected the neuro-epigenome of their piglets. We focused on the amygdala, frontal cortex, and hippocampus, brain regions related to emotionality, learning, memory, and stress response. Differentially methylated regions (DMRs) were investigated in these brain regions of male piglets born from sows kept in an enriched vs a barren environment. Within the latter group of piglets, we compared the brain methylomes of piglets born from sows expressing stereotypies vs sows not expressing stereotypies. DMRs emerged in each comparison. While the epigenome of the hippocampus and frontal cortex of piglets is mainly affected by the maternal environment, the epigenome of the amygdala is mainly affected by maternal stereotypies. The molecular pathways and mechanisms triggered in the brains of piglets by maternal environment or stereotypies are different, which is reflected on the differential gene function associated to the DMRs found in each piglets' brain region . The present study is the first to investigate the neuro-epigenomic effects of maternal enrichment in pigs' offspring and the first to investigate the neuro-epigenomic effects of maternal stereotypies in the offspring of a mammal.
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Affiliation(s)
- Patricia Tatemoto
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Animal Biotechnology Laboratory, Animal Science Department, University of São Paulo - Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Thiago Bernardino
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, Brazil
- Graduation Program in One Health, University of Santo Amaro, São Paulo Brazil
| | - Ricardo Zanella
- Faculty of Agronomy and Veterinary Medicine, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Carlos Guerrero-Bosagna
- Avian Behavioral Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
- Physiology and Environmental Toxicology Program, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Adroaldo José Zanella
- Center for Comparative Studies in Sustainability, Health and Welfare, Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, FMVZ, University of São Paulo, Pirassununga, São Paulo, Brazil
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Zhu Y, Kong L, Han T, Yan Q, Liu J. Machine learning identification and immune infiltration of disulfidptosis-related Alzheimer's disease molecular subtypes. Immun Inflamm Dis 2023; 11:e1037. [PMID: 37904698 PMCID: PMC10566450 DOI: 10.1002/iid3.1037] [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: 05/09/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a common neurodegenerative disorder. Disulfidptosis is a newly discovered form of programmed cell death that holds promise as a therapeutic strategy for various disorders. However, the functional roles of disulfidptosis-related genes (DRGs) in AD remain unknown. METHODS Microarray data and clinical information from patients with AD and healthy controls were downloaded from the Gene Expression Omnibus database. A thorough examination of DRG expression and immune characteristics in both groups was performed. Based on the identified DRGs, we performed an unsupervised clustering analysis to categorize the AD samples into various disulfidptosis-related molecular clusters. Weighted gene co-expression network analysis was performed to select hub genes specific to disulfidptosis-related AD clusters. The performances of various machine learning models were compared to determine the optimal predictive model. The predictive ability of the optimal model was assessed using nomogram analysis and five external datasets. RESULTS Eight DRGs showed differential expression between the AD and control samples. Two different molecular clusters were identified. The immune cell infiltration analysis revealed distinct differences in the immune microenvironment of the two clusters. The support vector machine model showed the highest performance, and a panel of five signature genes was identified, which showed excellent performance on the external validation datasets. The nomogram analysis also showed high accuracy in predicting AD. CONCLUSION We identified disulfidptosis-related molecular clusters in AD and established a novel risk model to assess the likelihood of developing AD. These findings revealed a complex association between disulfidptosis and AD, which may aid in identifying potential therapeutic targets for this debilitating disorder.
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Affiliation(s)
- Yidong Zhu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Lingyue Kong
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Tianxiong Han
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Qiongzhi Yan
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Jun Liu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
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Zhu M, Hou T, Jia L, Tan Q, Qiu C, Du Y. Development and validation of a 13-gene signature associated with immune function for the detection of Alzheimer's disease. Neurobiol Aging 2023; 125:62-73. [PMID: 36842362 DOI: 10.1016/j.neurobiolaging.2022.12.014] [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: 08/10/2022] [Revised: 12/05/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Current knowledge of Alzheimer's disease (AD) etiology and effective therapy remains limited. Thus, the identification of biomarkers is crucial to improve the detection and treatment of patients with AD. Using robust rank aggregation method to analyze the microarray data from Gene Expression Omnibus database, we identified 1138 differentially expressed genes in AD. We then explored 13 hub genes by weighted gene co-expression network analysis, least absolute shrinkage, and selection operator, and logistic regression in the training dataset. The detection model, which composed of CD163, CDC42SE1, CECR6, CSF1R, CYP27A1, EIF4E3, H2AFJ, IFIT2, IL10RA, KIAA1324, PSTPIP1, SLA, and TBC1D2 genes, along with APOE gene, showed that the area under the curve for detecting AD was 0.821 (95% confidence interval [CI] = 0.782-0.861) and the model was validated in ADNI dataset (area under the curve = 0.776; 95%CI = 0.686-0.865). Notably, the 13 genes in the model were highly enriched in immune function. These findings have implications for the detection and therapeutic target of AD.
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Affiliation(s)
- Min Zhu
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tingting Hou
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Longfei Jia
- Innovation Center for Neurological Disorders and Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Qihua Tan
- Department of Public Health, Epidemiology and Biostatistics, University of Southern Denmark, Odense, Denmark
| | - Chengxuan Qiu
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Neurobiology, Care Sciences and Society, Aging Research Center, Karolinska Institutet and Stockholm University, Stockholm, Sweden.
| | - Yifeng Du
- Department of Neurology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
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6
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Xia P, Ma H, Chen J, Liu Y, Cui X, Wang C, Zong S, Wang L, Liu Y, Lu Z. Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer's disease. BMC Med Genomics 2023; 16:56. [PMID: 36918839 PMCID: PMC10012531 DOI: 10.1186/s12920-023-01479-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: 09/24/2022] [Accepted: 03/06/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a progressive, neurodegenerative disorder with insidious onset. Some scholars believe that there is a close relationship between pyroptosis and AD. However, studies with evidence supporting this relationship are lacking. MATERIALS AND METHODS The microarray data of AD were retrieved from the Gene Expression Omnibus (GEO) database with the datasets merged using the R package inSilicoMerging. R software package Limma was used to perform the differential expression analysis to identify the differentially expressed genes (DEGs). We further performed the enrichment analyses of the DEGs based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases to identify the metabolic pathways with a significant difference. The Gene Set Enrichment Analysis (GSEA) was applied to identify the significant pathways. The protein-protein interaction (PPI) network was constructed based on the STRING database with the hub genes identified. Quantitative real-time PCR (qRT-PCR) analyses based on HT22 cells were performed to validate the findings based on the microarray analysis. Gene expression correlation heatmaps were generated to evaluate the relationships among the genes. RESULTS A new dataset was derived by merging 4 microarray datasets in the hippocampus of AD patients in the GEO database. Differential gene expression analysis yielded a volcano plot of a total of 20 DEGs (14 up-regulated and 6 down-regulated). GO analysis revealed a group of GO terms with a significant difference, e.g., cytoplasmic vesicle membrane, vesicle membrane, and monocyte chemotaxis. KEGG analysis detected the metabolic pathways with a significant difference, e.g., Rheumatoid arthritis and Fluid shear stress and atherosclerosis. The results of the Gene Set Enrichment Analysis of the microarray data showed that gene set ALZHEIMER_DISEASE and the gene set PYROPTOSIS were both up-regulated. PPI network showed that pyroptosis-related genes were divided into two groups. In the Aβ-induced HT22 cell model, three genes (i.e., BAX, IL18, and CYCS) were revealed with significant differences. Gene expression correlation heatmaps revealed strong correlations between pyroptotic genes and AD-related genes. CONCLUSION The pyroptosis-related genes BAX, IL18, and CYCS were significantly different between AD patients and normal controls.
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Affiliation(s)
- Pengcheng Xia
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Huijun Ma
- Clinical Laboratory, Qingdao Women and Children's Hospital, Qingdao, Shandong, China
| | - Jing Chen
- Discipline of Anatomy and Pathology, Shandong First Medical University, Jinan, Shandong, China
| | - Yingchao Liu
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Xiaolin Cui
- School of Medicine, Shandong University, Jinan, Shandong, China
| | - Cuicui Wang
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Shuai Zong
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Le Wang
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Yun Liu
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China.
| | - Zhiming Lu
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital, Shandong First Medical University, Jinan, Shandong, China.
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Piras IS, Brokaw D, Kong Y, Weisenberger DJ, Krate J, Delvaux E, Mahurkar S, Blattler A, Siegmund KD, Sue L, Serrano GE, Beach TG, Laird PW, Huentelman MJ, Coleman PD. Integrated DNA Methylation/RNA Profiling in Middle Temporal Gyrus of Alzheimer's Disease. Cell Mol Neurobiol 2023:10.1007/s10571-022-01307-3. [PMID: 36596913 DOI: 10.1007/s10571-022-01307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/08/2022] [Indexed: 01/05/2023]
Abstract
Alzheimer's disease is a neurodegenerative disorder clinically defined by gradual cognitive impairment and alteration in executive function. We conducted an epigenome-wide association study (EWAS) of a clinically and neuropathologically characterized cohort of 296 brains, including Alzheimer's disease (AD) and non-demented controls (ND), exploring the relationship with the RNA expression from matched donors. We detected 5246 CpGs and 832 regions differentially methylated, finding overlap with previous EWAS but also new associations. CpGs previously identified in ANK1, MYOC, and RHBDF2 were differentially methylated, and one of our top hits (GPR56) was not previously detected. ANK1 was differentially methylated at the region level, along with APOE and RHBDF2. Only a small number of genes showed a correlation between DNA methylation and RNA expression statistically significant. Multiblock partial least-squares discriminant analysis showed several CpG sites and RNAs discriminating AD and ND (AUC = 0.908) and strongly correlated with each other. Furthermore, the CpG site cg25038311 was negatively correlated with the expression of 22 genes. Finally, with the functional epigenetic module analysis, we identified a protein-protein network characterized by inverse RNA/DNA methylation correlation and enriched for "Regulation of insulin-like growth factor transport", with IGF1 as the hub gene. Our results confirm and extend the previous EWAS, providing new information about a brain region not previously explored in AD DNA methylation studies. The relationship between DNA methylation and gene expression is not significant for most of the genes in our sample, consistently with the complexities in the gene expression regulation.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Danielle Brokaw
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Yinfei Kong
- Department of Information Systems and Decision Sciences, California State University Fullerton, Fullerton, CA, 92831, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Biology, University of South California, Los Angeles, CA, 90033, USA
| | - Jonida Krate
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
- UnityPoint Clinic, Waterloo, IA, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Swapna Mahurkar
- UCLA Division of Digestive Diseases, University of California, Los Angeles, CA, 90024, USA
| | - Adam Blattler
- Department of Biochemistry and Molecular Biology, University of South California, Los Angeles, CA, 90033, USA
- Genetics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Kimberly D Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089-9175, USA
| | - Lucia Sue
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Geidy E Serrano
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Paul D Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85287, USA.
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Wang B, Liu W, Sun F. Nucleosome assembly protein 1-like 5 alleviates Alzheimer's disease-like pathological characteristics in a cell model. Front Mol Neurosci 2022; 15:1034766. [PMID: 36568274 PMCID: PMC9773259 DOI: 10.3389/fnmol.2022.1034766] [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: 09/02/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) remains one of the most common dementias of neurodegenerative disease-related diseases. Nucleosome assembly protein 1-like 5 (NAP1L5) belongs to the NAP1L protein family, which acts as a histone chaperone. However, the function and mechanism of NAP1L5 in AD are still unclear. Bioinformatics analysis, RT-qPCR, and Western blotting results showed that NAP1L5 was downregulated in the brain tissues of AD patients and a mouse cell model of AD. NAP1L5 overexpression alleviated (Amyloid-β precursor protein) APP metabolism and Tau phosphorylation. We further demonstrated that NAP1L5 regulated the AD-like pathological characteristics through the GSK3B/Wnt/β-Catenin signaling pathway. Moreover, we showed that the Wnt/β-Catenin signaling pathway, regulated by NAP1L5, was mediated by AQP1-mediated mechanism in N2a-APP695sw cell. In sum, these results suggested that NAP1L5 overexpression has neuroprotective effects and might act as potential biomarker and target for the diagnosis and treatment of AD.
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Affiliation(s)
- Bingyan Wang
- Department of Anesthesiology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Weiying Liu
- Department of Pathogen Biology, School of Basic Medicine, Tianjin Medical University, Tianjin, China,*Correspondence: Weiying Liu,
| | - Fengxian Sun
- Department of Physiology and Pathophysiology, School of Basic Medicine, Tianjin Medical University, Tianjin, China,Fengxian Sun,
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Alzheimer's disease large-scale gene expression portrait identifies exercise as the top theoretical treatment. Sci Rep 2022; 12:17189. [PMID: 36229643 PMCID: PMC9561721 DOI: 10.1038/s41598-022-22179-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/11/2022] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder that affects multiple brain regions and is difficult to treat. In this study we used 22 AD large-scale gene expression datasets to identify a consistent underlying portrait of AD gene expression across multiple brain regions. Then we used the portrait as a platform for identifying treatments that could reverse AD dysregulated expression patterns. Enrichment of dysregulated AD genes included multiple processes, ranging from cell adhesion to CNS development. The three most dysregulated genes in the AD portrait were the inositol trisphosphate kinase, ITPKB (upregulated), the astrocyte specific intermediate filament protein, GFAP (upregulated), and the rho GTPase, RHOQ (upregulated). 41 of the top AD dysregulated genes were also identified in a recent human AD GWAS study, including PNOC, C4B, and BCL11A. 42 transcription factors were identified that were both dysregulated in AD and that in turn affect expression of other AD dysregulated genes. Male and female AD portraits were highly congruent. Out of over 250 treatments, three datasets for exercise or activity were identified as the top three theoretical treatments for AD via reversal of large-scale gene expression patterns. Exercise reversed expression patterns of hundreds of AD genes across multiple categories, including cytoskeleton, blood vessel development, mitochondrion, and interferon-stimulated related genes. Exercise also ranked as the best treatment across a majority of individual region-specific AD datasets and meta-analysis AD datasets. Fluoxetine also scored well and a theoretical combination of fluoxetine and exercise reversed 549 AD genes. Other positive treatments included curcumin. Comparisons of the AD portrait to a recent depression portrait revealed a high congruence of downregulated genes in both. Together, the AD portrait provides a new platform for understanding AD and identifying potential treatments for AD.
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Liu S, Lu Y, Geng D. Molecular Subgroup Classification in Alzheimer's Disease by Transcriptomic Profiles. J Mol Neurosci 2022; 72:866-879. [PMID: 35080766 DOI: 10.1007/s12031-021-01957-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/08/2021] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a progressive cognitive disorder that occurs worldwide, and the lack of disease-modifying targets and pathways is a pressing issue. This study aimed to provide new targets and pathways by performing molecular subgroup classification. After normalizing the collected data, the subgroup number was confirmed with consensus clustering. Comparisons of clinical features among subgroups were conducted to clarify the clinical traits of each subgroup. Subgroup-specific genes were identified to perform weighted gene coexpression analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out. Next, gene set enrichment analysis (GSEA) was performed. Protein-protein interaction networks were built to screen core genes and in each subgroup to perform Spearman correlation analysis with clinical traits. Sequencing profiles of 1068 AD samples collected from 2 datasets were classified into 3 subgroups. Clinical comparisons revealed that patients in subgroup III tended to be younger, while their pathological grades were the most severe. WGCNA detected four gene modules, and the turquoise module, where the dopaminergic synapse pathway was enriched, was related to subgroup I. The neurotrophin signaling pathway and TGF-beta signaling pathway were robustly enriched in the blue and brown modules, respectively, in subgroup III. Moreover, 3 hub genes in subgroup I were negatively correlated with the sum of neurofibrillary tangle (Nft) density. Conversely, hub genes in subgroups II and III exhibited positive correlations with the sum of Nft density. These results provide new pathways and targets for AD treatment.
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Affiliation(s)
- Sha Liu
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, West Huaihai Road 99, Xuzhou, 221002, Jiangsu, China
| | - Yan Lu
- Department of Neurology, The Municipal Hospital, Xuzhou Medical University, Xuzhou, 221116, Jiangsu, China
| | - Deqin Geng
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, West Huaihai Road 99, Xuzhou, 221002, Jiangsu, China.
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Yuan L, Zou D, Yang X, Chen X, Lu Y, Zhang A, Zhang P, Wei F. Proteomics and functional study reveal kallikrein-6 enhances communicating hydrocephalus. Clin Proteomics 2021; 18:30. [PMID: 34915845 PMCID: PMC8903716 DOI: 10.1186/s12014-021-09335-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/07/2021] [Indexed: 01/22/2023] Open
Abstract
Background Communicating hydrocephalus (CH) is a common neurological disorder caused by a blockage of cerebrospinal fluid. In this study, we aimed to explore the potential molecular mechanism underlying CH development. Methods Quantitative proteomic analysis was performed to screen the differentially expressed proteins (DEPs) between patients with and without CH. A CH rat model was verified by Hoechst staining, and the co-localization of the target protein and neuron was detected using immunofluorescence staining. Loss-of-function experiments were performed to examine the effect of KLK6 on the synapse structure. Results A total of 11 DEPs were identified, and kallikrein 6 (KLK6) expression was found to be significantly upregulated in patients with CH compared with that in patients without CH. The CH rat model was successfully constructed, and KLK6 was found to be co-localized with neuronal nuclei in brain tissue. The expression level of IL-1β, TNF-α, and KLK6 in the CH group was higher than that in the control group. After knockdown of KLK6 expression using small-interfering RNA (siRNA), the expression levels of synapsin-1 and PSD95 in neuronal cells were increased, and the length, number, and structure of synapses were significantly improved. Following siRNA interference KLK6 expression, 5681 differentially expressed genes (DEGs) were identified in transcriptome profile. The upregulated DEGs of Appl2, Nav2, and Nrn1 may be involved in the recovery of synaptic structures after the interference of KLK6 expression. Conclusions Collectively, KLK6 participates in the development of CH and might provide a new target for CH treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09335-9.
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Affiliation(s)
- Lei Yuan
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
| | - Dongdong Zou
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
| | - Xia Yang
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
| | - Xin Chen
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China.
| | - Youming Lu
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
| | - Aijun Zhang
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
| | - Pengqi Zhang
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
| | - Fance Wei
- Department of Neurosurgery, The Affiliated Sixth People's Hospital, Shanghai Jiaotong University, NO. 600 Yishan Road, Shanghai, 200233, China
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12
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Liu J, Ottaviani D, Sefta M, Desbrousses C, Chapeaublanc E, Aschero R, Sirab N, Lubieniecki F, Lamas G, Tonon L, Dehainault C, Hua C, Fréneaux P, Reichman S, Karboul N, Biton A, Mirabal-Ortega L, Larcher M, Brulard C, Arrufat S, Nicolas A, Elarouci N, Popova T, Némati F, Decaudin D, Gentien D, Baulande S, Mariani O, Dufour F, Guibert S, Vallot C, Rouic LLL, Matet A, Desjardins L, Pascual-Pasto G, Suñol M, Catala-Mora J, Llano GC, Couturier J, Barillot E, Schaiquevich P, Gauthier-Villars M, Stoppa-Lyonnet D, Golmard L, Houdayer C, Brisse H, Bernard-Pierrot I, Letouzé E, Viari A, Saule S, Sastre-Garau X, Doz F, Carcaboso AM, Cassoux N, Pouponnot C, Goureau O, Chantada G, de Reyniès A, Aerts I, Radvanyi F. A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression. Nat Commun 2021; 12:5578. [PMID: 34552068 PMCID: PMC8458383 DOI: 10.1038/s41467-021-25792-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
Retinoblastoma is the most frequent intraocular malignancy in children, originating from a maturing cone precursor in the developing retina. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using multi-omics data, we demonstrate the existence of two retinoblastoma subtypes. Subtype 1, of earlier onset, includes most of the heritable forms. It harbors few genetic alterations other than the initiating RB1 inactivation and corresponds to differentiated tumors expressing mature cone markers. By contrast, subtype 2 tumors harbor frequent recurrent genetic alterations including MYCN-amplification. They express markers of less differentiated cone together with neuronal/ganglion cell markers with marked inter- and intra-tumor heterogeneity. The cone dedifferentiation in subtype 2 is associated with stemness features including low immune and interferon response, E2F and MYC/MYCN activation and a higher propensity for metastasis. The recognition of these two subtypes, one maintaining a cone-differentiated state, and the other, more aggressive, associated with cone dedifferentiation and expression of neuronal markers, opens up important biological and clinical perspectives for retinoblastomas.
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Affiliation(s)
- Jing Liu
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.452770.30000 0001 2226 6748Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Daniela Ottaviani
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.414531.60000 0001 0695 6255Precision Medicine, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Meriem Sefta
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Céline Desbrousses
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Elodie Chapeaublanc
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Rosario Aschero
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Nanor Sirab
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Fabiana Lubieniecki
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Gabriela Lamas
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Laurie Tonon
- grid.418116.b0000 0001 0200 3174Synergie Lyon Cancer, Plateforme de Bioinformatique “Gilles Thomas”, Centre Léon Bérard, 69008 Lyon, France
| | - Catherine Dehainault
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France
| | - Clément Hua
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Paul Fréneaux
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Sacha Reichman
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Narjesse Karboul
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Anne Biton
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U900, 75005 Paris, France ,Ecole des Mines ParisTech, 77305 Fontainebleau, France ,grid.428999.70000 0001 2353 6535Present Address: Institut Pasteur – Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, 75015 Paris, France
| | - Liliana Mirabal-Ortega
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Magalie Larcher
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Céline Brulard
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.411777.30000 0004 1765 1563Present Address: INSERM U930, CHU Bretonneau, 37000 Tours, France
| | - Sandrine Arrufat
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - André Nicolas
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Nabila Elarouci
- grid.452770.30000 0001 2226 6748Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Tatiana Popova
- grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France
| | - Fariba Némati
- grid.418596.70000 0004 0639 6384Département de Recherche Translationnelle, Institut Curie, 75005 Paris, France
| | - Didier Decaudin
- grid.418596.70000 0004 0639 6384Département de Recherche Translationnelle, Institut Curie, 75005 Paris, France
| | - David Gentien
- grid.418596.70000 0004 0639 6384Département de Recherche Translationnelle, Institut Curie, 75005 Paris, France
| | - Sylvain Baulande
- grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, NGS Platform, 75005 Paris, France
| | - Odette Mariani
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Florent Dufour
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Sylvain Guibert
- grid.425132.3GeCo Genomics Consulting, Integragen, 91000 Evry, France
| | - Céline Vallot
- grid.425132.3GeCo Genomics Consulting, Integragen, 91000 Evry, France
| | - Livia Lumbroso-Le Rouic
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France
| | - Alexandre Matet
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Paris, France
| | - Laurence Desjardins
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France
| | - Guillem Pascual-Pasto
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Mariona Suñol
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Department of Pathology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Jaume Catala-Mora
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Department of Ophthalmology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Genoveva Correa Llano
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Jérôme Couturier
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Emmanuel Barillot
- grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U900, 75005 Paris, France ,Ecole des Mines ParisTech, 77305 Fontainebleau, France
| | - Paula Schaiquevich
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Marion Gauthier-Villars
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France
| | - Dominique Stoppa-Lyonnet
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Paris, France
| | - Lisa Golmard
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France
| | - Claude Houdayer
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France ,grid.41724.34Present Address: Department of Genetics, Rouen University Hospital, 76000 Rouen, France
| | - Hervé Brisse
- grid.418596.70000 0004 0639 6384Département d’Imagerie Médicale, Institut Curie, 75005 Paris, France
| | - Isabelle Bernard-Pierrot
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Eric Letouzé
- grid.417925.cCentre de Recherche des Cordeliers, Sorbonne Universités, INSERM, 75006 Paris, France ,grid.508487.60000 0004 7885 7602Functional Genomics of Solid Tumors, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, France
| | - Alain Viari
- grid.418116.b0000 0001 0200 3174Synergie Lyon Cancer, Plateforme de Bioinformatique “Gilles Thomas”, Centre Léon Bérard, 69008 Lyon, France
| | - Simon Saule
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Xavier Sastre-Garau
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.414145.10000 0004 1765 2136Present Address: Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 94000 Créteil, France
| | - François Doz
- grid.508487.60000 0004 7885 7602Université de Paris, Paris, France ,grid.418596.70000 0004 0639 6384SIREDO Center (Care, Innovation and Research in Pediatric Adolescent and Young Adult Oncology), Institut Curie, 75005 Paris, France
| | - Angel M. Carcaboso
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Nathalie Cassoux
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Paris, France
| | - Celio Pouponnot
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Guillermo Chantada
- grid.414531.60000 0001 0695 6255Precision Medicine, Hospital J.P. Garrahan, Buenos Aires, Argentina ,grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain ,grid.423606.50000 0001 1945 2152National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Aurélien de Reyniès
- grid.452770.30000 0001 2226 6748Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Isabelle Aerts
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.418596.70000 0004 0639 6384SIREDO Center (Care, Innovation and Research in Pediatric Adolescent and Young Adult Oncology), Institut Curie, 75005 Paris, France
| | - François Radvanyi
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
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Li T, Liao Z, Mao Y, Hu J, Le D, Pei Y, Sun W, Lin J, Qiu Y, Zhu J, Chen Y, Qi C, Ye X, Su H, Yu E. Temporal dynamic changes of intrinsic brain activity in Alzheimer's disease and mild cognitive impairment patients: a resting-state functional magnetic resonance imaging study. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:63. [PMID: 33553356 PMCID: PMC7859807 DOI: 10.21037/atm-20-7214] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by memory impairment. Previous studies have largely focused on alterations of static brain activity occurring in patients with AD. Few studies to date have explored the characteristics of dynamic brain activity in cognitive impairment, and their predictive ability in AD patients. METHODS One hundred and eleven AD patients, 29 MCI patients, and 73 healthy controls (HC) were recruited. The dynamic amplitude of low-frequency fluctuation (dALFF) and the dynamic fraction amplitude of low-frequency fluctuation (dfALFF) were used to assess the temporal variability of local brain activity in patients with AD or mild cognitive impairment (MCI). Pearson's correlation coefficients were calculated between the metrics and subjects' behavioral scores. RESULTS The results of analysis of variance indicated that the AD, MCI, and HC groups showed significant variability of dALFF in the cerebellar posterior and middle temporal lobes. In AD patients, these brain regions had high dALFF variability. Significant dfALFF variability was found between the three groups in the left calcarine cortex and white matter. The AD group showed lower dfALFF than the MCI group in the left calcarine cortex. CONCLUSIONS Compared to HC, AD patients were found to have increased dALFF variability in the cerebellar posterior and temporal lobes. This abnormal pattern may diminish the capacity of the cerebellum and temporal lobes to participate in the cerebrocerebellar circuits and default mode network (DMN), which regulate cognition and emotion in AD. The findings above indicate that the analysis of dALFF and dfALFF based on functional magnetic resonance imaging data may give a new insight into the neurophysiological mechanisms of AD.
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Affiliation(s)
- Ting Li
- Zhejiang Provincial People’s Hospital, Qingdao University, Qingdao, China
| | - Zhengluan Liao
- Department of Psychiatry, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Yanping Mao
- Department of Psychological Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Jiaojiao Hu
- Department of Psychological Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Dansheng Le
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yangliu Pei
- Graduate faculty, Bengbu Medical College, Bengbu, China
| | - Wangdi Sun
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jixin Lin
- Department of Internal Medicine, Shengsi County People’s Hospital, Zhoushan, China
| | - Yaju Qiu
- Department of Psychiatry, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Junpeng Zhu
- Department of Psychiatry, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Yan Chen
- Department of Psychiatry, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Chang Qi
- Department of Psychiatry, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Xiangming Ye
- Department of Rehabilitation Medicine, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Heng Su
- Department of Psychiatry, Zhejiang Provincial People’s Hospital, Hangzhou, China
| | - Enyan Yu
- Department of Psychological Medicine, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
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Vishwanath N, Monis WJ, Hoffmann GA, Ramachandran B, DiGiacomo V, Wong JY, Smith ML, Layne MD. Mechanisms of aortic carboxypeptidase-like protein secretion and identification of an intracellularly retained variant associated with Ehlers-Danlos syndrome. J Biol Chem 2020; 295:9725-9735. [PMID: 32482891 DOI: 10.1074/jbc.ra120.013902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Indexed: 01/02/2023] Open
Abstract
Aortic carboxypeptidase-like protein (ACLP) is a collagen-binding extracellular matrix protein that has important roles in wound healing and fibrosis. ACLP contains thrombospondin repeats, a collagen-binding discoidin domain, and a catalytically inactive metallocarboxypeptidase domain. Recently, mutations in the ACLP-encoding gene, AE-binding protein 1 (AEBP1), have been discovered, leading to the identification of a new variant of Ehlers-Danlos syndrome causing connective tissue disruptions in multiple organs. Currently, little is known about the mechanisms of ACLP secretion or the role of post-translational modifications in these processes. We show here that the secreted form of ACLP contains N-linked glycosylation and that inhibition of glycosylation results in its intracellular retention. Using site-directed mutagenesis, we determined that glycosylation of Asn-471 and Asn-1030 is necessary for ACLP secretion and identified a specific N-terminal proteolytic ACLP fragment. To determine the contribution of secreted ACLP to extracellular matrix mechanical properties, we generated and mechanically tested wet-spun collagen ACLP composite fibers, finding that ACLP enhances the modulus (or stiffness), toughness, and tensile strength of the fibers. Some AEBP1 mutations were null alleles, whereas others resulted in expressed proteins. We tested the hypothesis that a recently discovered 40-amino acid mutation and insertion in the ACLP discoidin domain regulates collagen binding and assembly. Interestingly, we found that this protein variant is retained intracellularly and induces endoplasmic reticulum stress identified with an XBP1-based endoplasmic reticulum stress reporter. Our findings highlight the importance of N-linked glycosylation of ACLP for its secretion and contribute to our understanding of ACLP-dependent disease pathologies.
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Affiliation(s)
- Neya Vishwanath
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - William J Monis
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Gwendolyn A Hoffmann
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Bhavana Ramachandran
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Vincent DiGiacomo
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joyce Y Wong
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Michael L Smith
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
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15
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AEBP1 is a Novel Oncogene: Mechanisms of Action and Signaling Pathways. JOURNAL OF ONCOLOGY 2020; 2020:8097872. [PMID: 32565808 PMCID: PMC7273425 DOI: 10.1155/2020/8097872] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/13/2020] [Indexed: 12/29/2022]
Abstract
Adipocyte enhancer-binding protein 1 (AEBP1) is a transcriptional repressor involved in the regulation of critical biological processes including adipogenesis, mammary gland development, inflammation, macrophage cholesterol homeostasis, and atherogenesis. Several years ago, we first reported the ability of AEBP1 to exert a positive control over the canonical NF-κB pathway. Indeed, AEBP1 positively regulates NF-κB activity via its direct interaction with IκBα, a key NF-κB inhibitor. AEBP1 overexpression results in uncontrollable activation of NF-κB, which may have severe pathogenic outcomes. Recently, the regulatory relationship between AEBP1 and NF-κB pathway has been of great interest to many researchers primarily due to the implication of NF-κB signaling in critical cellular processes such as inflammation and cancer. Since constitutive activation of NF-κB is widely implicated in carcinogenesis, AEBP1 overexpression is associated with tumor development and progression. Recent studies sought to explore the effects of the overexpression of AEBP1, as a potential oncogene, in different types of cancer. In this review, we analyze the effects of AEBP1 overexpression in a variety of malignancies (e.g., breast cancer, glioblastoma, bladder cancer, gastric cancer, colorectal cancer, ovarian cancer, and skin cancer), with a specific focus on the AEBP1-mediated control over the canonical NF-κB pathway. We also underscore the ability of AEBP1 to regulate crucial cancer-related events like cell proliferation and apoptosis in light of other key pathways (e.g., PI3K-Akt, sonic hedgehog (Shh), p53, parthanatos (PARP-1), and PTEN). Identifying AEBP1 as a potential biomarker for cancer prognosis may lead to a novel therapeutic target for the prevention and/or treatment of various types of cancer.
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