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Nguyen HD, Jo WH, Cha JO, Hoang NHM, Kim MS. Elucidation of the effects of 2,5-hexandione as a metabolite of n-hexane on cognitive impairment in leptin-knockout mice (C57BL/6-Lepem1Shwl/Korl). Toxicol Res 2024; 40:389-408. [PMID: 38911537 PMCID: PMC11187033 DOI: 10.1007/s43188-024-00228-1] [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: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/17/2024] [Indexed: 06/25/2024] Open
Abstract
Exposure to n-hexane and its metabolite 2,5-hexandione (HD) is a well-known cause of neurotoxicity, particularly in the peripheral nervous system. To date, few studies have focused on the neurotoxic effects of HD on cognitive impairment. Exposure to HD and diabetes mellitus can exacerbate neurotoxicity. There are links among HD, diabetes mellitus, and cognitive impairment; however, the specific mechanisms underlying them remain unclear. Therefore, we aimed to elucidate the neurotoxic effects of HD on cognitive impairment in ob/ob (C57BL/6-Lepem1Shwl/Korl) mice. We found that HD induced cognitive impairment by altering the expression of genes (FN1, AGT, ACTA2, MYH11, MKI67, MET, CTGF, and CD44), miRNAs (mmu-miR15a-5p, mmu-miR-17-5p, and mmu-miR-29a-3p), transcription factors (transcription factor AP-2 alpha [TFAP2A], serum response factor [Srf], and paired box gene 4 [PAX4]), and signaling pathways (ERK/CERB, PI3K/AKT, GSK-3β/p-tau/amyloid-β), as well as by causing neuroinflammation (TREM1/DAP12/NF-κB), oxidative stress, and apoptosis. The prevalent use of n-hexane in various industrial applications (for instance, shoe manufacturing, printing inks, paints, and varnishes) suggests that individuals with elevated body weight and glucose levels and those employed in high-risk workplaces have greater probability of cognitive impairment. Therefore, implementing screening strategies for HD-induced cognitive dysfunction is crucial. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s43188-024-00228-1.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Won Hee Jo
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Jae Ok Cha
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Ngoc Hong Minh Hoang
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Min-Sun Kim
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922 Republic of Korea
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Rao C, Liu B, Qin H, Du Z. Enoyl coenzyme a hydratase 1 attenuates aortic valve calcification by suppressing Runx2 via Wnt5a/Ca 2+ pathway. J Cell Commun Signal 2024; 18:e12038. [PMID: 38946717 PMCID: PMC11208118 DOI: 10.1002/ccs3.12038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 07/02/2024] Open
Abstract
The morbidity and death rates of calcified aortic valves|calcific aortic valve (CAV) disease (CAVD) remain high for its limited therapeutic choices. Here, we investigated the function, therapeutic potential, and putative mechanisms of Enoyl coenzyme A hydratase 1 (ECH1) in CAVD by various in vitro and in vivo experiments. Single-cell sequencing revealed that ECH1 was predominantly expressed in valve interstitial cells and was significantly reduced in CAVs. Overexpression of ECH1 reduced aortic valve calcification in ApoE-/- mice treated with high cholesterol diet, while ECH1 silencing had the reverse effect. We also identified Wnt5a, a noncanonical Wnt ligand, was also altered when ECH1 expression was modulated. Mechanistically, we found that ECH1 exerted anti-calcific actions through suppressing Wnt signaling, since CHIR99021, a Wnt agonist, may significantly lessen the protective impact of ECH1 overexpression on the development of valve calcification. ChIP and luciferase assays all showed that ECH1 overexpression prevented Runx2 binding to its downstream gene promoters (osteopontin and osteocalcin), while CHIR99021 neutralized this protective effect. Collectively, our findings reveal a previously unrecognized mechanism of ECH1-Wnt5a/Ca2+ regulation in CAVD, implying that targeting ECH1 may be a potential therapeutic strategy to prevent CAVD development.
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Affiliation(s)
- Caijun Rao
- Department of GeriatricsTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Baoqing Liu
- Department of Cardiovascular SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Haojie Qin
- Clinic Center of Human Gene ResearchUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of CardiologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubeiChina
| | - Zhipeng Du
- Department of GastroenterologyInstitute of Liver and Gastrointestinal DiseasesTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Diaw SH, Delcambre S, Much C, Ott F, Kostic VS, Gajos A, Münchau A, Zittel S, Busch H, Grünewald A, Klein C, Lohmann K. DYT-THAP1: exploring gene expression in fibroblasts for potential biomarker discovery. Neurogenetics 2024; 25:141-147. [PMID: 38498291 DOI: 10.1007/s10048-024-00752-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Dystonia due to pathogenic variants in the THAP1 gene (DYT-THAP1) shows variable expressivity and reduced penetrance of ~ 50%. Since THAP1 encodes a transcription factor, modifiers influencing this variability likely operate at the gene expression level. This study aimed to assess the transferability of differentially expressed genes (DEGs) in neuronal cells related to pathogenic variants in the THAP1 gene, which were previously identified by transcriptome analyses. For this, we performed quantitative (qPCR) and Digital PCR (dPCR) in cultured fibroblasts. RNA was extracted from THAP1 manifesting (MMCs) and non-manifesting mutation carriers (NMCs) as well as from healthy controls. The expression profiles of ten of 14 known neuronal DEGs demonstrated differences in fibroblasts between these three groups. This included transcription factors and targets (ATF4, CLN3, EIF2A, RRM1, YY1), genes involved in G protein-coupled receptor signaling (BDKRB2, LPAR1), and a gene linked to apoptosis and DNA replication/repair (CRADD), which all showed higher expression levels in MMCs and NMCs than in controls. Moreover, the analysis of genes linked to neurological disorders (STXBP1, TOR1A) unveiled differences in expression patterns between MMCs and controls. Notably, the genes CUEDC2, DRD4, ECH1, and SIX2 were not statistically significantly differentially expressed in fibroblast cultures. With > 70% of the tested genes being DEGs also in fibroblasts, fibroblasts seem to be a suitable model for DYT-THAP1 research despite some restrictions. Furthermore, at least some of these DEGs may potentially also serve as biomarkers of DYT-THAP1 and influence its penetrance and expressivity.
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Affiliation(s)
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Christoph Much
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Fabian Ott
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Vladimir S Kostic
- Institute of Neurology, School of Medicine, University of Belgrade, Belgrade, 11000, Serbia
| | - Agata Gajos
- Department of Extrapyramidal Diseases, Medical University of Lodz, Lodz, 90-647, Poland
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, 23562, Lübeck, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hauke Busch
- Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4362, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany.
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Kelly J, Moyeed R, Carroll C, Luo S, Li X. Blood biomarker-based classification study for neurodegenerative diseases. Sci Rep 2023; 13:17191. [PMID: 37821485 PMCID: PMC10567903 DOI: 10.1038/s41598-023-43956-4] [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: 02/23/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
As the population ages, neurodegenerative diseases are becoming more prevalent, making it crucial to comprehend the underlying disease mechanisms and identify biomarkers to allow for early diagnosis and effective screening for clinical trials. Thanks to advancements in gene expression profiling, it is now possible to search for disease biomarkers on an unprecedented scale.Here we applied a selection of five machine learning (ML) approaches to identify blood-based biomarkers for Alzheimer's (AD) and Parkinson's disease (PD) with the application of multiple feature selection methods. Based on ROC AUC performance, one optimal random forest (RF) model was discovered for AD with 159 gene markers (ROC-AUC = 0.886), while one optimal RF model was discovered for PD (ROC-AUC = 0.743). Additionally, in comparison to traditional ML approaches, deep learning approaches were applied to evaluate their potential applications in future works. We demonstrated that convolutional neural networks perform consistently well across both the Alzheimer's (ROC AUC = 0.810) and Parkinson's (ROC AUC = 0.715) datasets, suggesting its potential in gene expression biomarker detection with increased tuning of their architecture.
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Affiliation(s)
- Jack Kelly
- Faculty of Medicine, Biology and Health, Centre for Biostatistics, School of Health Sciences, University of Manchester, Manchester, UK.
- Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK.
| | - Rana Moyeed
- Faculty of Science and Engineering, University of Plymouth, Plymouth, PL6 8BU, UK
| | - Camille Carroll
- Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK
| | - Shouqing Luo
- Faculty of Health, University of Plymouth, Plymouth, PL6 8BU, UK
| | - Xinzhong Li
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK.
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Plaschke K, Kopitz J, Gebert J, Wolf ND, Wolf RC. Proteomic Analysis Reveals Potential Exosomal Biomarkers in Patients With Sporadic Alzheimer Disease. Alzheimer Dis Assoc Disord 2023; 37:315-321. [PMID: 38015424 DOI: 10.1097/wad.0000000000000589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/18/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Despite substantial progress made in the past decades, the pathogenesis of sporadic Alzheimer disease (sAD) and related biological markers of the disease are still controversially discussed. Cerebrospinal fluid and functional brain imaging markers have been established to support the clinical diagnosis of sAD. Yet, due to the invasiveness of such diagnostics, less burdensome markers have been increasingly investigated in the past years. Among such markers, extracellular vesicles may yield promise in (early) diagnostics and treatment monitoring in sAD. MATERIALS AND METHODS In this pilot study, we collected the blood plasma of 18 patients with sAD and compared the proteome of extracted extracellular vesicles with the proteome of 11 age-matched healthy controls. The resulting proteomes were characterized by Gene Ontology terms and between-group statistics. RESULTS Ten distinct proteins were found to significantly differ between sAD patients and controls (P<0.05, False Discovery Rate, corrected). These proteins included distinct immunoglobulins, fibronectin, and apolipoproteins. CONCLUSIONS These findings lend further support for exosomal changes in neurodegenerative disorders, and particularly in sAD. Further proteomic research could decisively advance our knowledge of sAD pathophysiology as much as it could foster the development of clinically meaningful biomarkers.
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Affiliation(s)
| | | | | | - Nadine D Wolf
- Center for Psychosocial Medicine, Department of General Psychiatry, University Hospital Heidelberg, Heidelberg, Germany
| | - Robert Christian Wolf
- Center for Psychosocial Medicine, Department of General Psychiatry, University Hospital Heidelberg, Heidelberg, Germany
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Fissolo N, Calvo-Barreiro L, Eixarch H, Boschert U, Villar LM, Costa-Frossard L, Ferrer M, Sanchez A, Borràs E, Sabidó E, Espejo C, Montalban X, Comabella M. Molecular signature associated with cladribine treatment in patients with multiple sclerosis. Front Immunol 2023; 14:1233546. [PMID: 37559720 PMCID: PMC10408299 DOI: 10.3389/fimmu.2023.1233546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023] Open
Abstract
Introduction Little is known about the molecular profiling associated with the effect of cladribine in patients with multiple sclerosis (MS). Here, we aimed first to characterize the transcriptomic and proteomic profiles induced by cladribine in blood cells, and second to identify potential treatment response biomarkers to cladribine in patients with MS. Methods Gene, protein and microRNA (miRNA) expression profiles were determined by microarrays (genes, miRNAs) and mass spectrometry (proteins) in peripheral blood mononuclear cells (PBMCs) from MS patients after in vitro treatment with cladribine in its active and inactive forms. Two bioinformatics approaches to integrate the three obtained datasets were applied: (i) a multiomics discriminant analysis (DIABLO - Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies); and (ii) a multi-stage integration of features selected in differential expression analysis on each dataset and then merged. Selected molecules from the in vitro study were quantified by qPCR ex vivo in PBMCs from MS patients receiving cladribine. Results PBMCs treated in vitro with cladribine were characterized by a major downregulation of gene, protein, and miRNA expression compared with the untreated cells. An intermediate pattern between the cladribine-treated and untreated conditions was observed in PBMCs treated with cladribine in its inactive form. The differential expression analysis of each dataset led to the identification of four genes and their encoded proteins, and twenty-two miRNAs regulating their expression, that were associated with cladribine treatment. Two of these genes (PPIF and NHLRC2), and three miRNAs (miR-21-5p, miR-30b-5p, and miR-30e-5p) were validated ex vivo in MS patients treated with cladribine. Discussion By using a combination of omics data and bioinformatics approaches we were able to identify a multiomics molecular profile induced by cladribine in vitro in PBMCs. We also identified a number of biomarkers that were validated ex vivo in PBMCs from patients with MS treated with cladribine that have the potential to become treatment response biomarkers to this drug.
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Affiliation(s)
- Nicolas Fissolo
- Servei de Neurologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Calvo-Barreiro
- Servei de Neurologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Herena Eixarch
- Servei de Neurologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ursula Boschert
- Ares Trading SA, Eysins, Switzerland, an affiliate of Merck KGaA, Darmstadt, Germany
| | - Luisa M. Villar
- Department of Immunology, Multiple Sclerosis Unit, Hospital Ramon y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Lucienne Costa-Frossard
- Department of Neurology, Multiple Sclerosis Unit, Hospital Ramon y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Mireia Ferrer
- Statistics and Bioinformatics Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Alex Sanchez
- Statistics and Bioinformatics Unit, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Spain
| | - Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Carmen Espejo
- Servei de Neurologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Montalban
- Servei de Neurologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Manuel Comabella
- Servei de Neurologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
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7
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Tallgren A, Kager L, O’Grady G, Tuominen H, Körkkö J, Kuismin O, Feucht M, Wilson C, Behunova J, England E, Kurki MI, Palotie A, Hallman M, Kaarteenaho R, Laccone F, Boztug K, Hinttala R, Uusimaa J. Novel patients with NHLRC2 variants expand the phenotypic spectrum of FINCA disease. Front Neurosci 2023; 17:1123327. [PMID: 37179546 PMCID: PMC10173879 DOI: 10.3389/fnins.2023.1123327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/08/2023] [Indexed: 05/15/2023] Open
Abstract
Purpose FINCA disease (Fibrosis, Neurodegeneration and Cerebral Angiomatosis, OMIM 618278) is an infantile-onset neurodevelopmental and multiorgan disease. Since our initial report in 2018, additional patients have been described. FINCA is the first human disease caused by recessive variants in the highly conserved NHLRC2 gene. Our previous studies have shown that Nhlrc2-null mouse embryos die during gastrulation, indicating the essential role of the protein in embryonic development. Defect in NHLRC2 leads to cerebral neurodegeneration and severe pulmonary, hepatic and cardiac fibrosis. Despite having a structure suggestive of an enzymatic role and the clinical importance of NHLRC2 in multiple organs, the specific physiological role of the protein is unknown. Methods The clinical histories of five novel FINCA patients diagnosed with whole exome sequencing were reviewed. Segregation analysis of the biallelic, potentially pathogenic NHLRC2 variants was performed using Sanger sequencing. Studies on neuropathology and NHLRC2 expression in different brain regions were performed on autopsy samples of three previously described deceased FINCA patients. Results One patient was homozygous for the pathogenic variant c.442G > T, while the other four were compound heterozygous for this variant and two other pathogenic NHLRC2 gene variants. All five patients presented with multiorgan dysfunction with neurodevelopmental delay, recurrent infections and macrocytic anemia as key features. Interstitial lung disease was pronounced in infancy but often stabilized. Autopsy samples revealed widespread, albeit at a lower intensity than the control, NHLRC2 expression in the brain. Conclusion This report expands on the characteristic clinical features of FINCA disease. Presentation is typically in infancy, and although patients can live to late adulthood, the key clinical and histopathological features are fibrosis, infection susceptibility/immunodeficiency/intellectual disability, neurodevelopmental disorder/neurodegeneration and chronic anemia/cerebral angiomatosis (hence the acronym FINCA) that enable an early diagnosis confirmed by genetic investigations.
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Affiliation(s)
- Antti Tallgren
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Leo Kager
- St. Anna Children’s Hospital, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Gina O’Grady
- Paediatric Neuroservices, Starship Children’s Health, Te Whatu Ora Health New Zealand, Auckland, New Zealand
| | - Hannu Tuominen
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jarmo Körkkö
- Center for Intellectual Disability Care, Oulu University Hospital, Oulu, Finland
| | - Outi Kuismin
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Martha Feucht
- Department of Paediatrics, Center for Rare and Complex Epilepsies, Medical University of Vienna, Vienna, Austria
| | - Callum Wilson
- National Metabolic Service, Auckland City Hospital, Auckland, New Zealand
| | - Jana Behunova
- Department of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Eleina England
- Mendelian Genomics, Programme in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Mitja I. Kurki
- Programme in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Aarno Palotie
- Programme in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, United States
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mikko Hallman
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Clinic for Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Center of Internal Medicine and Respiratory Medicine and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Franco Laccone
- Department of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Kaan Boztug
- St. Anna Children’s Hospital, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Reetta Hinttala
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Johanna Uusimaa
- Research Unit of Clinical Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
- Clinic for Children and Adolescents, Oulu University Hospital, Oulu, Finland
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Li J, Qi L, Chen Y, Lv H, Bi H. Bioinformatics analysis of the potential mechanisms of Alzheimer's disease induced by exposure to combined triazine herbicides. Ann Hum Biol 2023; 50:442-451. [PMID: 37819172 DOI: 10.1080/03014460.2023.2259242] [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: 03/07/2023] [Accepted: 08/31/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND The development of Alzheimer's disease (AD) is promoted by a combination of genetic and environmental factors. Notably, combined exposure to triazine herbicides atrazine (ATR), simazine (SIM), and propazine (PRO) may promote the development of AD, but the mechanism is unknown. AIM To study the molecular mechanism of AD induced by triazine herbicides. METHODS Differentially expressed genes (DEGs) of AD patients and controls were identified. The intersectional targets of ATR, SIM, and PRO for possible associations with AD were screened through network pharmacology and used for gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis. The binding potentials between the core targets and herbicides were validated by molecular docking and molecular dynamics. RESULTS A total of 1,062 DEGs were screened between the AD patients and controls, which identified 148 intersectional targets of herbicides causing AD that were screened by network pharmacology analysis. GO and KEGG enrichment analysis revealed that cell cycling and cellular senescence were important signalling pathways. Finally, the core targets EGFR, FN1, and TYMS were screened and validated by molecular docking and molecular dynamics. CONCLUSION Our results suggest that combined exposure to triazine herbicides might promote the development of AD, thereby providing new insights for the prevention of AD.
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Affiliation(s)
- Jianan Li
- Department of Occupational and Environmental Health, College of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ling Qi
- Department of Occupational and Environmental Health, College of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Yuxin Chen
- Department of Occupational and Environmental Health, College of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Haoming Lv
- Department of Occupational and Environmental Health, College of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Haoran Bi
- Department of Biostatistics, College of Public Health, Xuzhou Medical University, Xuzhou, China
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9
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Zhang HY, Zong RQ, Wu FX, Li YR. Bioinformatics Analysis Identifies ASCL1 as the Key Transcription Factor in Hepatocellular Carcinoma Progression. DISEASE MARKERS 2023; 2023:3560340. [PMID: 36755802 PMCID: PMC9902118 DOI: 10.1155/2023/3560340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/12/2022] [Accepted: 11/25/2022] [Indexed: 01/31/2023]
Abstract
Methods Differentially transcription factors (DETFs) were identified from differentially expressed genes (DEGs) in GSE62232 and transcription factors. Then, they were analyzed by regulatory networks, prognostic risk model, and overall survival analyses to identify the key DETF. Combined with the regulatory networks and binding site analysis, the target mRNA of key DETF was determined, and its prognostic value in HCC was evaluated by survival, clinical characteristics analyses, and experiments. Finally, the expressions and functions of the key DETF on the DEmRNAs were investigated in HCC cells. Results Through multiple bioinformatics analyses, ASCL1 was identified as the key DETF, and SLC6A13 was predicted to be its target mRNA with the common binding site of CCAGCAACTGGCC, both downregulated in HCC. In survival analysis, high SLC6A13 was related to better HCC prognosis, and SLC6A13 was differentially expressed in HCC patients with clinical characteristics. Furthermore, cell experiments showed the mRNA expressions of ASCL1 and SLC6A13 were both reduced in HCC, and their overexpressions suppressed the growth, invasion, and migration of HCC cells. Besides, over-ASCL1 could upregulate SLC6A13 expression in HCC cells. Conclusion This study identifies two suppressor genes in HCC progression, ASCL1 and SLC6A13, and the key transcription factor ASCL1 suppresses HCC progression by targeting SLC6A13 mRNA. They are both potential treatment targets and prognostic biomarkers for HCC patients, which provides new clues for HCC research.
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Affiliation(s)
- Hong-yan Zhang
- Department of Intensive Care Medicine, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Rui-qing Zong
- Department of Intensive Care Medicine, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Fei-xiang Wu
- Department of Intensive Care Medicine, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yi-ran Li
- Department of Intensive Care Medicine, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
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Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through immune landscape analysis. NPJ AGING 2022; 8:15. [PMCID: PMC9636153 DOI: 10.1038/s41514-022-00096-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
AbstractMild cognitive impairment (MCI) is a clinical precursor of Alzheimer’s disease (AD). Recent genetic studies have reported on associations between AD risk genes and immunity. Here, we obtained samples and data from 317 AD, 432 MCI, and 107 cognitively normal (CN) subjects and investigated immune-cell type composition and immune clonal diversity of T-cell receptor (TRA, TRB, TRG, and TRD) and B-cell receptor (IGH, IGK, and IGL) repertoires through bulk RNA sequencing. We found the proportions of plasma cells, γδ T cells, neutrophils, and B cells were significantly different and the diversities of IGH, IGK, and TRA were significantly small with AD progression. We then identified a differentially expressed gene, WDR37, in terms of risk of MCI-to-AD conversion. Our prognosis prediction model using the potential blood-based biomarkers for early AD diagnosis, which combined two immune repertoires (IGK and TRA), WDR37, and clinical information, successfully classified MCI patients into two groups, low and high, in terms of risk of MCI-to-AD conversion (log-rank test P = 2.57e-3). It achieved a concordance index of 0.694 in a discovery cohort and of 0.643 in an independent validation cohort. We believe that further investigation, using larger sample sizes, will lead to practical clinical use in the near future.
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11
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Dietary Selenomethionine Reduce Mercury Tissue Levels and Modulate Methylmercury Induced Proteomic and Transcriptomic Alterations in Hippocampi of Adolescent BALB/c Mice. Int J Mol Sci 2022; 23:ijms232012242. [PMID: 36293098 PMCID: PMC9603801 DOI: 10.3390/ijms232012242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 12/02/2022] Open
Abstract
Methylmercury (MeHg) is a well-known environmental contaminant, particularly harmful to the developing brain. The main human dietary exposure to MeHg occurs through seafood consumption. However, seafood also contains several nutrients, including selenium, which has been shown to interact with MeHg and potentially ameliorate its toxicity. The aim of this study was to investigate the combined effects of selenium (as selenomethionine; SeMet) and MeHg on mercury accumulation in tissues and the effects concomitant dietary exposure of these compounds exert on the hippocampal proteome and transcriptome in mice. Adolescent male BALB/c mice were exposed to SeMet and two different doses of MeHg through their diet for 11 weeks. Organs, including the brain, were sampled for mercury analyses. Hippocampi were collected and analyzed using proteomics and transcriptomics followed by multi-omics bioinformatics data analysis. The dietary presence of SeMet reduced the amount of mercury in several organs, including the brain. Proteomic and RNA-seq analyses showed that both protein and RNA expression patterns were inversely regulated in mice receiving SeMet together with MeHg compared to MeHg alone. Several pathways, proteins and RNA transcripts involved in conditions such as immune responses and inflammation, oxidative stress, cell plasticity and Alzheimer’s disease were affected inversely by SeMet and MeHg, indicating that SeMet can ameliorate several toxic effects of MeHg in mice.
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12
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Yu G, Hao J, Pan X, Shi L, Zhang Y, Wang J, Fan H, Xiao Y, Yang F, Lou J, Chang W, Malnoë A, Li M. Structure of Arabidopsis SOQ1 lumenal region unveils C-terminal domain essential for negative regulation of photoprotective qH. NATURE PLANTS 2022; 8:840-855. [PMID: 35798975 DOI: 10.1038/s41477-022-01177-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx-NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.
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Affiliation(s)
- Guimei Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Jingfang Hao
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Xiaowei Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Science, Capital Normal University, Beijing, China
| | - Lifang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jifeng Wang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hongcheng Fan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yang Xiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Fuquan Yang
- University of Chinese Academy of Sciences, Beijing, P.R. China
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jizhong Lou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Wenrui Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Alizée Malnoë
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, Umeå, Sweden.
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China.
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13
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Pathak N, Vimal SK, Tandon I, Agrawal L, Hongyi C, Bhattacharyya S. Neurodegenerative Disorders of Alzheimer, Parkinsonism, Amyotrophic Lateral Sclerosis and Multiple Sclerosis: An Early Diagnostic Approach for Precision Treatment. Metab Brain Dis 2022; 37:67-104. [PMID: 34719771 DOI: 10.1007/s11011-021-00800-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/11/2021] [Indexed: 12/21/2022]
Abstract
Neurodegenerative diseases (NDs) are characterised by progressive dysfunction of synapses, neurons, glial cells and their networks. Neurodegenerative diseases can be classified according to primary clinical features (e.g., dementia, parkinsonism, or motor neuron disease), anatomic distribution of neurodegeneration (e.g., frontotemporal degenerations, extrapyramidal disorders, or spinocerebellar degenerations), or principal molecular abnormalities. The most common neurodegenerative disorders are amyloidosis, tauopathies, a-synucleinopathy, and TAR DNA-binding protein 43 (TDP-43) proteopathy. The protein abnormalities in these disorders have abnormal conformational properties along with altered cellular mechanisms, and they exhibit motor deficit, mitochondrial malfunction, dysfunctions in autophagic-lysosomal pathways, synaptic toxicity, and more emerging mechanisms such as the roles of stress granule pathways and liquid-phase transitions. Finally, for each ND, microglial cells have been reported to be implicated in neurodegeneration, in particular, because the microglial responses can shift from neuroprotective to a deleterious role. Growing experimental evidence suggests that abnormal protein conformers act as seed material for oligomerization, spreading from cell to cell through anatomically connected neuronal pathways, which may in part explain the specific anatomical patterns observed in brain autopsy sample. In this review, we mention the human pathology of select neurodegenerative disorders, focusing on how neurodegenerative disorders (i.e., Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis) represent a great healthcare problem worldwide and are becoming prevalent because of the increasing aged population. Despite many studies have focused on their etiopathology, the exact cause of these diseases is still largely unknown and until now with the only available option of symptomatic treatments. In this review, we aim to report the systematic and clinically correlated potential biomarker candidates. Although future studies are necessary for their use in early detection and progression in humans affected by NDs, the promising results obtained by several groups leads us to this idea that biomarkers could be used to design a potential therapeutic approach and preclinical clinical trials for the treatments of NDs.
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Affiliation(s)
- Nishit Pathak
- Department of Pharmaceutical Sciences and Chinese Traditional Medicine, Southwest University, Beibei, Chongqing, 400715, People's Republic of China
| | - Sunil Kumar Vimal
- Department of Pharmaceutical Sciences and Chinese Traditional Medicine, Southwest University, Beibei, Chongqing, 400715, People's Republic of China
| | - Ishi Tandon
- Amity University Jaipur, Rajasthan, Jaipur, Rajasthan, India
| | - Lokesh Agrawal
- Graduate School of Comprehensive Human Sciences, Kansei Behavioural and Brain Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Cao Hongyi
- Department of Pharmaceutical Sciences and Chinese Traditional Medicine, Southwest University, Beibei, Chongqing, 400715, People's Republic of China
| | - Sanjib Bhattacharyya
- Department of Pharmaceutical Sciences and Chinese Traditional Medicine, Southwest University, Beibei, Chongqing, 400715, People's Republic of China.
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14
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Tan MS, Cheah PL, Chin AV, Looi LM, Chang SW. A review on omics-based biomarkers discovery for Alzheimer's disease from the bioinformatics perspectives: Statistical approach vs machine learning approach. Comput Biol Med 2021; 139:104947. [PMID: 34678481 DOI: 10.1016/j.compbiomed.2021.104947] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disease that affects cognition and is the most common cause of dementia in the elderly. As the number of elderly individuals increases globally, the incidence and prevalence of AD are expected to increase. At present, AD is diagnosed clinically, according to accepted criteria. The essential elements in the diagnosis of AD include a patients history, a physical examination and neuropsychological testing, in addition to appropriate investigations such as neuroimaging. The omics-based approach is an emerging field of study that may not only aid in the diagnosis of AD but also facilitate the exploration of factors that influence the development of the disease. Omics techniques, including genomics, transcriptomics, proteomics and metabolomics, may reveal the pathways that lead to neuronal death and identify biomolecular markers associated with AD. This will further facilitate an understanding of AD neuropathology. In this review, omics-based approaches that were implemented in studies on AD were assessed from a bioinformatics perspective. Current state-of-the-art statistical and machine learning approaches used in the single omics analysis of AD were compared based on correlations of variants, differential expression, functional analysis and network analysis. This was followed by a review of the approaches used in the integration and analysis of multi-omics of AD. The strengths and limitations of multi-omics analysis methods were explored and the issues and challenges associated with omics studies of AD were highlighted. Lastly, future studies in this area of research were justified.
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Affiliation(s)
- Mei Sze Tan
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Phaik-Leng Cheah
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ai-Vyrn Chin
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lai-Meng Looi
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Siow-Wee Chang
- Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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15
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Matar M, Gokoglu SA, Prelich MT, Gallo CA, Iqbal AK, Britten RA, Prabhu RK, Myers JG. Machine Learning Models to Predict Cognitive Impairment of Rodents Subjected to Space Radiation. Front Syst Neurosci 2021; 15:713131. [PMID: 34588962 PMCID: PMC8473791 DOI: 10.3389/fnsys.2021.713131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
This research uses machine-learned computational analyses to predict the cognitive performance impairment of rats induced by irradiation. The experimental data in the analyses is from a rodent model exposed to ≤15 cGy of individual galactic cosmic radiation (GCR) ions: 4He, 16O, 28Si, 48Ti, or 56Fe, expected for a Lunar or Mars mission. This work investigates rats at a subject-based level and uses performance scores taken before irradiation to predict impairment in attentional set-shifting (ATSET) data post-irradiation. Here, the worst performing rats of the control group define the impairment thresholds based on population analyses via cumulative distribution functions, leading to the labeling of impairment for each subject. A significant finding is the exhibition of a dose-dependent increasing probability of impairment for 1 to 10 cGy of 28Si or 56Fe in the simple discrimination (SD) stage of the ATSET, and for 1 to 10 cGy of 56Fe in the compound discrimination (CD) stage. On a subject-based level, implementing machine learning (ML) classifiers such as the Gaussian naïve Bayes, support vector machine, and artificial neural networks identifies rats that have a higher tendency for impairment after GCR exposure. The algorithms employ the experimental prescreen performance scores as multidimensional input features to predict each rodent's susceptibility to cognitive impairment due to space radiation exposure. The receiver operating characteristic and the precision-recall curves of the ML models show a better prediction of impairment when 56Fe is the ion in question in both SD and CD stages. They, however, do not depict impairment due to 4He in SD and 28Si in CD, suggesting no dose-dependent impairment response in these cases. One key finding of our study is that prescreen performance scores can be used to predict the ATSET performance impairments. This result is significant to crewed space missions as it supports the potential of predicting an astronaut's impairment in a specific task before spaceflight through the implementation of appropriately trained ML tools. Future research can focus on constructing ML ensemble methods to integrate the findings from the methodologies implemented in this study for more robust predictions of cognitive decrements due to space radiation exposure.
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Affiliation(s)
- Mona Matar
- NASA Glenn Research Center, Cleveland, OH, United States
| | | | | | | | - Asad K. Iqbal
- ZIN Technologies, Inc., Cleveland, OH, United States
| | - Richard A. Britten
- Department of Radiation Oncology, Eastern Virginia Medical School, Norfolk, VA, United States
| | - R. K. Prabhu
- Universities Space Research Association, Cleveland, OH, United States
| | - Jerry G. Myers
- NASA Glenn Research Center, Cleveland, OH, United States
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16
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Amin M, Tang S, Shalamanova L, Taylor RL, Wylie S, Abdullah BM, Whitehead KA. Polyamine biomarkers as indicators of human disease. Biomarkers 2021; 26:77-94. [PMID: 33439737 DOI: 10.1080/1354750x.2021.1875506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The significant increase of periodontitis, chronic kidney disease (CKD), Alzheimer's disease and cancer can be attributed to an ageing population. Each disease produces a range of biomarkers that can be indicative of disease onset and progression. Biomarkers are defined as cellular (intra/extracellular components and whole cells), biochemical (metabolites, ions and toxins) or molecular (nucleic acids, proteins and lipids) alterations which are measurable in biological media such as human tissues, cells or fluids. An interesting group of biomarkers that merit further investigation are the polyamines. Polyamines are a group of molecules consisting of cadaverine, putrescine, spermine and spermidine and have been implicated in the development of a range of systemic diseases, in part due to their production in periodontitis. Cadaverine and putrescine within the periodontal environment have demonstrated cell signalling interfering abilities, by way of leukocyte migration disruption. The polyamines spermine and spermidine in tumour cells have been shown to inhibit cellular apoptosis, effectively prolonging tumorigenesis and continuation of cancer within the host. Polyamine degradation products such as acrolein have been shown to exacerbate renal damage in CKD patients. Thus, the use of such molecules has merit to be utilized in the early indication of such diseases in patients.
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Affiliation(s)
- Mohsin Amin
- Microbiology at Interfaces, Manchester Metropolitan University, Manchester, UK.,Department of Engineering and Technology, Built Environment, Liverpool John Moores University, Liverpool, UK
| | - Shiying Tang
- Microbiology at Interfaces, Manchester Metropolitan University, Manchester, UK.,Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Liliana Shalamanova
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Rebecca L Taylor
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Stephen Wylie
- Department of Engineering and Technology, Civil Engineering, Liverpool John Moores University, Liverpool, UK
| | - Badr M Abdullah
- Department of Engineering and Technology, Built Environment, Liverpool John Moores University, Liverpool, UK
| | - Kathryn A Whitehead
- Microbiology at Interfaces, Manchester Metropolitan University, Manchester, UK.,Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
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17
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Hiltunen AE, Kangas SM, Ohlmeier S, Pietilä I, Hiltunen J, Tanila H, McKerlie C, Govindan S, Tuominen H, Kaarteenaho R, Hallman M, Uusimaa J, Hinttala R. Variant in NHLRC2 leads to increased hnRNP C2 in developing neurons and the hippocampus of a mouse model of FINCA disease. Mol Med 2020; 26:123. [PMID: 33297935 PMCID: PMC7724728 DOI: 10.1186/s10020-020-00245-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
Background FINCA disease is a pediatric cerebropulmonary disease caused by variants in the NHL repeat-containing 2 (NHLRC2) gene. Neurological symptoms are among the first manifestations of FINCA disease, but the consequences of NHLRC2 deficiency in the central nervous system are currently unexplored. Methods The orthologous mouse gene is essential for development, and its complete loss leads to early embryonic lethality. In the current study, we used CRISPR/Cas9 to generate an Nhlrc2 knockin (KI) mouse line, harboring the FINCA patient missense mutation (c.442G > T, p.Asp148Tyr). A FINCA mouse model, resembling the compound heterozygote genotype of FINCA patients, was obtained by crossing the KI and Nhlrc2 knockout mouse lines. To reveal NHLRC2-interacting proteins in developing neurons, we compared cortical neuronal precursor cells of E13.5 FINCA and wild-type mouse embryos by two-dimensional difference gel electrophoresis. Results Despite the significant decrease in NHLRC2, the mice did not develop severe early onset multiorgan disease in either sex. We discovered 19 altered proteins in FINCA neuronal precursor cells; several of which are involved in vesicular transport pathways and actin dynamics which have been previously reported in other cell types including human to have an association with dysfunctional NHLRC2. Interestingly, isoform C2 of hnRNP C1/C2 was significantly increased in both developing neurons and the hippocampus of adult female FINCA mice, connecting NHLRC2 dysfunction with accumulation of RNA binding protein. Conclusions We describe here the first NHLRC2-deficient mouse model to overcome embryonic lethality, enabling further studies on predisposing and causative mechanisms behind FINCA disease. Our novel findings suggest that disrupted RNA metabolism may contribute to the neurodegeneration observed in FINCA patients.
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Affiliation(s)
- Anniina E Hiltunen
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland. .,Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Salla M Kangas
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Steffen Ohlmeier
- Proteomics Core Facility, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu, 90014, Finland
| | - Ilkka Pietilä
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, Uppsala, Sweden
| | - Jori Hiltunen
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Heikki Tanila
- A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, Canada.,Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Subashika Govindan
- Tissue Engineering Laboratory, Hepia/HES-SO, University of Applied Sciences Western Switzerland, Geneva, Switzerland
| | - Hannu Tuominen
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland.,Department of Pathology, Oulu University Hospital, Oulu, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, Respiratory Research, University of Oulu, Oulu, Finland.,Medical Research Center Oulu and Unit of Internal Medicine and Respiratory Medicine, Oulu University Hospital, Oulu, Finland
| | - Mikko Hallman
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Johanna Uusimaa
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland.,Clinic for Children and Adolescents, Paediatric Neurology Unit, Oulu University Hospital, Oulu, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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18
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Responsive Expression of MafF to β-Amyloid-Induced Oxidative Stress. DISEASE MARKERS 2020; 2020:8861358. [PMID: 33488846 PMCID: PMC7787795 DOI: 10.1155/2020/8861358] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/13/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
The small musculoaponeurotic fibrosarcoma (sMaf) proteins MafF, MafG, and MafK are basic region leucine zipper- (bZIP-) type transcription factors and display tissue- or stimulus-specific expression patterns. As the oxidative stress reactive proteins, sMafs are implicated in various neurological disorders. In the present study, the expressions of sMafs were investigated across five databases gathering transcriptomic data from 74 Alzheimer's disease (AD) patients and 66 controls in the Gene Expression Omnibus (GEO) database. The expression of MafF was increased in the hippocampus of AD patients, which was negatively correlated with the expression of the glutamate cysteine ligase catalytic subunit (GCLC). Furthermore, MafF was significantly increased in patients with Braak stage V-VI, compared to those with Braak stage III-IV. β-Amyloid (Aβ), a strong inducer of oxidative stress, plays a crucial role in the pathogenesis of AD. The responsive expressions of sMafs to Aβ-induced oxidative stress were studied in the APP/PS1 mouse model of AD, Aβ intrahippocampal injection rats, and several human cell lines from different tissue origins. This study revealed that only the induction of MafF was accompanied with reduction of GCLC and glutathione (GSH). MafF knockdown suppressed the increase of GSH induced by Aβ. Among sMafs, MafF is the most responsive to Aβ-induced oxidative stress and might potentiate the inhibition of antioxidation. These results provide a better understanding of sMaf modulation in AD and highlight MafF as a potential therapeutic target in AD.
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19
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Diniz Pereira J, Gomes Fraga V, Morais Santos AL, Carvalho MDG, Caramelli P, Braga Gomes K. Alzheimer's disease and type 2 diabetes mellitus: A systematic review of proteomic studies. J Neurochem 2020; 156:753-776. [PMID: 32909269 DOI: 10.1111/jnc.15166] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/15/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022]
Abstract
Similar to dementia, the risk for developing type 2 diabetes mellitus (T2DM) increases with age, and T2DM also increases the risk for dementia, particularly Alzheimer's disease (AD). Although T2DM is primarily a peripheral disorder and AD is a central nervous system disease, both share some common features as they are chronic and complex diseases, and both show involvement of oxidative stress and inflammation in their progression. These characteristics suggest that T2DM may be associated with AD, which gave rise to a new term, type 3 diabetes (T3DM). In this study, we searched for matching peripheral proteomic biomarkers of AD and T2DM based in a systematic review of the available literature. We identified 17 common biomarkers that were differentially expressed in both patients with AD or T2DM when compared with healthy controls. These biomarkers could provide a useful workflow for screening T2DM patients at risk to develop AD.
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Affiliation(s)
- Jessica Diniz Pereira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vanessa Gomes Fraga
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anna Luiza Morais Santos
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maria das Graças Carvalho
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paulo Caramelli
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Karina Braga Gomes
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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20
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Ma J, Ma C, Li J, Sun Y, Ye F, Liu K, Zhang H. Extracellular Matrix Proteins Involved in Alzheimer's Disease. Chemistry 2020; 26:12101-12110. [PMID: 32207199 DOI: 10.1002/chem.202000782] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/22/2020] [Indexed: 01/19/2023]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases and characterized by cognitive and memory impairments. Emerging evidence suggests that the extracellular matrix (ECM) in the brain plays an important role in the etiology of AD. It has been detected that the levels of ECM proteins have changed in the brains of AD patients and animal models. Some ECM components, for example, elastin and heparan sulfate proteoglycans, are considered to promote the upregulation of extracellular amyloid-beta (Aβ) proteins. In addition, collagen VI and laminin are shown to have interactions with Aβ peptides, which might lead to the clearance of those peptides. Thus, ECM proteins are involved in both amyloidosis and neuroprotection in the AD process. However, the molecular mechanism of neuronal ECM proteins on the pathophysiology of AD remains elusive. More investigation of ECM proteins with AD pathogenesis is needed, and this may lead to novel therapeutic strategies and biomarkers for AD.
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Affiliation(s)
- Jun Ma
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P.R. China.,State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China
| | - Chao Ma
- School of Engineering and Applied Sciences & Department of Physics, Harvard University, 29 Oxford Street, Cambridge, MA, 02138, USA
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China
| | - Yao Sun
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China
| | - Fangfu Ye
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P.R. China.,Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China.,Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China.,Department of Chemistry, Tsinghua University, Beijing, 100084, P.R. China
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21
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Shigemizu D, Mori T, Akiyama S, Higaki S, Watanabe H, Sakurai T, Niida S, Ozaki K. Identification of potential blood biomarkers for early diagnosis of Alzheimer's disease through RNA sequencing analysis. ALZHEIMERS RESEARCH & THERAPY 2020; 12:87. [PMID: 32677993 PMCID: PMC7367375 DOI: 10.1186/s13195-020-00654-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022]
Abstract
Background With demographic shifts toward older populations, the number of people with dementia is steadily increasing. Alzheimer’s disease (AD) is the most common cause of dementia, and no curative treatment is available. The current best strategy is to delay disease progression and to practice early intervention to reduce the number of patients that ultimately develop AD. Therefore, promising novel biomarkers for early diagnosis are urgently required. Methods To identify blood-based biomarkers for early diagnosis of AD, we performed RNA sequencing (RNA-seq) analysis of 610 blood samples, representing 271 patients with AD, 91 cognitively normal (CN) adults, and 248 subjects with mild cognitive impairment (MCI). We first estimated cell-type proportions among AD, MCI, and CN samples from the bulk RNA-seq data using CIBERSORT and then examined the differentially expressed genes (DEGs) between AD and CN samples. To gain further insight into the biological functions of the DEGs, we performed gene set enrichment analysis (GSEA) and network-based meta-analysis. Results In the cell-type distribution analysis, we found a significant association between the proportion of neutrophils and AD prognosis at a false discovery rate (FDR) < 0.05. Furthermore, a similar trend emerged in the results of routine blood tests from a large number of samples (n = 3,099: AD, 1,605; MCI, 994; CN, 500). In addition, GSEA and network-based meta-analysis based on DEGs between AD and CN samples revealed functional modules and important hub genes associated with the pathogenesis of AD. The risk prediction model constructed by using the proportion of neutrophils and the most important hub genes (EEF2 and RPL7) achieved a high AUC of 0.878 in a validation cohort; when further applied to a prospective cohort, the model achieved a high accuracy of 0.727. Conclusions Our model was demonstrated to be effective in prospective AD risk prediction. These findings indicate the discovery of potential biomarkers for early diagnosis of AD, and their further improvement may lead to future practical clinical use.
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Affiliation(s)
- Daichi Shigemizu
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan. .,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan. .,RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan.
| | - Taiki Mori
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan
| | - Shintaro Akiyama
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan
| | - Sayuri Higaki
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan
| | - Hiroshi Watanabe
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan
| | - Takashi Sakurai
- The Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Obu, 474-8511, Aichi, Japan.,Department of Cognitive and Behavioral Science, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Aichi, Japan
| | - Shumpei Niida
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan
| | - Kouichi Ozaki
- Medical Genome Center, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, 474-8511, Aichi, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan
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22
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Kelly J, Moyeed R, Carroll C, Luo S, Li X. Genetic networks in Parkinson's and Alzheimer's disease. Aging (Albany NY) 2020; 12:5221-5243. [PMID: 32205467 PMCID: PMC7138567 DOI: 10.18632/aging.102943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Parkinson’s disease (PD) and Alzheimer’s disease (AD) are the most common neurodegenerative diseases and there is increasing evidence that they share common physiological and pathological links. Here we have conducted the largest network analysis of PD and AD based on their gene expressions in blood to date. We identified modules that were not preserved between disease and healthy control (HC) networks, and important hub genes and transcription factors (TFs) in these modules. We highlighted that the PD module not preserved in HCs was associated with insulin resistance, and HDAC6 was identified as a hub gene in this module which may have the role of influencing tau phosphorylation and autophagic flux in neurodegenerative disease. The AD module associated with regulation of lipolysis in adipocytes and neuroactive ligand-receptor interaction was not preserved in healthy and mild cognitive impairment networks and the key hubs TRPC5 and BRAP identified as potential targets for therapeutic treatments of AD. Our study demonstrated that PD and AD share common disrupted genetics and identified novel pathways, hub genes and TFs that may be new areas for mechanistic study and important targets in both diseases.
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Affiliation(s)
- Jack Kelly
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Rana Moyeed
- Faculty of Science and Engineering, Plymouth University, Plymouth PL6 8BU, UK
| | - Camille Carroll
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Shouqing Luo
- Faculty of Health: Medicine, Dentistry and Human Sciences, Plymouth University, Plymouth PL6 8BU, UK
| | - Xinzhong Li
- School of Science, Engineering and Design, Teesside University, Middlesbrough TS1 3BX, UK
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23
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Mao X, Huang D, Rao C, Du M, Liang M, Li F, Liu B, Huang K. Enoyl coenzyme A hydratase 1 combats obesity and related metabolic disorders by promoting adipose tissue browning. Am J Physiol Endocrinol Metab 2020; 318:E318-E329. [PMID: 31961704 DOI: 10.1152/ajpendo.00424.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Browning of white adipose tissue (WAT) has been recognized as an important strategy for the treatment of obesity, insulin resistance, and diabetes. Enoyl coenzyme A hydratase 1 (ECH1) is a widely known enzyme involved in lipid metabolism. However, whether and how ECH1 is implicated in browning of WAT remain obscure. Adeno-associated, virus-mediated genetic engineering of ECH1 in adipose tissue was used in investigations in mouse models of obesity induced by a high-fat diet (HFD) or browning induced by cold exposure. Metabolic parameters showed that ECH1 overexpression decreased weight gain and improved insulin sensitivity and lipid profile after 8 wk of an HFD. Further work revealed that these changes were associated with enhanced energy expenditure and increased appearance of brown-like adipocytes in inguinal WAT, as verified by a remarkable increase in uncoupling protein 1 and thermogenic gene expression. In vitro, ECH1 induced brown fat-related gene expression in adipocytes differentiated from primary stromal vascular fractions, whereas knockdown of ECH1 reversed this effect. Mechanistically, ECH1 regulated the thermogenic program by inhibiting mammalian target of rapamycin signaling, which may partially explain the potential mechanism for ECH1 regulating adipose browning. In summary, ECH1 may participate in the pathology of obesity by regulating browning of WAT, which probably provides us with a new therapeutic strategy for combating obesity.
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Affiliation(s)
- Xiaoxiang Mao
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dandan Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Caijun Rao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Du
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minglu Liang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Baoqing Liu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Huang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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24
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Tang R, Liu H. Identification of Temporal Characteristic Networks of Peripheral Blood Changes in Alzheimer's Disease Based on Weighted Gene Co-expression Network Analysis. Front Aging Neurosci 2019; 11:83. [PMID: 31178714 PMCID: PMC6537635 DOI: 10.3389/fnagi.2019.00083] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease. The study of blood-based biomarkers has lasted for a long time in AD, because it supports the concept that peripheral changes are involved in AD pathology. But it is still unclear how peripheral blood is involved in the temporal characteristic molecular mechanisms of AD from aging to mild cognitive impairment (MCI) and which cells are responsible for the molecular mechanisms. The main purpose of our study is to gain a systematic and comprehensive understanding of temporal characteristic networks of peripheral blood in AD using whole blood samples with 329 case-control samples, including 104 normal elderly control subjects (CTL), 80 MCI who are susceptible to AD, and 145 AD, by the weighted gene co-expression network analysis (WGCNA). The module-trait relationships were constructed and module preservation was validated with independent datasets GSE63061, GSE97760, GSE18309, GSE29378, GSE28146, and GSE29652. Our results indicate that the down-regulated protein modification and ubiquitin degradation systems, and the up-regulated insulin resistance both play a major role in MCI, while the up-regulated inflammatory cascade dominates in AD, which is mainly mediated by monocytes, macrophages. Although there is mixed activation of M1 and M2 macrophages in all stages of AD, the immune neutral state or M2 polarization may predominate in MCI, and M1 polarization may predominate in AD. Moreover, we found that TRPV2, NDUFV1, ATF4, HSPA8, STAT3 and LUC7L3 may mediate the pathological changes in MCI, while SIRPA, LAMP-2, NDUFB5, HSPA8, STAT3 and FPR2 may mediate the conversion from MCI-AD or the pathological changes in AD, which provide a basis for the treatment based on the peripheral blood system. In addition, we also found that the combined diagnosis based on a panel of genes from the red, blue, and brown modules have a moderate diagnostic effect on distinguishing MCI and AD from CTL, suggesting that those panels of genes may be used for detection of MCI and prediction of this conversion from MCI to AD. Our research emphasizes that pathological changes, based on temporal characteristics of peripheral blood, provide a theoretical basis for targeted peripheral treatment based on appropriate times and identified several diagnostic markers.
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Affiliation(s)
- Runhong Tang
- Department of Neurology, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Huayan Liu
- Department of Neurology, First Affiliated Hospital, China Medical University, Shenyang, China
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25
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Paakkola T, Salokas K, Miinalainen I, Lehtonen S, Manninen A, Kaakinen M, Ruddock LW, Varjosalo M, Kaarteenaho R, Uusimaa J, Hinttala R. Biallelic mutations in human NHLRC2 enhance myofibroblast differentiation in FINCA disease. Hum Mol Genet 2019; 27:4288-4302. [PMID: 30239752 DOI: 10.1093/hmg/ddy298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/14/2018] [Indexed: 01/04/2023] Open
Abstract
The development of tissue fibrosis is complex and at the present time, not fully understood. Fibrosis, neurodegeneration and cerebral angiomatosis (FINCA disease) have been described in patients with mutations in NHL repeat-containing protein 2 (NHLRC2). However, the molecular functions of NHLRC2 are uncharacterized. Herein, we identified putative interacting partners for NHLRC2 using proximity-labeling mass spectrometry. We also investigated the function of NHLRC2 using immortalized cells cultured from skin biopsies of FINCA patients and normal fibroblasts with NHLRC2 knock-down and NHLRC2 overexpressing gene modifications. Transmission electron microscopy analysis of immortalized cell cultures from three FINCA patients demonstrated multilamellar bodies and distinctly organized vimentin filaments. Additionally, two of three cultures derived from patient skin biopsies contained cells that exhibited features characteristic of myofibroblasts. Altogether, the data presented in this study show for the first time that NHLRC2 is involved in cellular organization through regulation of the cytoskeleton and vesicle transport. We conclude that compound heterozygous p.Asp148Tyr and p.Arg201GlyfsTer6 mutations in NHLRC2 lead to severe tissue fibrosis in humans by enhancing the differentiation of fibroblasts to myofibroblasts.
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Affiliation(s)
- Teija Paakkola
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland.,Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, Finland, Helsinki, Finland.,Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Finland, Helsinki, Finland
| | | | | | - Aki Manninen
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Lloyd W Ruddock
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Finland, Helsinki, Finland.,Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Finland, Helsinki, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland.,Unit of Internal Medicine and Respiratory Medicine, Oulu University Hospital, OYS, Oulu, Finland.,Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Johanna Uusimaa
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland.,Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Reetta Hinttala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland.,Medical Research Center Oulu, University of Oulu, Oulu, Finland
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26
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Kelly J, Moyeed R, Carroll C, Albani D, Li X. Gene expression meta-analysis of Parkinson's disease and its relationship with Alzheimer's disease. Mol Brain 2019; 12:16. [PMID: 30819229 PMCID: PMC6396547 DOI: 10.1186/s13041-019-0436-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 02/15/2019] [Indexed: 12/16/2022] Open
Abstract
Parkinson’s disease (PD) and Alzheimer’s disease (AD) are the most common neurodegenerative diseases and have been suggested to share common pathological and physiological links. Understanding the cross-talk between them could reveal potentials for the development of new strategies for early diagnosis and therapeutic intervention thus improving the quality of life of those affected. Here we have conducted a novel meta-analysis to identify differentially expressed genes (DEGs) in PD microarray datasets comprising 69 PD and 57 control brain samples which is the biggest cohort for such studies to date. Using identified DEGs, we performed pathway, upstream and protein-protein interaction analysis. We identified 1046 DEGs, of which a majority (739/1046) were downregulated in PD. YWHAZ and other genes coding 14–3-3 proteins are identified as important DEGs in signaling pathways and in protein-protein interaction networks (PPIN). Perturbed pathways also include mitochondrial dysfunction and oxidative stress. There was a significant overlap in DEGs between PD and AD, and over 99% of these were differentially expressed in the same up or down direction across the diseases. REST was identified as an upstream regulator in both diseases. Our study demonstrates that PD and AD share significant common DEGs and pathways, and identifies novel genes, pathways and upstream regulators which may be important targets for therapy in both diseases.
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Affiliation(s)
- Jack Kelly
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, PL6 8BU, UK
| | - Rana Moyeed
- Faculty of Science and Engineering, Plymouth University, Plymouth, PL6 8BU, UK
| | - Camille Carroll
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, PL6 8BU, UK
| | - Diego Albani
- Department of Neuroscience, IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri" Via La Masa 19, 20156, Milan, Italy
| | - Xinzhong Li
- Faculty of Medicine and Dentistry, Plymouth University, Plymouth, PL6 8BU, UK. .,School of Science, Engineering & Design, Teesside University, Middlesbrough, TS1 3BX, UK.
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27
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Neuner SM, Heuer SE, Zhang JG, Philip VM, Kaczorowski CC. Identification of Pre-symptomatic Gene Signatures That Predict Resilience to Cognitive Decline in the Genetically Diverse AD-BXD Model. Front Genet 2019; 10:35. [PMID: 30787942 PMCID: PMC6372563 DOI: 10.3389/fgene.2019.00035] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/18/2019] [Indexed: 12/23/2022] Open
Abstract
Across the population, individuals exhibit a wide variation of susceptibility or resilience to developing Alzheimer’s disease (AD). Identifying specific factors that promote resilience would provide insight into disease mechanisms and nominate potential targets for therapeutic intervention. Here, we use transcriptome profiling to identify gene networks present in the pre-symptomatic AD mouse brain relating to neuroinflammation, brain vasculature, extracellular matrix organization, and synaptic signaling that predict cognitive performance at an advanced age. We highlight putative drivers of these observed relationships, including Itgb2, Fcgr2b, Slc6a14, and Gper1, which represent prime targets through which to promote resilience prior to overt symptom onset. In addition, we identify a genomic region on chromosome 2 containing variants that directly modulate resilience network expression. Overall, work here highlights new potential drivers of resilience to AD and contributes significantly to our understanding of early, potentially causal, disease mechanisms.
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Affiliation(s)
- Sarah M Neuner
- University of Tennessee Health Science Center, Memphis, TN, United States.,The Jackson Laboratory, Bar Harbor, ME, United States
| | - Sarah E Heuer
- The Jackson Laboratory, Bar Harbor, ME, United States.,Tufts University Sackler School of Graduate Biomedical Sciences, Boston, MA, United States
| | - Ji-Gang Zhang
- The Jackson Laboratory, Bar Harbor, ME, United States
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28
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Surendranathan A, Su L, Mak E, Passamonti L, Hong YT, Arnold R, Vázquez Rodríguez P, Bevan-Jones WR, Brain SAE, Fryer TD, Aigbirhio FI, Rowe JB, O’Brien JT. Early microglial activation and peripheral inflammation in dementia with Lewy bodies. Brain 2018; 141:3415-3427. [PMID: 30403785 PMCID: PMC6262214 DOI: 10.1093/brain/awy265] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/31/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
Inflammation is increasingly recognized as part of the pathology of neurodegenerative conditions such as Alzheimer's disease and Parkinson's disease, but its role in dementia with Lewy bodies remains unclear. Using multimodal imaging and peripheral cytokine analysis, we therefore investigated central and peripheral inflammation in this common form of dementia. Nineteen participants with probable dementia with Lewy bodies and 16 similarly aged controls underwent 3 T MRI and PET imaging with 11C-PK11195, a marker of microglial activation in vivo. Peripheral blood inflammatory cytokines were also measured in all subjects, as well as in an additional 10 controls, using the Mesoscale Human Cytokine 36 plex panel and additional assays for high sensitivity c-reactive protein, tumour necrosis factor receptor 1, IL-34, YKL-40 (chitinase-3-like protein 1) and colony stimulating factor 1. To test for the presence of in vivo amyloid, 11C-Pittsburgh compound B PET imaging was also performed in 16 of the dementia with Lewy body participants. Microglial activation was elevated in dementia with Lewy bodies subjects with mild disease when compared to those with moderate/severe impairment, where disease severity was indexed by cognitive performance on the revised Addenbrooke's Cognitive Examination. In patients, strong correlations were found between cognitive performance and 11C-PK11195 non-displaceable binding potential in several regions including the caudate nucleus (R = 0.83, P = 0.00008) and cuneus (R = 0.77, P = 0.0005). Several inflammatory cytokines were altered in the patients compared to controls, with elevated macrophage inflammatory protein-3 (P = 0.001), IL-17A (P = 0.008) and IL-2 (P = 0.046) and reduced IL-8 (P = 0.024). There was no correlation between cortical 11C-Pittsburgh compound B standardized uptake value ratio and clinical features, regional 11C-PK11195 binding or peripheral cytokine levels. Nor was there any regional correlation between 11C-PK11195 non-displaceable binding potentials and 11C-Pittsburgh compound B standardized uptake value ratios. Our findings provide evidence for both central and peripheral inflammatory changes in dementia with Lewy bodies, with microglial activation occurring early in the disease in key regions known to be associated with pathology, before declining as cognition declines. Raised peripheral cytokines associated with T cell function further suggest a role for the adaptive immune system in the pathogenesis of the disease.
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Affiliation(s)
| | - Li Su
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Sino-Britain Centre for Cognition and Ageing Research, Faculty of Psychology, Southwest University, Chongqing, China
| | - Elijah Mak
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Luca Passamonti
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Young T Hong
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wolfson Brain Imaging Centre, University of Cambridge, Cambridge, UK
| | - Robert Arnold
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | | | | | | | - Tim D Fryer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wolfson Brain Imaging Centre, University of Cambridge, Cambridge, UK
| | - Franklin I Aigbirhio
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wolfson Brain Imaging Centre, University of Cambridge, Cambridge, UK
| | - James B Rowe
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - John T O’Brien
- Department of Psychiatry, University of Cambridge, Cambridge, UK
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29
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Systematic Analysis and Biomarker Study for Alzheimer's Disease. Sci Rep 2018; 8:17394. [PMID: 30478411 PMCID: PMC6255913 DOI: 10.1038/s41598-018-35789-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/28/2018] [Indexed: 12/31/2022] Open
Abstract
Revealing the relationship between dysfunctional genes in blood and brain tissues from patients with Alzheimer’s Disease (AD) will help us to understand the pathology of this disease. In this study, we conducted the first such large systematic analysis to identify differentially expressed genes (DEGs) in blood samples from 245 AD cases, 143 mild cognitive impairment (MCI) cases, and 182 healthy control subjects, and then compare these with DEGs in brain samples. We evaluated our findings using two independent AD blood datasets and performed a gene-based genome-wide association study to identify potential novel risk genes. We identified 789 and 998 DEGs common to both blood and brain of AD and MCI subjects respectively, over 77% of which had the same regulation directions across tissues and disease status, including the known ABCA7, and the novel TYK2 and TCIRG1. A machine learning classification model containing NDUFA1, MRPL51, and RPL36AL, implicating mitochondrial and ribosomal function, was discovered which discriminated between AD patients and controls with 85.9% of area under the curve and 78.1% accuracy (sensitivity = 77.6%, specificity = 78.9%). Moreover, our findings strongly suggest that mitochondrial dysfunction, NF-κB signalling and iNOS signalling are important dysregulated pathways in AD pathogenesis.
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30
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Zhang F, Wei J, Li X, Ma C, Gao Y. Early Candidate Urine Biomarkers for Detecting Alzheimer’s Disease Before Amyloid-β Plaque Deposition in an APP (swe)/PSEN1dE9 Transgenic Mouse Model. J Alzheimers Dis 2018; 66:613-637. [DOI: 10.3233/jad-180412] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fanshuang Zhang
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wei
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Xundou Li
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Neuroscience Center; Joint Laboratory of Anesthesia and Pain, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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31
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Biterova E, Ignatyev A, Uusimaa J, Hinttala R, Ruddock LW. Structural analysis of human NHLRC2, mutations of which are associated with FINCA disease. PLoS One 2018; 13:e0202391. [PMID: 30138417 PMCID: PMC6107167 DOI: 10.1371/journal.pone.0202391] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 11/21/2022] Open
Abstract
NHLRC2 (NHL repeat-containing protein 2) is an essential protein. Mutations of NHLRC2, including Asp148Tyr, have been recently associated with a novel FINCA disease (fibrosis, neurodegeneration, cerebral angiomatosis), which is fatal in early childhood. To gain insight into the mechanisms of action of this essential protein, we determined the crystal structure of the Trx-like and NHL repeat β-propeller domains of human NHLRC2 to a resolution of 2.7 Å. The structure reveals two domains adjacent to each other that form a cleft containing a conserved CCINC motif. A SAXS structure of full-length NHLRC2 reveals that the non-conserved C-terminal domain does not pack against the N-terminal domains. Analysis of the surface properties of the protein identifies an extended negative electrostatic potential in the surface of the cleft formed by the two domains, which likely forms a binding site for a ligand or interaction partner(s). Bioinformatics analysis discovers homologs across a range of eukaryotic and prokaryotic species and conserved residues map mostly to the adjacent surfaces of the Trx-like and β-propeller domains that form the cleft, suggesting both that this forms the potential functional site of NHLRC2 and that the function is conserved across species. Asp148 is located in the Trx-like domain and is not conserved across species. The Asp148Tyr mutation destabilizes the structure of the protein by 2°C. The NHLRC2 structure, the first of any of its homologs, provides an important step towards more focused structure-function studies of this essential protein.
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Affiliation(s)
- Ekaterina Biterova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Alexander Ignatyev
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Johanna Uusimaa
- Biocenter Oulu, University of Oulu, Oulu, Finland
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Reetta Hinttala
- Biocenter Oulu, University of Oulu, Oulu, Finland
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Lloyd W. Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
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32
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Uusimaa J, Kaarteenaho R, Paakkola T, Tuominen H, Karjalainen MK, Nadaf J, Varilo T, Uusi-Mäkelä M, Suo-Palosaari M, Pietilä I, Hiltunen AE, Ruddock L, Alanen H, Biterova E, Miinalainen I, Salminen A, Soininen R, Manninen A, Sormunen R, Kaakinen M, Vuolteenaho R, Herva R, Vieira P, Dunder T, Kokkonen H, Moilanen JS, Rantala H, Nogee LM, Majewski J, Rämet M, Hallman M, Hinttala R. NHLRC2 variants identified in patients with fibrosis, neurodegeneration, and cerebral angiomatosis (FINCA): characterisation of a novel cerebropulmonary disease. Acta Neuropathol 2018; 135:727-742. [PMID: 29423877 DOI: 10.1007/s00401-018-1817-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 11/26/2022]
Abstract
A novel multi-organ disease that is fatal in early childhood was identified in three patients from two non-consanguineous families. These children were born asymptomatic but at the age of 2 months they manifested progressive multi-organ symptoms resembling no previously known disease. The main clinical features included progressive cerebropulmonary symptoms, malabsorption, progressive growth failure, recurrent infections, chronic haemolytic anaemia and transient liver dysfunction. In the affected children, neuropathology revealed increased angiomatosis-like leptomeningeal, cortical and superficial white matter vascularisation and congestion, vacuolar degeneration and myelin loss in white matter, as well as neuronal degeneration. Interstitial fibrosis and previously undescribed granuloma-like lesions were observed in the lungs. Hepatomegaly, steatosis and collagen accumulation were detected in the liver. A whole-exome sequencing of the two unrelated families with the affected children revealed the transmission of two heterozygous variants in the NHL repeat-containing protein 2 (NHLRC2); an amino acid substitution p.Asp148Tyr and a frameshift 2-bp deletion p.Arg201GlyfsTer6. NHLRC2 is highly conserved and expressed in multiple organs and its function is unknown. It contains a thioredoxin-like domain; however, an insulin turbidity assay on human recombinant NHLRC2 showed no thioredoxin activity. In patient-derived fibroblasts, NHLRC2 levels were low, and only p.Asp148Tyr was expressed. Therefore, the allele with the frameshift deletion is likely non-functional. Development of the Nhlrc2 null mouse strain stalled before the morula stage. Morpholino knockdown of nhlrc2 in zebrafish embryos affected the integrity of cells in the midbrain region. This is the first description of a fatal, early-onset disease; we have named it FINCA disease based on the combination of pathological features that include fibrosis, neurodegeneration, and cerebral angiomatosis.
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Affiliation(s)
- Johanna Uusimaa
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland.
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland.
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, Respiratory Research, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Medical Research Center Oulu and Unit of Internal Medicine and Respiratory Medicine, Oulu University Hospital, PO Box 20, 90029, Oulu, Finland
| | - Teija Paakkola
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Hannu Tuominen
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Department of Pathology, Oulu University Hospital, PO Box 50, 90029, Oulu, Finland
| | - Minna K Karjalainen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Javad Nadaf
- McGill University and Génome Québec Innovation Centre, Montreal, QC, H3A 0G1, Canada
- St. Jude Children's Research Hospital (SJCRH), 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Teppo Varilo
- Department of Medical Genetics, University of Helsinki, Haartmaninkatu 8, 00251, Helsinki, Finland
| | - Meri Uusi-Mäkelä
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Maria Suo-Palosaari
- Department of Diagnostic Radiology and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, PO Box 50, 90029, Oulu, Finland
| | - Ilkka Pietilä
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Anniina E Hiltunen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Lloyd Ruddock
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Heli Alanen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Ekaterina Biterova
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Ilkka Miinalainen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Annamari Salminen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Raija Soininen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Aki Manninen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Raija Sormunen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Mika Kaakinen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | | | - Riitta Herva
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Päivi Vieira
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Teija Dunder
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab, Oulu University Hospital, PO Box 500, 90029, Oulu, Finland
- Department of Clinical Chemistry and Medical Research Center Oulu, University Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Jukka S Moilanen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Heikki Rantala
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Lawrence M Nogee
- Division of Neonatology, Johns Hopkins University School of Medicine, CMSC 6-104A, 600 N. Wolfe St., Baltimore, MD, 21287, USA
| | - Jacek Majewski
- McGill University and Génome Québec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Mika Rämet
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mikko Hallman
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Reetta Hinttala
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
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33
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Grand Moursel L, van Roon-Mom WMC, Kiełbasa SM, Mei H, Buermans HPJ, van der Graaf LM, Hettne KM, de Meijer EJ, van Duinen SG, Laros JFJ, van Buchem MA, 't Hoen PAC, van der Maarel SM, van der Weerd L. Brain Transcriptomic Analysis of Hereditary Cerebral Hemorrhage With Amyloidosis-Dutch Type. Front Aging Neurosci 2018; 10:102. [PMID: 29706885 PMCID: PMC5908973 DOI: 10.3389/fnagi.2018.00102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/26/2018] [Indexed: 11/23/2022] Open
Abstract
Hereditary cerebral hemorrhage with amyloidosis-Dutch type (HCHWA-D) is an early onset hereditary form of cerebral amyloid angiopathy (CAA) caused by a point mutation resulting in an amino acid change (NP_000475.1:p.Glu693Gln) in the amyloid precursor protein (APP). Post-mortem frontal and occipital cortical brain tissue from nine patients and nine age-related controls was used for RNA sequencing to identify biological pathways affected in HCHWA-D. Although previous studies indicated that pathology is more severe in the occipital lobe in HCHWA-D compared to the frontal lobe, the current study showed similar changes in gene expression in frontal and occipital cortex and the two brain regions were pooled for further analysis. Significantly altered pathways were analyzed using gene set enrichment analysis (GSEA) on 2036 significantly differentially expressed genes. Main pathways over-represented by down-regulated genes were related to cellular aerobic respiration (including ATP synthesis and carbon metabolism) indicating a mitochondrial dysfunction. Principal up-regulated pathways were extracellular matrix (ECM)–receptor interaction and ECM proteoglycans in relation with an increase in the transforming growth factor beta (TGFβ) signaling pathway. Comparison with the publicly available dataset from pre-symptomatic APP-E693Q transgenic mice identified overlap for the ECM–receptor interaction pathway, indicating that ECM modification is an early disease specific pathomechanism.
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Affiliation(s)
- Laure Grand Moursel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Szymon M Kiełbasa
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Netherlands
| | - Hailiang Mei
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, Netherlands
| | - Henk P J Buermans
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linda M van der Graaf
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Kristina M Hettne
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Emile J de Meijer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Sjoerd G van Duinen
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.,Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Mark A van Buchem
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Louise van der Weerd
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
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34
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Nishi K, Iwaihara Y, Tsunoda T, Doi K, Sakata T, Shirasawa S, Ishikura S. ROS-induced cleavage of NHLRC2 by caspase-8 leads to apoptotic cell death in the HCT116 human colon cancer cell line. Cell Death Dis 2017; 8:3218. [PMID: 29242562 PMCID: PMC5870588 DOI: 10.1038/s41419-017-0006-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 12/14/2022]
Abstract
Excess production of reactive oxygen species (ROS) is known to cause apoptotic cell death. However, the molecular mechanisms whereby ROS induce apoptosis remain elusive. Here we show that the NHL-repeat-containing protein 2 (NHLRC2) thioredoxin-like domain protein is cleaved by caspase-8 in ROS-induced apoptosis in the HCT116 human colon cancer cell line. Treatment of HCT116 cells with the oxidant tert-butyl hydroperoxide (tBHP) induced apoptosis and reduced NHLRC2 protein levels, whereas pretreatment with the antioxidant N-acetyl-l-cysteine prevented apoptosis and the decrease in NHLRC2 protein levels seen in tBHP-treated cells. Furthermore, the ROS-induced decrease in NHLRC2 protein levels was relieved by the caspase inhibitor z-VAD-fmk. We found that the thioredoxin-like domain of NHLRC2 interacted with a proenzyme form of caspase-8, and that caspase-8 cleaved NHLRC2 protein at Asp580 in vitro. Furthermore, siRNA-mediated knockdown of caspase-8 blocked the ROS-induced decrease in NHLRC2 protein levels. Both shRNA and CRISPR-Cas9-mediated loss of NHLRC2 resulted in an increased susceptibility of HCT116 cells to ROS-induced apoptosis. These results suggest that excess ROS production causes a caspase-8-mediated decrease in NHLRC2 protein levels, leading to apoptotic cell death in colon cancer cells, and indicate an important role of NHLRC2 in the regulation of ROS-induced apoptosis.
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Affiliation(s)
- Kensuke Nishi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan.,Department of Otorhinolaryngology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Yuri Iwaihara
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Keiko Doi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Toshifumi Sakata
- Department of Otorhinolaryngology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180, Japan. .,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180, Japan.
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