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Bakulin A, Teyssier NB, Kampmann M, Khoroshkin M, Goodarzi H. pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease. PLoS Comput Biol 2024; 20:e1012346. [PMID: 39236079 DOI: 10.1371/journal.pcbi.1012346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 07/22/2024] [Indexed: 09/07/2024] Open
Abstract
Inferring the driving regulatory programs from comparative analysis of gene expression data is a cornerstone of systems biology. Many computational frameworks were developed to address this problem, including our iPAGE (information-theoretic Pathway Analysis of Gene Expression) toolset that uses information theory to detect non-random patterns of expression associated with given pathways or regulons. Our recent observations, however, indicate that existing approaches are susceptible to the technical biases that are inherent to most real world annotations. To address this, we have extended our information-theoretic framework to account for specific biases and artifacts in biological networks using the concept of conditional information. To showcase pyPAGE, we performed a comprehensive analysis of regulatory perturbations that underlie the molecular etiology of Alzheimer's disease (AD). pyPAGE successfully recapitulated several known AD-associated gene expression programs. We also discovered several additional regulons whose differential activity is significantly associated with AD. We further explored how these regulators relate to pathological processes in AD through cell-type specific analysis of single cell and spatial gene expression datasets. Our findings showcase the utility of pyPAGE as a precise and reliable biomarker discovery in complex diseases such as Alzheimer's disease.
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Affiliation(s)
- Artemy Bakulin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Noam B Teyssier
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
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2
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Babalola JA, Lang M, George M, Stracke A, Tam-Amersdorfer C, Itxaso I, Lucija D, Tadic J, Schilcher I, Loeffler T, Flunkert S, Prokesch M, Leitinger G, Lass A, Hutter-Paier B, Panzenboeck U, Hoefler G. Astaxanthin enhances autophagy, amyloid beta clearance and exerts anti-inflammatory effects in in vitro models of Alzheimer's disease-related blood brain barrier dysfunction and inflammation. Brain Res 2023; 1819:148518. [PMID: 37579986 DOI: 10.1016/j.brainres.2023.148518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 08/16/2023]
Abstract
Defective degradation and clearance of amyloid-β as well as inflammation per se are crucial players in the pathology of Alzheimer's disease (AD). A defective transport across the blood-brain barrier is causative for amyloid-β (Aβ) accumulation in the brain, provoking amyloid plaque formation. Using primary porcine brain capillary endothelial cells and murine organotypic hippocampal slice cultures as in vitro models of AD, we investigated the effects of the antioxidant astaxanthin (ASX) on Aβ clearance and neuroinflammation. We report that ASX enhanced the clearance of misfolded proteins in primary porcine brain capillary endothelial cells by inducing autophagy and altered the Aβ processing pathway. We observed a reduction in the expression levels of intracellular and secreted amyloid precursor protein/Aβ accompanied by an increase in ABC transporters ABCA1, ABCG1 as well as low density lipoprotein receptor-related protein 1 mRNA levels. Furthermore, ASX treatment increased autophagic flux as evidenced by increased lipidation of LC3B-II as well as reduced protein expression of phosphorylated S6 ribosomal protein and mTOR. In LPS-stimulated brain slices, ASX exerted anti-inflammatory effects by reducing the secretion of inflammatory cytokines while shifting microglia polarization from M1 to M2 phenotype. Our data suggest ASX as potential therapeutic compound ameliorating AD-related blood brain barrier impairment and inflammation.
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Affiliation(s)
| | - Magdalena Lang
- Otto Loewi Research Center, Division of Immunology, Medical University of Graz, Austria
| | - Meekha George
- Department of Obstetrics and Gynaecology, Medical University of Graz, Austria
| | - Anika Stracke
- Otto Loewi Research Center, Division of Immunology, Medical University of Graz, Austria
| | | | | | | | - Jelena Tadic
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | | | | | | | - Gerd Leitinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Austria
| | - Achim Lass
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | - Ute Panzenboeck
- Otto Loewi Research Center, Division of Immunology, Medical University of Graz, Austria
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria.
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3
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Common Genetic Factors and Pathways in Alzheimer's Disease and Ischemic Stroke: Evidences from GWAS. Genes (Basel) 2023; 14:genes14020353. [PMID: 36833280 PMCID: PMC9957001 DOI: 10.3390/genes14020353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide association studies (GWASs) revealed that there were common risk genes between AD and IS, indicating common molecular pathways and their common pathophysiology. In this review, we summarize AD and IS risk single nucleotide polymorphisms (SNPs) and their representative genes from the GWAS Catalog database, and find thirteen common risk genes, but no common risk SNPs. Furthermore, the common molecular pathways associated with these risk gene products are summarized from the GeneCards database and clustered into inflammation and immunity, G protein-coupled receptor, and signal transduction. At least seven of these thirteen genes can be regulated by 23 microRNAs identified from the TargetScan database. Taken together, the imbalance of these molecular pathways may give rise to these two common brain disorders. This review sheds light on the pathogenesis of comorbidity of AD and IS, and provides molecular targets for disease prevention, manipulation, and brain health maintenance.
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4
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Kretzschmar GC, Alencar NM, da Silva SSL, Sulzbach CD, Meissner CG, Petzl-Erler ML, Souza RLR, Boldt ABW. GWAS-Top Polymorphisms Associated With Late-Onset Alzheimer Disease in Brazil: Pointing Out Possible New Culprits Among Non-Coding RNAs. Front Mol Biosci 2021; 8:632314. [PMID: 34291080 PMCID: PMC8287568 DOI: 10.3389/fmolb.2021.632314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/31/2021] [Indexed: 01/06/2023] Open
Abstract
Several genome-wide association studies (GWAS) have been carried out with late-onset Alzheimer's disease (LOAD), mainly in European and Asian populations. Different polymorphisms were associated, but several of them without a functional explanation. GWAS are fundamental for identifying loci associated with diseases, although they often do not point to causal polymorphisms. In this sense, functional investigations are a fundamental tool for discovering causality, although the failure of this validation does not necessarily indicate a non-causality. Furthermore, the allele frequency of associated genetic variants may vary widely between populations, requiring replication of these associations in other ethnicities. In this sense, our study sought to replicate in 150 AD patients and 114 elderly controls from the South Brazilian population 18 single-nucleotide polymorphisms (SNPs) associated with AD in European GWAS, with further functional investigation using bioinformatic tools for the associated SNPs. Of the 18 SNPs investigated, only four were associated in our population: rs769449 (APOE), rs10838725 (CELF1), rs6733839, and rs744373 (BIN1-CYP27C1). We identified 54 variants in linkage disequilibrium (LD) with the associated SNPs, most of which act as expression or splicing quantitative trait loci (eQTLs/sQTLs) in genes previously associated with AD or with a possible functional role in the disease, such as CELF1, MADD, MYBPC3, NR1H3, NUP160, SPI1, and TOMM40. Interestingly, eight of these variants are located within long non-coding RNA (lncRNA) genes that have not been previously investigated regarding AD. Some of these polymorphisms can result in changes in these lncRNAs' secondary structures, leading to either loss or gain of microRNA (miRNA)-binding sites, deregulating downstream pathways. Our pioneering work not only replicated LOAD association with polymorphisms not yet associated in the Brazilian population but also identified six possible lncRNAs that may interfere in LOAD development. The results lead us to emphasize the importance of functional exploration of associations found in large-scale association studies in different populations to base personalized and inclusive medicine in the future.
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Affiliation(s)
- Gabriela Canalli Kretzschmar
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Nina Moura Alencar
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Saritha Suellen Lopes da Silva
- Laboratory of Polymorphism and Linkage, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Carla Daniela Sulzbach
- Laboratory of Polymorphism and Linkage, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Caroline Grisbach Meissner
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Ricardo Lehtonen R. Souza
- Laboratory of Polymorphism and Linkage, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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Zhao L, Lei W, Deng C, Wu Z, Sun M, Jin Z, Song Y, Yang Z, Jiang S, Shen M, Yang Y. The roles of liver X receptor α in inflammation and inflammation-associated diseases. J Cell Physiol 2020; 236:4807-4828. [PMID: 33305467 DOI: 10.1002/jcp.30204] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/19/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
Liver X receptor α (LXRα; also known as NR1H3), an isoform of LXRs, is a member of the nuclear receptor family of transcription factors and plays essential roles in the transcriptional control of cholesterol homeostasis. Previous in-depth phenotypic analyses of mouse models with deficient LXRα have also demonstrated various physiological functions of this receptor within inflammatory responses. LXRα activation exerts a combination of metabolic and anti-inflammatory actions resulting in the modulation and the amelioration of inflammatory disorders. The tight "repercussions" between LXRα and inflammation, as well as cholesterol homeostasis, have suggested that LXRα could be pharmacologically targeted in pathologies such as atherosclerosis, acute lung injury, and Alzheimer's disease. This review gives an overview of the recent advances in understanding the roles of LXRα in inflammation and inflammation-associated diseases, which will help in the design of future experimental researches on the potential of LXRα and advance the investigation of LXRα as pharmacological inflammatory targets.
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Affiliation(s)
- Lin Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education Life of Sciences, Northwest University, Xi'an, China.,Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Wangrui Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education Life of Sciences, Northwest University, Xi'an, China
| | - Chao Deng
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhen Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education Life of Sciences, Northwest University, Xi'an, China
| | - Meng Sun
- Department of Cardiology, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhenxiao Jin
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yanbin Song
- Department of Cardiology, Affiliated Hospital, Yan'an University, China
| | - Zhi Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education Life of Sciences, Northwest University, Xi'an, China
| | - Shuai Jiang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education Life of Sciences, Northwest University, Xi'an, China
| | - Mingzhi Shen
- Hainan Hospital of PLA General Hospital, The Second School of Clinical Medicine, Southern Medical University, Sanya, Hainan, China.,Hainan Branch of National Clinical Reasearch Center of Geriatrics Disease, Sanya, Hainan, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education Life of Sciences, Northwest University, Xi'an, China
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6
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Karki R, Madan S, Gadiya Y, Domingo-Fernández D, Kodamullil AT, Hofmann-Apitius M. Data-Driven Modeling of Knowledge Assemblies in Understanding Comorbidity Between Type 2 Diabetes Mellitus and Alzheimer's Disease. J Alzheimers Dis 2020; 78:87-95. [PMID: 32925069 PMCID: PMC7683056 DOI: 10.3233/jad-200752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background: Recent studies have suggested comorbid association between Alzheimer’s disease (AD) and type 2 diabetes mellitus (T2DM) through identification of shared molecular mechanisms. However, the inference is pre-dominantly literature-based and lacks interpretation of pre-disposed genomic variants and transcriptomic measurables. Objective: In this study, we aim to identify shared genetic variants and dysregulated genes in AD and T2DM and explore their functional roles in the comorbidity between the diseases. Methods: The genetic variants for AD and T2DM were retrieved from GWAS catalog, GWAS central, dbSNP, and DisGeNet and subjected to linkage disequilibrium analysis. Next, shared variants were prioritized using RegulomeDB and Polyphen-2. Afterwards, a knowledge assembly embedding prioritized variants and their corresponding genes was created by mining relevant literature using Biological Expression Language. Finally, coherently perturbed genes from gene expression meta-analysis were mapped to the knowledge assembly to pinpoint biological entities and processes and depict a mechanistic link between AD and T2DM. Results: Our analysis identified four genes (i.e., ABCG1, COMT, MMP9, and SOD2) that could have dual roles in both AD and T2DM. Using cartoon representation, we have illustrated a set of causal events surrounding these genes which are associated to biological processes such as oxidative stress, insulin resistance, apoptosis and cognition. Conclusion: Our approach of using data as the driving force for unraveling disease etiologies eliminates literature bias and enables identification of novel entities that serve as the bridge between comorbid conditions.
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Affiliation(s)
- Reagon Karki
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Bonn, Germany
| | - Sumit Madan
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Yojana Gadiya
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Bonn, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Alpha Tom Kodamullil
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Bonn, Germany
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7
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Mouzat K, Chudinova A, Polge A, Kantar J, Camu W, Raoul C, Lumbroso S. Regulation of Brain Cholesterol: What Role Do Liver X Receptors Play in Neurodegenerative Diseases? Int J Mol Sci 2019; 20:E3858. [PMID: 31398791 PMCID: PMC6720493 DOI: 10.3390/ijms20163858] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022] Open
Abstract
Liver X Receptors (LXR) alpha and beta are two members of nuclear receptor superfamily documented as endogenous cholesterol sensors. Following conversion of cholesterol in oxysterol, both LXR isoforms detect intracellular concentrations and act as transcription factors to promote expression of target genes. Among their numerous physiological roles, they act as central cholesterol-lowering factors. In the central nervous system (CNS), cholesterol has been shown to be an essential determinant of brain function, particularly as a major constituent of myelin and membranes. In the brain, LXRs act as cholesterol central regulators, and, beyond this metabolic function, LXRs have additional roles such as providing neuroprotective effects and lowering neuroinflammation. In many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), and multiple sclerosis (MS), dysregulations of cholesterol and oxysterol have been reported. In this paper, we propose to focus on recent advances in the knowledge of the LXRs roles on brain cholesterol and oxysterol homeostasis, neuroinflammation, neuroprotection, and their putative involvement in neurodegenerative disorders. We will discuss their potential use as candidates for both molecular diagnosis and as promising pharmacological targets in the treatment of ALS, AD, or MS patients.
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Affiliation(s)
- Kevin Mouzat
- Motoneuron Disease: Pathophysiology and Therapy, The Neuroscience Institute of Montpellier, University of Montpellier, Montpellier, Laboratoire de Biochimie et Biologie Moléculaire, Nimes University Hospital, 30029 Nîmes, France.
| | - Aleksandra Chudinova
- Motoneuron Disease: Pathophysiology and Therapy, The Neuroscience Institute of Montpellier, University of Montpellier, Montpellier, Laboratoire de Biochimie et Biologie Moléculaire, Nimes University Hospital, 30029 Nîmes, France
| | - Anne Polge
- Laboratoire de Biochimie et Biologie Moléculaire, Nimes University Hospital, University of Montpellier, 30029 Nîmes, France
| | - Jovana Kantar
- Motoneuron Disease: Pathophysiology and Therapy, The Neuroscience Institute of Montpellier, University of Montpellier, Montpellier, Laboratoire de Biochimie et Biologie Moléculaire, Nimes University Hospital, 30029 Nîmes, France
| | - William Camu
- ALS Reference Center, Montpellier University Hospital and University of Montpellier, Inserm UMR1051, 34000 Montpellier, France
| | - Cédric Raoul
- The Neuroscience Institute of Montpellier, Inserm UMR1051, University of Montpellier, 34091 Montpellier, France
| | - Serge Lumbroso
- Motoneuron Disease: Pathophysiology and Therapy, The Neuroscience Institute of Montpellier, University of Montpellier, Montpellier, Laboratoire de Biochimie et Biologie Moléculaire, Nimes University Hospital, 30029 Nîmes, France
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8
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Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, Soininen H, Haapasalo A, Pike I, Hiltunen M. A multiomic approach to characterize the temporal sequence in Alzheimer's disease-related pathology. Neurobiol Dis 2018; 124:454-468. [PMID: 30557660 DOI: 10.1016/j.nbd.2018.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/15/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023] Open
Abstract
No single-omic approach completely elucidates the multitude of alterations taking place in Alzheimer's disease (AD). Here, we coupled transcriptomic and phosphoproteomic approaches to determine the temporal sequence of changes in mRNA, protein, and phosphopeptide expression levels from human temporal cortical samples, with varying degree of AD-related pathology. This approach highlighted fluctuation in synaptic and mitochondrial function as the earliest pathological events in brain samples with AD-related pathology. Subsequently, increased expression of inflammation and extracellular matrix-associated gene products was observed. Interaction network assembly for the associated gene products, emphasized the complex interplay between these processes and the role of addressing post-translational modifications in the identification of key regulators. Additionally, we evaluate the use of decision trees and random forests in identifying potential biomarkers differentiating individuals with different degree of AD-related pathology. This multiomic and temporal sequence-based approach provides a better understanding of the sequence of events leading to AD.
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Affiliation(s)
- Mikael Marttinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Antonio Neme
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Vikram Mitra
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mari Takalo
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Kaisa M A Paldanius
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Michael Bremang
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mitja I Kurki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Psychiatry, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Neurosurgery of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital and University of Eastern Finland, Kuopio 70029, Finland
| | - Ville Leinonen
- Neurosurgery of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland
| | - Hilkka Soininen
- Neurology of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland; Institute of Clinical Medicine/Neurology, University of Eastern Finland, Kuopio 70210, Finland
| | - Annakaisa Haapasalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Ian Pike
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland.
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9
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Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Natunen T, Haapasalo A, Herukka SK, Kuusisto J, Soininen H, Kivipelto M, Laakso M, Hiltunen M. Decreased plasma C-reactive protein levels in APOE ε4 allele carriers. Ann Clin Transl Neurol 2018; 5:1229-1240. [PMID: 30349858 PMCID: PMC6186931 DOI: 10.1002/acn3.639] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Objective Apolipoprotein E (APOE) ε4 allele is a well‐established risk factor in Alzheimer's disease (AD). Here, we assessed the effects of APOE polymorphism on cardiovascular, metabolic, and inflammation‐related parameters in population‐based cohorts. Methods Association of cardiovascular, metabolic, and inflammation‐related parameters with the APOE polymorphism in a large Finnish Metabolic Syndrome in Men (METSIM) cohort and Finnish Geriatric Intervention study to prevent cognitive impairment and disability (FINGER) were investigated. Brain‐specific effects were addressed in postmortem brain samples. Results Individuals carrying the APOE ε4 allele displayed significantly elevated serum/plasma LDL cholesterol and apolipoprotein B levels. APOE ε3ε4 and ε4ε4 significantly associated with lower levels of plasma high‐sensitivity C‐reactive protein (hs‐CRP). Plasma amyloid‐β 42 (Aβ42) and reduced hs‐CRP levels showed an association independently of the APOE status. Interpretation These data suggest that the APOE ε4 allele associates with lower levels of hs‐CRP in individuals without dementia. Moreover, Aβ42 may encompass anti‐inflammatory effects reflected by reduced hs‐CRP levels.
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Affiliation(s)
- Henna Martiskainen
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland
| | - Mari Takalo
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Alina Solomon
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Division of Clinical Geriatrics Center for Alzheimer Research NVS, Karolinska Institutet Novum 5th floor Huddinge 14157 Sweden
| | - Alena Stančáková
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland
| | - Mikael Marttinen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Teemu Natunen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Annakaisa Haapasalo
- A.I Virtanen Institute for Molecular Sciences University of Eastern Finland Neulaniementie 2 Kuopio 70211 Finland
| | - Sanna-Kaisa Herukka
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Neurocenter Neurology Kuopio University Hospital Kuopio Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Kuopio University Hospital Kuopio Finland
| | - Hilkka Soininen
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Neurocenter Neurology Kuopio University Hospital Kuopio Finland
| | - Miia Kivipelto
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Division of Clinical Geriatrics Center for Alzheimer Research NVS, Karolinska Institutet Novum 5th floor Huddinge 14157 Sweden.,Department of Public Health Solutions Public Health Promotion Unit National Institute for Health and Welfare PO Box 30 Helsinki 00271 Finland
| | - Markku Laakso
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Kuopio University Hospital Kuopio Finland
| | - Mikko Hiltunen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
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10
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Hiebl V, Ladurner A, Latkolik S, Dirsch VM. Natural products as modulators of the nuclear receptors and metabolic sensors LXR, FXR and RXR. Biotechnol Adv 2018; 36:1657-1698. [PMID: 29548878 DOI: 10.1016/j.biotechadv.2018.03.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 01/25/2023]
Abstract
Nuclear receptors (NRs) represent attractive targets for the treatment of metabolic syndrome-related diseases. In addition, natural products are an interesting pool of potential ligands since they have been refined under evolutionary pressure to interact with proteins or other biological targets. This review aims to briefly summarize current basic knowledge regarding the liver X (LXR) and farnesoid X receptors (FXR) that form permissive heterodimers with retinoid X receptors (RXR). Natural product-based ligands for these receptors are summarized and the potential of LXR, FXR and RXR as targets in precision medicine is discussed.
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Affiliation(s)
- Verena Hiebl
- University of Vienna, Department of Pharmacognosy, Althanstrasse 14, 1090 Vienna, Austria
| | - Angela Ladurner
- University of Vienna, Department of Pharmacognosy, Althanstrasse 14, 1090 Vienna, Austria.
| | - Simone Latkolik
- University of Vienna, Department of Pharmacognosy, Althanstrasse 14, 1090 Vienna, Austria
| | - Verena M Dirsch
- University of Vienna, Department of Pharmacognosy, Althanstrasse 14, 1090 Vienna, Austria
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11
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Liver X Receptor Genes Variants Modulate ALS Phenotype. Mol Neurobiol 2017; 55:1959-1965. [PMID: 28244008 DOI: 10.1007/s12035-017-0453-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/09/2017] [Indexed: 12/14/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is one of the most severe motor neuron (MN) disorders in adults. Phenotype of ALS patients is highly variable and may be influenced by modulators of energy metabolism. Recent works have implicated the liver X receptors α and β (LXRs), either in the propagation process of ALS or in the maintenance of MN survival. LXRs are nuclear receptors activated by oxysterols, modulating cholesterol levels, a suspected modulator of ALS severity. In a cohort of 438 ALS patients and 330 healthy controls, the influence of LXR genes on ALS risk and phenotype was studied using single nucleotide polymorphisms (SNPs). The two LXRα SNPs rs2279238 and rs7120118 were shown to be associated with age at onset in ALS patients. Consistently, homozygotes were twice more correlated than were heterozygotes to delayed onset. The onset was thus delayed by 3.9 years for rs2279238 C/T carriers and 7.8 years for T/T carriers. Similar results were obtained for rs7120118 (+2.1 years and +6.7 years for T/C and C/C genotypes, respectively). The LXRβ SNP rs2695121 was also shown to be associated with a 30% increase of ALS duration (p = 0.0055, FDR = 0.044). The tested genotypes were not associated with ALS risk. These findings add further evidence to the suspected implication of LXR genes in the disease process of ALS and might open new perspectives in ALS therapeutics.
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12
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Mouzat K, Raoul C, Polge A, Kantar J, Camu W, Lumbroso S. Liver X receptors: from cholesterol regulation to neuroprotection-a new barrier against neurodegeneration in amyotrophic lateral sclerosis? Cell Mol Life Sci 2016; 73:3801-8. [PMID: 27510420 PMCID: PMC11108529 DOI: 10.1007/s00018-016-2330-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 12/13/2022]
Abstract
Cholesterol plays a central role in numerous nervous system functions. Cholesterol is the major constituent of myelin sheaths, is essential for synapse and dendrite formation, axon guidance as well as neurotransmission. Among regulators of cholesterol homeostasis, liver X receptors (LXRs), two members of the nuclear receptor superfamily, play a determinant role. LXRs act as cholesterol sensors and respond to high intracellular cholesterol concentration by decreasing plasmatic and intracellular cholesterol content. Beyond their cholesterol-lowering role, LXRs have been proposed as regulators of immunity and anti-inflammatory factors. Dysregulation of cholesterol metabolism combined to neuroinflammatory context have been described in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). ALS is characterized by the progressive loss of motoneurons in the brain and spinal cord, leading to severe paralytic condition and death of patients in a median time of 3 years. Motoneuron degeneration is accompanied by chronic neuroinflammatory response, involving microglial and astrocytic activation, infiltration of blood-derived immune cells and release of pro-inflammatory factors. We propose to discuss here the role of LXRs as a molecular link between the central nervous system cholesterol metabolism, neuroinflammation, motoneuron survival and their potential as promising therapeutic candidates for ALS therapy.
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Affiliation(s)
- Kevin Mouzat
- Department of Biochemistry and Molecular Biology, Nîmes University Hospital, Nîmes, France.
- University of Montpellier, Montpellier, France.
- INSERM UMR1051, The Neuroscience Institute of Montpellier (INM), Saint Eloi Hospital, Montpellier, France.
| | - Cédric Raoul
- INSERM UMR1051, The Neuroscience Institute of Montpellier (INM), Saint Eloi Hospital, Montpellier, France
| | - Anne Polge
- Department of Biochemistry and Molecular Biology, Nîmes University Hospital, Nîmes, France
| | - Jovana Kantar
- Department of Biochemistry and Molecular Biology, Nîmes University Hospital, Nîmes, France
- INSERM UMR1051, The Neuroscience Institute of Montpellier (INM), Saint Eloi Hospital, Montpellier, France
| | - William Camu
- University of Montpellier, Montpellier, France
- INSERM UMR1051, The Neuroscience Institute of Montpellier (INM), Saint Eloi Hospital, Montpellier, France
- Neurology Department, ALS Center, Gui de Chauliac Hospital, Montpellier, France
| | - Serge Lumbroso
- Department of Biochemistry and Molecular Biology, Nîmes University Hospital, Nîmes, France
- University of Montpellier, Montpellier, France
- INSERM UMR1051, The Neuroscience Institute of Montpellier (INM), Saint Eloi Hospital, Montpellier, France
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13
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Kurkinen KMA, Marttinen M, Turner L, Natunen T, Mäkinen P, Haapalinna F, Sarajärvi T, Gabbouj S, Kurki M, Paananen J, Koivisto AM, Rauramaa T, Leinonen V, Tanila H, Soininen H, Lucas FR, Haapasalo A, Hiltunen M. SEPT8 modulates β-amyloidogenic processing of APP by affecting the sorting and accumulation of BACE1. J Cell Sci 2016; 129:2224-38. [PMID: 27084579 DOI: 10.1242/jcs.185215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/11/2016] [Indexed: 12/21/2022] Open
Abstract
Dysfunction and loss of synapses are early pathogenic events in Alzheimer's disease. A central step in the generation of toxic amyloid-β (Aβ) peptides is the cleavage of amyloid precursor protein (APP) by β-site APP-cleaving enzyme (BACE1). Here, we have elucidated whether downregulation of septin (SEPT) protein family members, which are implicated in synaptic plasticity and vesicular trafficking, affects APP processing and Aβ generation. SEPT8 was found to reduce soluble APPβ and Aβ levels in neuronal cells through a post-translational mechanism leading to decreased levels of BACE1 protein. In the human temporal cortex, we identified alterations in the expression of specific SEPT8 transcript variants in a manner that correlated with Alzheimer's-disease-related neurofibrillary pathology. These changes were associated with altered β-secretase activity. We also discovered that the overexpression of a specific Alzheimer's-disease-associated SEPT8 transcript variant increased the levels of BACE1 and Aβ peptides in neuronal cells. These changes were related to an increased half-life of BACE1 and the localization of BACE1 in recycling endosomes. These data suggest that SEPT8 modulates β-amyloidogenic processing of APP through a mechanism affecting the intracellular sorting and accumulation of BACE1.
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Affiliation(s)
- Kaisa M A Kurkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Mikael Marttinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Laura Turner
- Eisai Ltd., Bernard Katz Building, University College London, London WC1E 6BT, UK
| | - Teemu Natunen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Fanni Haapalinna
- Institute of Clinical Medicine - Neurology, School of Medicine, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Timo Sarajärvi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Sami Gabbouj
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Mitja Kurki
- Institute of Clinical Medicine - Neurosurgery, School of Medicine, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Jussi Paananen
- Institute of Clinical Medicine - Neurosurgery, School of Medicine, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Anne M Koivisto
- Institute of Clinical Medicine - Neurology, School of Medicine, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Tuomas Rauramaa
- Institute of Clinical Medicine - Pathology, School of Medicine, University of Eastern Finland and Department of Pathology, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Ville Leinonen
- Institute of Clinical Medicine - Neurosurgery, School of Medicine, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Heikki Tanila
- Department of Neurobiology, A.I. Virtanen, Institute for Molecular Sciences, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology, School of Medicine, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Fiona R Lucas
- Eisai Ltd., Bernard Katz Building, University College London, London WC1E 6BT, UK
| | - Annakaisa Haapasalo
- Institute of Clinical Medicine - Neurology, School of Medicine, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, 70211 Kuopio, Finland Department of Neurobiology, A.I. Virtanen, Institute for Molecular Sciences, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland Institute of Clinical Medicine - Neurology, School of Medicine, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, 70211 Kuopio, Finland
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14
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Natunen T, Takalo M, Kemppainen S, Leskelä S, Marttinen M, Kurkinen KMA, Pursiheimo JP, Sarajärvi T, Viswanathan J, Gabbouj S, Solje E, Tahvanainen E, Pirttimäki T, Kurki M, Paananen J, Rauramaa T, Miettinen P, Mäkinen P, Leinonen V, Soininen H, Airenne K, Tanzi RE, Tanila H, Haapasalo A, Hiltunen M. Relationship between ubiquilin-1 and BACE1 in human Alzheimer's disease and APdE9 transgenic mouse brain and cell-based models. Neurobiol Dis 2015; 85:187-205. [PMID: 26563932 DOI: 10.1016/j.nbd.2015.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 09/13/2015] [Accepted: 11/07/2015] [Indexed: 11/16/2022] Open
Abstract
Accumulation of β-amyloid (Aβ) and phosphorylated tau in the brain are central events underlying Alzheimer's disease (AD) pathogenesis. Aβ is generated from amyloid precursor protein (APP) by β-site APP-cleaving enzyme 1 (BACE1) and γ-secretase-mediated cleavages. Ubiquilin-1, a ubiquitin-like protein, genetically associates with AD and affects APP trafficking, processing and degradation. Here, we have investigated ubiquilin-1 expression in human brain in relation to AD-related neurofibrillary pathology and the effects of ubiquilin-1 overexpression on BACE1, tau, neuroinflammation, and neuronal viability in vitro in co-cultures of mouse embryonic primary cortical neurons and microglial cells under acute neuroinflammation as well as neuronal cell lines, and in vivo in the brain of APdE9 transgenic mice at the early phase of the development of Aβ pathology. Ubiquilin-1 expression was decreased in human temporal cortex in relation to the early stages of AD-related neurofibrillary pathology (Braak stages 0-II vs. III-IV). There was a trend towards a positive correlation between ubiquilin-1 and BACE1 protein levels. Consistent with this, ubiquilin-1 overexpression in the neuron-microglia co-cultures with or without the induction of neuroinflammation resulted in a significant increase in endogenously expressed BACE1 levels. Sustained ubiquilin-1 overexpression in the brain of APdE9 mice resulted in a moderate, but insignificant increase in endogenous BACE1 levels and activity, coinciding with increased levels of soluble Aβ40 and Aβ42. BACE1 levels were also significantly increased in neuronal cells co-overexpressing ubiquilin-1 and BACE1. Ubiquilin-1 overexpression led to the stabilization of BACE1 protein levels, potentially through a mechanism involving decreased degradation in the lysosomal compartment. Ubiquilin-1 overexpression did not significantly affect the neuroinflammation response, but decreased neuronal viability in the neuron-microglia co-cultures under neuroinflammation. Taken together, these results suggest that ubiquilin-1 may mechanistically participate in AD molecular pathogenesis by affecting BACE1 and thereby APP processing and Aβ accumulation.
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Affiliation(s)
- Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Mari Takalo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland; Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Susanna Kemppainen
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Stina Leskelä
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mikael Marttinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Kaisa M A Kurkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Juha-Pekka Pursiheimo
- Department of Medical Biochemistry and Genetics, Institute of Biomedicine, Turku, Finland
| | - Timo Sarajärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Jayashree Viswanathan
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
| | - Sami Gabbouj
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Eino Solje
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
| | - Eveliina Tahvanainen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
| | - Tiina Pirttimäki
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mitja Kurki
- Neurosurgery sIA Group, Kuopio University Hospital, Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital, Kuopio, Finland; Institute of Clinical Medicine - Pathology, University of Eastern Finland, Kuopio, Finland
| | - Pasi Miettinen
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Leinonen
- Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland; Neurosurgery of NeuroCenter, University of Eastern Finland, Kuopio, Finland
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Kari Airenne
- The Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, Boston, MA 02129, United States; Harvard Medical School, Boston, MA 02129, United States
| | - Heikki Tanila
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Annakaisa Haapasalo
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland.
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland.
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Transcriptomics and mechanistic elucidation of Alzheimer's disease risk genes in the brain and in vitro models. Neurobiol Aging 2014; 36:1221.e15-28. [PMID: 25281018 DOI: 10.1016/j.neurobiolaging.2014.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/08/2014] [Accepted: 09/01/2014] [Indexed: 01/10/2023]
Abstract
In this study, we have assessed the expression and splicing status of genes involved in the pathogenesis or affecting the risk of Alzheimer's disease (AD) in the postmortem inferior temporal cortex samples obtained from 60 subjects with varying degree of AD-related neurofibrillary pathology. These subjects were grouped based on neurofibrillary pathology into 3 groups: Braak stages 0-II, Braak stages III-IV, and Braak stages V-VI. We also examined the right frontal cortical biopsies obtained during life from 22 patients with idiopathic shunt-responding normal pressure hydrocephalus, a disease that displays similar pathologic alterations as seen in AD. These 22 patients were categorized according to dichotomized amyloid-β positive or negative pathology in the biopsies. We observed that the expression of FRMD4A significantly decreased, and the expression of MS4A6A significantly increased in relation to increasing AD-related neurofibrillary pathology. Moreover, the expression of 2 exons in both CLU and TREM2 significantly increased with increase in AD-related neurofibrillary pathology. However, a similar trend toward increased expression in CLU and TREM2 was observed with most of the studied exons, suggesting a global change in the expression rather than altered splicing. Correlation of gene expression with well-established AD-related factors, such as α-, β-, and γ-secretase activities, brain amyloid-β42 levels, and cerebrospinal fluid biomarkers, revealed a positive correlation between β-secretase activity and the expression of TREM2 and BIN1. In expression quantitative trait loci analysis, we did not detect significant effects of the risk alleles on gene expression or splicing. Analysis of the normal pressure hydrocephalus biopsies revealed no differences in the expression or splicing profiles of the studied genes between amyloid-β positive and negative patients. Using the protein-protein interaction-based in vitro pathway analysis tools, we found that downregulation of FRMD4A associated with increased APP-β-secretase interaction, increased amyloid-β40 secretion, and altered phosphorylation of tau. Taken together, our results suggest that the expression of FRMD4A, MS4A6A, CLU, and TREM2 is altered in relation to increasing AD-related neurofibrillary pathology, and that FRMD4A may play a role in amyloidogenic and tau-related pathways in AD. Therefore, investigation of gene expression changes in the brain and effects of the identified genes on disease-associated pathways in vitro may provide mechanistic insights on how alterations in these genes may contribute to AD pathogenesis.
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Liu F, Wang W, Xu Y, Wang Y, Chen LF, Fang Q, Yan XW. ABCG1 rs57137919G>a polymorphism is functionally associated with varying gene expression and apoptosis of macrophages. PLoS One 2014; 9:e97044. [PMID: 24972087 PMCID: PMC4074052 DOI: 10.1371/journal.pone.0097044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/14/2014] [Indexed: 01/16/2023] Open
Abstract
ATP-binding cassette transporter G1 (ABCG1) is a transmembrane cholesterol transporter involved in macrophage sterol homeostasis, reverse cholesterol transport (RCT), and atherosclerosis. The role of ABCG1 in atherosclerosis remains controversial, especially in animal models. Our previous study showed that single nucleotide polymorphism rs57137919 (-367G>A) in the ABCG1 promoter region was associated with reduced risk for atherosclerotic coronary artery disease (CAD). This study was designed to provide functional evidence for the role of rs57137919G>A in atherosclerosis in humans. We combined in vitro and ex vivo studies using cell lines and human monocyte-derived macrophages to investigate the functional consequences of the promoter polymorphism by observing the effects of the rs57137919A allele on promoter activity, transcription factor binding, gene expression, cholesterol efflux, and apoptosis levels. The results showed that the rs57137919A allele was significantly associated with decreased ABCG1 gene expression possibly due to the impaired ability of protein-DNA binding. ABCG1-mediated cholesterol efflux decreased by 23% with rs57137919 A/A versus the G/G genotype. Cholesterol-loaded macrophage apoptosis was induced 2-fold with the A/A genotype compared with the G/G genotype. Proapoptotic genes Bok and Bid mRNA levels were significantly increased in macrophages from the A/A genotype compared with those from the G/G genotype. These findings demonstrated that the ABCG1 promoter rs57137919G>A variant had an allele-specific effect on ABCG1 expression and was associated with an increased apoptosis in cholesterol-loaded macrophages, providing functional evidence to explain the reduced risk for atherosclerosis in subjects with the ABCG1 promoter rs57137919A allele as reported in our previous study.
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Affiliation(s)
- Fang Liu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Xu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lian-Feng Chen
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Quan Fang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao-Wei Yan
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail:
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