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Chu D, Lei L, Gu S, Liu F, Wu F. Dual-specificity tyrosine phosphorylation-regulated kinase 1A promotes the inclusion of amyloid precursor protein exon 7. Biochem Pharmacol 2024; 224:116233. [PMID: 38663682 DOI: 10.1016/j.bcp.2024.116233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Extracellular amyloid plaques made of Amyloid-β (Aβ) derived from amyloid precursor protein (APP) is one of the major neuropathological hallmarks of Alzheimer's disease (AD). There are three major isoforms of APP, APP770, APP751, and APP695 generated by alternative splicing of exons 7 and 8. Exon 7 encodes the Kunitz protease inhibitor (KPI) domain. Its inclusion generates APP isoforms containing KPI, APPKPI+, which is elevated in AD and Down syndrome (DS) brains and associated with increased Aβ deposition. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (Dyrk1A) phosphorylates many splicing factors and regulates the alternative splicing of pre-mRNA. It is upregulated in DS and AD brain. However, it is not yet clear whether Dyrk1A could regulate APP alternative splicing. In the present study, we overexpressed or knocked down Dyrk1A in cultured cells and observed that Dyrk1A promoted the inclusion of both APP exons 7 and 8. Moreover, a significant increase in APP exon7 inclusion was also detected in the forebrain and hippocampus of human Dyrk1A transgenic mice - Tg/Dyrk1A. Screening for splicing factors regulated by Dyrk1A revealed that serine/arginine-rich protein 9G8 inhibited APP exon7 inclusion and interacted with APP pre-mRNA. In vitro, expression of exon 7 facilitated APP cleavage. In human Dyrk1A transgenic mice, we also found an increase in Aβ production. These findings suggest that Dyrk1A inhibits the splicing factor 9G8 and promotes APP exon 7 inclusion, leading to more APPKPI+ expression and APP cleavage and potentially contributing to Aβ production in vivo.
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Affiliation(s)
- Dandan Chu
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China; Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA; Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Leyi Lei
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China
| | - Shu Gu
- Nantong No.1 High School of Jiangsu Province, Nantong 226300, China
| | - Fei Liu
- Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA.
| | - Feng Wu
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China; Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA.
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Kim Y, You JH, Ryu Y, Park G, Lee U, Moon HE, Park HR, Song CW, Ku JL, Park SH, Paek SH. ELAVL2 loss promotes aggressive mesenchymal transition in glioblastoma. NPJ Precis Oncol 2024; 8:79. [PMID: 38548861 PMCID: PMC10978835 DOI: 10.1038/s41698-024-00566-1] [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: 05/16/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Glioblastoma (GBM), the most lethal primary brain cancer, exhibits intratumoral heterogeneity and molecular plasticity, posing challenges for effective treatment. Despite this, the regulatory mechanisms underlying such plasticity, particularly mesenchymal (MES) transition, remain poorly understood. In this study, we elucidate the role of the RNA-binding protein ELAVL2 in regulating aggressive MES transformation in GBM. We found that ELAVL2 is most frequently deleted in GBM compared to other cancers and associated with distinct clinical and molecular features. Transcriptomic analysis revealed that ELAVL2-mediated alterations correspond to specific GBM subtype signatures. Notably, ELAVL2 expression negatively correlated with epithelial-to-mesenchymal transition (EMT)-related genes, and its loss promoted MES process and chemo-resistance in GBM cells, whereas ELAVL2 overexpression exerted the opposite effect. Further investigation via tissue microarray analysis demonstrated that high ELAVL2 protein expression confers a favorable survival outcome in GBM patients. Mechanistically, ELAVL2 was shown to directly bind to the transcripts of EMT-inhibitory molecules, SH3GL3 and DNM3, modulating their mRNA stability, potentially through an m6A-dependent mechanism. In summary, our findings identify ELAVL2 as a critical tumor suppressor and mRNA stabilizer that regulates MES transition in GBM, underscoring its role in transcriptomic plasticity and glioma progression.
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Affiliation(s)
- Yona Kim
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Ji Hyeon You
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeonjoo Ryu
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Gyuri Park
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Urim Lee
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Eun Moon
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Ran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Chang W Song
- Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Advanced Institute of Convergence Technology, Seoul National University, Suwon, Korea.
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Frazel PW, Labib D, Fisher T, Brosh R, Pirjanian N, Marchildon A, Boeke JD, Fossati V, Liddelow SA. Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols. Nat Neurosci 2023; 26:1726-1738. [PMID: 37697111 PMCID: PMC10763608 DOI: 10.1038/s41593-023-01424-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence during the development of the brain and spinal cord. Here we used single-cell/single-nucleus RNA sequencing (scRNA-seq/snRNA-seq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human-induced pluripotent stem cells. We computationally identify candidate genes involved in the fate specification of glia in both species and report heterogeneous expression of astrocyte surface markers across differentiating cells. We then used our transcriptomic data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multi-omic, dual single-nuclei (sn)RNA-seq/snATAC-seq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets will enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.
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Affiliation(s)
- Paul W Frazel
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA.
| | - David Labib
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Theodore Fisher
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York City, NY, USA
| | - Nicolette Pirjanian
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Anne Marchildon
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York City, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA.
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York City, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York City, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York City, NY, USA.
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Salvato I, Ricciardi L, Dal Col J, Nigro A, Giurato G, Memoli D, Sellitto A, Lamparelli EP, Crescenzi MA, Vitale M, Vatrella A, Nucera F, Brun P, Caicci F, Dama P, Stiff T, Castellano L, Idrees S, Johansen MD, Faiz A, Wark PA, Hansbro PM, Adcock IM, Caramori G, Stellato C. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation. Front Immunol 2023; 14:1192028. [PMID: 37483631 PMCID: PMC10360199 DOI: 10.3389/fimmu.2023.1192028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss. Results RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression. Discussion Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.
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Affiliation(s)
- Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Assunta Sellitto
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Erwin Pavel Lamparelli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Maria Assunta Crescenzi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Monica Vitale
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Paola Dama
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Thomas Stiff
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Leandro Castellano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Alen Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Peter A. Wark
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, London, United Kingdom
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
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Emerging Roles for the RNA-Binding Protein HuD (ELAVL4) in Nervous System Diseases. Int J Mol Sci 2022; 23:ijms232314606. [PMID: 36498933 PMCID: PMC9736382 DOI: 10.3390/ijms232314606] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
The main goal of this review is to provide an updated overview of the involvement of the RNA-binding protein (RBP) HuD, encoded by the ELAVL4 gene, in nervous system development, maintenance, and function, and its emerging role in nervous system diseases. A particular focus is on recent studies reporting altered HuD levels, or activity, in disease models and patients. Substantial evidence suggests HuD involvement in Parkinson's disease (PD), Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS). Interestingly, while possible disease-causing mutations in the ELAVL4 gene remain elusive, a common theme in these diseases seems to be the altered regulation of HuD at multiple steps, including post-transcriptional and post-translational levels. In turn, the changed activity of HuD can have profound implications for its target transcripts, which are overly stabilized in case of HuD gain of function (as proposed in PD and ALS) or reduced in case of decreased HuD binding (as suggested by some studies in AD). Moreover, the recent discovery that HuD is a component of pathological cytoplasmic inclusion in both familial and sporadic ALS patients might help uncover the common molecular mechanisms underlying such complex diseases. We believe that deepening our understanding of the involvement of HuD in neurodegeneration could help developing new diagnostic and therapeutic tools.
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Sun T, Zeng L, Cai Z, Liu Q, Li Z, Liu R. Comprehensive analysis of dysregulated circular RNAs and construction of a ceRNA network involved in the pathology of Alzheimer's disease in a 5 × FAD mouse model. Front Aging Neurosci 2022; 14:1020699. [PMID: 36466608 PMCID: PMC9712785 DOI: 10.3389/fnagi.2022.1020699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 09/21/2023] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) causes a decline in cognitive function that poses a significant hazard to human health. However, the exact pathogenesis of AD and effective treatment have both proven elusive. Circular RNAs (circRNAs), which were initially deemed as meaningless non-coding RNAs, have been shown to participate in a variety of physiological and pathological processes. However, the variations and characteristics of circRNAs are not fairly well understood during the occurrence and development of AD. METHODS In this study, we performed RNA sequencing analyses, identified circRNA expression profiles, and explored the circRNA-associated competing endogenous RNA (ceRNA) relationship in the hippocampus of five familial AD (5 × FAD) mice with cognitive dysfunction. RESULTS The RNA sequencing results identified 34 dysregulated circRNAs in the hippocampus of 5 × FAD mice, including 17 upregulated and 17 downregulated circRNAs. The circRNA-miRNA interaction network for the dysregulated circRNAs was generated, and it was found to include 34 circRNAs and 711 miRNAs. Next, 2067 mRNAs potentially modulated by upregulated circRNA-interacting miRNAs and 2297 mRNAs potentially modulated by downregulated circRNA-interacting miRNAs were identified. Pathway enrichment analyses revealed that the circRNA-miRNA-mRNA network modulated AD development via multiple pathways, such as axon guidance, mitogen-activated protein kinase, and neurotrophin. The associated biological processes were mainly related to neuron projection development, cell morphogenesis, and head development. Their corresponding distributions were especially high in the axon, postsynapse, and neuronal body. We constructed a ceRNA network that included five circRNAs, four miRNAs, and 188 mRNAs. In this network, the differential expressions of three circRNAs (circRNA04655, circRNA00723, and circRNA01891), two miRNAs (miR-3470b and miR-6240), and 13 mRNAs (Vgll3, Nhsl2, Rab7, Tardbp, Vps33b, Fam107a, Tacr1, Ankrd40, Creb1, Snap23, Csnk1a1, Bmi1, and Bfar) in the hippocampus of 5 × FAD mice using qRT-PCR analyses were consistent with the RNA sequencing results. Another one circRNAs (circRNA00747) and two mRNAs (Zfp37 and Polr1e) had similar expression trends to the sequencing data, while circRNA03723 and Mapk10 had deviated expression trends to the sequencing data. CONCLUSIONS In conclusion, our study uncovered dysregulated circRNA expression profiles in the hippocampus of 5 × FAD mice, stretched comprehension of ceRNA biology, investigated the potential role of this ceRNA network in pathogenesis and progression, and identified potential biomarkers and therapeutic targets for AD.
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Affiliation(s)
- Ting Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Zeng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongdi Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingshan Liu
- Key Laboratory of Ethnomedicine of Ministry of Education, School of Pharmarcy, Minzu University of China, Beijing, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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van der Linden RJ, Gerritsen JS, Liao M, Widomska J, Pearse RV, White FM, Franke B, Young-Pearse TL, Poelmans G. RNA-binding protein ELAVL4/HuD ameliorates Alzheimer's disease-related molecular changes in human iPSC-derived neurons. Prog Neurobiol 2022; 217:102316. [PMID: 35843356 PMCID: PMC9912016 DOI: 10.1016/j.pneurobio.2022.102316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/18/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022]
Abstract
The RNA binding protein ELAVL4/HuD regulates the translation and splicing of multiple Alzheimer's disease (AD) candidate genes. We generated ELAVL4 knockout (KO) human induced pluripotent stem cell-derived neurons to study the effect that ELAVL4 has on AD-related cellular phenotypes. ELAVL4 KO significantly increased the levels of specific APP isoforms and intracellular phosphorylated tau, molecular changes that are related to the pathological hallmarks of AD. Overexpression of ELAVL4 in wild-type neurons and rescue experiments in ELAVL4 KO cells showed opposite effects and also led to a reduction of the extracellular amyloid-beta (Aβ)42/40 ratio. All these observations were made in familial AD (fAD) and fAD-corrected neurons. To gain insight into the molecular cascades involved in neuronal ELAVL4 signaling, we conducted pathway and upstream regulator analyses of transcriptomic and proteomic data from the generated neurons. These analyses revealed that ELAVL4 affects multiple biological pathways linked to AD, including those involved in synaptic function, as well as gene expression downstream of APP and tau signaling. The analyses also suggest that ELAVL4 expression is regulated by insulin receptor-FOXO1 signaling in neurons. Taken together, ELAVL4 expression ameliorates AD-related molecular changes in neurons and affects multiple synaptic pathways, making it a promising target for novel drug development.
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Affiliation(s)
- Robert J van der Linden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Meichen Liao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joanna Widomska
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands; Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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8
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1-L Transcription in Alzheimer's Disease. Curr Issues Mol Biol 2022; 44:3533-3551. [PMID: 36005139 PMCID: PMC9406503 DOI: 10.3390/cimb44080243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer’s disease is a very complex disease and better explanations and models are needed to understand how neurons are affected and microglia are activated. A new model of Alzheimer’s disease is presented here, the β-amyloid peptide is considered an important RNA recognition/binding peptide. 1-L transcription revealed compatible sequences with AAUAAA (PAS signal) and UUUC (class III ARE rich in U) in the Aβ peptide, supporting the peptide–RNA regulatory model. When a hypothetical model of fibril selection with the prionic character of amyloid assemblies is added to the peptide-RNA regulatory model, the downregulation of the PI3K-Akt pathway and the upregulation of the PLC-IP3 pathway are well explained. The model explains why neurons are less protected from inflammation and why microglia are activated; why mitochondria are destabilized; why the autophagic flux is destabilized; and why the post-transcriptional attenuation of the axonal signal “noise” is interrupted. For example, the model suggests that Aβ peptide may post-transcriptionally control ELAVL2 (ELAV-like RNA binding protein 2) and DCP2 (decapping mRNA protein 2), which are known to regulate RNA processing, transport, and stability.
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9
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Cui X, Hao C, Gong L, Kajitani N, Schwartz S. HnRNP D activates production of HPV16 E1 and E6 mRNAs by promoting intron retention. Nucleic Acids Res 2022; 50:2782-2806. [PMID: 35234917 PMCID: PMC8934624 DOI: 10.1093/nar/gkac132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/26/2022] [Accepted: 02/11/2022] [Indexed: 12/13/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) E1 and E6 proteins are produced from mRNAs with retained introns, but it has been unclear how these mRNAs are generated. Here, we report that hnRNP D act as a splicing inhibitor of HPV16 E1/E2- and E6/E7-mRNAs thereby generating intron-containing E1- and E6-mRNAs, respectively. N- and C-termini of hnRNP D contributed to HPV16 mRNA splicing control differently. HnRNP D interacted with the components of splicing machinery and with HPV16 RNA to exert its inhibitory function. As a result, the cytoplasmic levels of intron-retained HPV16 mRNAs were increased in the presence of hnRNP D. Association of hnRNP D with HPV16 mRNAs in the cytoplasm was observed, and this may correlate with unexpected inhibition of HPV16 E1- and E6-mRNA translation. Notably, hnRNP D40 interacted with HPV16 mRNAs in an HPV16-driven tonsillar cancer cell line and in HPV16-immortalized human keratinocytes. Furthermore, knockdown of hnRNP D in HPV16-driven cervical cancer cells enhanced production of the HPV16 E7 oncoprotein. Our results suggest that hnRNP D plays significant roles in the regulation of HPV gene expression and HPV-associated cancer development.
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Affiliation(s)
- Xiaoxu Cui
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Chengyu Hao
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Lijing Gong
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,China Institute of Sport and Health Sciences, Beijing Sport University, Haidian District, Beijing 100084, China
| | - Naoko Kajitani
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
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10
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Gourdomichali O, Zonke K, Kattan FG, Makridakis M, Kontostathi G, Vlahou A, Doxakis E. In Situ Peroxidase Labeling Followed by Mass-Spectrometry Reveals TIA1 Interactome. BIOLOGY 2022; 11:biology11020287. [PMID: 35205152 PMCID: PMC8869308 DOI: 10.3390/biology11020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 01/15/2023]
Abstract
TIA1 is a broadly expressed DNA/RNA binding protein that regulates multiple aspects of RNA metabolism. It is best known for its role in stress granule assembly during the cellular stress response. Three RNA recognition motifs mediate TIA1 functions along with a prion-like domain that supports multivalent protein-protein interactions that are yet poorly characterized. Here, by fusing the enhanced ascorbate peroxidase 2 (APEX2) biotin-labeling enzyme to TIA1 combined with mass spectrometry, the proteins in the immediate vicinity of TIA1 were defined in situ. Eighty-six and 203 protein partners, mostly associated with ribonucleoprotein complexes, were identified in unstressed control and acute stress conditions, respectively. Remarkably, the repertoire of TIA1 protein partners was highly dissimilar between the two cellular states. Under unstressed control conditions, the biological processes associated with the TIA1 interactome were enriched for cytosolic ontologies related to mRNA metabolism, such as translation initiation, nucleocytoplasmic transport, and RNA catabolism, while the protein identities were primarily represented by RNA binding proteins, ribosomal subunits, and eicosanoid regulators. Under acute stress, TIA1-labeled partners displayed a broader subcellular distribution that included the chromosomes and mitochondria. The enriched biological processes included splicing, translation, and protein synthesis regulation, while the molecular function of the proteins was enriched for RNA binding activity, ribosomal subunits, DNA double-strand break repair, and amide metabolism. Altogether, these data highlight the TIA1 spatial environment with its different partners in diverse cellular states and pave the way to dissect TIA1 role in these processes.
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Affiliation(s)
- Olga Gourdomichali
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Department of Biology, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Katerina Zonke
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Fedon-Giasin Kattan
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Manousos Makridakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Georgia Kontostathi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Antonia Vlahou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; (O.G.); (K.Z.); (F.-G.K.); (M.M.); (G.K.); (A.V.)
- Correspondence:
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11
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Diaz-Garcia S, Ko VI, Vazquez-Sanchez S, Chia R, Arogundade OA, Rodriguez MJ, Traynor BJ, Cleveland D, Ravits J. Nuclear depletion of RNA-binding protein ELAVL3 (HuC) in sporadic and familial amyotrophic lateral sclerosis. Acta Neuropathol 2021; 142:985-1001. [PMID: 34618203 PMCID: PMC8568872 DOI: 10.1007/s00401-021-02374-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/07/2022]
Abstract
Amyotrophic lateral sclerosis is a progressive fatal neurodegenerative disease caused by loss of motor neurons and characterized neuropathologically in almost all cases by nuclear depletion and cytoplasmic aggregation of TDP-43, a nuclear RNA-binding protein (RBP). We identified ELAVL3 as one of the most downregulated genes in our transcriptome profiles of laser captured microdissection of motor neurons from sporadic ALS nervous systems and the most dysregulated of all RBPs. Neuropathological characterizations showed ELAVL3 nuclear depletion in a great percentage of remnant motor neurons, sometimes accompanied by cytoplasmic accumulations. These abnormalities were common in sporadic cases with and without intermediate expansions in ATXN2 and familial cases carrying mutations in C9orf72 and SOD1. Depletion of ELAVL3 occurred at both the RNA and protein levels and a short protein isoform was identified, but it is not related to a TDP-43-dependent cryptic exon in intron 3. Strikingly, ELAVL3 abnormalities were more frequent than TDP-43 abnormalities and occurred in motor neurons still with normal nuclear TDP-43 present, but all neurons with abnormal TDP-43 also had abnormal ELAVL3. In a neuron-like cell culture model using SH-SY5Y cells, ELAVL3 mislocalization occurred weeks before TDP-43 abnormalities were seen. We interrogated genetic databases, but did not identify association of ELAVL3 genetic structure with ALS. Taken together, these findings suggest that ELAVL3 is an important RBP in ALS pathogenesis acquired early and the neuropathological data suggest that it is involved by loss of function rather than cytoplasmic toxicity.
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Affiliation(s)
- Sandra Diaz-Garcia
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
| | - Vivian I. Ko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
| | - Sonia Vazquez-Sanchez
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0670 USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA USA
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3707 USA
| | | | - Maria J. Rodriguez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
| | - Bryan J. Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-3707 USA
| | - Don Cleveland
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0670 USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA USA
| | - John Ravits
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093-0670 USA
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12
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Chalkiadaki K, Statoulla E, Markou M, Bellou S, Bagli E, Fotsis T, Murphy C, Gkogkas CG. Translational control in neurovascular brain development. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211088. [PMID: 34659781 PMCID: PMC8511748 DOI: 10.1098/rsos.211088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The human brain carries out complex tasks and higher functions and is crucial for organismal survival, as it senses both intrinsic and extrinsic environments. Proper brain development relies on the orchestrated development of different precursor cells, which will give rise to the plethora of mature brain cell-types. Within this process, neuronal cells develop closely to and in coordination with vascular cells (endothelial cells (ECs), pericytes) in a bilateral communication process that relies on neuronal activity, attractive or repulsive guidance cues for both cell types and on tight-regulation of gene expression. Translational control is a master regulator of the gene-expression pathway and in particular for neuronal and ECs, it can be localized in developmentally relevant (axon growth cone, endothelial tip cell) and mature compartments (synapses, axons). Herein, we will review mechanisms of translational control relevant to brain development in neurons and ECs in health and disease.
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Affiliation(s)
- Kleanthi Chalkiadaki
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Elpida Statoulla
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Maria Markou
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Sofia Bellou
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Eleni Bagli
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Theodore Fotsis
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Carol Murphy
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Christos G. Gkogkas
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
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13
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RNA-Binding Protein HuD as a Versatile Factor in Neuronal and Non-Neuronal Systems. BIOLOGY 2021; 10:biology10050361. [PMID: 33922479 PMCID: PMC8145660 DOI: 10.3390/biology10050361] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary Tight regulation of gene expression is critical for various biological processes such as proliferation, development, differentiation, and death; its dysregulation is linked to the pathogenesis of diseases. Gene expression is dynamically regulated by numerous factors at DNA, RNA, and protein levels, and RNA binding proteins (RBPs) and non–coding RNAs play important roles in the regulation of RNA metabolisms. RBPs govern a diverse spectrum of RNA metabolism by recognizing and binding to the secondary structure or the certain sequence of target mRNAs, and their malfunctions caused by aberrant expression or mutation are implicated in disease pathology. HuD, an RBP in the human antigen (Hu) family, has been studied as a pivotal regulator of gene expression in neuronal systems; however, accumulating evidence reveals the significance of HuD in non–neuronal systems including certain types of cancer cells or endocrine cells in the lung, pancreas, and adrenal gland. In addition, the abnormal function of HuD suggests its pathological association with neurological disorders, cancers, and diabetes. Thus, this review discusses HuD–mediated gene regulation in neuronal and non–neuronal systems to address how it works to orchestrate gene expression and how its expression is controlled in the stress response of pathogenesis of diseases. Abstract HuD (also known as ELAVL4) is an RNA–binding protein belonging to the human antigen (Hu) family that regulates stability, translation, splicing, and adenylation of target mRNAs. Unlike ubiquitously distributed HuR, HuD is only expressed in certain types of tissues, mainly in neuronal systems. Numerous studies have shown that HuD plays essential roles in neuronal development, differentiation, neurogenesis, dendritic maturation, neural plasticity, and synaptic transmission by regulating the metabolism of target mRNAs. However, growing evidence suggests that HuD also functions as a pivotal regulator of gene expression in non–neuronal systems and its malfunction is implicated in disease pathogenesis. Comprehensive knowledge of HuD expression, abundance, molecular targets, and regulatory mechanisms will broaden our understanding of its role as a versatile regulator of gene expression, thus enabling novel treatments for diseases with aberrant HuD expression. This review focuses on recent advances investigating the emerging role of HuD, its molecular mechanisms of target gene regulation, and its disease relevance in both neuronal and non–neuronal systems.
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14
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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15
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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16
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Carrasco J, Rauer M, Hummel B, Grzejda D, Alfonso-Gonzalez C, Lee Y, Wang Q, Puchalska M, Mittler G, Hilgers V. ELAV and FNE Determine Neuronal Transcript Signatures through EXon-Activated Rescue. Mol Cell 2020; 80:156-163.e6. [PMID: 33007255 DOI: 10.1016/j.molcel.2020.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
The production of alternative RNA variants contributes to the tissue-specific regulation of gene expression. In the animal nervous system, a systematic shift toward distal sites of transcription termination produces transcript signatures that are crucial for neuron development and function. Here, we report that, in Drosophila, the highly conserved protein ELAV globally regulates all sites of neuronal 3' end processing and directly binds to proximal polyadenylation sites of target mRNAs in vivo. We uncover an endogenous strategy of functional gene rescue that safeguards neuronal RNA signatures in an ELAV loss-of-function context. When not directly repressed by ELAV, the transcript encoding the ELAV paralog FNE acquires a mini-exon, generating a new protein able to translocate to the nucleus and rescue ELAV-mediated alternative polyadenylation and alternative splicing. We propose that exon-activated functional rescue is a more widespread mechanism that ensures robustness of processes regulated by a hierarchy, rather than redundancy, of effectors.
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Affiliation(s)
- Judit Carrasco
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwig University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), 79108 Freiburg, Germany
| | - Michael Rauer
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Barbara Hummel
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Dominika Grzejda
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwig University, 79104 Freiburg, Germany; International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), 79108 Freiburg, Germany
| | - Carlos Alfonso-Gonzalez
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, Albert Ludwig University, 79104 Freiburg, Germany; International Max Planck Research School for Immunology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany
| | - Yeon Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Qingqing Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Monika Puchalska
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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17
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Jakubauskienė E, Vilys L, Pečiulienė I, Kanopka A. The role of hypoxia on Alzheimer's disease-related APP and Tau mRNA formation. Gene 2020; 766:145146. [PMID: 32941952 DOI: 10.1016/j.gene.2020.145146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/24/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022]
Abstract
The removal of introns from mRNA precursors (pre-mRNAs) is an essential step in eukaryotic gene expression. The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many diseases, including Alzheimer's disease (AD). In the presented study, we have examined the influence of cellular hypoxia on mRNA splice variant formation from Alzheimer's disease-related Tau and APP genes in brain cells. We have shown that the hypoxic microenvironment influenced the formation of Tau mRNA splice variants, but had no effect on APP mRNA splice variant formation. Additionally, our presented results indicate that splicing factor SRSF1 but not SRSF5 alters the formation of Tau cellular mRNA splice variants in hypoxic cells. Obtained results have also shown that hypoxic brain cells possess enhanced CLK1-4 kinase mRNA levels. This study underlines that cellular hypoxia can influence disease development through changing pre-mRNA splicing.
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Affiliation(s)
| | - Laurynas Vilys
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Inga Pečiulienė
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Arvydas Kanopka
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.
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18
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Shah S, Molinaro G, Liu B, Wang R, Huber KM, Richter JD. FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism. Cell Rep 2020; 30:4459-4472.e6. [PMID: 32234480 PMCID: PMC7179797 DOI: 10.1016/j.celrep.2020.02.076] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/24/2019] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Silencing of FMR1 and loss of its gene product, FMRP, results in fragile X syndrome (FXS). FMRP binds brain mRNAs and inhibits polypeptide elongation. Using ribosome profiling of the hippocampus, we find that ribosome footprint levels in Fmr1-deficient tissue mostly reflect changes in RNA abundance. Profiling over a time course of ribosome runoff in wild-type tissue reveals a wide range of ribosome translocation rates; on many mRNAs, the ribosomes are stalled. Sucrose gradient ultracentrifugation of hippocampal slices after ribosome runoff reveals that FMRP co-sediments with stalled ribosomes, and its loss results in decline of ribosome stalling on specific mRNAs. One such mRNA encodes SETD2, a lysine methyltransferase that catalyzes H3K36me3. Chromatin immunoprecipitation sequencing (ChIP-seq) demonstrates that loss of FMRP alters the deployment of this histone mark. H3K36me3 is associated with alternative pre-RNA processing, which we find occurs in an FMRP-dependent manner on transcripts linked to neural function and autism spectrum disorders.
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Affiliation(s)
- Sneha Shah
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gemma Molinaro
- Department of Neuroscience, University of Texas Southwestern Medical School, Dallas, TX 75390, USA
| | - Botao Liu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ruijia Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kimberly M Huber
- Department of Neuroscience, University of Texas Southwestern Medical School, Dallas, TX 75390, USA.
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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19
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Paschou M, Maier L, Papazafiri P, Selescu T, Dedos SG, Babes A, Doxakis E. Neuronal microRNAs modulate TREK two-pore domain K + channel expression and current density. RNA Biol 2020; 17:651-662. [PMID: 31994436 DOI: 10.1080/15476286.2020.1722450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The TREK family of leak potassium channels has been found to play critical roles in nociception, sensitivity to general anaesthetics, neuroprotection, and memory. The three members of the family, TREK1, TREK2 and TRAAK establish the resting potential and modify the duration, frequency and amplitude of action potentials. Despite their apparent importance, the repertoire of regulatory interactions utilized by cells to control their expression is poorly understood. Herein, the contribution of miRNAs in the regulation of their post-transcriptional gene expression has been examined. Using different assays, miR-124 and to a lesser extent miR-128 and miR-183 were found to reduce TREK1 and TREK2 levels through specific binding to their 3'UTRs. In contrast, miR-9 which was predicted to bind to TRAAK 3'UTR, did not alter its expression. Expression of miR-124, miR-128 and miR-183 was found to mirror that of Trek1 and Trek2 mRNAs during brain development. Moreover, application of proinflammatory mediators in dorsal root ganglion (DRG) neurons revealed an inverse correlation between miR-124 and Trek1 and Trek2 mRNA expression. Voltage clamp recordings of TREK2-mediated currents showed that miR-124 reduced the sensitivity of TREK2-expressing cells to non-aversive warmth stimulation. Overall, these findings reveal a significant regulatory mechanism by which TREK1 and TREK2 expression and hence activity are controlled in neurons and uncover new druggable targets for analgesia and neuroprotection.Abbreviations: microRNA: miRNA; UTR: untranslated region; K2p channels: two-pore domain K+channels; DRG: dorsal root ganglion; CNS: central nervous system; FBS: fetal bovine serum; TuD: Tough Decoy; TREK: tandem P-domain weak inward rectifying K+ (TWIK)-related K+ channel 1; TRAAK: TWIK-related arachidonic acid K+.
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Affiliation(s)
- Maria Paschou
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Larisa Maier
- Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Panagiota Papazafiri
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Tudor Selescu
- Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Skarlatos G Dedos
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandru Babes
- Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Epaminondas Doxakis
- Center for Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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20
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Otsuka H, Fukao A, Funakami Y, Duncan KE, Fujiwara T. Emerging Evidence of Translational Control by AU-Rich Element-Binding Proteins. Front Genet 2019; 10:332. [PMID: 31118942 PMCID: PMC6507484 DOI: 10.3389/fgene.2019.00332] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/28/2019] [Indexed: 12/27/2022] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of posttranscriptional gene expression and control many important biological processes including cell proliferation, development, and differentiation. RBPs bind specific motifs in their target mRNAs and regulate mRNA fate at many steps. The AU-rich element (ARE) is one of the major cis-regulatory elements in the 3′ untranslated region (UTR) of labile mRNAs. Many of these encode factors requiring very tight regulation, such as inflammatory cytokines and growth factors. Disruption in the control of these factors’ expression can cause autoimmune diseases, developmental disorders, or cancers. Therefore, these mRNAs are strictly regulated by various RBPs, particularly ARE-binding proteins (ARE-BPs). To regulate mRNA metabolism, ARE-BPs bind target mRNAs and affect some factors on mRNAs directly, or recruit effectors, such as mRNA decay machinery and protein kinases to target mRNAs. Importantly, some ARE-BPs have stabilizing roles, whereas others are destabilizing, and ARE-BPs appear to compete with each other when binding to target mRNAs. The function of specific ARE-BPs is modulated by posttranslational modifications (PTMs) including methylation and phosphorylation, thereby providing a means for cellular signaling pathways to regulate stability of specific target mRNAs. In this review, we summarize recent studies which have revealed detailed molecular mechanisms of ARE-BP-mediated regulation of gene expression and also report on the importance of ARE-BP function in specific physiological contexts and how this relates to disease. We also propose an mRNP regulatory network based on competition between stabilizing ARE-BPs and destabilizing ARE-BPs.
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Affiliation(s)
- Hiroshi Otsuka
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | | | | | - Kent E Duncan
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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21
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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Sobu Y, Furukori K, Chiba K, Nairn AC, Kinjo M, Hata S, Suzuki T. Phosphorylation of multiple sites within an acidic region of Alcadein α is required for kinesin-1 association and Golgi exit of Alcadein α cargo. Mol Biol Cell 2017; 28:3844-3856. [PMID: 29093024 PMCID: PMC5739299 DOI: 10.1091/mbc.e17-05-0301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/18/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022] Open
Abstract
Alcadein a (Alca) is reported to function as a cargo receptor when associated with kinesin-1. Phosphorylation of three serine residues in the acidic region located between the two WD motifs of Alca is required for interaction with kinesin-1 and Golgi exit of Alca cargo. Alcadein α (Alcα) is a major cargo of kinesin-1 that is subjected to anterograde transport in neuronal axons. Two tryptophan- and aspartic acid-containing (WD) motifs located in its cytoplasmic domain directly bind the tetratricopeptide repeat (TPR) motifs of the kinesin light chain (KLC), which activate kinesin-1 and recruit kinesin-1 to Alcα cargo. We found that phosphorylation of three serine residues in the acidic region located between the two WD motifs is required for interaction with KLC. Phosphorylation of these serine residues may alter the disordered structure of the acidic region to induce direct association with KLC. Replacement of these serines with Ala results in a mutant that is unable to bind kinesin-1, which impairs exit of Alcα cargo from the Golgi. Despite this deficiency, the compromised Alcα mutant was still transported, albeit improperly by vesicles following missorting of the Alcα mutant with amyloid β-protein precursor (APP) cargo. This suggests that APP partially compensates for defective Alcα in anterograde transport by providing an alternative cargo receptor for kinesin-1.
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Affiliation(s)
- Yuriko Sobu
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Keiko Furukori
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.,Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508
| | - Kyoko Chiba
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06508
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Saori Hata
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Toshiharu Suzuki
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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