1
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Sato K, Takayama KI, Inoue S. Stress granule-mediated RNA regulatory mechanism in Alzheimer's disease. Geriatr Gerontol Int 2024; 24 Suppl 1:7-14. [PMID: 37726158 DOI: 10.1111/ggi.14663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/20/2023] [Accepted: 08/27/2023] [Indexed: 09/21/2023]
Abstract
Living organisms experience a range of stresses. To cope effectively with these stresses, eukaryotic cells have evolved a sophisticated mechanism involving the formation of stress granules (SGs), which play a crucial role in protecting various types of RNA species under stress, such as mRNAs and long non-coding RNAs (lncRNAs). SGs are non-membranous cytoplasmic ribonucleoprotein (RNP) granules, and the RNAs they contain are translationally stalled. Importantly, SGs have been thought to contribute to the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD). SGs also contain multiple RNA-binding proteins (RBPs), several of which have been implicated in AD progression. SGs are transient structures that dissipate after stress relief. However, the chronic stresses associated with aging lead to the persistent formation of SGs and subsequently to solid-like pathological SGs, which could impair cellular RNA metabolism and also act as a nidus for the aberrant aggregation of AD-associated proteins. In this paper, we provide a comprehensive summary of the physical basis of SG-enriched RNAs and SG-resident RBPs. We then review the characteristics of AD-associated gene transcripts and their similarity to the SG-enriched RNAs. Furthermore, we summarize and discuss the functional implications of SGs in neuronal RNA metabolism and the aberrant aggregation of AD-associated proteins mediated by SG-resident RBPs in the context of AD pathogenesis. Geriatr Gerontol Int 2024; 24: 7-14.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- Integrated Research Initiative for Living Well with Dementia, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
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2
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Takeiwa T, Ikeda K, Horie K, Inoue S. Role of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer. RNA Biol 2024; 21:1-17. [PMID: 38551131 PMCID: PMC10984136 DOI: 10.1080/15476286.2024.2332855] [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] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
RNA-binding proteins (RBPs) play crucial roles in the functions and homoeostasis of various tissues by regulating multiple events of RNA processing including RNA splicing, intracellular RNA transport, and mRNA translation. The Drosophila behavior and human splicing (DBHS) family proteins including PSF/SFPQ, NONO, and PSPC1 are ubiquitously expressed RBPs that contribute to the physiology of several tissues. In mammals, DBHS proteins have been reported to contribute to neurological diseases and play crucial roles in cancers, such as prostate, breast, and liver cancers, by regulating cancer-specific gene expression. Notably, in recent years, multiple small molecules targeting DBHS family proteins have been developed for application as cancer therapeutics. This review provides a recent overview of the functions of DBHS family in physiology and pathophysiology, and discusses the application of DBHS family proteins as promising diagnostic and therapeutic targets for cancers.
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Affiliation(s)
- Toshihiko Takeiwa
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo, Japan
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo, Japan
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
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3
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Nikom D, Zheng S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat Rev Neurosci 2023; 24:457-473. [PMID: 37336982 DOI: 10.1038/s41583-023-00717-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Alternative splicing generates a myriad of RNA products and protein isoforms of different functions from a single gene. Dysregulated alternative splicing has emerged as a new mechanism broadly implicated in the pathogenesis of neurodegenerative diseases such as Alzheimer disease, amyotrophic lateral sclerosis, frontotemporal dementia, Parkinson disease and repeat expansion diseases. Understanding the mechanisms and functional outcomes of abnormal splicing in neurological disorders is vital in developing effective therapies to treat mis-splicing pathology. In this Review, we discuss emerging research and evidence of the roles of alternative splicing defects in major neurodegenerative diseases and summarize the latest advances in RNA-based therapeutic strategies to target these disorders.
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Affiliation(s)
- David Nikom
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA
| | - Sika Zheng
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA.
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA.
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
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4
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Takayama KI, Matsuoka S, Adachi S, Honma T, Yoshida M, Doi T, Shin-ya K, Yoshida M, Osada H, Inoue S. Identification of small-molecule inhibitors against the interaction of RNA-binding protein PSF and its target RNA for cancer treatment. PNAS NEXUS 2023; 2:pgad203. [PMID: 37388923 PMCID: PMC10304769 DOI: 10.1093/pnasnexus/pgad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023]
Abstract
Diverse cellular activities are modulated through a variety of RNAs, including long noncoding RNAs (lncRNAs), by binding to certain proteins. The inhibition of oncogenic proteins or RNAs is expected to suppress cancer cell proliferation. We have previously demonstrated that PSF interaction with its target RNAs, such as androgen-induced lncRNA CTBP1-AS, is critical for hormone therapy resistance in prostate and breast cancers. However, the action of protein-RNA interactions remains almost undruggable to date. High-throughput screening (HTS) has facilitated the discovery of drugs for protein-protein interactions. In the present study, we developed an in vitro alpha assay using Flag peptide-conjugated lncRNA, CTBP1-AS, and PSF. We then constructed an effective HTS screening system to explore small compounds that inhibit PSF-RNA interactions. Thirty-six compounds were identified and dose-dependently inhibited PSF-RNA interaction in vitro. Moreover, chemical optimization of these lead compounds and evaluation of cancer cell proliferation revealed two promising compounds, N-3 and C-65. These compounds induced apoptosis and inhibited cell growth in prostate and breast cancer cells. By inhibiting PSF-RNA interaction, N-3 and C-65 up-regulated signals that are repressed by PSF, such as the cell cycle signals by p53 and p27. Furthermore, using a mouse xenograft model for hormone therapy-resistant prostate cancer, we revealed that N-3 and C-65 can significantly suppress tumor growth and downstream target gene expression, such as the androgen receptor (AR). Thus, our findings highlight a therapeutic strategy through the development of inhibitors for RNA-binding events in advanced cancers.
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Affiliation(s)
- Ken-ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, itabashi-ku, Tokyo 173-0015, Japan
| | - Seiji Matsuoka
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shungo Adachi
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Masahito Yoshida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Drug Discovery Chemical Bank Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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5
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Taylor R, Hamid F, Fielding T, Gordon PM, Maloney M, Makeyev EV, Houart C. Prematurely terminated intron-retaining mRNAs invade axons in SFPQ null-driven neurodegeneration and are a hallmark of ALS. Nat Commun 2022; 13:6994. [PMID: 36414621 PMCID: PMC9681851 DOI: 10.1038/s41467-022-34331-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/21/2022] [Indexed: 11/23/2022] Open
Abstract
Loss of SFPQ is a hallmark of motor degeneration in ALS and prevents maturation of motor neurons when occurring during embryogenesis. Here, we show that in zebrafish, developing motor neurons lacking SFPQ exhibit axon extension, branching and synaptogenesis defects, prior to degeneration. Subcellular transcriptomics reveals that loss of SFPQ in neurons produces a complex set of aberrant intron-retaining (IR) transcripts coding for neuron-specific proteins that accumulate in neurites. Some of these local IR mRNAs are prematurely terminated within the retained intron (PreT-IR). PreT-IR mRNAs undergo intronic polyadenylation, nuclear export, and localise to neurites in vitro and in vivo. We find these IR and PreT-IR mRNAs enriched in RNAseq datasets of tissue from patients with familial and sporadic ALS. This shared signature, between SFPQ-depleted neurons and ALS, functionally implicates SFPQ with the disease and suggests that neurite-centred perturbation of alternatively spliced isoforms drives the neurodegenerative process.
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Affiliation(s)
- Richard Taylor
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK.
| | - Fursham Hamid
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Megan Maloney
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology & Neuroscience, Guy's Campus, King's College London, London, SE1 1UL, UK.
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6
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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7
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SFPQ-ABL1 and BCR-ABL1 utilize different signalling networks to drive B-cell acute lymphoblastic leukaemia. Blood Adv 2022; 6:2373-2387. [PMID: 35061886 PMCID: PMC9006296 DOI: 10.1182/bloodadvances.2021006076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
SFPQ-ABL1 is localized to the nuclear compartment and is a relatively weaker driver of cellular proliferation compared with BCR-ABL1. SFPQ-ABL1 and BCR-ABL1 activate distinct signaling networks, both of which converge on inhibiting apoptosis and driving proliferation.
Philadelphia-like (Ph-like) acute lymphoblastic leukemia (ALL) is a high-risk subtype of B-cell ALL characterized by a gene expression profile resembling Philadelphia chromosome–positive ALL (Ph+ ALL) in the absence of BCR-ABL1. Tyrosine kinase–activating fusions, some involving ABL1, are recurrent drivers of Ph-like ALL and are targetable with tyrosine kinase inhibitors (TKIs). We identified a rare instance of SFPQ-ABL1 in a child with Ph-like ALL. SFPQ-ABL1 expressed in cytokine-dependent cell lines was sufficient to transform cells and these cells were sensitive to ABL1-targeting TKIs. In contrast to BCR-ABL1, SFPQ-ABL1 localized to the nuclear compartment and was a weaker driver of cellular proliferation. Phosphoproteomics analysis showed upregulation of cell cycle, DNA replication, and spliceosome pathways, and downregulation of signal transduction pathways, including ErbB, NF-κB, vascular endothelial growth factor (VEGF), and MAPK signaling in SFPQ-ABL1–expressing cells compared with BCR-ABL1–expressing cells. SFPQ-ABL1 expression did not activate phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling and was associated with phosphorylation of G2/M cell cycle proteins. SFPQ-ABL1 was sensitive to navitoclax and S-63845 and promotes cell survival by maintaining expression of Mcl-1 and Bcl-xL. SFPQ-ABL1 has functionally distinct mechanisms by which it drives ALL, including subcellular localization, proliferative capacity, and activation of cellular pathways. These findings highlight the role that fusion partners have in mediating the function of ABL1 fusions.
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8
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Katano-Toki A, Yoshino S, Nakajima Y, Tomaru T, Nishikido A, Ishida E, Horiguchi K, Saito T, Ozawa A, Satoh T, Yamada M. SFPQ associated with a co-activator for PPARγ, HELZ2, regulates key nuclear factors for adipocyte differentiation. Biochem Biophys Res Commun 2021; 562:139-145. [PMID: 34052659 DOI: 10.1016/j.bbrc.2021.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
We recently isolated a novel co-activator of peroxisome proliferator-activated receptor γ, helicase with zinc finger 2 (HELZ2). HELZ2 null mice were resistant to diet-induced obesity and NAFFL/NASH, and HELZ2 was phosphorylated at tyrosine residues. In order to find a factor related to HELZ2, we analyzed products co-immunoprecipitated with phosphorylated HELZ2 by mass spectrometry analyses. We identified proline- and glutamine-rich (SFPQ) as a protein associating with tyrosine-phosphorylated HELZ2. The knockdown of SFPQ in 3T3-L1 cells downregulated mRNA levels of transcription factors including Krox20, Cebpβ, and Cebpδ: key factors for early-stage adipocyte differentiation. In addition, knockdown of SFPQ inhibited 3T3-L1 cell differentiation to mature adipocytes. These findings demonstrated that SFPQ associating with HELZ2 is an important novel transcriptional regulator of adipocyte differentiation.
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Affiliation(s)
- Akiko Katano-Toki
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan.
| | - Satoshi Yoshino
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yasuyo Nakajima
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Takuya Tomaru
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Ayaka Nishikido
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Emi Ishida
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuhiko Horiguchi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tsugumichi Saito
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Atsushi Ozawa
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tetsurou Satoh
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Masanobu Yamada
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
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9
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Takayama KI, Honma T, Suzuki T, Kondoh Y, Osada H, Suzuki Y, Yoshida M, Inoue S. Targeting Epigenetic and Posttranscriptional Gene Regulation by PSF Impairs Hormone Therapy-Refractory Cancer Growth. Cancer Res 2021; 81:3495-3508. [PMID: 33975881 DOI: 10.1158/0008-5472.can-20-3819] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/05/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
RNA-binding protein PSF functions as an epigenetic modifier by interacting with long noncoding RNAs and the corepressor complex. PSF also promotes RNA splicing events to enhance oncogenic signals. In this study, we conducted an in vitro chemical array screen and identified multiple small molecules that interact with PSF. Several molecules inhibited RNA binding by PSF and decreased prostate cancer cell viability. Among these molecules and its derivatives was a promising molecule, No. 10-3 [7,8-dihydroxy-4-(4-methoxyphenyl)chromen-2-one], that was the most effective at blocking PSF RNA-binding ability and suppressing treatment-resistant prostate and breast cancer cell proliferation. Exposure to No. 10-3 inhibited PSF target gene expression at the mRNA level. Treatment with No. 10-3 reversed epigenetically repressed PSF downstream targets, such as cell-cycle inhibitors, at the transcriptional level. Chromatin immunoprecipitation sequencing in prostate cancer cells revealed that No. 10-3 enhances histone acetylation to induce expression of apoptosis as well as cell-cycle inhibitors. Furthermore, No. 10-3 exhibited antitumor efficacy in a hormone therapy-resistant prostate cancer xenograft mouse model, suppressing treatment-resistant tumor growth. Taken together, this study highlights the feasibility of targeting PSF-mediated epigenetic and RNA-splicing activities for the treatment of aggressive cancers. SIGNIFICANCE: This study identifies small molecules that target PSF-RNA interactions and suppress hormone therapy-refractory cancer growth, suggesting the potential of targeting PSF-mediated gene regulation for cancer treatment.
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Affiliation(s)
- Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Drug Discovery Chemical Bank Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Drug Discovery Chemical Bank Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.,Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan. .,Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
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10
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Biamonti G, Amato A, Belloni E, Di Matteo A, Infantino L, Pradella D, Ghigna C. Alternative splicing in Alzheimer's disease. Aging Clin Exp Res 2021; 33:747-758. [PMID: 31583531 DOI: 10.1007/s40520-019-01360-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/19/2019] [Indexed: 12/25/2022]
Abstract
Alzheimer's disease (AD) is the most frequent neurodegenerative disorder in the elderly, occurring in approximately 20% of people older than 80. The molecular causes of AD are still poorly understood. However, recent studies have shown that Alternative Splicing (AS) is involved in the gene expression reprogramming associated with the functional changes observed in AD patients. In particular, mutations in cis-acting regulatory sequences as well as alterations in the activity and sub-cellular localization of trans-acting splicing factors and components of the spliceosome machinery are associated with splicing abnormalities in AD tissues, which may influence the onset and progression of the disease. In this review, we discuss the current molecular understanding of how alterations in the AS process contribute to AD pathogenesis. Finally, recent therapeutic approaches targeting aberrant AS regulation in AD are also reviewed.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy.
| | - Angela Amato
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy
| | - Elisa Belloni
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy
| | - Anna Di Matteo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy
| | - Lucia Infantino
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy
| | - Davide Pradella
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy
| | - Claudia Ghigna
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), via Abbiategrasso, 207, 27100, Pavia, Italy
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11
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Gordon PM, Hamid F, Makeyev EV, Houart C. A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons. Nat Commun 2021; 12:1918. [PMID: 33771997 PMCID: PMC7997972 DOI: 10.1038/s41467-021-22098-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
The RNA-binding protein SFPQ plays an important role in neuronal development and has been associated with several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease. Here, we report that loss of sfpq leads to premature termination of multiple transcripts due to widespread activation of previously unannotated cryptic last exons (CLEs). These SFPQ-inhibited CLEs appear preferentially in long introns of genes with neuronal functions and can dampen gene expression outputs and/or give rise to short peptides interfering with the normal gene functions. We show that one such peptide encoded by the CLE-containing epha4b mRNA isoform is responsible for neurodevelopmental defects in the sfpq mutant. The uncovered CLE-repressive activity of SFPQ is conserved in mouse and human, and SFPQ-inhibited CLEs are found expressed across ALS iPSC-derived neurons. These results greatly expand our understanding of SFPQ function and uncover a gene regulation mechanism with wide relevance to human neuropathologies.
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Affiliation(s)
- Patricia M Gordon
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, IoPPN, Guy's Campus, King's College London, London, SE1 1UL, UK.
| | - Fursham Hamid
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, IoPPN, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, IoPPN, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, IoPPN, Guy's Campus, King's College London, London, SE1 1UL, UK.
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12
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Murine Long Noncoding RNA Morrbid Contributes in the Regulation of NRAS Splicing in Hepatocytes In Vitro. Int J Mol Sci 2020; 21:ijms21165605. [PMID: 32764370 PMCID: PMC7460575 DOI: 10.3390/ijms21165605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 12/19/2022] Open
Abstract
The coupling of alternative splicing with the nonsense-mediated decay (NMD) pathway maintains quality control of the transcriptome in eukaryotes by eliminating transcripts with premature termination codons (PTC) and fine-tunes gene expression. Long noncoding RNA (lncRNA) can regulate multiple cellular processes, including alternative splicing. Previously, murine Morrbid (myeloid RNA repressor of Bcl2l11 induced death) lncRNA was described as a locus-specific controller of the lifespan of short-living myeloid cells via transcription regulation of the apoptosis-related Bcl2l11 protein. Here, we report that murine Morrbid lncRNA in hepatocytes participates in the regulation of proto-oncogene NRAS (neuroblastoma RAS viral oncogene homolog) splicing, including the formation of the isoform with PTC. We observed a significant increase of the NRAS isoform with PTC in hepatocytes with depleted Morrbid lncRNA. We demonstrated that the NRAS isoform with PTC is degraded via the NMD pathway. This transcript is presented almost only in the nucleus and has a half-life ~four times lower than other NRAS transcripts. Additionally, in UPF1 knockdown hepatocytes (the key NMD factor), we observed a significant increase of the NRAS isoform with PTC. By a modified capture hybridization (CHART) analysis of the protein targets, we uncovered interactions of Morrbid lncRNA with the SFPQ (splicing factor proline and glutamine rich)-NONO (non-POU domain-containing octamer-binding protein) splicing complex. Finally, we propose the regulation mechanism of NRAS splicing in murine hepatocytes by alternative splicing coupled with the NMD pathway with the input of Morrbid lncRNA.
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13
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Takayama K, Fujiwara K, Inoue S. Amyloid precursor protein, an androgen‐regulated gene, is targeted by RNA‐binding protein PSF/SFPQ in neuronal cells. Genes Cells 2019; 24:719-730. [DOI: 10.1111/gtc.12721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/09/2019] [Accepted: 09/14/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Ken‐ichi Takayama
- Department of Systems Aging Science and Medicine Tokyo Metropolitan Institute of Gerontology Tokyo Japan
| | - Kyoko Fujiwara
- Department of Medicine Nihon University School of Medicine Tokyo Japan
- Department of Anatomy Nihon University School of Dentistry Tokyo Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine Tokyo Metropolitan Institute of Gerontology Tokyo Japan
- Division of Gene Regulation and Signal Transduction Research Center for Genomic Medicine Saitama Medical University Hidaka Saitama Japan
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14
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Takeuchi A, Iida K, Tsubota T, Hosokawa M, Denawa M, Brown JB, Ninomiya K, Ito M, Kimura H, Abe T, Kiyonari H, Ohno K, Hagiwara M. Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain. Cell Rep 2019; 23:1326-1341. [PMID: 29719248 DOI: 10.1016/j.celrep.2018.03.141] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/19/2018] [Accepted: 03/30/2018] [Indexed: 12/13/2022] Open
Abstract
Genes specifically expressed in neurons contain members with extended long introns. Longer genes present a problem with respect to fulfilment of gene length transcription, and evidence suggests that dysregulation of long genes is a mechanism underlying neurodegenerative and psychiatric disorders. Here, we report the discovery that RNA-binding protein Sfpq is a critical factor for maintaining transcriptional elongation of long genes. We demonstrate that Sfpq co-transcriptionally binds to long introns and is required for sustaining long-gene transcription by RNA polymerase II through mediating the interaction of cyclin-dependent kinase 9 with the elongation complex. Phenotypically, Sfpq disruption caused neuronal apoptosis in developing mouse brains. Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases. The identified molecular machinery yields directions for targeted investigations of the association between long-gene transcriptopathy and neuronal diseases.
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Affiliation(s)
- Akihide Takeuchi
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kei Iida
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Toshiaki Tsubota
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masatsugu Denawa
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - J B Brown
- Laboratory for Molecular Biosciences, Life Science Informatics Research Unit, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takaya Abe
- Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Hiroshi Kiyonari
- Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan; Animal Resource Development Unit, R IKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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15
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Bartys N, Kierzek R, Lisowiec-Wachnicka J. The regulation properties of RNA secondary structure in alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194401. [PMID: 31323437 DOI: 10.1016/j.bbagrm.2019.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
Abstract
The RNA secondary structure is important for many functional processes in the cell. The secondary and tertiary structures of cellular RNAs are essential for the activity of these molecules in processes such as transcription, splicing, translation, and localization. New high-throughput analytical methods, including next generation sequencing, have allowed for the in-depth characterization of the 'RNA structurome': a new term describing how the RNA structure controls the activity of RNA by itself and how it regulates the expression of genes. In this review, we present many examples of the influence of structural motifs of RNA, long range interactions and global RNA structure on the alternative splicing processes. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Natalia Bartys
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
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16
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Baskota SU, Lopez OL, Greenamyre JT, Kofler J. Spectrum of tau pathologies in Huntington's disease. J Transl Med 2019; 99:1068-1077. [PMID: 30573872 PMCID: PMC9342691 DOI: 10.1038/s41374-018-0166-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Huntington's disease (HD) is an autosomal dominant disorder caused by a trinucleotide expansion in the huntingtin gene. Recently, a new role for tau has been implicated in the pathogenesis of HD, whereas others have argued that postmortem tau pathology findings are attributable to concurrent Alzheimer's disease pathology. The frequency of other well-defined common age-related tau pathologies in HD has not been examined in detail. In this single center, retrospective analysis, we screened seven cases of Huntington's disease (5 females, 2 males, age at death: 47-73 years) for neuronal and glial tau pathology using phospho-tau immunohistochemistry. All seven cases showed presence of neuronal tau pathology. Five cases met diagnostic criteria for primary age-related tauopathy (PART), with three cases classified as definite PART and two cases as possible PART, all with a Braak stage of I. One case was diagnosed with low level of Alzheimer's disease neuropathologic change. In the youngest case, rare perivascular aggregates of tau-positive neurons, astrocytes and processes were identified at sulcal depths, meeting current neuropathological criteria for stage 1 chronic traumatic encephalopathy (CTE). Although the patient had no history of playing contact sports, he experienced several falls, but no definitive concussions during his disease course. Three of the PART cases and the CTE-like case showed additional evidence of aging-related tau astrogliopathy. None of the cases showed significant tau pathology in the striatum. In conclusion, while we found evidence for tau hyperphosphorylation and aggregation in all seven of our HD cases, the tau pathology was readily classifiable into known diagnostic entities and most likely represents non-specific age- or perhaps trauma-related changes. As the tau pathology was very mild in all cases and not unexpected for a population of this age range, it does not appear that the underlying HD may have promoted or accelerated tau accumulation.
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Affiliation(s)
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Timothy Greenamyre
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, Pittsburgh, PA, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.
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17
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Tan J, Yang L, Ong AAL, Shi J, Zhong Z, Lye ML, Liu S, Lisowiec-Wachnicka J, Kierzek R, Roca X, Chen G. A Disease-Causing Intronic Point Mutation C19G Alters Tau Exon 10 Splicing via RNA Secondary Structure Rearrangement. Biochemistry 2019; 58:1565-1578. [DOI: 10.1021/acs.biochem.9b00001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiazi Tan
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Lixia Yang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Alan Ann Lerk Ong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Jiahao Shi
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Zhensheng Zhong
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Mun Leng Lye
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Shiyi Liu
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Gang Chen
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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18
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Lu J, Shu R, Zhu Y. Dysregulation and Dislocation of SFPQ Disturbed DNA Organization in Alzheimer's Disease and Frontotemporal Dementia. J Alzheimers Dis 2019; 61:1311-1321. [PMID: 29376859 DOI: 10.3233/jad-170659] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SFPQ (Splicing factor proline- and glutamine-rich) is a DNA and RNA binding protein involved in transcription, pre-mRNA splicing, and DNA damage repair. SFPQ was found dysregulated in a few tauopathies such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). In addition, knock-down of SFPQ induced FTD-like behavior in mouse. To confirm the role of SFPQ in AD and FTD, we analyzed the brain sections from the AD and FTD brain samples with SFPQ upregulation and dislocation. Specifically, we observed SFPQ dislocated to the cytoplasm and nuclear envelopes, and DNA structures and organizations were associated with these dislocation phenotypes in AD and FTD brains. Consistently, we also found decreased DAPI intensities and smaller chromocenters associated with SFPQ dislocation in nerural-2a (N2a) cells. As the upregulation and hyperphosphorylation of tau protein is a hallmark of AD and FTD, our study sought to investigate potential interactions between tau and SFPQ by co-transfection and co-immunoprecipitation assays in N2a cells. SFPQ dislocation was found enhanced with tau co-transfection and tau co-transfection further resulted in extended DNA disorganization in N2a cells. Overall, our results indicate that dysregulation and dislocation of SFPQ and subsequent DNA disorganization might be a novel pathway in the progression of AD and FTD.
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Affiliation(s)
- Jing Lu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.,Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Runzhe Shu
- Hudson Institute of Medical Research, Monash University, Melbourne, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Monash University, Melbourne, Australia
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19
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Flather D, Nguyen JHC, Semler BL, Gershon PD. Exploitation of nuclear functions by human rhinovirus, a cytoplasmic RNA virus. PLoS Pathog 2018; 14:e1007277. [PMID: 30142213 PMCID: PMC6126879 DOI: 10.1371/journal.ppat.1007277] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/06/2018] [Accepted: 08/11/2018] [Indexed: 12/17/2022] Open
Abstract
Protein production, genomic RNA replication, and virion assembly during infection by picornaviruses like human rhinovirus and poliovirus take place in the cytoplasm of infected human cells, making them the quintessential cytoplasmic pathogens. However, a growing body of evidence suggests that picornavirus replication is promoted by a number of host proteins localized normally within the host cell nucleus. To systematically identify such nuclear proteins, we focused on those that appear to re-equilibrate from the nucleus to the cytoplasm during infection of HeLa cells with human rhinovirus via quantitative protein mass spectrometry. Our analysis revealed a highly selective re-equilibration of proteins with known mRNA splicing and transport-related functions over nuclear proteins of all other functional classes. The multifunctional splicing factor proline and glutamine rich (SFPQ) was identified as one such protein. We found that SFPQ is targeted for proteolysis within the nucleus by viral proteinase 3CD/3C, and a fragment of SFPQ was shown to migrate to the cytoplasm at mid-to-late times of infection. Cells knocked down for SFPQ expression showed significantly reduced rhinovirus titers, viral protein production, and viral RNA accumulation, consistent with SFPQ being a pro-viral factor. The SFPQ fragment that moved into the cytoplasm was able to bind rhinovirus RNA either directly or indirectly. We propose that the truncated form of SFPQ promotes viral RNA stability or replication, or virion morphogenesis. More broadly, our findings reveal dramatic changes in protein compartmentalization during human rhinovirus infection, allowing the virus to systematically hijack the functions of proteins not normally found at its cytoplasmic site of replication. We explored the dynamics of host cell protein relocalization from the nucleus to the cytoplasm during an infection by human rhinovirus using quantitative mass spectrometry, confocal imaging, and Western blot analysis. We discovered a highly selective re-equilibration of proteins with known mRNA splicing and transport-related functions, including splicing factor proline and glutamine rich (SFPQ). Using RNAi experiments and viral replication assays, we demonstrated that SFPQ is a pro-viral factor required for rhinovirus growth. Our studies provide new insights into how this cytoplasmic RNA virus is able to alter and hijack the functions of host proteins that normally reside in the nucleus.
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Affiliation(s)
- Dylan Flather
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States of America
- Center for Virus Research, University of California, Irvine, California, United States of America
| | - Joseph H. C. Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States of America
- Center for Virus Research, University of California, Irvine, California, United States of America
| | - Bert L. Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States of America
- Center for Virus Research, University of California, Irvine, California, United States of America
- * E-mail: (BLS); (PDG)
| | - Paul D. Gershon
- Center for Virus Research, University of California, Irvine, California, United States of America
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, United States of America
- * E-mail: (BLS); (PDG)
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20
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Singh G, Rife BD, Seufzer B, Salemi M, Rendahl A, Boris-Lawrie K. Identification of conserved, primary sequence motifs that direct retrovirus RNA fate. Nucleic Acids Res 2018; 46:7366-7378. [PMID: 29846681 PMCID: PMC6101577 DOI: 10.1093/nar/gky369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/20/2018] [Accepted: 05/16/2018] [Indexed: 12/16/2022] Open
Abstract
Precise stoichiometry of genome-length transcripts and alternatively spliced mRNAs is a hallmark of retroviruses. We discovered short, guanosine and adenosine sequence motifs in the 5'untranslated region of several retroviruses and ascertained the reasons for their conservation using a representative lentivirus and genetically simpler retrovirus. We conducted site-directed mutagenesis of the GA-motifs in HIV molecular clones and observed steep replication delays in T-cells. Quantitative RNA analyses demonstrate the GA-motifs are necessary to retain unspliced viral transcripts from alternative splicing. Mutagenesis of the GA-motifs in a C-type retrovirus validate the similar downregulation of unspliced transcripts and virion structural protein. The evidence from cell-based co-precipitation studies shows the GA-motifs in the 5'untranslated region confer binding by SFPQ/PSF, a protein co-regulated with T-cell activation. Diminished SFPQ/PSF or mutation of either GA-motif attenuates the replication of HIV. The interaction of SFPQ/PSF with both GA-motifs is crucial for maintaining the stoichiometry of the viral transcripts and does not affect packaging of HIV RNA. Our results demonstrate the conserved GA-motifs direct the fate of retrovirus RNA. These findings have exposed an RNA-based molecular target to attenuate retrovirus replication.
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Affiliation(s)
- Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Brittany D Rife
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Bradley Seufzer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Aaron Rendahl
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
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21
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Ishigaki S, Fujioka Y, Okada Y, Riku Y, Udagawa T, Honda D, Yokoi S, Endo K, Ikenaka K, Takagi S, Iguchi Y, Sahara N, Takashima A, Okano H, Yoshida M, Warita H, Aoki M, Watanabe H, Okado H, Katsuno M, Sobue G. Altered Tau Isoform Ratio Caused by Loss of FUS and SFPQ Function Leads to FTLD-like Phenotypes. Cell Rep 2017; 18:1118-1131. [PMID: 28147269 DOI: 10.1016/j.celrep.2017.01.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 12/16/2016] [Accepted: 01/05/2017] [Indexed: 12/13/2022] Open
Abstract
Fused in sarcoma (FUS) and splicing factor, proline- and glutamine-rich (SFPQ) are RNA binding proteins that regulate RNA metabolism. We found that alternative splicing of the Mapt gene at exon 10, which generates 4-repeat tau (4R-T) and 3-repeat tau (3R-T), is regulated by interactions between FUS and SFPQ in the nuclei of neurons. Hippocampus-specific FUS- or SFPQ-knockdown mice exhibit frontotemporal lobar degeneration (FTLD)-like behaviors, reduced adult neurogenesis, accumulation of phosphorylated tau, and hippocampal atrophy with neuronal loss through an increased 4R-T/3R-T ratio. Normalization of this increased ratio by 4R-T-specific silencing results in recovery of the normal phenotype. These findings suggest a biological link among FUS/SFPQ, tau isoform alteration, and phenotypic expression, which may function in the early pathomechanism of FTLD.
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Affiliation(s)
- Shinsuke Ishigaki
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Department of Therapeutics for Intractable Neurological Disorders, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
| | - Yusuke Fujioka
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yohei Okada
- Department of Neurology, Aichi Medical University, School of Medicine, Aichi 480-1195, Japan
| | - Yuichi Riku
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Aichi 480-1195, Japan
| | - Tsuyoshi Udagawa
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Daiyu Honda
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Satoshi Yokoi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kuniyuki Endo
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Shinnosuke Takagi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yohei Iguchi
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Naruhiko Sahara
- Department of Functional Brain Imaging Research, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Akihiko Takashima
- Faculty of Science, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Aichi 480-1195, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Hirohisa Watanabe
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Brain and Mind Research Center, Nagoya University, Nagoya, Aichi 466-8550, Japan
| | - Haruo Okado
- Department of Brain Development and Neural Regeneration, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Gen Sobue
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Brain and Mind Research Center, Nagoya University, Nagoya, Aichi 466-8550, Japan; Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
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22
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
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Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
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Pachima YI, Zhou LY, Lei P, Gozes I. Microtubule-Tau Interaction as a Therapeutic Target for Alzheimer's Disease. J Mol Neurosci 2016; 58:145-52. [PMID: 26816082 DOI: 10.1007/s12031-016-0715-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yanina Ivashko Pachima
- Lily and Avraham Gildor Chair for the Investigation of Growth Factors, Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Liu-yao Zhou
- Department of Neurology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China
| | - Peng Lei
- Department of Neurology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, 610041, China. .,Oxidation Biology Unit, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, 3052, VIC, Australia.
| | - Illana Gozes
- Lily and Avraham Gildor Chair for the Investigation of Growth Factors, Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 69978, Israel.
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Knott GJ, Bond CS, Fox AH. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res 2016; 44:3989-4004. [PMID: 27084935 PMCID: PMC4872119 DOI: 10.1093/nar/gkw271] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Nuclear proteins are often given a concise title that captures their function, such as 'transcription factor,' 'polymerase' or 'nuclear-receptor.' However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein-protein and protein-nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Archa H Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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25
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Methyl-Arginine Profile of Brain from Aged PINK1-KO+A53T-SNCA Mice Suggests Altered Mitochondrial Biogenesis. PARKINSONS DISEASE 2016; 2016:4686185. [PMID: 27034888 PMCID: PMC4791501 DOI: 10.1155/2016/4686185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 11/29/2022]
Abstract
Hereditary Parkinson's disease can be triggered by an autosomal dominant overdose of alpha-Synuclein (SNCA) or the autosomal recessive deficiency of PINK1. We recently showed that the combination of PINK1-knockout with overexpression of A53T-SNCA in double mutant (DM) mice potentiates phenotypes and reduces survival. Now we studied brain hemispheres of DM mice at age of 18 months in a hypothesis-free approach, employing a quantitative label-free global proteomic mass spectrometry scan of posttranslational modifications focusing on methyl-arginine. The strongest effects were documented for the adhesion modulator CMAS, the mRNA decapping/deadenylation factor PATL1, and the synaptic plasticity mediator CRTC1/TORC1. In addition, an intriguing effect was observed for the splicing factor PSF/SFPQ, known to interact with the dopaminergic differentiation factor NURR1 as well as with DJ-1, the protein responsible for the autosomal recessive PARK7 variant of PD. CRTC1, PSF, and DJ-1 are modulators of PGC1alpha and of mitochondrial biogenesis. This pathway was further stressed by dysregulations of oxygen sensor EGLN3 and of nuclear TMPO. PSF and TMPO cooperate with dopaminergic differentiation factors LMX1B and NURR1. Further dysregulations concerned PRR18, TRIO, HNRNPA1, DMWD, WAVE1, ILDR2, DBNDD1, and NFM. Thus, we report selective novel endogenous stress responses in brain, which highlight early dysregulations of mitochondrial homeostasis and midbrain vulnerability.
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26
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Lisowiec J, Magner D, Kierzek E, Lenartowicz E, Kierzek R. Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biol 2015; 12:330-42. [PMID: 25826665 DOI: 10.1080/15476286.2015.1017214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative splicing at the MAPT gene exon 10 yields similar levels of the 3R and 4R tau protein isoforms. (1) The presence of mutations, particularly in exon 10 and intron 10-11, changes the quantity of tau isoforms. Domination each of the isoform yields tau protein aggregation and frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Here, we report for the first time the secondary structure of the 194/195 nucleotide region for the wild type (WT) and 10 mutants of the MAPT gene pre-mRNA determined using both chemical and microarray mapping. Thermodynamic analyses indicate that single nucleotide mutations in the splicing regulatory element (SRE) that form a hairpin affect its stability by up to 4 and 7 kcal/mol. Moreover, binding the regulatory hairpin of small molecule ligands (neomycin, kanamycin, tobramycin and mitoxantrone) enhance its stability depending on the nature of the ligands and the RNA mutations. Experiments using the cos-7 cell line indicate that the presence of ligands and modified antisense oligonucleotides affect the quantity of 3R and 4R isoforms. This finding correlates with the thermodynamic stability of the regulatory hairpin. An alternative splicing regulation mechanism for exon 10 is postulated based on our experimental data and on published data.
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Key Words
- AD, Alzheimer disease
- DMS, dimethyl sulfide
- ESE, exonic splicing enhancer
- ESS, exonic splicing silencer
- FTD, frontotemporal dementia
- FTDP-17, frontotemporal dementia and Parkinsonism linked to chromosome 17
- ISM, intronic splicing modulator
- ISS, intronic splicing silencer
- MAPT, microtubule-associated protein tau
- NMIA, N-methylisotoic anhydride
- NMR, nuclear magnetic resonance
- PPE, polypurine enhancer
- RNA structure
- RNA thermodynamics
- RT-PCR, reverse transcription polymerase chain reaction
- SHAPE, selective 2′-hydroxyl acylation analyzed by primer extension
- SMA, spinal muscular atrophy
- SRE, splicing regulatory element
- U1 snRNP, U1 small nuclear ribonucleoprotein
- WT, wild type
- alternative splicing regulation
- antisense oligonucleotides
- neurodegradation
- pre-mRNA, pre-messenger RNA
- small molecule binding
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Affiliation(s)
- Jolanta Lisowiec
- a Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Noskowskiego, Poland
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27
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Liu G, Liu C, Zhang XN. Comparison of the neuropsychological mechanisms of 2,6-diisopropylphenol and N-methyl-D-aspartate receptor antagonist against electroconvulsive therapy-induced learning and memory impairment in depressed rats. Mol Med Rep 2015; 12:3297-3308. [PMID: 25998151 PMCID: PMC4526078 DOI: 10.3892/mmr.2015.3803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 04/14/2015] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to examine the neurophysiological mechanisms of the 2,6-diisopropylphenol and N-methyl-D-aspartate (NMDA) receptor antagonist against learning and memory impairment, induced by electroconvulsive therapy (ECT). A total of 48 adult depressed rats without olfactory bulbs were randomly divided into six experimental groups: i) saline; ii) 10 mg/kg MK‑801; iii) 10 mg/kg MK‑801 and a course of ECT; iv) 200 mg/kg 2,6‑diisopropylphenol; v) 200 mg/kg 2,6‑diisopropylphenol and a course of ECT; and vi) saline and a course of ECT. The learning and memory abilities of the rats were assessed using a Morris water maze 1 day after a course of ECT. The hippocampus was removed 1 day after assessment using the Morris water maze assessment. The content of glutamate in the hippocampus was detected using high‑performance liquid chromatography. The expression levels of p‑AT8Ser202 and GSK‑3β1H8 in the hippocampus were determined using immunohistochemical staining and western blot analysis. The results demonstrated that the 2,6‑diisopropylphenol NMDA receptor antagonist, MK‑801 and ECT induced learning and memory impairment in the depressed rats. The glutamate content was significantly upregulated by ECT, reduced by 2,6‑diisopropylphenol, and was unaffected by the NMDA receptor antagonist in the hippocampus of the depressed rats. Tau protein hyperphosphorylation in the hippocampus was upregulated by ECT, but was reduced by 2,6‑diisopropylphenol and the MK‑801 NMDA receptor antagonist. It was also demonstrated that 2,6‑diisopropylphenol prevented learning and memory impairment and reduced the hyperphosphorylation of the Tau protein, which was induced by eECT. GSK‑3β was found to be the key protein involved in this signaling pathway. The ECT reduced the learning and memory impairment, caused by hyperphosphorylation of the Tau protein, in the depressed rats by upregulating the glutamate content.
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Affiliation(s)
- Gang Liu
- Department of Anesthesiology, General Hospital of Beijing Military Area of PLA, Beijing 100700, P.R. China
| | - Chao Liu
- Department of Anesthesiology, Tianjin Chest Hospital, Tianjin 300222, P.R. China
| | - Xue-Ning Zhang
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
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Yarosh CA, Iacona JR, Lutz CS, Lynch KW. PSF: nuclear busy-body or nuclear facilitator? WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:351-67. [PMID: 25832716 PMCID: PMC4478221 DOI: 10.1002/wrna.1280] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 01/25/2023]
Abstract
PTB-associated splicing factor (PSF) is an abundant and essential nucleic acid-binding protein that participates in a wide range of gene regulatory processes and cellular response pathways. At the protein level, PSF consists of multiple domains, many of which remain poorly characterized. Although grouped in a family with the proteins p54nrb/NONO and PSPC1 based on sequence homology, PSF contains additional protein sequence not included in other family members. Consistently, PSF has also been implicated in functions not ascribed to p54nrb/NONO or PSPC1. Here, we provide a review of the cellular activities in which PSF has been implicated and what is known regarding the mechanisms by which PSF functions in each case. We propose that the complex domain arrangement of PSF allows for its diversity of function and integration of activities. Finally, we discuss recent evidence that individual activities of PSF can be regulated independently from one another through the activity of domain-specific co-factors.
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Affiliation(s)
- Christopher A Yarosh
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph R Iacona
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences-New Jersey Medical School, Newark, NJ, USA
| | - Carol S Lutz
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences-New Jersey Medical School, Newark, NJ, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
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29
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Cho S, Moon H, Loh TJ, Oh HK, Williams DR, Liao DJ, Zhou J, Green MR, Zheng X, Shen H. PSF contacts exon 7 of SMN2 pre-mRNA to promote exon 7 inclusion. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:517-25. [PMID: 24632473 DOI: 10.1016/j.bbagrm.2014.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 12/23/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease and a leading cause of infant mortality. Deletions or mutations of SMN1 cause SMA, a gene that encodes a SMN protein. SMN is important for the assembly of Sm proteins onto UsnRNA to UsnRNP. SMN has also been suggested to direct axonal transport of β-actin mRNA in neurons. Humans contain a second SMN gene called SMN2 thus SMA patients produce some SMN but not with sufficient levels. The majority of SMN2 mRNA does not include exon 7. Here we show that increased expression of PSF promotes inclusion of exon 7 in the SMN2 whereas reduced expression of PSF promotes exon 7 skipping. In addition, we present evidence showing that PSF interacts with the GAAGGA enhancer in exon 7. We also demonstrate that a mutation in this enhancer abolishes the effects of PSF on exon 7 splicing. Furthermore we show that the RNA target sequences of PSF and tra2β in exon 7 are partially overlapped. These results lead us to conclude that PSF interacts with an enhancer in exon 7 to promote exon 7 splicing of SMN2 pre-mRNA.
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Affiliation(s)
- Sunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Heegyum Moon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hyun Kyung Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Darren Reese Williams
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - D Joshua Liao
- Hormel Institute, University of Minnesota, Austin, MN, USA
| | | | - Michael R Green
- Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
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30
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Qian W, Liu F. Regulation of alternative splicing of tau exon 10. Neurosci Bull 2014; 30:367-77. [PMID: 24627328 DOI: 10.1007/s12264-013-1411-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/03/2014] [Indexed: 12/22/2022] Open
Abstract
The neuronal microtubule-associated protein tau is abnormally hyperphosphorylated and aggregated into neurofibrillary tangles in the brains of individuals with Alzheimer's disease and related neurodegenerative disorders. The adult human brain expresses six isoforms of tau generated by alternative splicing of exons 2, 3, and 10 of its pre-mRNA. Exon 10 encodes the second microtubule-binding repeat of tau. Its alternative splicing produces tau isoforms with either three or four microtubule-binding repeats, termed 3R-tau and 4Rtau. In the normal adult human brain, the level of 3R-tau is approximately equal to that of 4R-tau. Several silent and intronic mutations of the tau gene associated with FTDP-17T (frontotemporal dementia with Parkinsonism linked to chromosome 17 and specifically characterized by tau pathology) only disrupt exon 10 splicing, but do not influence the primary sequence of the tau protein. Thus, abnormal exon 10 splicing is sufficient to cause neurodegeneration and dementia. Here, we review the regulation of tau exon 10 splicing by cis-elements and trans-factors and summarize all the mutations associated with FTDP-17T and related tauopathies. The findings suggest that correction of exon 10 splicing may be a potential target for tau exon 10 splicing-related tauopathies.
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Affiliation(s)
- Wei Qian
- Department of Biochemistry and Molecular Biology, School of Medicine, Nantong University, Nantong, 226001, China
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31
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Schirer Y, Malishkevich A, Ophir Y, Lewis J, Giladi E, Gozes I. Novel marker for the onset of frontotemporal dementia: early increase in activity-dependent neuroprotective protein (ADNP) in the face of Tau mutation. PLoS One 2014; 9:e87383. [PMID: 24489906 PMCID: PMC3906161 DOI: 10.1371/journal.pone.0087383] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/22/2013] [Indexed: 12/14/2022] Open
Abstract
Tauopathy, a major pathology in Alzheimer's disease, is also found in ∼50% of frontotemporal dementias (FTDs). Tau transcript, a product of a single gene, undergoes alternative splicing to yield 6 protein species, each with either 3 or 4 microtubule binding repeat domains (tau 3R or 4R, associated with dynamic and stable microtubules, respectively). While the healthy human brain shows a 1/1 ratio of tau 3R/4R, this ratio may be dramatically changed in the FTD brain. We have previously discovered that activity-dependent neuroprotective protein (ADNP) is essential for brain formation in the mouse, with ADNP+/− mice exhibiting tauopathy, age-driven neurodegeneration and behavioral deficits. Here, in transgenic mice overexpressing a mutated tau 4R species, in the cerebral cortex but not in the cerebellum, we showed significantly increased ADNP expression (∼3-fold transcripts) in the cerebral cortex of young transgenic mice (∼disease onset), but not in the cerebellum, as compared to control littermates. The transgene-age-related increased ADNP expression paralleled augmented dynamic tau 3R transcript level compared to control littermates. Blocking mutated tau 4R transgene expression resulted in normalization of ADNP and tau 3R expression. ADNP was previously shown to be a member of the SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling complex. Here, Brahma (Brm), a component of the SWI/SNF complex regulating alternative splicing, showed a similar developmental expression pattern to ADNP. Immunoprecipitations further suggested Brm-ADNP interaction coupled to ADNP - polypyrimidine tract-binding protein (PTB)-associated splicing factor (PSF)-binding, with PSF being a direct regulator of tau transcript splicing. It should be noted that although we have shown a correlation between levels of ADNP and tau isoform expression three months of age, we are not presenting evidence of a direct link between the two. Future research into ADNP/tau relations is warranted.
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Affiliation(s)
- Yulie Schirer
- The Adams Super Center for Brain Studies, The Lily and Avraham Gildor Chair for the Investigation of Growth Factors, The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Anna Malishkevich
- The Adams Super Center for Brain Studies, The Lily and Avraham Gildor Chair for the Investigation of Growth Factors, The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Yotam Ophir
- The Adams Super Center for Brain Studies, The Lily and Avraham Gildor Chair for the Investigation of Growth Factors, The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Jada Lewis
- Center for Translational Research in Neurodegenerative Disease, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Eliezer Giladi
- The Adams Super Center for Brain Studies, The Lily and Avraham Gildor Chair for the Investigation of Growth Factors, The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Illana Gozes
- The Adams Super Center for Brain Studies, The Lily and Avraham Gildor Chair for the Investigation of Growth Factors, The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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32
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Iqbal K, Liu F, Gong CX. Alzheimer disease therapeutics: focus on the disease and not just plaques and tangles. Biochem Pharmacol 2014; 88:631-9. [PMID: 24418409 DOI: 10.1016/j.bcp.2014.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/26/2013] [Accepted: 01/02/2014] [Indexed: 12/13/2022]
Abstract
The bulk of AD research during the last 25 years has been Aβ-centric based on a strong faith in the Amyloid Cascade Hypothesis which is not supported by the data on humans. To date, Aβ-based therapeutic clinical trials on sporadic cases of AD have been negative. Although most likely the major reason for the failure is that Aβ is not an effective therapeutic target for sporadic AD, initiation of the treatment at mild to moderate stages of the disease is blamed as too late to be effective. Clinical trials on presymptomatic familial AD cases have been initiated with the logic that Aβ is a trigger of the disease and hence initiation of the Aβ immunotherapies several years before any clinical symptoms would be effective. There is an urgent need to explore targets other than Aβ. There is now increasing interest in inhibiting tau pathology, which does have a far more compelling rationale than Aβ. AD is multifactorial and over 99% of the cases are the sporadic form of the disease. Understanding of the various etiopathogenic mechanisms of sporadic AD and generation of the disease-relevant animal models are required to develop rational therapeutic targets and therapies. Treatment of AD will require both inhibition of neurodegeneration and regeneration of the brain.
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Affiliation(s)
- Khalid Iqbal
- Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA.
| | - Fei Liu
- Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
| | - Cheng-Xin Gong
- Department of Neurochemistry, Inge Grundke-Iqbal Research Floor, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA
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33
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Zhou Y, Liu S, Liu G, Öztürk A, Hicks GG. ALS-associated FUS mutations result in compromised FUS alternative splicing and autoregulation. PLoS Genet 2013; 9:e1003895. [PMID: 24204307 PMCID: PMC3814325 DOI: 10.1371/journal.pgen.1003895] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 09/05/2013] [Indexed: 12/13/2022] Open
Abstract
The gene encoding a DNA/RNA binding protein FUS/TLS is frequently mutated in amyotrophic lateral sclerosis (ALS). Mutations commonly affect its carboxy-terminal nuclear localization signal, resulting in varying deficiencies of FUS nuclear localization and abnormal cytoplasmic accumulation. Increasing evidence suggests deficiencies in FUS nuclear function may contribute to neuron degeneration. Here we report a novel FUS autoregulatory mechanism and its deficiency in ALS-associated mutants. Using FUS CLIP-seq, we identified significant FUS binding to a highly conserved region of exon 7 and the flanking introns of its own pre-mRNAs. We demonstrated that FUS is a repressor of exon 7 splicing and that the exon 7-skipped splice variant is subject to nonsense-mediated decay (NMD). Overexpression of FUS led to the repression of exon 7 splicing and a reduction of endogenous FUS protein. Conversely, the repression of exon 7 was reduced by knockdown of FUS protein, and moreover, it was rescued by expression of EGFP-FUS. This dynamic regulation of alternative splicing describes a novel mechanism of FUS autoregulation. Given that ALS-associated FUS mutants are deficient in nuclear localization, we examined whether cells expressing these mutants would be deficient in repressing exon 7 splicing. We showed that FUS harbouring R521G, R522G or ΔExon15 mutation (minor, moderate or severe cytoplasmic localization, respectively) directly correlated with respectively increasing deficiencies in both exon 7 repression and autoregulation of its own protein levels. These data suggest that compromised FUS autoregulation can directly exacerbate the pathogenic accumulation of cytoplasmic FUS protein in ALS. We showed that exon 7 skipping can be induced by antisense oligonucleotides targeting its flanking splice sites, indicating the potential to alleviate abnormal cytoplasmic FUS accumulation in ALS. Taken together, FUS autoregulation by alternative splicing provides insight into a molecular mechanism by which FUS-regulated pre-mRNA processing can impact a significant number of targets important to neurodegeneration.
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Affiliation(s)
- Yueqin Zhou
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Songyan Liu
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, Manitoba, Canada
- Faculty of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guodong Liu
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Arzu Öztürk
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Geoffrey G. Hicks
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Regenerative Medicine Program, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Martinez NM, Lynch KW. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev 2013; 253:216-36. [PMID: 23550649 PMCID: PMC3621013 DOI: 10.1111/imr.12047] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most mammalian pre-mRNAs are alternatively spliced in a manner that alters the resulting open reading frame. Consequently, alternative pre-mRNA splicing provides an important RNA-based layer of protein regulation and cellular function. The ubiquitous nature of alternative splicing coupled with the advent of technologies that allow global interrogation of the transcriptome have led to an increasing awareness of the possibility that widespread changes in splicing patterns contribute to lymphocyte function during an immune response. Indeed, a few notable examples of alternative splicing have clearly been demonstrated to regulate T-cell responses to antigen. Moreover, several proteins key to the regulation of splicing in T cells have recently been identified. However, much remains to be done to truly identify the spectrum of genes that are regulated at the level of splicing in immune cells and to determine how many of these are controlled by currently known factors and pathways versus unknown mechanisms. Here, we describe the proteins, pathways, and mechanisms that have been shown to regulate alternative splicing in human T cells and discuss what is and is not known about the genes regulated by such factors. Finally, we highlight unifying themes with regards to the mechanisms and consequences of alternative splicing in the adaptive immune system and give our view of important directions for future studies.
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Affiliation(s)
- Nicole M Martinez
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6059, USA
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2, 6-Diisopropylphenol Protects Against The Impairment of Learning-memory and Reduces The Hyperphosphorylation of Protein Tau Induced by Electroconvulsive Shock in The Depression Model Rats Whose Olfactory Bulbs Were Removed*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Impaired Post-transcriptional Regulation in Alzheimer′s Disease*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2012.00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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MicroRNAs and the Regulation of Tau Metabolism. Int J Alzheimers Dis 2012; 2012:406561. [PMID: 22720189 PMCID: PMC3374946 DOI: 10.1155/2012/406561] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/19/2012] [Indexed: 11/17/2022] Open
Abstract
Abnormal regulation of tau phosphorylation and/or alternative splicing is associated with the development of a large (>20) group of neurodegenerative disorders collectively known as tauopathies, the most common being Alzheimer's disease. Despite intensive research, little is known about the molecular mechanisms that participate in the transcriptional and posttranscriptional regulation of endogenous tau, especially in neurons. Recently, we showed that mice lacking Dicer in the forebrain displayed progressive neurodegeneration accompanied by disease-like changes in tau phosphorylation and splicing. Dicer is a key enzyme in the biogenesis of microRNAs (miRNAs), small noncoding RNAs that function as part of the RNA-induced silencing complex (RISC) to repress gene expression at the posttranscriptional level. We identified miR-16 and miR-132 as putative endogenous modulators of neuronal tau phosphorylation and tau exon 10 splicing, respectively. Interestingly, these miRNAs have been implicated in cell survival and function, whereas changes in miR-16/132 levels correlate with tau pathology in human neurodegenerative disorders. Thus, understanding how miRNA networks influence tau metabolism and possibly other biological systems might provide important clues into the molecular causes of tauopathies, particularly the more common but less understood sporadic forms.
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Sumanasekera C, Kelemen O, Beullens M, Aubol BE, Adams JA, Sunkara M, Morris A, Bollen M, Andreadis A, Stamm S. C6 pyridinium ceramide influences alternative pre-mRNA splicing by inhibiting protein phosphatase-1. Nucleic Acids Res 2011; 40:4025-39. [PMID: 22210893 PMCID: PMC3351148 DOI: 10.1093/nar/gkr1289] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Alternative pre-mRNA processing is a central element of eukaryotic gene regulation. The cell frequently alters the use of alternative exons in response to physiological stimuli. Ceramides are lipid-signaling molecules composed of sphingosine and a fatty acid. Previously, water-insoluble ceramides were shown to change alternative splicing and decrease SR-protein phosphorylation by activating protein phosphatase-1 (PP1). To gain further mechanistical insight into ceramide-mediated alternative splicing, we analyzed the effect of C6 pyridinium ceramide (PyrCer) on alternative splice site selection. PyrCer is a water-soluble ceramide analog that is under investigation as a cancer drug. We found that PyrCer binds to the PP1 catalytic subunit and inhibits the dephosphorylation of several splicing regulatory proteins containing the evolutionarily conserved RVxF PP1-binding motif (including PSF/SFPQ, Tra2-beta1 and SF2/ASF). In contrast to natural ceramides, PyrCer promotes phosphorylation of splicing factors. Exons that are regulated by PyrCer have in common suboptimal splice sites, are unusually short and share two 4-nt motifs, GAAR and CAAG. They are dependent on PSF/SFPQ, whose phosphorylation is regulated by PyrCer. Our results indicate that lipids can influence pre-mRNA processing by regulating the phosphorylation status of specific regulatory factors, which is mediated by protein phosphatase activity.
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Affiliation(s)
- Chiranthani Sumanasekera
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
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