1
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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2
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Lin CC, Chang TC, Wang Y, Guo L, Gao Y, Bikorimana E, Lemoff A, Fang YV, Zhang H, Zhang Y, Ye D, Soria-Bretones I, Servetto A, Lee KM, Luo X, Otto JJ, Akamatsu H, Napolitano F, Mani R, Cescon DW, Xu L, Xie Y, Mendell JT, Hanker AB, Arteaga CL. PRMT5 is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer. Nat Commun 2024; 15:2287. [PMID: 38480701 PMCID: PMC10937713 DOI: 10.1038/s41467-024-46495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with estrogen receptor-positive (ER+) breast cancer. However, patients treated with CDK4/6i eventually develop drug resistance and progress. RB1 loss-of-function alterations confer resistance to CDK4/6i, but the optimal therapy for these patients is unclear. Through a genome-wide CRISPR screen, we identify protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in ER+/RB1-knockout breast cancer cells. Inhibition of PRMT5 blocks the G1-to-S transition in the cell cycle independent of RB, leading to growth arrest in RB1-knockout cells. Proteomics analysis uncovers fused in sarcoma (FUS) as a downstream effector of PRMT5. Inhibition of PRMT5 results in dissociation of FUS from RNA polymerase II, leading to hyperphosphorylation of serine 2 in RNA polymerase II, intron retention, and subsequent downregulation of proteins involved in DNA synthesis. Furthermore, treatment with the PRMT5 inhibitor pemrametostat and a selective ER degrader fulvestrant synergistically inhibits growth of ER+/RB-deficient cell-derived and patient-derived xenografts. These findings highlight dual ER and PRMT5 blockade as a potential therapeutic strategy to overcome resistance to CDK4/6i in ER+/RB-deficient breast cancer.
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Affiliation(s)
- Chang-Ching Lin
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunpeng Gao
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Emmanuel Bikorimana
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Lemoff
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yisheng V Fang
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yanfeng Zhang
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dan Ye
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Alberto Servetto
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Kyung-Min Lee
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Xuemei Luo
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joseph J Otto
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Hiroaki Akamatsu
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Fabiana Napolitano
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ram Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - David W Cescon
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ariella B Hanker
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carlos L Arteaga
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
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3
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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4
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Zhu Q, Hu Y, Jiang W, Ou ZL, Yao YB, Zai HY. Circ-CCT2 Activates Wnt/β-catenin Signaling to Facilitate Hepatoblastoma Development by Stabilizing PTBP1 mRNA. Cell Mol Gastroenterol Hepatol 2023; 17:175-197. [PMID: 37866478 PMCID: PMC10758885 DOI: 10.1016/j.jcmgh.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND & AIMS Circ-CCT2 (hsa_circ_0000418) is a novel circular RNA that stems from the CCT2 gene. However, the expression of circ-CCT2 and its roles in hepatoblastoma are unknown. Our study aims to study the circ-CCT2 roles in hepatoblastoma development. METHODS Hepatoblastoma specimens were collected for examining the expression of circ-CCT2, TAF15, and PTBP1. CCK-8 and colony formation assays were applied for cell proliferation analysis. Migratory and invasive capacities were evaluated through wound healing and Transwell assays. The interaction between circ-CCT2, TAF15, and PTBP1 was validated by fluorescence in situ hybridization, RNA pull-down, and RNA immunoprecipitation. SKL2001 was used as an agonist of the Wnt/β-catenin pathway. A subcutaneous mouse model of hepatoblastoma was established for examining the function of circ-CCT2 in hepatoblastoma in vivo. RESULTS Circ-CCT2 was significantly up-regulated in hepatoblastoma. Overexpression of circ-CCT2 activated Wnt/β-catenin signaling and promoted hepatoblastoma progression, whereas knockdown of circ-CCT2 exerted opposite effects. Moreover, both TAF15 and PTBP1 were up-regulated in hepatoblastoma tissues and cells. TAF15 was positively correlated with the expression of circ-CCT2 and PTBP1 in hepatoblastoma. Furthermore, circ-CCT2 recruited and up-regulated TAF15 protein to stabilize PTBP1 mRNA and trigger Wnt/β-catenin signaling in hepatoblastoma. Overexpression of TAF15 or PTBP1 reversed knockdown of circ-CCT2-mediated suppression of hepatoblastoma progression. SKL2001-mediated activation of Wnt/β-catenin signaling reversed the anti-tumor effects of silencing of circ-CCT2, TAF15, or PTBP1. CONCLUSIONS Circ-CCT2 stabilizes PTBP1 mRNA and activates Wnt/β-catenin signaling through recruiting and up-regulating TAF15 protein, thus promoting hepatoblastoma progression. Our findings deepen the understanding of hepatoblastoma pathogenesis and suggest potential therapeutic targets.
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Affiliation(s)
- Qin Zhu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Yu Hu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Wei Jiang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Zheng-Lin Ou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Yuan-Bing Yao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China
| | - Hong-Yan Zai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan Province, P.R. China.
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5
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Dupuy M, Lamoureux F, Mullard M, Postec A, Regnier L, Baud’huin M, Georges S, Brounais-Le Royer B, Ory B, Rédini F, Verrecchia F. Ewing sarcoma from molecular biology to the clinic. Front Cell Dev Biol 2023; 11:1248753. [PMID: 37752913 PMCID: PMC10518617 DOI: 10.3389/fcell.2023.1248753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
In Europe, with an incidence of 7.5 cases per million, Ewing sarcoma (ES) is the second most common primary malignant bone tumor in children, adolescents and young adults, after osteosarcoma. Since the 1980s, conventional treatment has been based on the use of neoadjuvant and adjuvant chemotherapeutic agents combined with surgical resection of the tumor when possible. These treatments have increased the patient survival rate to 70% for localized forms, which drops drastically to less than 30% when patients are resistant to chemotherapy or when pulmonary metastases are present at diagnosis. However, the lack of improvement in these survival rates over the last decades points to the urgent need for new therapies. Genetically, ES is characterized by a chromosomal translocation between a member of the FET family and a member of the ETS family. In 85% of cases, the chromosomal translocation found is (11; 22) (q24; q12), between the EWS RNA-binding protein and the FLI1 transcription factor, leading to the EWS-FLI1 fusion protein. This chimeric protein acts as an oncogenic factor playing a crucial role in the development of ES. This review provides a non-exhaustive overview of ES from a clinical and biological point of view, describing its main clinical, cellular and molecular aspects.
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Affiliation(s)
- Maryne Dupuy
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Université d'Angers, Nantes, France
| | | | | | | | | | | | | | | | | | | | - Franck Verrecchia
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Université d'Angers, Nantes, France
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6
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Eraso P, Mazón MJ, Jiménez V, Pizarro-García P, Cuevas EP, Majuelos-Melguizo J, Morillo-Bernal J, Cano A, Portillo F. New Functions of Intracellular LOXL2: Modulation of RNA-Binding Proteins. Molecules 2023; 28:molecules28114433. [PMID: 37298909 DOI: 10.3390/molecules28114433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) was initially described as an extracellular enzyme involved in extracellular matrix remodeling. Nevertheless, numerous recent reports have implicated intracellular LOXL2 in a wide variety of processes that impact on gene transcription, development, differentiation, proliferation, migration, cell adhesion, and angiogenesis, suggesting multiple different functions for this protein. In addition, increasing knowledge about LOXL2 points to a role in several types of human cancer. Moreover, LOXL2 is able to induce the epithelial-to-mesenchymal transition (EMT) process-the first step in the metastatic cascade. To uncover the underlying mechanisms of the great variety of functions of intracellular LOXL2, we carried out an analysis of LOXL2's nuclear interactome. This study reveals the interaction of LOXL2 with numerous RNA-binding proteins (RBPs) involved in several aspects of RNA metabolism. Gene expression profile analysis of cells silenced for LOXL2, combined with in silico identification of RBPs' targets, points to six RBPs as candidates to be substrates of LOXL2's action, and that deserve a more mechanistic analysis in the future. The results presented here allow us to hypothesize novel LOXL2 functions that might help to comprehend its multifaceted role in the tumorigenic process.
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Affiliation(s)
- Pilar Eraso
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - María J Mazón
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Victoria Jiménez
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Patricia Pizarro-García
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Eva P Cuevas
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Jara Majuelos-Melguizo
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Jesús Morillo-Bernal
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Amparo Cano
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco Portillo
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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7
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Li X, Du Y, Chen X, Liu C. Emerging roles of O-glycosylation in regulating protein aggregation, phase separation, and functions. Curr Opin Chem Biol 2023; 75:102314. [PMID: 37156204 DOI: 10.1016/j.cbpa.2023.102314] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023]
Abstract
Protein O-glycosylation is widely identified in various proteins involved in diverse biological processes. Recent studies have demonstrated that O-glycosylation plays crucial and multifaceted roles in modulating protein amyloid aggregation and liquid-liquid phase separation (LLPS) under physiological conditions. Dysregulation of these processes is closely associated with human diseases such as neurodegenerative diseases (NDs) and cancers. In this review, we first summarize the distinct roles of O-glycosylation in regulating pathological aggregation of different amyloid proteins related to NDs and elaborate the underlying mechanisms of how O-glycosylation modulates protein aggregation kinetics, induces new aggregated structures, and mediates the pathogenesis of amyloid aggregates under diseased conditions. Furthermore, we introduce recent discoveries on O-GlcNAc-mediated regulation of synaptic LLPS and phase separation potency of low-complexity domain-enriched proteins. Finally, we identify challenges in future research and highlight the potential for developing new therapeutic strategies of NDs by targeting protein O-glycosylation.
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Affiliation(s)
- Xiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yifei Du
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
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8
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Selig EE, Bhura R, White MR, Akula S, Hoffman RD, Tovar CN, Xu X, Booth RE, Libich DS. Biochemical and biophysical characterization of the nucleic acid binding properties of the RNA/DNA binding protein EWS. Biopolymers 2023; 114:e23536. [PMID: 36929870 PMCID: PMC10233817 DOI: 10.1002/bip.23536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
EWS is a member of the FET family of RNA/DNA binding proteins that regulate crucial phases of nucleic acid metabolism. EWS comprises an N-terminal low-complexity domain (LCD) and a C-terminal RNA-binding domain (RBD). The RBD is further divided into three RG-rich regions, which flank an RNA-recognition motif (RRM) and a zinc finger (ZnF) domain. Recently, EWS was shown to regulate R-loops in Ewing sarcoma, a pediatric bone and soft-tissue cancer in which a chromosomal translocation fuses the N-terminal LCD of EWS to the C-terminal DNA binding domain of the transcription factor FLI1. Though EWS was shown to directly bind R-loops, the binding mechanism was not elucidated. In the current study, the RBD of EWS was divided into several constructs, which were subsequently assayed for binding to various nucleic acid structures expected to form at R-loops, including RNA stem-loops, DNA G-quadruplexes, and RNA:DNA hybrids. EWS interacted with all three nucleic acid structures with varying affinities and multiple domains contributed to binding each substrate. The RRM and RG2 region appear to bind nucleic acids promiscuously while the ZnF displayed more selectivity for single-stranded structures. With these results, the structural underpinnings of EWS recognition and binding of R-loops and other nucleic acid structures is better understood.
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Affiliation(s)
- Emily E Selig
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| | - Roohi Bhura
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Matthew R White
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Shivani Akula
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Renee D Hoffman
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Carmel N Tovar
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - Xiaoping Xu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
| | - Rachell E Booth
- Department of Chemistry and Biochemistry, University of the Incarnate Word, San Antonio, Texas, 78209, USA
| | - David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229, USA
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9
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Giannattasio T, Testa E, Palombo R, Chellini L, Franceschini F, Crevenna Á, Petkov PM, Paronetto MP, Barchi M. The RNA-binding protein FUS/TLS interacts with SPO11 and PRDM9 and localize at meiotic recombination hotspots. Cell Mol Life Sci 2023; 80:107. [PMID: 36967403 PMCID: PMC10040399 DOI: 10.1007/s00018-023-04744-5] [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: 01/24/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
In mammals, meiotic recombination is initiated by the introduction of DNA double strand breaks (DSBs) into narrow segments of the genome, defined as hotspots, which is carried out by the SPO11/TOPOVIBL complex. A major player in the specification of hotspots is PRDM9, a histone methyltransferase that, following sequence-specific DNA binding, generates trimethylation on lysine 4 (H3K4me3) and lysine 36 (H3K36me3) of histone H3, thus defining the hotspots. PRDM9 activity is key to successful meiosis, since in its absence DSBs are redirected to functional sites and synapsis between homologous chromosomes fails. One protein factor recently implicated in guiding PRDM9 activity at hotspots is EWS, a member of the FET family of proteins that also includes TAF15 and FUS/TLS. Here, we demonstrate that FUS/TLS partially colocalizes with PRDM9 on the meiotic chromosome axes, marked by the synaptonemal complex component SYCP3, and physically interacts with PRDM9. Furthermore, we show that FUS/TLS also interacts with REC114, one of the axis-bound SPO11-auxiliary factors essential for DSB formation. This finding suggests that FUS/TLS is a component of the protein complex that promotes the initiation of meiotic recombination. Accordingly, we document that FUS/TLS coimmunoprecipitates with SPO11 in vitro and in vivo. The interaction occurs with both SPO11β and SPO11α splice isoforms, which are believed to play distinct functions in the formation of DSBs in autosomes and male sex chromosomes, respectively. Finally, using chromatin immunoprecipitation experiments, we show that FUS/TLS is localized at H3K4me3-marked hotspots in autosomes and in the pseudo-autosomal region, the site of genetic exchange between the XY chromosomes.
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Affiliation(s)
- Teresa Giannattasio
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Erika Testa
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Ramona Palombo
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy
| | - Flavia Franceschini
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Álvaro Crevenna
- European Molecular Biology Laboratory, Neurobiology and Epigenetics Unit, Monterotondo, Italy
| | | | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy.
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135, Rome, Italy.
| | - Marco Barchi
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy.
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10
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Lv L, Huang B, Yi L, Zhang L. Long non-coding RNA SNHG4 enhances RNF14 mRNA stability to promote the progression of colorectal cancer by recruiting TAF15 protein. Apoptosis 2022; 28:414-431. [PMID: 36482019 DOI: 10.1007/s10495-022-01781-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
Abstract
SNHG4 is a lncRNA that was previously reported to promote colorectal cancer (CRC) progression via molecular sponge mechanism. Bioinformatic analysis suggested SNHG4 might scaffold TAF15 protein-RNF14 mRNA interaction. We aimed to investigate the mechanisms of potential SNHG4/TAF15/RNF14 axis in promoting CRC malignant phenotypes. Protein-RNA interaction was determined using RNA immunoprecipitation, pull-down and fluorescence in situ hybridization (FISH) combined immunofluorescence assays. Cell apoptosis rates were quantified using flow cytometry. CCK-8 and colony formation were adopted to determine cell proliferation. Wound healing and transwell assays were employed to assess cell migration and invasion, respectively. Xenograft tumor model was applied to assess the effects of SNHG4 on CRC tumorigenesis in vivo. SNHG4, TAF15 and RNF14 were up-regulated in CRC tissues. SNHG4 overexpression promoted cell proliferation, migration, invasion, and Wnt/β-catenin pathway activation in vitro, as well as tumor growth in vivo. The inhibited malignant phenotypes caused by SNHG4 knockdown were impeded by TAF15 or RNF14 overexpression. Mechanistically, SNHG4 recruited TAF15 protein and thus promoted the interaction between TAF15 protein and RNF14 mRNA, leading to the increased RNF14 mRNA stability. This in turn facilitated the Wnt/β-catenin signal transduction. SNHG4 enhanced RNF14 mRNA stability and activated the Wnt/β-catenin pathway to promote the progression of colorectal cancer by recruiting TAF15 protein.
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Affiliation(s)
- Lv Lv
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, NO.8, Wenchang Road, Liuzhou, 545006, Guangxi, People's Republic of China.
| | - Bojie Huang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Lu Yi
- Department of Dermatology & Venerology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Li Zhang
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, NO.8, Wenchang Road, Liuzhou, 545006, Guangxi, People's Republic of China
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11
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TIF1γ inhibits lung adenocarcinoma EMT and metastasis by interacting with the TAF15/TBP complex. Cell Rep 2022; 41:111513. [DOI: 10.1016/j.celrep.2022.111513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
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12
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Potential Involvement of ewsr1-w Gene in Ovarian Development of Chinese Tongue Sole, Cynoglossus semilaevis. Animals (Basel) 2022; 12:ani12192503. [PMID: 36230245 PMCID: PMC9559465 DOI: 10.3390/ani12192503] [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: 08/01/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Sexual dimorphism is a phenomenon commonly existing in animals. Chinese tongue sole Cynoglossus semilaevis is an economical marine fish with obvious female-biased size dimorphism. So, it is important to explore the molecular mechanism beyond gonadal development for sex control in aquaculture industry. RNA-binding protein Ewing Sarcoma protein-like (ewsr1) gene is important for mouse gonadal development and reproduction, however there are limited studies on this gene in teleost. In this study, two ewsr1 genes were cloned and characterized from C. semilaevis. The ewsr1-w gene, located in W chromosomes, showed female-biased expression during C. semilaevis gonadal development. In addition, knock-down effect and transcriptional regulation of Cs-ewsr1-w further suggested its essential role in ovarian development. This study broadened our understanding on ewsr1 function in teleost, and provided genetic resources for the further development of sex control breeding techniques in C. semilaevis aquaculture. Abstract Ewsr1 encodes a protein that acts as a multifunctional molecule in a variety of cellular processes. The full-length of Cs-ewsr1-w and Cs-ewsr1-z were cloned in Chinese tongue sole (Cynoglossus semilaevis). The open reading frame (ORF) of Cs-ewsr1-w was 1,767 bp that encoded 589 amino acids, while Cs-ewsr1-z was 1,794 bp that encoded 598 amino acids. Real-time PCR assays showed that Cs-ewsr1-w exhibited significant female-biased expression and could be hardly detected in male. It has the most abundant expression in ovaries among eight healthy tissues. Its expression in ovary increased gradually from 90 d to 3 y with C. semilaevis ovarian development and reached the peak at 3 y. After Cs-ewsr1-w knockdown with siRNA interference, several genes related to gonadal development including foxl2, sox9b and pou5f1 were down-regulated in ovarian cell line, suggesting the possible participation of Cs-ewsr1-w in C. semilaevis ovarian development. The dual-luciferase reporter assay revealed that the -733/-154 bp Cs-ewsr1-w promoter fragment exhibited strong transcription activity human embryonic kidney (HEK) 293T cell line. The mutation of a MAF BZIP Transcription Factor K (Mafk) binding site located in this fragment suggested that transcription factor Mafk might play an important role in Cs-ewsr1-w basal transcription. Our results will provide clues on the gene expression level, transcriptional regulation and knock-down effect of ewsr1 gene during ovarian development in teleost.
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13
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Verdile V, Svetoni F, La Rosa P, Ferrante G, Cesari E, Sette C, Paronetto M. EWS splicing regulation contributes to balancing Foxp1 isoforms required for neuronal differentiation. Nucleic Acids Res 2022; 50:3362-3378. [PMID: 35253879 PMCID: PMC8989529 DOI: 10.1093/nar/gkac154] [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: 07/26/2021] [Revised: 01/27/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is a key regulatory process underlying the amplification of genomic information and the expansion of proteomic diversity, particularly in brain. Here, we identify the Ewing sarcoma protein (EWS) as a new player of alternative splicing regulation during neuronal differentiation. Knockdown of EWS in neuronal progenitor cells leads to premature differentiation. Transcriptome profiling of EWS-depleted cells revealed global changes in splicing regulation. Bioinformatic analyses and biochemical experiments demonstrated that EWS regulates alternative exons in a position-dependent fashion. Notably, several EWS-regulated splicing events are physiologically modulated during neuronal differentiation and EWS depletion in neuronal precursors anticipates the splicing-pattern of mature neurons. Among other targets, we found that EWS controls the alternative splicing of the forkhead family transcription factor FOXP1, a pivotal transcriptional regulator of neuronal differentiation, possibly contributing to the switch of gene expression underlying the neuronal differentiation program.
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Affiliation(s)
- Veronica Verdile
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Francesca Svetoni
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Piergiorgio La Rosa
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Gabriele Ferrante
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
| | - Eleonora Cesari
- GSTEP-Organoids Core Facility, IRCCS Fondazione Policlinico Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- GSTEP-Organoids Core Facility, IRCCS Fondazione Policlinico Agostino Gemelli, 00168 Rome, Italy
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, 00168 Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143 Rome, Italy
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14
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Zhao L, Guo Y, Guo Y, Ji X, Fan D, Chen C, Yuan W, Sun Z, Ji Z. Effect and mechanism of circRNAs in tumor angiogenesis and clinical application. Int J Cancer 2021; 150:1223-1232. [PMID: 34724210 DOI: 10.1002/ijc.33863] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022]
Abstract
Tumor blood vessels provide oxygen and necessary nutrients for the tumor, which provides the basis for tumor metastasis. Therefore, tumor angiogenesis plays a very important role in tumor growth and metastasis. In contrast to linear RNAs, circRNAs represent a type of closed-loop RNA with diverse biological functions. At the same time, circRNAs have strong stability, timeliness, tissue specificity and disease specificity. With the rapid development of next-generation sequencing and bioinformatics, there have been an increasing number of studies on circRNAs. At present, a large number of studies have reported that circRNAs regulate tumor growth, invasion, metastasis, tumor metabolism, tumor immunity and other biological functions. Increasing evidence has shown that circRNAs also play an important role in tumor angiogenesis. In this review, we briefly introduced tumor angiogenesis and circRNAs and outlined the main ways that circRNAs affect tumor angiogenesis from multiple aspects. Finally, we further explored the potential clinical application value of circRNAs in the context of tumor angiogenesis.
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Affiliation(s)
- Luyang Zhao
- BGI College, Zhengzhou University, Zhengzhou, Henan, China.,Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuying Guo
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yaxin Guo
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan, China.,Department of Basic Medical, Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang Ji
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Dandan Fan
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Chen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenyu Ji
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan, China.,Department of Basic Medical, Academy of Medical Sciences of Zhengzhou University, Zhengzhou, Henan, China
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15
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Choi HJ, Lee JY, Cha SJ, Han YJ, Yoon JH, Kim HJ, Kim K. FUS-induced neurotoxicity is prevented by inhibiting GSK-3β in a drosophila model of amyotrophic lateral sclerosis. Hum Mol Genet 2021; 31:850-862. [PMID: 34605896 DOI: 10.1093/hmg/ddab290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 09/12/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS)-linked mutations in fused in sarcoma (FUS) lead to the formation of cytoplasmic aggregates in neurons. They are believed play a critical role in the pathogenesis of FUS-associated ALS. Therefore, the clearance and degradation of cytoplasmic FUS aggregates in neurons may be considered a therapeutic strategy for ALS. However, the molecular pathogenic mechanisms behind FUS-associated ALS remain poorly understood. Here, we report GSK-3β as a potential modulator of FUS-induced toxicity. We demonstrated that RNAi-mediated knockdown of Drosophila ortholog Shaggy in FUS-expressing flies suppresses defective phenotypes, including retinal degeneration, motor defects, motor neuron degeneration, and mitochondrial dysfunction. Furthermore, we found that cytoplasmic FUS aggregates were significantly reduced by Shaggy knockdown. In addition, we found that the levels of FUS proteins were significantly reduced by co-overexpression of Slimb, a F-box protein, in FUS-expressing flies, indicating that Slimb is critical for the suppressive effect of Shaggy/GSK-3β inhibition on FUS-induced toxicity in Drosophila. These findings revealed a novel mechanism of neuronal protective effect through SCFSlimb-mediated FUS degradation via GSK-3β inhibition, and provided in vivo evidence of the potential for modulating FUS-induced ALS progression using GSK-3β inhibitors.
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Affiliation(s)
- Hyun-Jun Choi
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea.,Department of Integrated Biomedical Sciences, Soonchunhyang University, Cheonan 31151, Korea
| | - Ji Young Lee
- Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Korea
| | - Sun Joo Cha
- Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea
| | - Yeo Jeong Han
- Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Korea.,Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea
| | - Ja Hoon Yoon
- Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Korea
| | - Hyung-Jun Kim
- Dementia Research Group, Korea Brain Research Institute (KBRI), Daegu 41068, Korea
| | - Kiyoung Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Korea.,Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea
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16
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Liu Q, Guo L, Qi H, Lou M, Wang R, Hai B, Xu K, Zhu L, Ding Y, Li C, Xie L, Shen J, Xiang X, Shao J. A MYBL2 complex for RRM2 transactivation and the synthetic effect of MYBL2 knockdown with WEE1 inhibition against colorectal cancer. Cell Death Dis 2021; 12:683. [PMID: 34234118 PMCID: PMC8263627 DOI: 10.1038/s41419-021-03969-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022]
Abstract
Ribonucleotide reductase (RR) is a unique enzyme for the reduction of NDPs to dNDPs, the building blocks for DNA synthesis and thus essential for cell proliferation. Pan-cancer profiling studies showed that RRM2, the small subunit M2 of RR, is abnormally overexpressed in multiple types of cancers; however, the underlying regulatory mechanisms in cancers are still unclear. In this study, through searching in cancer-omics databases and immunohistochemistry validation with clinical samples, we showed that the expression of MYBL2, a key oncogenic transcriptional factor, was significantly upregulated correlatively with RRM2 in colorectal cancer (CRC). Ectopic expression and knockdown experiments indicated that MYBL2 was essential for CRC cell proliferation, DNA synthesis, and cell cycle progression in an RRM2-dependent manner. Mechanistically, MYBL2 directly bound to the promoter of RRM2 gene and promoted its transcription during S-phase together with TAF15 and MuvB components. Notably, knockdown of MYBL2 sensitized CRC cells to treatment with MK-1775, a clinical trial drug for inhibition of WEE1, which is involved in a degradation pathway of RRM2. Finally, mouse xenograft experiments showed that the combined suppression of MYBL2 and WEE1 synergistically inhibited CRC growth with a low systemic toxicity in vivo. Therefore, we propose a new regulatory mechanism for RRM2 transcription for CRC proliferation, in which MYBL2 functions by constituting a dynamic S-phase transcription complex following the G1/early S-phase E2Fs complex. Doubly targeting the transcription and degradation machines of RRM2 could produce a synthetic inhibitory effect on RRM2 level with a novel potential for CRC treatment.
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Affiliation(s)
- Qian Liu
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijuan Guo
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongyan Qi
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Meng Lou
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Rui Wang
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Boning Hai
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kailun Xu
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijun Zhu
- Key Laboratory of Pancreatic Disease of Zhejiang Province, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Pancreatic Disease of Zhejiang Province, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chen Li
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingdan Xie
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Shen
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueping Xiang
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jimin Shao
- Department of Pathology & Pathophysiology, and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang University Cancer Center, Key Laboratory of Disease Proteomics of Zhejiang Province, Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China.
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17
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Amyotrophic Lateral Sclerosis: Molecular Mechanisms, Biomarkers, and Therapeutic Strategies. Antioxidants (Basel) 2021; 10:antiox10071012. [PMID: 34202494 PMCID: PMC8300638 DOI: 10.3390/antiox10071012] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/16/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with the progressive loss of motor neurons, leading to a fatal paralysis. According to whether there is a family history of ALS, ALS can be roughly divided into two types: familial and sporadic. Despite decades of research, the pathogenesis of ALS is still unelucidated. To this end, we review the recent progress of ALS pathogenesis, biomarkers, and treatment strategies, mainly discuss the roles of immune disorders, redox imbalance, autophagy dysfunction, and disordered iron homeostasis in the pathogenesis of ALS, and introduce the effects of RNA binding proteins, ALS-related genes, and non-coding RNA as biomarkers on ALS. In addition, we also mention other ALS biomarkers such as serum uric acid (UA), cardiolipin (CL), chitotriosidase (CHIT1), and neurofilament light chain (NFL). Finally, we discuss the drug therapy, gene therapy, immunotherapy, and stem cell-exosomal therapy for ALS, attempting to find new therapeutic targets and strategies. A challenge is to study the various mechanisms of ALS as a syndrome. Biomarkers that have been widely explored are indispensable for the diagnosis, treatment, and prevention of ALS. Moreover, the development of new genes and targets is an urgent task in this field.
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18
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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19
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Martónez-Ferníndez V, Navarro F. Rpb5, a subunit shared by eukaryotic RNA polymerases, cooperates with prefoldin-like Bud27/URI. AIMS GENETICS 2021. [DOI: 10.3934/genet.2018.1.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractRpb5 is one of the five common subunits to all eukaryotic RNA polymerases, which is conserved in archaea, but not in bacteria. Among these common subunits, it is the only one that is not interchangeable between yeasts and humans, and accounts for the functional incompatibility of yeast and human subunits. Rpb5 has been proposed to contribute to the gene-specific activation of RNA pol II, notably during the infectious cycle of the hepatitis B virus, and also to participate in general transcription mediated by all eukaryotic RNA pol. The structural analysis of Rpb5 and its interaction with different transcription factors, regulators and DNA, accounts for Rpb5 being necessary to maintain the correct conformation of the shelf module of RNA pol II, which favors the proper organization of the transcription bubble and the clamp closure of the enzyme.In this work we provide details about subunit Rpb5's structure, conservation and the role it plays in transcription regulation by analyzing the different interactions with several factors, as well as its participation in the assembly of the three RNA pols, in cooperation with prefoldin-like Bud27/URI.
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Affiliation(s)
- Veránica Martónez-Ferníndez
- Department of Experimental Biology, Faculty of Experimental Sciences, University of JaÉn, Paraje de las Lagunillas, s/n, 23071, JaÉn, Spain
| | - Francisco Navarro
- Department of Experimental Biology, Faculty of Experimental Sciences, University of JaÉn, Paraje de las Lagunillas, s/n, 23071, JaÉn, Spain
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20
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Martin JC, Hoegel TJ, Lynch ML, Woloszynska A, Melendy T, Ohm JE. Exploiting Replication Stress as a Novel Therapeutic Intervention. Mol Cancer Res 2020; 19:192-206. [PMID: 33020173 DOI: 10.1158/1541-7786.mcr-20-0651] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/01/2020] [Accepted: 09/29/2020] [Indexed: 11/16/2022]
Abstract
Ewing sarcoma is an aggressive pediatric tumor of the bone and soft tissue. The current standard of care is radiation and chemotherapy, and patients generally lack targeted therapies. One of the defining molecular features of this tumor type is the presence of significantly elevated levels of replication stress as compared with both normal cells and many other types of cancers, but the source of this stress is poorly understood. Tumors that harbor elevated levels of replication stress rely on the replication stress and DNA damage response pathways to retain viability. Understanding the source of the replication stress in Ewing sarcoma may reveal novel therapeutic targets. Ewing sarcomagenesis is complex, and in this review, we discuss the current state of our knowledge regarding elevated replication stress and the DNA damage response in Ewing sarcoma, one contributor to the disease process. We will also describe how these pathways are being successfully targeted therapeutically in other tumor types, and discuss possible novel, evidence-based therapeutic interventions in Ewing sarcoma. We hope that this consolidation will spark investigations that uncover new therapeutic targets and lead to the development of better treatment options for patients with Ewing sarcoma. IMPLICATIONS: This review uncovers new therapeutic targets in Ewing sarcoma and highlights replication stress as an exploitable vulnerability across multiple cancers.
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Affiliation(s)
- Jeffrey C Martin
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Tamara J Hoegel
- Department of Pediatric Hematology and Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Miranda L Lynch
- Hauptman-Woodward Medical Research Institute, Buffalo, New York
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Thomas Melendy
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, New York
| | - Joyce E Ohm
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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21
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Primary Intracranial Mesenchymal Tumor with EWSR1-CREM Gene Fusion: A Case Report and Literature Review. World Neurosurg 2020; 142:318-324. [PMID: 32668333 DOI: 10.1016/j.wneu.2020.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/29/2023]
Abstract
BACKGROUND The prevalence of gene translocation in some mesenchymal tumors can be used as highly specific molecular diagnostic markers in clinic and pathology. EWSR1 is a partner gene in a large, diverse range of mesenchymal tumors. CASE DESCRIPTION This paper describes the case of a 31-year-old man who was diagnosed with a primary intracranial mesenchymal tumor with EWSR1-CREM gene fusion and eventually returned to a normal live with no signs of tumor recurrence or metastasis after treatment, including surgery therapy, radiotherapy, and 6 cycles of vincristine-doxorubicin-cyclophosphamide chemotherapy, even though the classification and grade of the tumor are still controversial. CONCLUSIONS This case is a novel entity of intracranial mesenchymal neoplasm with EWSR1-CREM gene fusion which was confirmed by histopathology, molecular pathology, and next-generation sequencing (NGS). The literature review shows only 5 cases of intracranial tumor harboring EWSR1-CREM gene fusion with similar features. With the further application of molecular pathology and NGS in clinical practice, there will be more intracranial mesenchymal tumor cases with EWSR1-CREM gene fusion found in the future, which may lead to further understanding of the diagnosis and clinical features of this neoplasm.
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22
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Singh AK, Kapoor V, Thotala D, Hallahan DE. TAF15 contributes to the radiation-inducible stress response in cancer. Oncotarget 2020; 11:2647-2659. [PMID: 32676166 PMCID: PMC7343639 DOI: 10.18632/oncotarget.27663] [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: 02/19/2020] [Accepted: 06/15/2020] [Indexed: 12/28/2022] Open
Abstract
Resistance to radiation therapy is a significant problem in the treatment of non-small cell lung cancer (NSCLC). There is an unmet need to discover new molecular targets for drug development in combination with standard of care cancer therapy. We found that TAF15 was radiation-inducible using phage-displayed peptide libraries. In this study, we report that overexpression of TAF15 is correlated with worsened survival in NSCLC patients. Radiation treatment led to surface induction of TAF15 in vitro and in vivo. We genetically silenced TAF15 which led to a significant reduction in proliferation of NSCLC cells. Cells depleted of TAF15 exhibited cell cycle arrest and enhanced apoptosis through activation and accumulation of p53. In combination with radiation, TAF15 knockdown led to a significant reduction in the surviving fraction of NSCLC cell lines. To determine the importance of TAF15 surface expression, we targeted TAF15 with an antibody. In combination with radiation, the anti-TAF15 antibody led to a reduction in the surviving fraction of cancer cells. These studies show that TAF15 is a radiation-inducible molecular target that is accessible to anti-cancer antibodies and enhances cell viability in response to radiation.
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Affiliation(s)
- Abhay Kumar Singh
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dinesh Thotala
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dennis E Hallahan
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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23
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Bourefis AR, Campanari ML, Buee-Scherrer V, Kabashi E. Functional characterization of a FUS mutant zebrafish line as a novel genetic model for ALS. Neurobiol Dis 2020; 142:104935. [PMID: 32380281 DOI: 10.1016/j.nbd.2020.104935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/22/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in Fused in sarcoma (FUS), an RNA-binding protein, are known to cause Amyotrophic Lateral Sclerosis (ALS). However, molecular mechanisms due to loss of FUS function remain unclear and controversial. Here, we report the characterization and phenotypic analysis of a deletion mutant of the unique FUS orthologue in zebrafish where Fus protein levels are depleted. The homozygous mutants displayed a reduced lifespan as well as impaired motor abilities associated with specific cellular deficits, including decreased motor neurons length and neuromuscular junctions (NMJ) fragmentation. Furthermore, we demonstrate that these cellular impairments are linked to the misregulation of mRNA expression of acetylcholine receptor (AChR) subunits and histone deacetylase 4, markers of denervation and reinnervation processes observed in ALS patients. In addition, fus loss of function alters tau transcripts favoring the expression of small tau isoforms. Overall, this new animal model extends our knowledge on FUS and supports the relevance of FUS loss of function in ALS physiopathology.
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Affiliation(s)
- Annis-Rayan Bourefis
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
| | - Maria-Letizia Campanari
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
| | | | - Edor Kabashi
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France.
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24
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Gipson AB, Giloteaux L, Hanson MR, Bentolila S. Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1. PLANTS 2020; 9:plants9030307. [PMID: 32121603 PMCID: PMC7154859 DOI: 10.3390/plants9030307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023]
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins.
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25
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Hock EM, Maniecka Z, Hruska-Plochan M, Reber S, Laferrière F, Sahadevan M K S, Ederle H, Gittings L, Pelkmans L, Dupuis L, Lashley T, Ruepp MD, Dormann D, Polymenidou M. Hypertonic Stress Causes Cytoplasmic Translocation of Neuronal, but Not Astrocytic, FUS due to Impaired Transportin Function. Cell Rep 2020; 24:987-1000.e7. [PMID: 30044993 DOI: 10.1016/j.celrep.2018.06.094] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/14/2018] [Accepted: 06/22/2018] [Indexed: 12/20/2022] Open
Abstract
The primarily nuclear RNA-binding protein FUS (fused in sarcoma) forms pathological cytoplasmic inclusions in a subset of early-onset amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients. In response to cellular stress, FUS is recruited to cytoplasmic stress granules, which are hypothesized to act as precursors of pathological inclusions. We monitored the stress-induced nucleocytoplasmic shuttling of endogenous FUS in an ex vivo mouse CNS model and human neural networks. We found that hyperosmolar, but not oxidative, stress induced robust cytoplasmic translocation of neuronal FUS, with transient nuclear clearance and loss of function. Surprisingly, this reaction is independent of stress granule formation and the molecular pathways activated by hyperosmolarity. Instead, it represents a mechanism mediated by cytoplasmic redistribution of Transportin 1/2 and is potentiated by transcriptional inhibition. Importantly, astrocytes, which remain unaffected in ALS/FTD-FUS, are spared from this stress reaction that may signify the initial event in the development of FUS pathology.
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Affiliation(s)
- Eva-Maria Hock
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Zuzanna Maniecka
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Marian Hruska-Plochan
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefan Reber
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Florent Laferrière
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Sonu Sahadevan M K
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Helena Ederle
- BioMedical Center (BMC), Ludwig-Maximiians-University Munich, 82152 Planegg-Martinsried, Germany; Graduate School of Systemic Neurosciences (GSN), 82152 Planegg-Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Lauren Gittings
- Queen Square Brain Bank for Neurological Diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 1PJ, UK
| | - Lucas Pelkmans
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Luc Dupuis
- Faculty of Medicine, INSERM UMR-S1118 and Fédération de Médecine Translationnelle, Université de Strasbourg, Strasbourg, France
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Diseases, Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 1PJ, UK
| | - Marc-David Ruepp
- UK Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Dorothee Dormann
- BioMedical Center (BMC), Ludwig-Maximiians-University Munich, 82152 Planegg-Martinsried, Germany; Graduate School of Systemic Neurosciences (GSN), 82152 Planegg-Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Magdalini Polymenidou
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland.
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26
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Shotwell CR, Cleary JD, Berglund JA. The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1573. [PMID: 31680457 DOI: 10.1002/wrna.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/21/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Eukaroytic RNA-binding proteins (RBPs) recognize and process RNAs through recognition of their sequence motifs via RNA-binding domains (RBDs). RBPs usually consist of one or more RBDs and can include additional functional domains that modify or cleave RNA. Engineered RBPs have been used to answer basic biology questions, control gene expression, locate viral RNA in vivo, as well as many other tasks. Given the growing number of diseases associated with RNA and RBPs, engineered RBPs also have the potential to serve as therapeutics. This review provides an in depth description of recent advances in engineered RBPs and discusses opportunities and challenges in the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Methods > RNA Nanotechnology RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Carl R Shotwell
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida
| | - John D Cleary
- RNA Institute, University at Albany, Albany, New York
| | - J Andrew Berglund
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York
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27
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Krasnopolsky S, Marom L, Victor RA, Kuzmina A, Schwartz JC, Fujinaga K, Taube R. Fused in sarcoma silences HIV gene transcription and maintains viral latency through suppressing AFF4 gene activation. Retrovirology 2019; 16:16. [PMID: 31238957 PMCID: PMC6593535 DOI: 10.1186/s12977-019-0478-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Background The human immunodeficiency virus (HIV) cell reservoir is currently a main obstacle towards complete eradication of the virus. This infected pool is refractory to anti-viral therapy and harbors integrated proviruses that are transcriptionally repressed but replication competent. As transcription silencing is key for establishing the HIV reservoir, significant efforts have been made to understand the mechanism that regulate HIV gene transcription, and the role of the elongation machinery in promoting this step. However, while the role of the super elongation complex (SEC) in enhancing transcription activation of HIV is well established, the function of SEC in modulating viral latency is less defined and its cell partners are yet to be identified. Results In this study we identify fused in sarcoma (FUS) as a partner of AFF4 in cells. FUS inhibits the activation of HIV transcription by AFF4 and ELL2, and silences overall HIV gene transcription. Concordantly, depletion of FUS elevates the occupancy of AFF4 and Cdk9 on the viral promoter and activates HIV gene transcription. Live cell imaging demonstrates that FUS co-localizes with AFF4 within nuclear punctuated condensates, which are disrupted upon treating cells with aliphatic alcohol. In HIV infected cells, knockout of FUS delays the gradual entry of HIV into latency, and similarly promotes viral activation in a T cell latency model that is treated with JQ1. Finally, effects of FUS on HIV gene transcription are also exhibited genome wide, where FUS mainly occupies gene promoters at transcription starting sites, while its knockdown leads to an increase in AFF4 and Cdk9 occupancy on gene promoters of FUS affected genes. Conclusions Towards eliminating the HIV infected reservoir, understanding the mechanisms by which the virus persists in the face of therapy is important. Our observations show that FUS regulates both HIV and global gene transcription and modulates viral latency, thus can potentially serve as a target for future therapy that sets to reactivate HIV from its latent state. Electronic supplementary material The online version of this article (10.1186/s12977-019-0478-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simona Krasnopolsky
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Lital Marom
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Rachel A Victor
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Alona Kuzmina
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel
| | - Jacob C Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Koh Fujinaga
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel.
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28
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Ouyang H, Zhang K, Fox-Walsh K, Yang Y, Zhang C, Huang J, Li H, Zhou Y, Fu XD. The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. Nucleic Acids Res 2019; 45:12481-12495. [PMID: 30053258 PMCID: PMC5716145 DOI: 10.1093/nar/gkx912] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/27/2017] [Indexed: 12/13/2022] Open
Abstract
The Ewing Sarcoma protein (EWS) is a multifaceted RNA binding protein (RBP) with established roles in transcription, pre-mRNA processing and DNA damage response. By generating high quality EWS-RNA interactome, we uncovered its specific and prevalent interaction with a large subset of primary microRNAs (pri-miRNAs) in mammalian cells. Knockdown of EWS reduced, whereas overexpression enhanced, the expression of its target miRNAs. Biochemical analysis revealed that multiple elements in target pri-miRNAs, including the sequences flanking the stem-loop region, contributed to high affinity EWS binding and sequence swap experiments between target and non-target demonstrated that the flanking sequences provided the specificity for enhanced pri-miRNA processing by the Microprocessor Drosha/DGCR8. Interestingly, while repressing Drosha expression, as reported earlier, we found that EWS was able to enhance the recruitment of Drosha to chromatin. Together, these findings suggest that EWS may positively and negatively regulate miRNA biogenesis via distinct mechanisms, thus providing a new foundation to understand the function of EWS in development and disease.
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Affiliation(s)
- Huiwu Ouyang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kristi Fox-Walsh
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yang Yang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Huang
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yu Zhou
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Institue of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang-Dong Fu
- State Key Laboratory of Virology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
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29
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Abstract
This chapter describes the main neuropathological features of the most common age associated neurodegenerative diseases including Alzheimer's disease, Lewy body diseases, vascular dementia and the various types of frontotemporal lobar degeneration. In addition, the more recent concepts of primary age-related tauopathy and ageing-related tau astrogliopathy as well as chronic traumatic encephalopathy are briefly described. One section is dedicated to cerebral multi-morbidity as it is becoming increasingly clear that the old brain is characterised by the presence of multiple pathologies (to varying extent) rather than by one single, disease specific pathology alone. The main aim of this chapter is to inform the reader about the neuropathological basics of age associated neurodegenerative diseases as we feel this is crucial to meaningfully interpret the vast literature that is published in the broad field of dementia research.
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Affiliation(s)
- Lauren Walker
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Kirsty E McAleese
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Erskine
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Johannes Attems
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.
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30
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Kang J, Lim L, Lu Y, Song J. A unified mechanism for LLPS of ALS/FTLD-causing FUS as well as its modulation by ATP and oligonucleic acids. PLoS Biol 2019; 17:e3000327. [PMID: 31188823 PMCID: PMC6590835 DOI: 10.1371/journal.pbio.3000327] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 06/24/2019] [Accepted: 05/30/2019] [Indexed: 12/22/2022] Open
Abstract
526-residue Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) for its functions, which can further transit into pathological aggregation. ATP and nucleic acids, the universal cellular actors, were shown to modulate LLPS of FUS in a unique manner: enhancement and then dissolution. Currently, the driving force for LLPS of FUS is still under debate, while the mechanism for the modulation remains completely undefined. Here, by NMR and differential interference contrast (DIC) imaging, we characterized conformations, dynamics, and LLPS of FUS and its domains and subsequently their molecular interactions with oligonucleic acids, including one RNA and two single-stranded DNA (ssDNA) molecules, as well as ATP, Adenosine monophosphate (AMP), and adenosine. The results reveal 1) both a prion-like domain (PLD) rich in Tyr but absent of Arg/Lys and a C-terminal domain (CTD) abundant in Arg/Lys fail to phase separate. By contrast, the entire N-terminal domain (NTD) containing the PLD and an Arg-Gly (RG)-rich region efficiently phase separate, indicating that the π-cation interaction is the major driving force; 2) despite manifesting distinctive NMR observations, ATP has been characterized to modulate LLPS by specific binding as oligonucleic acids but with much lower affinity. Our results together establish a unified mechanism in which the π-cation interaction acts as the major driving force for LLPS of FUS and also serves as the target for modulation by ATP and oligonucleic acids through specific binding. This mechanism predicts that a myriad of proteins unrelated to RNA-binding proteins (RBPs) but with Arg/Lys-rich disordered regions could be modulated by ATP and nucleic acids, thus rationalizing the pathological association of Amyotrophic lateral sclerosis (ALS)-causing C9ORF72 dipeptides with any nucleic acids to manifest cytotoxicity.
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Affiliation(s)
- Jian Kang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
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31
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Abstract
Among the various genes that can be rearranged in soft tissue neoplasms associated with nonrandom chromosomal translocations, EWSR1 is the most frequent one to partner with other genes to generate recurrent fusion genes. This leads to a spectrum of clinically and pathologically diverse mesenchymal and nonmesenchymal neoplasms, variably manifesting as small round cell, spindle cell, clear cell or adipocytic tumors, or tumors with distinctive myxoid stroma. This review summarizes the growing list of mesenchymal neoplasms that are associated with EWSR1 gene rearrangements.
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Affiliation(s)
- Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK.
| | - Cyril Fisher
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital NHS Foundation Trust, Robert Aitken Institute for Clinical Research, University of Birmingham, Birmingham B15 2TT, UK
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32
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Chen C, Ding X, Akram N, Xue S, Luo SZ. Fused in Sarcoma: Properties, Self-Assembly and Correlation with Neurodegenerative Diseases. Molecules 2019; 24:molecules24081622. [PMID: 31022909 PMCID: PMC6514960 DOI: 10.3390/molecules24081622] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Fused in sarcoma (FUS) is a DNA/RNA binding protein that is involved in RNA metabolism and DNA repair. Numerous reports have demonstrated by pathological and genetic analysis that FUS is associated with a variety of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and polyglutamine diseases. Traditionally, the fibrillar aggregation of FUS was considered to be the cause of those diseases, especially via its prion-like domains (PrLDs), which are rich in glutamine and asparagine residues. Lately, a nonfibrillar self-assembling phenomenon, liquid–liquid phase separation (LLPS), was observed in FUS, and studies of its functions, mechanism, and mutual transformation with pathogenic amyloid have been emerging. This review summarizes recent studies on FUS self-assembling, including both aggregation and LLPS as well as their relationship with the pathology of ALS, FTLD, and other neurodegenerative diseases.
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Affiliation(s)
- Chen Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiufang Ding
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Nimrah Akram
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Song Xue
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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33
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Verdile V, De Paola E, Paronetto MP. Aberrant Phase Transitions: Side Effects and Novel Therapeutic Strategies in Human Disease. Front Genet 2019; 10:173. [PMID: 30967892 PMCID: PMC6440380 DOI: 10.3389/fgene.2019.00173] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
Phase separation is a physiological process occurring spontaneously when single-phase molecular complexes separate in two phases, a concentrated phase and a more diluted one. Eukaryotic cells employ phase transition strategies to promote the formation of intracellular territories not delimited by membranes with increased local RNA concentration, such as nucleolus, paraspeckles, P granules, Cajal bodies, P-bodies, and stress granules. These organelles contain both proteins and coding and non-coding RNAs and play important roles in different steps of the regulation of gene expression and in cellular signaling. Recently, it has been shown that most human RNA-binding proteins (RBPs) contain at least one low-complexity domain, called prion-like domain (PrLD), because proteins harboring them display aggregation properties like prion proteins. PrLDs support RBP function and contribute to liquid–liquid phase transitions that drive ribonucleoprotein granule assembly, but also render RBPs prone to misfolding by promoting the formation of pathological aggregates that lead to toxicity in specific cell types. Protein–protein and protein-RNA interactions within the separated phase can enhance the transition of RBPs into solid aberrant aggregates, thus causing diseases. In this review, we highlight the role of phase transition in human disease such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and in cancer. Moreover, we discuss novel therapeutic strategies focused to control phase transitions by preventing the conversion into aberrant aggregates. In this regard, the stimulation of chaperone machinery to disassemble membrane-less organelles, the induction of pathways that could inhibit aberrant phase separation, and the development of antisense oligonucleotides (ASOs) to knockdown RNAs could be evaluated as novel therapeutic strategies for the treatment of those human diseases characterized by aberrant phase transition aggregates.
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Affiliation(s)
- Veronica Verdile
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
| | - Elisa De Paola
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
| | - Maria Paola Paronetto
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
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34
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Martinez-Macias MI, Moore DA, Green RL, Gomez-Herreros F, Naumann M, Hermann A, Van Damme P, Hafezparast M, Caldecott KW. FUS (fused in sarcoma) is a component of the cellular response to topoisomerase I-induced DNA breakage and transcriptional stress. Life Sci Alliance 2019; 2:2/2/e201800222. [PMID: 30808650 PMCID: PMC6391683 DOI: 10.26508/lsa.201800222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
Abstract
This work shows that the ALS-associated protein FUS is a component of the cellular response to transcriptional stress induced by topoisomerase I–induced DNA breakage, thereby accumulating at sites of nucleolar rRNA synthesis. FUS (fused in sarcoma) plays a key role in several steps of RNA metabolism, and dominant mutations in this protein are associated with neurodegenerative diseases. Here, we show that FUS is a component of the cellular response to topoisomerase I (TOP1)–induced DNA breakage; relocalising to the nucleolus in response to RNA polymerase II (Pol II) stalling at sites of TOP1-induced DNA breaks. This relocalisation is rapid and dynamic, reversing following the removal of TOP1-induced breaks and coinciding with the recovery of global transcription. Importantly, FUS relocalisation following TOP1-induced DNA breakage is associated with increased FUS binding at sites of RNA polymerase I transcription in ribosomal DNA and reduced FUS binding at sites of RNA Pol II transcription, suggesting that FUS relocates from sites of stalled RNA Pol II either to regulate pre-mRNA processing during transcriptional stress or to modulate ribosomal RNA biogenesis. Importantly, FUS-mutant patient fibroblasts are hypersensitive to TOP1-induced DNA breakage, highlighting the possible relevance of these findings to neurodegeneration.
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Affiliation(s)
| | - Duncan Aq Moore
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Ryan L Green
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Fernando Gomez-Herreros
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, England.,Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocio-Centro Superior de Investigaciones Cientificas-Universidad de Sevilla, Seville, Spain
| | - Marcel Naumann
- Department of Neurology, Technische Universität Dresden, and German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Andreas Hermann
- Department of Neurology, Technische Universität Dresden, and German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany.,Center for Transdisciplinary Neurosciences Rostock, University Medical Center Rostock, University of Rostock, Rostock, Germany.,Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | | | - Majid Hafezparast
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, England
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35
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Wells C, Brennan SE, Keon M, Saksena NK. Prionoid Proteins in the Pathogenesis of Neurodegenerative Diseases. Front Mol Neurosci 2019; 12:271. [PMID: 31780895 PMCID: PMC6861308 DOI: 10.3389/fnmol.2019.00271] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
There is a growing body of evidence that prionoid protein behaviors are a core element of neurodegenerative diseases (NDs) that afflict humans. Common elements in pathogenesis, pathological effects and protein-level behaviors exist between Alzheimer's Disease (AD), Parkinson's Disease (PD), Huntington's Disease (HD) and Amyotrophic Lateral Sclerosis (ALS). These extend beyond the affected neurons to glial cells and processes. This results in a complicated system of disease progression, which often takes advantage of protective processes to promote the propagation of pathological protein aggregates. This review article provides a current snapshot of knowledge on these proteins and their intrinsic role in the pathogenesis and disease progression seen across NDs.
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36
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Riancho J, Gonzalo I, Ruiz-Soto M, Berciano J. Why do motor neurons degenerate? Actualisation in the pathogenesis of amyotrophic lateral sclerosis. NEUROLOGÍA (ENGLISH EDITION) 2019. [DOI: 10.1016/j.nrleng.2015.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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Riancho J, Gonzalo I, Ruiz-Soto M, Berciano J. ¿Por qué degeneran las motoneuronas? Actualización en la patogenia de la esclerosis lateral amiotrófica. Neurologia 2019; 34:27-37. [DOI: 10.1016/j.nrl.2015.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/06/2015] [Indexed: 12/11/2022] Open
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38
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Di Gregorio SE, Duennwald ML. ALS Yeast Models-Past Success Stories and New Opportunities. Front Mol Neurosci 2018; 11:394. [PMID: 30425620 PMCID: PMC6218427 DOI: 10.3389/fnmol.2018.00394] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
In the past two decades, yeast models have delivered profound insights into basic mechanisms of protein misfolding and the dysfunction of key cellular pathways associated with amyotrophic lateral sclerosis (ALS). Expressing ALS-associated proteins, such as superoxide dismutase (SOD1), TAR DNA binding protein 43 (TDP-43) and Fused in sarcoma (FUS), in yeast recapitulates major hallmarks of ALS pathology, including protein aggregation, mislocalization and cellular toxicity. Results from yeast have consistently been recapitulated in other model systems and even specimens from human patients, thus providing evidence for the power and validity of ALS yeast models. Focusing on impaired ribonucleic acid (RNA) metabolism and protein misfolding and their cytotoxic consequences in ALS, we summarize exemplary discoveries that originated from work in yeast. We also propose previously unexplored experimental strategies to modernize ALS yeast models, which will help to decipher the basic pathomechanisms underlying ALS and thus, possibly contribute to finding a cure.
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Affiliation(s)
- Sonja E Di Gregorio
- Schulich School of Medicine and Dentistry, Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Martin L Duennwald
- Schulich School of Medicine and Dentistry, Pathology and Laboratory Medicine, Western University, London, ON, Canada
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39
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Zhang T, Jiang X, Xu M, Wang H, Sang X, Qin M, Bao P, Wang R, Zhang C, Lu H, Li Y, Ren J, Chang HC, Yan J, Sun Q, Xu J. Sleep and circadian abnormalities precede cognitive deficits in R521C FUS knockin rats. Neurobiol Aging 2018; 72:159-170. [PMID: 30273830 DOI: 10.1016/j.neurobiolaging.2018.08.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022]
Abstract
Mutations in fused in sarcoma (Fus) cause familial amyotrophic lateral sclerosis (ALS) and occasionally frontotemporal dementia. Here we report the establishment and characterization of a novel knockin (KI) rat model expressing a Fus point mutation (R521C) via CRISPR/Cas9. The mutant animals developed adult-onset learning and memory behavioral deficits, with reduced spine density in hippocampal neurons. Remarkably, sleep-wake cycle and circadian abnormalities preceded the onset of cognitive deficit. RNA-seq study further demonstrated altered expression of some key sleep and circadian regulators, such as orexin/hypocretin receptor type 2 and casein kinase 1 epsilon, in the mutant rats. Therefore, we have established a rodent model expressing physiological level of a pathogenic mutant FUS, and we found cognitive impairment as a main behavioral deficit at mid age. Furthermore, we have revealed a new role of FUS in sleep and circadian regulation and demonstrated that functional change in FUS could cause sleep-wake and circadian disturbance as early symptoms.
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Affiliation(s)
- Tao Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Xin Jiang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China
| | - Min Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Sang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meiling Qin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Puhua Bao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ruiqi Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chenchen Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Huiping Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuzhuo Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Ren
- Center for Drug Safety Evaluation and Research, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hung-Chun Chang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Jin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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40
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Zagrovic B, Bartonek L, Polyansky AA. RNA-protein interactions in an unstructured context. FEBS Lett 2018; 592:2901-2916. [PMID: 29851074 PMCID: PMC6175095 DOI: 10.1002/1873-3468.13116] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/12/2018] [Accepted: 05/13/2018] [Indexed: 02/02/2023]
Abstract
Despite their importance, our understanding of noncovalent RNA-protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA-protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains. Specifically, we articulate the claim that the universal genetic code reflects the binding specificity between nucleobases and protein side chains and that, in turn, the code may be seen as the Rosetta stone for understanding RNA-protein interactions in general.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria
| | - Lukas Bartonek
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria
| | - Anton A. Polyansky
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria,MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
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41
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Ernst EH, Nielsen J, Ipsen MB, Villesen P, Lykke-Hartmann K. Transcriptome Analysis of Long Non-coding RNAs and Genes Encoding Paraspeckle Proteins During Human Ovarian Follicle Development. Front Cell Dev Biol 2018; 6:78. [PMID: 30087896 PMCID: PMC6066568 DOI: 10.3389/fcell.2018.00078] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence indicated that many long non-coding (lnc)RNAs function in multiple biological processes and dysregulation of their expression can cause diseases. Most regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression through epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling. Interestingly, differential lncRNA expression profiles in human oocytes and cumulus cells was recently assessed, however, lncRNAs in human follicle development has not previously been described. In this study, transcriptome dynamics in human primordial, primary and small antral follicles were interrogated and revealed information of lncRNA genes. It is known that some lncRNAs form a complex with paraspeckle proteins and therefore, we extended our transcriptional analysis to include genes encoding paraspeckle proteins. Primordial, primary follicles and small antral follicles was isolated using laser capture micro-dissection from ovarian tissue donated by three women having ovarian tissue cryopreserved before chemotherapy. After RN sequencing, a bioinformatic class comparison was performed and primordial, primary and small antral follicles were found to express several lncRNA and genes encoding paraspeckle proteins. Of particular interest, we detected the lncRNAs XIST, NEAT1, NEAT2 (MALAT1), and GAS5. Moreover, we noted a high expression of FUS, TAF15, and EWS components of the paraspeckles, proteins that belong to the FET (previously TET) family of RNA-binding proteins and are implicated in central cellular processes such as regulation of gene expression, maintenance of genomic integrity, and mRNA/microRNA processing. We also interrogated the intra-ovarian localization of the FUS, TAF15, and EWS proteins using immunofluorescence. The presence and the dynamics of genes that encode lncRNA and paraspeckle proteins may suggest that these may mediate functions in the cyclic recruitment and differentiation of human follicles and could participate in biological processes known to be associated with lncRNAs and paraspeckle proteins, such as gene expression control, scaffold formation and epigenetic control through human follicle development. This comprehensive transcriptome analysis of lncRNAs and genes encoding paraspeckle proteins expressed in human follicles could potentially provide biomarkers of oocyte quality for the development of non-invasive tests to identify embryos with high developmental potential.
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Affiliation(s)
- Emil H. Ernst
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Julie Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Malene B. Ipsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Palle Villesen
- Bioinformatic Research Centre, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Lykke-Hartmann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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42
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Ishigaki S, Sobue G. Importance of Functional Loss of FUS in FTLD/ALS. Front Mol Biosci 2018; 5:44. [PMID: 29774215 PMCID: PMC5943504 DOI: 10.3389/fmolb.2018.00044] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
Fused in sarcoma (FUS) is an RNA binding protein that regulates RNA metabolism including alternative splicing, transcription, and RNA transportation. FUS is genetically and pathologically involved in frontotemporal lobar degeneration (FTLD)/amyotrophic lateral sclerosis (ALS). Multiple lines of evidence across diverse models suggest that functional loss of FUS can lead to neuronal dysfunction and/or neuronal cell death. Loss of FUS in the nucleus can impair alternative splicing and/or transcription, whereas dysfunction of FUS in the cytoplasm, especially in the dendritic spines of neurons, can cause mRNA destabilization. Alternative splicing of the MAPT gene at exon 10, which generates 4-repeat Tau (4R-Tau) and 3-repeat Tau (3R-Tau), is one of the most impactful targets regulated by FUS. Additionally, loss of FUS function can affect dendritic spine maturations by destabilizing mRNAs such as Glutamate receptor 1 (GluA1), a major AMPA receptor, and Synaptic Ras GTPase-activating protein 1 (SynGAP1). Moreover, FUS is involved in axonal transport and morphological maintenance of neurons. These findings indicate that a biological link between loss of FUS function, Tau isoform alteration, aberrant post-synaptic function, and phenotypic expression might lead to the sequential cascade culminating in FTLD. Thus, to facilitate development of early disease markers and/or therapeutic targets of FTLD/ALS it is critical that the functions of FUS and its downstream pathways are unraveled.
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Affiliation(s)
- Shinsuke Ishigaki
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Therapeutics for Intractable Neurological Disorders, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Gen Sobue
- Brain and Mind Research Center, Nagoya University, Nagoya, Japan.,Research Division of Dementia and Neurodegenerative Disease, Nagoya University Graduate School of Medicine, Nagoya, Japan
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43
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Conic S, Desplancq D, Ferrand A, Fischer V, Heyer V, Reina San Martin B, Pontabry J, Oulad-Abdelghani M, Babu N K, Wright GD, Molina N, Weiss E, Tora L. Imaging of native transcription factors and histone phosphorylation at high resolution in live cells. J Cell Biol 2018; 217:1537-1552. [PMID: 29440513 PMCID: PMC5881509 DOI: 10.1083/jcb.201709153] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/15/2017] [Accepted: 01/18/2018] [Indexed: 01/16/2023] Open
Abstract
Conic et al. introduce a versatile antibody-based imaging approach to track endogenous nuclear factors in living cells. It allows efficient intracellular delivery of any fluorescent dye–conjugated antibody, or Fab fragment, into a variety of cell types. The dynamics of nuclear targets or posttranslational modifications can be monitored with high precision using confocal and super-resolution microscopy. Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types. Live-cell imaging permits following the labeled probes bound to their endogenous targets. By using conventional and super-resolution imaging we show dynamic changes in the distribution of several nuclear transcription factors (i.e., RNA polymerase II or TAF10), and specific phosphorylated histones (γH2AX), upon distinct biological stimuli at the nanometer scale. Hence, considering the large panel of available antibodies and the simplicity of their implementation, VANIMA can be used to uncover novel biological information based on the dynamic behavior of transcription factors or posttranslational modifications in the nucleus of single live cells.
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Affiliation(s)
- Sascha Conic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina San Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Pontabry
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epigenetics and Stem Cells, München, Germany
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Kishore Babu N
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Etienne Weiss
- Institut de Recherche de l'ESBS, UMR 7242, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,School of Biological Sciences, Nanyang Technological University, Singapore
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Svetoni F, De Paola E, La Rosa P, Mercatelli N, Caporossi D, Sette C, Paronetto MP. Post-transcriptional regulation of FUS and EWS protein expression by miR-141 during neural differentiation. Hum Mol Genet 2018; 26:2732-2746. [PMID: 28453628 DOI: 10.1093/hmg/ddx160] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/21/2017] [Indexed: 12/31/2022] Open
Abstract
Brain development involves proliferation, migration and specification of neural progenitor cells, culminating in neuronal circuit formation. Mounting evidence indicates that improper regulation of RNA binding proteins (RBPs), including members of the FET (FUS, EWS, TAF15) family, results in defective cortical development and/or neurodegenerative disorders. However, in spite of their physiological relevance, the precise pattern of FET protein expression in developing neurons is largely unknown. Herein, we found that FUS, EWS and TAF15 expression is differentially regulated during brain development, both in time and in space. In particular, our study identifies a fine-tuned regulation of FUS and EWS during neuronal differentiation, whereas TAF15 appears to be more constitutively expressed. Mechanistically FUS and EWS protein expression is regulated at the post-transcriptional level during neuron differentiation and brain development. Moreover, we identified miR-141 as a key regulator of these FET proteins that modulate their expression levels in differentiating neuronal cells. Thus, our studies uncover a novel link between post-transcriptional regulation of FET proteins expression and neurogenesis.
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Affiliation(s)
- Francesca Svetoni
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Piergiorgio La Rosa
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Neri Mercatelli
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
| | - Daniela Caporossi
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy
| | - Claudio Sette
- Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", 00135 Rome, Italy.,Laboratories of Cellular and Molecular Neurobiology and of Neuroembryology, Fondazione Santa Lucia, 00143 Rome, Italy
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Eom H, Park SJ, Kim MK, Kim H, Kang H, Lee I. TAF15b, involved in the autonomous pathway for flowering, represses transcription of FLOWERING LOCUS C. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:79-91. [PMID: 29086456 DOI: 10.1111/tpj.13758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 10/25/2017] [Indexed: 05/03/2023]
Abstract
TATA-binding protein-associated factors (TAFs) are general transcription factors within the transcription factor IID (TFIID) complex, which recognizes the core promoter of genes. In addition to their biochemical function, it is known that several TAFs are involved in the regulation of developmental processes. In this study, we found that TAF15b affects flowering time, especially through the autonomous pathway (AP) in Arabidopsis. The mutant taf15b shows late flowering compared with the wild type plant during both long and short days, and vernalization accelerates the flowering time of taf15b. In addition, taf15b shows strong upregulation of FLOWERING LOCUS C (FLC), a flowering repressor in Arabidopsis, and the flc taf15b double mutant completely offsets the late flowering of taf15b, indicating that TAF15b is a typical AP gene. The taf15b mutant also shows increased transcript levels of COOLAIR, an antisense transcript of FLC. Consistently, chromatin immunoprecipitation (ChIP) analyses showed that the TAF15b protein is enriched around both sense and antisense transcription start sites of the FLC locus. In addition, co-immunoprecipitation showed that TAF15b interacts with RNA polymerase II (Pol II), while ChIP showed increased enrichment of the phosphorylated forms, both serine 2 (Ser2) and Ser5, of the C-terminal domain of Pol II at the FLC locus, which is indicative of transcriptional elongation. Finally, taf15b showed higher enrichment of the active histone marker, H3K4me3, on FLC chromatin. Taken together, our results suggest that TAF15b affects flowering time through transcriptional repression of FLC in Arabidopsis.
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Affiliation(s)
- Hyunjoo Eom
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Korea
| | - Su Jung Park
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Min Kyung Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Hoyeun Kim
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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Li KKC, Chau BL, Lee KAW. Differential interaction of PRMT1 with RGG-boxes of the FET family proteins EWS and TAF15. Protein Sci 2017; 27:633-642. [PMID: 29193371 DOI: 10.1002/pro.3354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 12/31/2022]
Abstract
The FET sub-family (FUS/TLS, EWS, TAF15) of RNA-binding proteins have remarkably similar overall structure but diverse biological and pathological roles. The molecular basis for FET protein specialization is largely unknown. Gly-Arg-Rich regions (RGG-boxes) within FET proteins are targets for methylation by Protein-Arginine-Methyl-Transferase-1 (PRMT1) and substrate capture is thought to involve electrostatic attraction between positively charged polyRGG substrates and negatively charged surface channels of PRMT1. Unlike FUS and EWS, a high proportion of TAF15 RGG-boxes are embedded within neutrally charged YGGDR(S/G)G repeats, suggesting that they might not bind well to PRMT1. This notion runs contrary however to a report that YGGDR(S/G)G repeats are methylated by PRMT1. Using peptide-based polyRGG substrates and a novel 2-hybrid binding assay, we find that the Asp residue in YGGDR(S/G)G repeats confers poor binding to PRMT1. Our results therefore indicate that YGGDR(S/G)G repeats may contribute to TAF15 specialization by enabling differential interactions with PRMT1 and reduced overall levels of TAF15 methylation compared with other FET proteins. By analogy with molecular recognition of other disordered polyvalent ligands by globular protein partners, we also propose a dynamic polyelectrostatic model for substrate capture by PRMT1.
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Affiliation(s)
- Kim K C Li
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, S.A.R, China
| | - Bess L Chau
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, S.A.R, China
| | - Kevin A W Lee
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, S.A.R, China
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Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. Int J Mol Sci 2017; 18:ijms18122761. [PMID: 29257115 PMCID: PMC5751360 DOI: 10.3390/ijms18122761] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/15/2022] Open
Abstract
Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs.
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Kapeli K, Martinez FJ, Yeo GW. Genetic mutations in RNA-binding proteins and their roles in ALS. Hum Genet 2017; 136:1193-1214. [PMID: 28762175 PMCID: PMC5602095 DOI: 10.1007/s00439-017-1830-7] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/17/2017] [Indexed: 12/11/2022]
Abstract
Mutations in genes that encode RNA-binding proteins (RBPs) have emerged as critical determinants of neurological diseases, especially motor neuron disorders such as amyotrophic lateral sclerosis (ALS). RBPs are involved in all aspects of RNA processing, controlling the life cycle of RNAs from synthesis to degradation. Hallmark features of RBPs in neuron dysfunction include misregulation of RNA processing, mislocalization of RBPs to the cytoplasm, and abnormal aggregation of RBPs. Much progress has been made in understanding how ALS-associated mutations in RBPs drive pathogenesis. Here, we focus on several key RBPs involved in ALS—TDP-43, HNRNP A2/B1, HNRNP A1, FUS, EWSR1, and TAF15—and review our current understanding of how mutations in these proteins cause disease.
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Affiliation(s)
- Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore
| | - Fernando J Martinez
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Singapore.
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Molecular Engineering Laboratory, A*STAR, Singapore, 138673, Singapore.
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Efimova AD, Ovchinnikov RK, Roman AY, Maltsev AV, Grigoriev VV, Kovrazhkina EA, Skvortsova VI. The FUS protein: Physiological functions and a role in amyotrophic lateral sclerosis. Mol Biol 2017. [DOI: 10.1134/s0026893317020091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hock EM, Polymenidou M. Prion-like propagation as a pathogenic principle in frontotemporal dementia. J Neurochem 2017; 138 Suppl 1:163-83. [PMID: 27502124 PMCID: PMC6680357 DOI: 10.1111/jnc.13668] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/22/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022]
Abstract
Frontotemporal dementia is a devastating neurodegenerative disease causing stark alterations in personality and language. Characterized by severe atrophy of the frontal and temporal brain lobes, frontotemporal dementia (FTD) shows extreme heterogeneity in clinical presentation, genetic causes, and pathological findings. Like most neurodegenerative diseases, the initial symptoms of FTD are subtle, but increase in severity over time, as the disease progresses. Clinical progression is paralleled by exacerbation of pathological findings and the involvement of broader brain regions, which currently lack mechanistic explanation. Yet, a flurry of studies indicate that protein aggregates accumulating in neurodegenerative diseases can act as propagating entities, amplifying their pathogenic conformation, in a way similar to infectious prions. In this prion‐centric view, FTD can be divided into three subtypes, TDP‐43 or FUS proteinopathy and tauopathy. Here, we review the current evidence that FTD‐linked pathology propagates in a prion‐like manner and discuss the implications of these findings for disease progression and heterogeneity.
Frontotemporal dementia (FTD) is a progressive neurodegenerative disease causing severe personality dysfunctions, characterized by profound heterogeneity. Accumulation of tau, TDP‐43 or FUS cytoplasmic aggregates characterize molecularly distinct and non‐overlapping FTD subtypes. Here, we discuss the current evidence suggesting that prion‐like propagation and cell‐to‐cell spread of each of these cytoplasmic aggregates may underlie disease progression and heterogeneity.
This article is part of the Frontotemporal Dementia special issue.
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Affiliation(s)
- Eva-Maria Hock
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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