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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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2
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Ferruzo PYM, Boell VK, Russo LC, Oliveira CC, Forti FL. DUSP3 modulates IRES-dependent translation of mRNAs through dephosphorylation of the HNRNPC protein in cells under genotoxic stimulus. Biol Cell 2024; 116:e2300128. [PMID: 38538536 DOI: 10.1111/boc.202300128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND INFORMATION The dual-specificity phosphatase 3 (DUSP3) regulates cell cycle progression, proliferation, senescence, and DNA repair pathways under genotoxic stress. This phosphatase interacts with HNRNPC protein suggesting an involvement in the regulation of HNRNPC-ribonucleoprotein complex stability. In this work, we investigate the impact of DUSP3 depletion on functions of HNRNPC aiming to suggest new roles for this enzyme. RESULTS The DUSP3 knockdown results in the tyrosine hyperphosphorylation state of HNRNPC increasing its RNA binding ability. HNRNPC is present in the cytoplasm where it interacts with IRES trans-acting factors (ITAF) complex, which recruits the 40S ribosome on mRNA during protein synthesis, thus facilitating the translation of mRNAs containing IRES sequence in response to specific stimuli. In accordance with that, we found that DUSP3 is present in the 40S, monosomes and polysomes interacting with HNRNPC, just like other previously identified DUSP3 substrates/interacting partners such as PABP and NCL proteins. By downregulating DUSP3, Tyr-phosphorylated HNRNPC preferentially binds to IRES-containing mRNAs within ITAF complexes preferentially in synchronized or stressed cells, as evidenced by the higher levels of proteins such as c-MYC and XIAP, but not their mRNAs such as measured by qPCR. Under DUSP3 absence, this increased phosphorylated-HNRNPC/RNA interaction reduces HNRNPC-p53 binding in presence of RNAs releasing p53 for specialized cellular responses. Similarly, to HNRNPC, PABP physically interacts with DUSP3 in an RNA-dependent manner. CONCLUSIONS AND SIGNIFICANCE Overall, DUSP3 can modulate cellular responses to genotoxic stimuli at the translational level by maintaining the stability of HNRNPC-ITAF complexes and regulating the intensity and specificity of RNA interactions with RRM-domain proteins.
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Affiliation(s)
- Pault Y M Ferruzo
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Viktor K Boell
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Lilian C Russo
- Laboratory of Genome Instability, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Carla C Oliveira
- Laboratory of Post-transcriptional Control of Gene Expression, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Fabio L Forti
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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3
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Ma W, Ma B, Ma J, Zhu R. RB1 5́UTR contains an IRES related to cell cycle control and cancer progression. Gene 2023; 887:147724. [PMID: 37604323 DOI: 10.1016/j.gene.2023.147724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Retinoblastoma gene1 (RB1) is the first tumor suppressor gene that stands as the guardian of the gate of the G1 period and plays a central role in proliferation and differentiation. However, no reports focused on the possible internal ribosome entry site (IRES) function of the RB1 gene flanking sequence. In this study, we constructed a bicistronic reporter with the RB1 5'untranslated region (5́UTR) inserted between two reporter coding regions. We found RB1 5'UTR harbors an IRES and has higher activity in cancer cell lines than normal cells. Besides, RB1 IRES acquired the highest activity in the G0/G1 phase of the cell cycle, and the RB1 5'UTR mutation collected from retinoblastoma decreased IRES activity compared with RB1 5'UTR wild-type. These data indicated that RB1 IRES is a mechanism of stress regulation and is related to cell cycle control and cancer progression.
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Affiliation(s)
- Wennan Ma
- Changzhou Capmus of Hohai University, Changzhou, Jiangsu Province 213022, PR China
| | - Bei Ma
- Changzhou Capmus of Hohai University, Changzhou, Jiangsu Province 213022, PR China
| | - Jing Ma
- Nanjing Kingsley Biotechnology Co., Ltd, Nanjing, Jiangsu Province 210000, PR China
| | - Ruiyu Zhu
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu Province 214122, PR China.
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Li Y, Li C, Liu M, Liu S, Liu F, Wang L. The RNA-binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling. Development 2023; 150:dev201890. [PMID: 37874038 PMCID: PMC10652045 DOI: 10.1242/dev.201890] [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: 04/17/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
In vertebrates, the earliest hematopoietic stem and progenitor cells (HSPCs) are derived from a subset of specialized endothelial cells, hemogenic endothelial cells, in the aorta-gonad-mesonephros region through endothelial-to-hematopoietic transition. HSPC generation is efficiently and accurately regulated by a variety of factors and signals; however, the precise control of these signals remains incompletely understood. Post-transcriptional regulation is crucial for gene expression, as the transcripts are usually bound by RNA-binding proteins (RBPs) to regulate RNA metabolism. Here, we report that the RBP protein Csde1-mediated translational control is essential for HSPC generation during zebrafish early development. Genetic mutants and morphants demonstrated that depletion of csde1 impaired HSPC production in zebrafish embryos. Mechanistically, Csde1 regulates HSPC generation through modulating Wnt/β-catenin signaling activity. We demonstrate that Csde1 binds to ctnnb1 mRNAs (encoding β-catenin, an effector of Wnt signaling) and regulates translation but not stability of ctnnb1 mRNA, which further enhances β-catenin protein level and Wnt signal transduction activities. Together, we identify Csde1 as an important post-transcriptional regulator and provide new insights into how Wnt/β-catenin signaling is precisely regulated at the post-transcriptional level.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Can Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Mengyao Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shicheng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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5
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Kakumani PK, Ko Y, Ramakrishna S, Christopher G, Dodgson M, Shrinet J, Harvey LM, Shin C, Simard M. CSDE1 promotes miR-451 biogenesis. Nucleic Acids Res 2023; 51:9385-9396. [PMID: 37493604 PMCID: PMC10516617 DOI: 10.1093/nar/gkad619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023] Open
Abstract
MicroRNAs are sequentially processed by RNase III enzymes Drosha and Dicer. miR-451 is a highly conserved miRNA in vertebrates which bypasses Dicer processing and instead relies on AGO2 for its maturation. miR-451 is highly expressed in erythrocytes and regulates the differentiation of erythroblasts into mature red blood cells. However, the mechanistic details underlying miR-451 biogenesis in erythrocytes remains obscure. Here, we report that the RNA binding protein CSDE1 which is required for the development of erythroblasts into erythrocytes, controls the expression of miR-451 in erythroleukemia cells. CSDE1 binds miR-451 and regulates AGO2 processing of pre-miR-451 through its N-terminal domains. CSDE1 further interacts with PARN and promotes the trimming of intermediate miR-451 to the mature length. Together, our results demonstrate that CSDE1 promotes biogenesis of miR-451 in erythroid progenitors.
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Affiliation(s)
- Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Yunkoo Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sushmitha Ramakrishna
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Grace Christopher
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Maria Dodgson
- Department of Biochemistry, Memorial University of Newfoundland, 45 Arctic Avenue, St. John's NL A1C 5S7, Canada
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Louis-Mathieu Harvey
- Oncology Division, Centre Hospitalier Universitaire de Québec-Université Laval Research Center (L’Hôtel-Dieu de Québec), Quebec City, Québec G1R 3S3, Canada
- Laval University Cancer Research Centre, Québec City, Québec G1R 3S3, Canada
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Martin J Simard
- Oncology Division, Centre Hospitalier Universitaire de Québec-Université Laval Research Center (L’Hôtel-Dieu de Québec), Quebec City, Québec G1R 3S3, Canada
- Laval University Cancer Research Centre, Québec City, Québec G1R 3S3, Canada
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6
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Jia R, Che X, Jia J, Guo J. FOXM1a Isoform of Oncogene FOXM1 Is a Tumor Suppressor Suppressed by hnRNP C in Oral Squamous Cell Carcinoma. Biomolecules 2023; 13:1331. [PMID: 37759731 PMCID: PMC10526205 DOI: 10.3390/biom13091331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
FOXM1 is an oncogenic transcriptional factor and includes several isoforms generated by alternative splicing. Inclusion of alternative exon 9 produces FOXM1a, a transcriptionally inactive isoform. However, the role of FOXM1a in tumorigenesis remains unknown. In addition, the regulatory mechanisms of exon 9 splicing are also unclear. In the present study, we found that overexpression of FOXM1a significantly reduced cell proliferation and colony formation of oral squamous cell carcinoma (OSCC) cell proliferation in vitro. Importantly, OSCC cells with FOXM1a overexpression showed significantly slower tumor formation in nude mice. Moreover, we identified a U-rich exonic splicing suppressor (ESS) which is responsible for exon 9 skipping. Splicing factor heterogeneous nuclear ribonucleoprotein C (hnRNP C) can bind to the ESS and suppress exon 9 inclusion and FOXM1a expression. Silence of hnRNP C also significantly suppresses OSCC cell proliferation. HnRNP C is significantly co-expressed with FOXM1 in cancers. Our study uncovered a novel regulatory mechanism of oncogene FOXM1 expression in OSCC.
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Affiliation(s)
- Rong Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
| | - Xiaoxuan Che
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
| | - Jun Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China
| | - Jihua Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China
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7
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Niggl E, Bouman A, Briere LC, Hoogenboezem RM, Wallaard I, Park J, Admard J, Wilke M, Harris-Mostert EDRO, Elgersma M, Bain J, Balasubramanian M, Banka S, Benke PJ, Bertrand M, Blesson AE, Clayton-Smith J, Ellingford JM, Gillentine MA, Goodloe DH, Haack TB, Jain M, Krantz I, Luu SM, McPheron M, Muss CL, Raible SE, Robin NH, Spiller M, Starling S, Sweetser DA, Thiffault I, Vetrini F, Witt D, Woods E, Zhou D, Elgersma Y, van Esbroeck ACM. HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder. Am J Hum Genet 2023; 110:1414-1435. [PMID: 37541189 PMCID: PMC10432175 DOI: 10.1016/j.ajhg.2023.07.005] [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: 01/26/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
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Affiliation(s)
- Eva Niggl
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Lauren C Briere
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Ilse Wallaard
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; NGS Competence Center Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Emilio D R O Harris-Mostert
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Minetta Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
| | - Jennifer Bain
- Department of Neurology Division of Child Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK; Department of Oncology & Metabolism, University of Sheffield, S5 7AU Sheffield, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Paul J Benke
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL 33021, USA
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Alyssa E Blesson
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | - Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL Manchester, UK
| | | | - Dana H Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany; Center for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Mahim Jain
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ian Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon M Luu
- Waisman Center, University of Wisconsin Hospitals and Clinics, Madison, WI 53704, USA; Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Molly McPheron
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Candace L Muss
- Nemours / AI DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Sarah E Raible
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Michael Spiller
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Susan Starling
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - David A Sweetser
- Center for Genomic Medicine and Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Thiffault
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA; Undiagnosed Rare Disease Clinic (URDC), Indiana University, Indianapolis, IN 46202, USA
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Emily Woods
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy, Kansas City, MO 64108, USA; School of Medicine, University of Missouri- Kansas City, Kansas City, MO 64108, USA
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands.
| | - Annelot C M van Esbroeck
- Department of Clinical Genetics, Erasmus MC, 3015 GD Rotterdam, the Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, 3015 GD Rotterdam, the Netherlands
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8
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Saunders JT, Kumar S, Benavides-Serrato A, Holmes B, Benavides KE, Bashir MT, Nishimura RN, Gera J. Translation of circHGF RNA encodes an HGF protein variant promoting glioblastoma growth through stimulation of c-MET. J Neurooncol 2023; 163:207-218. [PMID: 37162666 DOI: 10.1007/s11060-023-04331-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/28/2023] [Indexed: 05/11/2023]
Abstract
INTRODUCTION HGF/c-MET signaling is a significant driver of glioblastoma (GBM) growth and disease progression. Unfortunately, c-MET targeted therapies have been found to be largely ineffective suggesting additional redundant mechanisms of c-MET activation. METHODS Utilizing RNA-sequencing (RNA-seq) and ribosome profiling analyses of circular RNAs, circ-HGF (hsa_circ_0080914) was identified as markedly upregulated in primary GBM and found to potentially encode an HGF protein variant (C-HGF) 119 amino acids in length. This candidate HGF variant was characterized and evaluated for its ability to mediate c-MET activation and regulate PDX GBM cell growth, motility and invasive potential in vitro and tumor burden in intracranial xenografts in mice. RESULTS An internal ribosome entry site (IRES) was identified within the circ-HGF RNA which mediated translation of the cross-junctional ORF encoding C-HGF and was observed to be highly expressed in GBM relative to normal brain tissue. C-HGF was also found to be secreted from GBM cells and concentrated cell culture supernatants or recombinant C-HGF activated known signaling cascades downstream of c-MET. C-HGF was shown to interact directly with the c-MET receptor resulting in its autophosphorylation and activation in PDX GBM lines. Knockdown of C-HGF resulted in suppression of c-MET signaling and marked inhibition of cell growth, motility and invasiveness, whereas overexpression of C-HGF displayed the opposite effects. Additionally, modulation of C-HGF expression regulated tumor growth in intracranial xenografted PDX GBM models. CONCLUSIONS These results reveal an alternative mechanism of c-MET activation via a circular RNA encoded HGF protein variant which is relevant in GBM biology. Targeting C-HGF may offer a promising approach for GBM clinical management.
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Affiliation(s)
- Jacquelyn T Saunders
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Sunil Kumar
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Angelica Benavides-Serrato
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Brent Holmes
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Kennedy E Benavides
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Muhammad T Bashir
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Robert N Nishimura
- Department of Neurology, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, USA
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA
| | - Joseph Gera
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA.
- Jonnson Comprehensive Cancer Center, University of California-Los Angeles, Greater Los Angeles Veterans Affairs Healthcare System, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA.
- Molecular Biology Institute, University of California-Los Angeles, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA.
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, 16111 Plummer Street (151), Building 1, Room C111A, Los Angeles, CA, 91343, USA.
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9
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Persistent Enterovirus Infection: Little Deletions, Long Infections. Vaccines (Basel) 2022; 10:vaccines10050770. [PMID: 35632526 PMCID: PMC9143164 DOI: 10.3390/vaccines10050770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Enteroviruses have now been shown to persist in cell cultures and in vivo by a novel mechanism involving the deletion of varying amounts of the 5′ terminal genomic region termed domain I (also known as the cloverleaf). Molecular clones of coxsackievirus B3 (CVB3) genomes with 5′ terminal deletions (TD) of varying length allow the study of these mutant populations, which are able to replicate in the complete absence of wildtype virus genomes. The study of TD enteroviruses has revealed numerous significant differences from canonical enteroviral biology. The deletions appear and become the dominant population when an enterovirus replicates in quiescent cell populations, but can also occur if one of the cis-acting replication elements of the genome (CRE-2C) is artificially mutated in the element’s stem and loop structures. This review discusses how the TD genomes arise, how they interact with the host, and their effects on host biology.
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10
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Avolio R, Inglés-Ferrándiz M, Ciocia A, Coll O, Bonnin S, Guitart T, Ribó A, Gebauer F. Coordinated post-transcriptional control of oncogene-induced senescence by UNR/CSDE1. Cell Rep 2022; 38:110211. [PMID: 35021076 DOI: 10.1016/j.celrep.2021.110211] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 08/27/2021] [Accepted: 12/14/2021] [Indexed: 02/06/2023] Open
Abstract
Oncogene-induced senescence (OIS) is a form of stable cell-cycle arrest arising in response to oncogenic stimulation. OIS must be bypassed for transformation, but the mechanisms of OIS establishment and bypass remain poorly understood, especially at the post-transcriptional level. Here, we show that the RNA-binding protein UNR/CSDE1 enables OIS in primary mouse keratinocytes. Depletion of CSDE1 leads to senescence bypass, cell immortalization, and tumor formation, indicating that CSDE1 behaves as a tumor suppressor. Unbiased high-throughput analyses uncovered that CSDE1 promotes OIS by two independent molecular mechanisms: enhancement of the stability of senescence-associated secretory phenotype (SASP) factor mRNAs and repression of Ybx1 mRNA translation. Importantly, depletion of YBX1 from immortal keratinocytes rescues senescence and uncouples proliferation arrest from the SASP, revealing multilayered mechanisms exerted by CSDE1 to coordinate senescence. Our data highlight the relevance of post-transcriptional control in the regulation of senescence.
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Affiliation(s)
- Rosario Avolio
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Marta Inglés-Ferrándiz
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Annagiulia Ciocia
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Olga Coll
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Sarah Bonnin
- Bioinformatics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Anna Ribó
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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11
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Wang Y, Lin S, Zhao Z, Xu P, Gao K, Qian H, Zhang Z, Guo X. Functional analysis of a putative Bombyx mori cypovirus miRNA BmCPV-miR-10 and its effect on virus replication. INSECT MOLECULAR BIOLOGY 2021; 30:552-565. [PMID: 34296485 DOI: 10.1111/imb.12725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Bombyx mori cypovirus (BmCPV) is an important pathogen of silkworm (B. mori), the economically beneficial insect. The mechanism of its interaction with host immune defence system in the process of infection is still not yet completely clear. Researches have demonstrated that virus-encoded microRNAs (miRNA) play a crucial role in regulating host-pathogen interaction, but few reports are available so far on miRNAs encoded by insect viruses, especially the RNA viruses. In this study, a putative miRNA encoded by the 10th segment of BmCPV genomic RNA, BmCPV-miR-10, was identified and functionally analysed. The expression of the putative BmCPV-miR-10 could be detected via stem-loop RT-PCR (reverse transcription-Polymerase Chain Reaction) in the midgut of silkworm larvae infected with BmCPV. BmCSDE1 (B. mori cold shock domain E1 protein) gene was predicted to be a candidate target gene for BmCPV-miR-10 with the miRNA binding site located in 3' untranslated region of its mRNA. The regulation effect of the putative BmCPV-miR-10 on BmCSDE1 was verified in HEK293 cells by lentiviral expression system, in BmN cells by transfecting BmCPV-miR-10 mimics. The qRT-PCR (quantitative real-time PCR) results showed that the putative BmCPV-miR-10 could suppress the expression of BmCSDE1. By injection of BmCPV-miR-10 mimics into the silkworm larvae infected with BmCPV, it was further proved that the putative BmCPV-miR-10 could suppress the expression of BmCSDE1 in vivo, then inhibit the expression of BmApaf-1 (B. mori apoptotic protease activating factor 1), while enhance the replication of BmCPV genomic RNAs to a certain extent. These results implied that the putative BmCPV-miR-10 could down-regulate the expression of BmCSDE1, then suppress the expression of BmApaf-1, thereby created a favourable intracellular environment for virus replication and proliferation.
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Affiliation(s)
- Y Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - S Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Z Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - P Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - K Gao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - H Qian
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Z Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - X Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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12
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Nadeem MS, Hosawi S, Alshehri S, Ghoneim MM, Imam SS, Murtaza BN, Kazmi I. Symptomatic, Genetic, and Mechanistic Overlaps between Autism and Alzheimer's Disease. Biomolecules 2021; 11:1635. [PMID: 34827633 PMCID: PMC8615882 DOI: 10.3390/biom11111635] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 02/02/2023] Open
Abstract
Autism spectrum disorder (ASD) and Alzheimer's disease (AD) are neurodevelopmental and neurodegenerative disorders affecting two opposite ends of life span, i.e., childhood and old age. Both disorders pose a cumulative threat to human health, with the rate of incidences increasing considerably worldwide. In the context of recent developments, we aimed to review correlated symptoms and genetics, and overlapping aspects in the mechanisms of the pathogenesis of ASD and AD. Dementia, insomnia, and weak neuromuscular interaction, as well as communicative and cognitive impairments, are shared symptoms. A number of genes and proteins linked with both disorders have been tabulated, including MECP2, ADNP, SCN2A, NLGN, SHANK, PTEN, RELN, and FMR1. Theories about the role of neuron development, processing, connectivity, and levels of neurotransmitters in both disorders have been discussed. Based on the recent literature, the roles of FMRP (Fragile X mental retardation protein), hnRNPC (heterogeneous ribonucleoprotein-C), IRP (Iron regulatory proteins), miRNAs (MicroRNAs), and α-, β0, and γ-secretases in the posttranscriptional regulation of cellular synthesis and processing of APP (amyloid-β precursor protein) have been elaborated to describe the parallel and overlapping routes and mechanisms of ASD and AD pathogenesis. However, the interactive role of genetic and environmental factors, oxidative and metal ion stress, mutations in the associated genes, and alterations in the related cellular pathways in the development of ASD and AD needs further investigation.
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Affiliation(s)
- Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.S.N.); (S.H.)
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.S.N.); (S.H.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Syed Sarim Imam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Bibi Nazia Murtaza
- Department of Zoology, Abbottabad University of Science and Technology (AUST), Abbottabad 22310, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.S.N.); (S.H.)
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13
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Grzybowska EA, Wakula M. Protein Binding to Cis-Motifs in mRNAs Coding Sequence Is Common and Regulates Transcript Stability and the Rate of Translation. Cells 2021; 10:2910. [PMID: 34831133 PMCID: PMC8616275 DOI: 10.3390/cells10112910] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
Protein binding to the non-coding regions of mRNAs is relatively well characterized and its functionality has been described in many examples. New results obtained by high-throughput methods indicate that binding to the coding sequence (CDS) by RNA-binding proteins is also quite common, but the functions thereof are more obscure. As described in this review, CDS binding has a role in the regulation of mRNA stability, but it has also a more intriguing role in the regulation of translational efficiency. Global approaches, which suggest the significance of CDS binding along with specific examples of CDS-binding RBPs and their modes of action, are outlined here, pointing to the existence of a relatively less-known regulatory network controlling mRNA stability and translation on yet another level.
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Affiliation(s)
- Ewa A. Grzybowska
- Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland;
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14
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El Khouri E, Ghoumid J, Haye D, Giuliano F, Drevillon L, Briand-Suleau A, De La Grange P, Nau V, Gaillon T, Bienvenu T, Jacquemin-Sablon H, Goossens M, Amselem S, Giurgea I. Wnt/β-catenin pathway and cell adhesion deregulation in CSDE1-related intellectual disability and autism spectrum disorders. Mol Psychiatry 2021; 26:3572-3585. [PMID: 33867523 DOI: 10.1038/s41380-021-01072-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
Among the genetic factors playing a key role in the etiology of intellectual disabilities (IDs) and autism spectrum disorders (ASDs), several encode RNA-binding proteins (RBPs). In this study, we deciphered the molecular and cellular bases of ID-ASD in a patient followed from birth to the age of 21, in whom we identified a de novo CSDE1 (Cold Shock Domain-containing E1) nonsense variation. CSDE1 encodes an RBP that regulates multiple cellular pathways by monitoring the translation and abundance of target transcripts. Analyses performed on the patient's primary fibroblasts showed that the identified CSDE1 variation leads to haploinsufficiency. We identified through RNA-seq assays the Wnt/β-catenin signaling and cellular adhesion as two major deregulated pathways. These results were further confirmed by functional studies involving Wnt-specific luciferase and substrate adhesion assays. Additional data support a disease model involving APC Down-Regulated-1 (APCDD1) and cadherin-2 (CDH2), two components of the Wnt/β-catenin pathway, CDH2 being also pivotal for cellular adhesion. Our study, which relies on both the deep phenotyping and long-term follow-up of a patient with CSDE1 haploinsufficiency and on ex vivo studies, sheds new light on the CSDE1-dependent deregulated pathways in ID-ASD.
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Affiliation(s)
- E El Khouri
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - J Ghoumid
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - D Haye
- Service de Génétique Médicale Centre, Hospitalo-Universitaire de Nice, Nice, France
| | - F Giuliano
- Service de Génétique Médicale Centre, Hospitalo-Universitaire de Nice, Nice, France
| | - L Drevillon
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,CHU Caen Normandie, Caen, France
| | - A Briand-Suleau
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.,Service de Génétique et Biologie Moléculaires, Hôpital Cochin, INSERM UMR1266 - Institute of Psychiatry and Neuroscience of Paris (IPNP) and University of Paris, Paris, France
| | | | - V Nau
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - T Gaillon
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France
| | - T Bienvenu
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, INSERM UMR1266 - Institute of Psychiatry and Neuroscience of Paris (IPNP) and University of Paris, Paris, France
| | - H Jacquemin-Sablon
- INSERM UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - M Goossens
- Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France
| | - S Amselem
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France
| | - I Giurgea
- Sorbonne Université, INSERM, Maladies génétiques d'expression pédiatrique, Département de Génétique médicale, Assistance Publique Hôpitaux de Paris, Hôpital Trousseau, Paris, France. .,Département de Génétique, Groupe Hospitalier Henri Mondor, Créteil, France.
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15
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CSDE1 attenuates microRNA-mediated silencing of PMEPA1 in melanoma. Oncogene 2021; 40:3231-3244. [PMID: 33833398 DOI: 10.1038/s41388-021-01767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
MicroRNAs and RNA-binding proteins (RBPs) primarily target the 3' UTR of mRNAs to control their translation and stability. However, their co-regulatory effects on specific mRNAs in physiology and disease are yet to be fully explored. CSDE1 is an RBP that promotes metastasis in melanoma and mechanisms underlying its oncogenic activities need to be completely defined. Here we report that CSDE1 interacts with specific miRNA-induced silencing complexes (miRISC) in melanoma. We find an association of CSDE1 with AGO2, the essential component of miRISC, which is facilitated by target mRNAs and depends on the first cold shock domain of CSDE1. Both CSDE1 and AGO2 bind to 3' UTR of PMEPA1. CSDE1 counters AGO2 binding, leading to an increase of PMEPA1 expression. We also identify a miRNA, miR-129-5p, that represses PMEPA1 expression in melanoma. Collectively, our results show that PMEPA1 promotes tumorigenic traits and that CSDE1 along with miR-129-5p/AGO2 miRISC act antagonistically to fine-tune PMEPA1 expression toward the progression of melanoma.
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16
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Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions. Nat Genet 2021; 53:729-741. [PMID: 33821006 PMCID: PMC8825242 DOI: 10.1038/s41588-021-00830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023]
Abstract
The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5' untranslated regions (UTRs) in noncanonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5' UTRs decreased gene expression, and extremely conserved 5' UTRs possess cis-regulatory elements that promote cell-type-specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a new methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5' UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
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17
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Kim W, Shin JC, Lee KH, Kim KT. PTBP1 Positively Regulates the Translation of Circadian Clock Gene, Period1. Int J Mol Sci 2020; 21:ijms21186921. [PMID: 32967200 PMCID: PMC7555454 DOI: 10.3390/ijms21186921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
Circadian oscillations of mRNAs and proteins are the main features of circadian clock genes. Among them, Period1 (Per1) is a key component in negative-feedback regulation, which shows a robust diurnal oscillation and the importance of circadian rhythm and translational regulation of circadian clock genes has been recognized. In the present study, we investigated the 5'-untranslated region (5'-UTR) of the mouse core clock gene, Per1, at the posttranscriptional level, particularly its translational regulation. The 5'-UTR of Per1 was found to promote its translation via an internal ribosomal entry site (IRES). We found that polypyrimidine tract-binding protein 1 (PTBP1) binds to the 5'-UTR of Per1 and positively regulates the IRES-mediated translation of Per1 without affecting the levels of Per1 mRNA. The reduction of PTBP1 level also decreased the endogenous levels of the PER1 protein but not of its mRNA. As for the oscillation of PER1 expression, the disruption of PTBP1 levels lowered the PER1 expression but not the phase of the oscillation. PTBP1 also changed the amplitudes of the mRNAs of other circadian clock genes, such as Cryptochrome 1 (Cry1) and Per3. Our results suggest that the PTBP1 is important for rhythmic translation of Per1 and it fine-tunes the overall circadian system.
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Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | | | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
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18
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Su Z, Liu X, Xu Y, Hu W, Zhao C, Zhao H, Feng X, Zhang S, Yang J, Shi X, Peng J. Novel reciprocal fusion genes involving HNRNPC and RARG in acute promyelocytic leukemia lacking RARA rearrangement. Haematologica 2020; 105:e376-e378. [PMID: 32354871 DOI: 10.3324/haematol.2019.244715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Zhan Su
- Department of Haematology, The Affiliated Hospital of Qingdao University, Qingdao .,Department of Haematology, Qilu Hospital, Cheeloo College of Medcine, Shandong University, Jinan
| | - Xin Liu
- Department of Stem Cell Transplantation, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Blood Diseases Hospital & Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin
| | - Yan Xu
- Department of Lymphoma & Myloma, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Blood Diseases Hospital & Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin
| | - Weiyu Hu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Qingdao University, Qingdao
| | - Chunting Zhao
- Department of Haematology, The Affiliated Hospital of Qingdao University, Qingdao
| | - Hongguo Zhao
- Department of Haematology, The Affiliated Hospital of Qingdao University, Qingdao
| | - Xianqi Feng
- Department of Haematology, The Affiliated Hospital of Qingdao University, Qingdao
| | - Shuchao Zhang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jie Yang
- Department of Haematology, The Affiliated Hospital of Qingdao University, Qingdao
| | - Xue Shi
- Department of Haematology, The Affiliated Hospital of Qingdao University, Qingdao
| | - Jun Peng
- Department of Haematology, Qilu Hospital, Cheeloo College of Medcine, Shandong University, Jinan
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19
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Kakumani PK, Harvey LM, Houle F, Guitart T, Gebauer F, Simard MJ. CSDE1 controls gene expression through the miRNA-mediated decay machinery. Life Sci Alliance 2020; 3:3/4/e201900632. [PMID: 32161113 PMCID: PMC7067469 DOI: 10.26508/lsa.201900632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022] Open
Abstract
In animals, miRNAs are the most prevalent small non-coding RNA molecules controlling posttranscriptional gene regulation. The Argonaute proteins (AGO) mediate miRNA-guided gene silencing by recruiting multiple factors involved in translational repression, deadenylation, and decapping. Here, we report that CSDE1, an RNA-binding protein linked to stem cell maintenance and metastasis in cancer, interacts with AGO2 within miRNA-induced silencing complex and mediates gene silencing through its N-terminal domains. We show that CSDE1 interacts with LSM14A, a constituent of P-body assembly and further associates to the DCP1-DCP2 decapping complex, suggesting that CSDE1 could promote the decay of miRNA-induced silencing complex-targeted mRNAs. Together, our findings uncover a hitherto unknown mechanism used by CSDE1 in the control of gene expression mediated by the miRNA pathway.
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Affiliation(s)
- Pavan Kumar Kakumani
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada .,Laval University Cancer Research Centre, Québec City, Canada
| | - Louis-Mathieu Harvey
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada.,Laval University Cancer Research Centre, Québec City, Canada
| | - François Houle
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada.,Laval University Cancer Research Centre, Québec City, Canada
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin J Simard
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, L'Hôtel-Dieu de Québec, Québec City, Canada .,Laval University Cancer Research Centre, Québec City, Canada
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20
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Guo AX, Cui JJ, Wang LY, Yin JY. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun Signal 2020; 18:14. [PMID: 31987048 PMCID: PMC6986143 DOI: 10.1186/s12964-019-0496-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract CSDE1 (cold shock domain containing E1) plays a key role in translational reprogramming, which determines the fate of a number of RNAs during biological processes. Interestingly, the role of CSDE1 is bidirectional. It not only promotes and represses the translation of RNAs but also increases and decreases the abundance of RNAs. However, the mechanisms underlying this phenomenon are still unknown. In this review, we propose a “protein-RNA connector” model to explain this bidirectional role and depict its three versions: sequential connection, mutual connection and facilitating connection. As described in this molecular model, CSDE1 binds to RNAs and cooperates with other protein regulators. CSDE1 connects with different RNAs and their regulators for different purposes. The triple complex of CSDE1, a regulator and an RNA reprograms translation in different directions for each transcript. Meanwhile, a number of recent studies have found important roles for CSDE1 in human diseases. This model will help us to understand the role of CSDE1 in translational reprogramming and human diseases. Video Abstract
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Affiliation(s)
- Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Jia-Jia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, People's Republic of China. .,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, People's Republic of China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China. .,Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, 410078, People's Republic of China. .,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, 410078, People's Republic of China.
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21
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Guo H, Li Y, Shen L, Wang T, Jia X, Liu L, Xu T, Ou M, Hoekzema K, Wu H, Gillentine MA, Liu C, Ni H, Peng P, Zhao R, Zhang Y, Phornphutkul C, Stegmann APA, Prada CE, Hopkin RJ, Shieh JT, McWalter K, Monaghan KG, van Hasselt PM, van Gassen K, Bai T, Long M, Han L, Quan Y, Chen M, Zhang Y, Li K, Zhang Q, Tan J, Zhu T, Liu Y, Pang N, Peng J, Scott DA, Lalani SR, Azamian M, Mancini GMS, Adams DJ, Kvarnung M, Lindstrand A, Nordgren A, Pevsner J, Osei-Owusu IA, Romano C, Calabrese G, Galesi O, Gecz J, Haan E, Ranells J, Racobaldo M, Nordenskjold M, Madan-Khetarpal S, Sebastian J, Ball S, Zou X, Zhao J, Hu Z, Xia F, Liu P, Rosenfeld JA, de Vries BBA, Bernier RA, Xu ZQD, Li H, Xie W, Hufnagel RB, Eichler EE, Xia K. Disruptive variants of CSDE1 associate with autism and interfere with neuronal development and synaptic transmission. SCIENCE ADVANCES 2019; 5:eaax2166. [PMID: 31579823 PMCID: PMC6760934 DOI: 10.1126/sciadv.aax2166] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/27/2019] [Indexed: 05/30/2023]
Abstract
RNA binding proteins are key players in posttranscriptional regulation and have been implicated in neurodevelopmental and neuropsychiatric disorders. Here, we report a significant burden of heterozygous, likely gene-disrupting variants in CSDE1 (encoding a highly constrained RNA binding protein) among patients with autism and related neurodevelopmental disabilities. Analysis of 17 patients identifies common phenotypes including autism, intellectual disability, language and motor delay, seizures, macrocephaly, and variable ocular abnormalities. HITS-CLIP revealed that Csde1-binding targets are enriched in autism-associated gene sets, especially FMRP targets, and in neuronal development and synaptic plasticity-related pathways. Csde1 knockdown in primary mouse cortical neurons leads to an overgrowth of the neurites and abnormal dendritic spine morphology/synapse formation and impaired synaptic transmission, whereas mutant and knockdown experiments in Drosophila result in defects in synapse growth and synaptic transmission. Our study defines a new autism-related syndrome and highlights the functional role of CSDE1 in synapse development and synaptic transmission.
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Affiliation(s)
- Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ying Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tianyun Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xiangbin Jia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lijuan Liu
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Tao Xu
- Department of Neurobiology, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Laboratory of Brain Disorders (Ministry of Science and Technology), Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Mengzhu Ou
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Huidan Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Madelyn A. Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Cenying Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hailun Ni
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Pengwei Peng
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rongjuan Zhao
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yu Zhang
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Chanika Phornphutkul
- Division of Human Genetics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI, USA
| | | | - Carlos E. Prada
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children’s Hospital, Cincinnati, OH, USA
| | - Robert J. Hopkin
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children’s Hospital, Cincinnati, OH, USA
| | - Joseph T. Shieh
- Institute for Human Genetics and Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Ting Bai
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Min Long
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lin Han
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yingting Quan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meilin Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaowen Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kuokuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jieqiong Tan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Zhu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaning Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Grazia M. S. Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Darius J. Adams
- Goryeb Children’s Hospital, Atlantic Health System, Morristown, NJ, USA
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, USA
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ikeoluwa A. Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, USA
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | | | - Jozef Gecz
- School of Medicine and the Robinson Research Institute, University of Adelaide at the Women’s and Children’s Hospital, Adelaide, South Australia, Australia
| | - Eric Haan
- Adult Genetics Unit, Royal Adelaide Hospital, and School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Judith Ranells
- Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Melissa Racobaldo
- Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Magnus Nordenskjold
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Susie Ball
- Central Washington Genetics Program, Virginia Mason Memorial, Yakima, WA, USA
| | - Xiaobing Zou
- Children Development Behavior Center of the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingping Zhao
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bert B. A. de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Zhi-Qing David Xu
- Department of Neurobiology, Beijing Key Laboratory of Neural Regeneration and Repair, Beijing Laboratory of Brain Disorders (Ministry of Science and Technology), Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Honghui Li
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Wei Xie
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, China
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Key Laboratory of Medical Information Research, Central South University, Changsha, Hunan, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai 200030, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan 410078, China
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22
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Booy EP, McRae EK, Ezzati P, Choi T, Gussakovsky D, McKenna SA. Comprehensive analysis of the BC200 ribonucleoprotein reveals a reciprocal regulatory function with CSDE1/UNR. Nucleic Acids Res 2019; 46:11575-11591. [PMID: 30247708 PMCID: PMC6265466 DOI: 10.1093/nar/gky860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
BC200 is a long non-coding RNA primarily expressed in brain but aberrantly expressed in various cancers. To gain a further understanding of the function of BC200, we performed proteomic analyses of the BC200 ribonucleoprotein (RNP) by transfection of 3′ DIG-labelled BC200. Protein binding partners of the functionally related murine RNA BC1 as well as a scrambled BC200 RNA were also assessed in both human and mouse cell lines. Stringent validation of proteins identified by mass spectrometry confirmed 14 of 84 protein binding partners and excluded eight proteins that did not appreciably bind BC200 in reverse experiments. Gene ontology analyses revealed general roles in RNA metabolic processes, RNA processing and splicing. Protein/RNA interaction sites were mapped with a series of RNA truncations revealing three distinct modes of interaction involving either the 5′ Alu-domain, 3′ A-rich or 3′ C-rich regions. Due to their high enrichment values in reverse experiments, CSDE1 and STRAP were further analyzed demonstrating a direct interaction between CSDE1 and BC200 and indirect binding of STRAP to BC200 via heterodimerization with CSDE1. Knock-down studies identified a reciprocal regulatory relationship between CSDE1 and BC200 and immunofluorescence analysis of BC200 knock-down cells demonstrated a dramatic reorganization of CSDE1 into distinct nuclear foci.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ewan Ks McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Section of Biomedical Proteomics, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba and Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Taegi Choi
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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23
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Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
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24
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Culjkovic-Kraljacic B, Borden KLB. The Impact of Post-transcriptional Control: Better Living Through RNA Regulons. Front Genet 2018; 9:512. [PMID: 30455716 PMCID: PMC6230556 DOI: 10.3389/fgene.2018.00512] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Traditionally, cancer is viewed as a disease driven by genetic mutations and/or epigenetic and transcriptional dysregulation. While these are undoubtedly important drivers, many recent studies highlight the disconnect between the proteome and the genome or transcriptome. At least in part, this disconnect arises as a result of dysregulated RNA metabolism which underpins the altered proteomic landscape observed. Thus, it is important to understand the basic mechanisms governing post-transcriptional control and how these processes can be co-opted to drive cancer cell phenotypes. In some cases, groups of mRNAs that encode protein involved in specific oncogenic processes can be co-regulated at multiple processing levels in order to turn on entire biochemical pathways. Indeed, the RNA regulon model was postulated as a means to understand how cells coordinately regulate transcripts encoding proteins in the same biochemical pathways. In this review, we describe some of the basic mRNA processes that are dysregulated in cancer and the biological impact this has on the cell. This dysregulation can affect networks of RNAs simultaneously thereby underpinning the oncogenic phenotypes observed.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
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25
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Wu Y, Zhao W, Liu Y, Tan X, Li X, Zou Q, Xiao Z, Xu H, Wang Y, Yang X. Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response. EMBO J 2018; 37:embj.201899017. [PMID: 30158112 PMCID: PMC6276880 DOI: 10.15252/embj.201899017] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/02/2018] [Accepted: 08/07/2018] [Indexed: 01/03/2023] Open
Abstract
Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG‐I was responsible for such tumor‐inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double‐stranded RNA (dsRNA), the binding ligand of RIG‐I. These up‐regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre‐mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well‐characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down‐stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.
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Affiliation(s)
- Yusheng Wu
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenwei Zhao
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Liu
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Xiangtian Tan
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Li
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Qin Zou
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Zhengtao Xiao
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Hui Xu
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuting Wang
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, China
| | - Xuerui Yang
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China .,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
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26
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Moore KS, Yagci N, van Alphen F, Meijer AB, ‘t Hoen PAC, von Lindern M. Strap associates with Csde1 and affects expression of select Csde1-bound transcripts. PLoS One 2018; 13:e0201690. [PMID: 30138317 PMCID: PMC6107111 DOI: 10.1371/journal.pone.0201690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 07/22/2018] [Indexed: 02/06/2023] Open
Abstract
Erythropoiesis is regulated at many levels, including control of mRNA translation. Changing environmental conditions, such as hypoxia or the availability of nutrients and growth factors, require a rapid response enacted by the enhanced or repressed translation of existing transcripts. Cold shock domain protein e1 (Csde1/Unr) is an RNA-binding protein required for erythropoiesis and strongly upregulated in erythroblasts relative to other hematopoietic progenitors. The aim of this study is to identify the Csde1-containing protein complexes and investigate their role in post-transcriptional expression control of Csde1-bound transcripts. We show that Serine/Threonine kinase receptor-associated protein (Strap/Unrip), was the protein most strongly associated with Csde1 in erythroblasts. Strap is a WD40 protein involved in signaling and RNA splicing, but its role when associated with Csde1 is unknown. Reduced expression of Strap did not alter the pool of transcripts bound by Csde1. Instead, it altered the mRNA and/or protein expression of several Csde1-bound transcripts that encode for proteins essential for translational regulation during hypoxia, such as Hmbs, eIF4g3 and Pabpc4. Also affected by Strap knockdown were Vim, a Gata-1 target crucial for erythrocyte enucleation, and Elavl1, which stabilizes Gata-1 mRNA. The major cellular processes affected by both Csde1 and Strap were ribosome function and cell cycle control.
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Affiliation(s)
- Kat S. Moore
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Nurcan Yagci
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floris van Alphen
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
| | - Alexander B. Meijer
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter A. C. ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marieke von Lindern
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Moore KS, von Lindern M. RNA Binding Proteins and Regulation of mRNA Translation in Erythropoiesis. Front Physiol 2018; 9:910. [PMID: 30087616 PMCID: PMC6066521 DOI: 10.3389/fphys.2018.00910] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Control of gene expression in erythropoiesis has to respond to signals that may emerge from intracellular processes or environmental factors. Control of mRNA translation allows for relatively rapid modulation of protein synthesis from the existing transcriptome. For instance, the protein synthesis rate needs to be reduced when reactive oxygen species or unfolded proteins accumulate in the cells, but also when iron supply is low or when growth factors are lacking in the environment. In addition, regulation of mRNA translation can be important as an additional layer of control on top of gene transcription, in which RNA binding proteins (RBPs) can modify translation of a set of transcripts to the cell’s actual protein requirement. The 5′ and 3′ untranslated regions of mRNA (5′UTR, 3′UTR) contain binding sites for general and sequence specific translation factors. They also contain secondary structures that may hamper scanning of the 5′UTR by translation complexes or may help to recruit translation factors. In addition, the term 5′UTR is not fully correct because many transcripts contain small open reading frames in their 5′UTR that are translated and contribute to regulation of mRNA translation. It is becoming increasingly clear that the transcriptome only partly predicts the proteome. The aim of this review is (i) to summarize how the availability of general translation initiation factors can selectively regulate transcripts because the 5′UTR contains secondary structures or short translated sequences, (ii) to discuss mechanisms that control the length of the mRNA poly(A) tail in relation to mRNA translation, and (iii) to give examples of sequence specific RBPs and their targets. We focused on transcripts and RBPs required for erythropoiesis. Whereas differentiation of erythroblasts to erythrocytes is orchestrated by erythroid transcription factors, the production of erythrocytes needs to respond to the availability of growth factors and nutrients, particularly the availability of iron.
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Affiliation(s)
- Kat S Moore
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
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Sepulveda G, Antkowiak M, Brust-Mascher I, Mahe K, Ou T, Castro NM, Christensen LN, Cheung L, Jiang X, Yoon D, Huang B, Jao LE. Co-translational protein targeting facilitates centrosomal recruitment of PCNT during centrosome maturation in vertebrates. eLife 2018; 7:34959. [PMID: 29708497 PMCID: PMC5976437 DOI: 10.7554/elife.34959] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/30/2018] [Indexed: 12/16/2022] Open
Abstract
As microtubule-organizing centers of animal cells, centrosomes guide the formation of the bipolar spindle that segregates chromosomes during mitosis. At mitosis onset, centrosomes maximize microtubule-organizing activity by rapidly expanding the pericentriolar material (PCM). This process is in part driven by the large PCM protein pericentrin (PCNT), as its level increases at the PCM and helps recruit additional PCM components. However, the mechanism underlying the timely centrosomal enrichment of PCNT remains unclear. Here, we show that PCNT is delivered co-translationally to centrosomes during early mitosis by cytoplasmic dynein, as evidenced by centrosomal enrichment of PCNT mRNA, its translation near centrosomes, and requirement of intact polysomes for PCNT mRNA localization. Additionally, the microtubule minus-end regulator, ASPM, is also targeted co-translationally to mitotic spindle poles. Together, these findings suggest that co-translational targeting of cytoplasmic proteins to specific subcellular destinations may be a generalized protein targeting mechanism. Before a cell divides, it creates a copy of its genetic material (DNA) and evenly distributes it between the new ‘daughter’ cells with the help of a complex called the mitotic spindle. This complex is made of long cable-like protein chains called microtubules. To ensure that each daughter cell receives an equal amount of DNA, structures known as centrosomes organize the microtubules during the division process. Centrosomes have two rigid cores, called centrioles, which are surrounded by a matrix of proteins called the pericentriolar material. It is from this material that the microtubules are organized. The pericentriolar material is a dynamic structure and changes its size by assembling and disassembling its protein components. The larger the pericentriolar material, the more microtubules can form. Before a cell divides, it rapidly expands in a process called centrosome maturation. A protein called pericentrin initiates the maturation by helping to recruit other proteins to the centrosome. Pericentrin molecules are large, and it takes the cell between 10 and 20 minutes to make each one. Nevertheless, the cell can produce and deliver large quantities of pericentrin to the centrosome in a matter of minutes. We do not yet know how this happens. To investigate this further, Sepulveda, Antkowiak, Brust-Mascher et al. used advanced microscopy to study zebrafish embryos and human cells grown in the laboratory. The results showed that cells build and transport pericentrin at the same time. Cells use messenger RNA molecules as templates to build proteins. These feed into protein factories called ribosomes, which assemble the building blocks in the correct order. Rather than waiting for the pericentrin production to finish, the cell moves the active factories to the centrosome with the help of a molecular motor called dynein. By the time the pericentrin molecules are completely made by ribosomes, they are already at the centrosome, ready to help with the recruitment of other proteins during centrosome maturation. These findings improve our understanding of centrosome maturation. The next step is to find out how the cell coordinates this process with the recruitment of other proteins to the centrosome. It is also possible that the cell uses similar processes to deliver other proteins to different parts of the cell.
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Affiliation(s)
- Guadalupe Sepulveda
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Mark Antkowiak
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Ingrid Brust-Mascher
- Department of Anatomy, Physiology and Cell Biology, University of California, Davis School of Veterinary Medicine, Davis, United States
| | - Karan Mahe
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Tingyoung Ou
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Noemi M Castro
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Lana N Christensen
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Lee Cheung
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Xueer Jiang
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Daniel Yoon
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Li-En Jao
- Department of Cell Biology and Human Anatomy, University of California, Davis School of Medicine, Davis, United States
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Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line. Sci Rep 2018; 8:2628. [PMID: 29422612 PMCID: PMC5805679 DOI: 10.1038/s41598-018-20518-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/18/2018] [Indexed: 01/12/2023] Open
Abstract
Expression of the RNA-binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis compared to other hematopoietic lineages. Csde1 expression is impaired in the severe congenital anemia Diamond Blackfan Anemia (DBA), and reduced expression of Csde1 in healthy erythroblasts impaired their proliferation and differentiation. To investigate the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1 in erythroid cells. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. For instance, protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced indicating more efficient translation of Pabpc1 followed by negative feedback on mRNA stability. Overall, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. Clones with complete loss of Csde1, however, could not be generated. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression.
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Lampe S, Kunze M, Scholz A, Brauß TF, Winslow S, Simm S, Keller M, Heidler J, Wittig I, Brüne B, Schmid T. Identification of the TXNIP IRES and characterization of the impact of regulatory IRES trans-acting factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:147-157. [PMID: 29378331 DOI: 10.1016/j.bbagrm.2018.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Sebastian Lampe
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Michael Kunze
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Thilo F Brauß
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Sofia Winslow
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Simm
- Department of Molecular Cell Biology of Plants, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mario Keller
- Department of Molecular Cell Biology of Plants, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.
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A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells. Nat Commun 2017; 8:1456. [PMID: 29129916 PMCID: PMC5682285 DOI: 10.1038/s41467-017-01744-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 10/11/2017] [Indexed: 12/29/2022] Open
Abstract
While the transcriptional network of human embryonic stem cells (hESCs) has been extensively studied, relatively little is known about how post-transcriptional modulations determine hESC function. RNA-binding proteins play central roles in RNA regulation, including translation and turnover. Here we show that the RNA-binding protein CSDE1 (cold shock domain containing E1) is highly expressed in hESCs to maintain their undifferentiated state and prevent default neural fate. Notably, loss of CSDE1 accelerates neural differentiation and potentiates neurogenesis. Conversely, ectopic expression of CSDE1 impairs neural differentiation. We find that CSDE1 post-transcriptionally modulates core components of multiple regulatory nodes of hESC identity, neuroectoderm commitment and neurogenesis. Among these key pro-neural/neuronal factors, CSDE1 binds fatty acid binding protein 7 (FABP7) and vimentin (VIM) mRNAs, as well as transcripts involved in neuron projection development regulating their stability and translation. Thus, our results uncover CSDE1 as a central post-transcriptional regulator of hESC identity and neurogenesis. Unlike transcriptional regulation of hESC identity, little is known post-transcriptionally. Here, the authors show that the RNA binding protein CSDE1 regulates core components of hESC identity, neurectoderm commitment and neurogenesis to maintain pluripotency and prevent neural differentiation.
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32
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Aviner R, Hofmann S, Elman T, Shenoy A, Geiger T, Elkon R, Ehrlich M, Elroy-Stein O. Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis. Nucleic Acids Res 2017; 45:5945-5957. [PMID: 28460002 PMCID: PMC5449605 DOI: 10.1093/nar/gkx326] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/16/2017] [Indexed: 12/16/2022] Open
Abstract
Precise regulation of mRNA translation is critical for proper cell division, but little is known about the factors that mediate it. To identify mRNA-binding proteins that regulate translation during mitosis, we analyzed the composition of polysomes from interphase and mitotic cells using unbiased quantitative mass-spectrometry (LC–MS/MS). We found that mitotic polysomes are enriched with a subset of proteins involved in RNA processing, including alternative splicing and RNA export. To demonstrate that these may indeed be regulators of translation, we focused on heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a test case and confirmed that it is recruited to elongating ribosomes during mitosis. Then, using a combination of pulsed SILAC, metabolic labeling and ribosome profiling, we showed that knockdown of hnRNP C affects both global and transcript-specific translation rates and found that hnRNP C is specifically important for translation of mRNAs that encode ribosomal proteins and translation factors. Taken together, our results demonstrate how proteomic analysis of polysomes can provide insight into translation regulation under various cellular conditions of interest and suggest that hnRNP C facilitates production of translation machinery components during mitosis to provide daughter cells with the ability to efficiently synthesize proteins as they enter G1 phase.
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Affiliation(s)
- Ranen Aviner
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sarah Hofmann
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Elman
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anjana Shenoy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcelo Ehrlich
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Orna Elroy-Stein
- Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Esnault S, Shen ZJ, Malter JS. Protein Translation and Signaling in Human Eosinophils. Front Med (Lausanne) 2017; 4:150. [PMID: 28971096 PMCID: PMC5609579 DOI: 10.3389/fmed.2017.00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/01/2017] [Indexed: 01/01/2023] Open
Abstract
We have recently reported that, unlike IL-5 and GM-CSF, IL-3 induces increased translation of a subset of mRNAs. In addition, we have demonstrated that Pin1 controls the activity of mRNA binding proteins, leading to enhanced mRNA stability, GM-CSF protein production and prolonged eosinophil (EOS) survival. In this review, discussion will include an overview of cap-dependent protein translation and its regulation by intracellular signaling pathways. We will address the more general process of mRNA post-transcriptional regulation, especially regarding mRNA binding proteins, which are critical effectors of protein translation. Furthermore, we will focus on (1) the roles of IL-3-driven sustained signaling on enhanced protein translation in EOS, (2) the mechanisms regulating mRNA binding proteins activity in EOS, and (3) the potential targeting of IL-3 signaling and the signaling leading to mRNA binding activity changes to identify therapeutic targets to treat EOS-associated diseases.
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Affiliation(s)
- Stephane Esnault
- Department of Medicine, Allergy, Pulmonary, and Critical Care Medicine Division, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States
| | - Zhong-Jian Shen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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Martinez-Useros J, Georgiev-Hristov T, Fernández-Aceñero MJ, Borrero-Palacios A, Indacochea A, Guerrero S, Li W, Cebrián A, Gómez del Pulgar T, Puime-Otin A, del Puerto-Nevado L, Rodríguez-Remírez M, Pérez N, Celdrán A, Gebauer F, Garcia-Foncillas J. UNR/CDSE1 expression as prognosis biomarker in resectable pancreatic ductal adenocarcinoma patients: A proof-of-concept. PLoS One 2017; 12:e0182044. [PMID: 28763470 PMCID: PMC5538752 DOI: 10.1371/journal.pone.0182044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/11/2017] [Indexed: 12/25/2022] Open
Abstract
Pancreatic ductal adenocarcinoma is an aggressive form of pancreatic cancer and the fourth leading cause of cancer-related death. When possible, curative approaches are based on surgical resection, though not every patient is a candidate for surgery. There are clinical guidelines for the management of these patients that offer different treatment options depending on the clinical and pathologic characteristics. However, the survival rates seen in this kind of patients are still low. The CDSE1 gene is located upstream of NRAS and encodes an RNA-binding protein termed UNR. The aim of this study was to analyze UNR expression and its correlation with outcome in patients with resectable pancreatic ductal adenocarcinoma (PDAC). For this, samples from resectable PDAC patients who underwent duodenopancreatectomy were used to evaluate UNR protein expression by immunohistochemistry using a tissue microarray. Here, we observed that low UNR expression was significantly associated with shorter progression-free survival after surgery (P = 0.010). Moreover, this prognostic marker remained significant after Cox proportional hazards model (P = 0.036). We further studied the role of CDSE1 expression in patient's prognosis using data from public repositories (GEO and TGCA), confirming our results. Interestingly, CDSE1 expression correlated with that of genes characteristic of an immunogenic molecular subtype of pancreatic cancer. Based on these findings, UNR may be considered a potential prognostic biomarker for resectable PDAC and may serve to guide subsequent adjuvant treatment decisions.
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Affiliation(s)
- Javier Martinez-Useros
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | | | | | - Aurea Borrero-Palacios
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | - Alberto Indacochea
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Oncology and Molecular Pathology Research Group-VHIR- Vall d' Hebron Institut de Recerca-Vall d' Hebron Hospital, P/ de la Vall d'Hebron, Barcelona, Spain
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Weiyao Li
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | - Arancha Cebrián
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | - Teresa Gómez del Pulgar
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | - Alberto Puime-Otin
- Department of Pathology, University Hospital Fundacion Jimenez Diaz, Madrid, Spain
| | - Laura del Puerto-Nevado
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | - María Rodríguez-Remírez
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
| | - Nuria Pérez
- Department of Pathology, University Hospital Fundacion Jimenez Diaz, Madrid, Spain
| | - Angel Celdrán
- Hepatobiliary and Pancreatic Surgery Unit, General and Digestive Tract Surgery Department, Fundacion Jimenez Diaz University Hospital, Madrid, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jesus Garcia-Foncillas
- Translational Oncology Division, OncoHealth Institute, University Hospital Fundacion Jimenez Diaz (FJD), Madrid, Spain
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Wurth L, Papasaikas P, Olmeda D, Bley N, Calvo GT, Guerrero S, Cerezo-Wallis D, Martinez-Useros J, García-Fernández M, Hüttelmaier S, Soengas MS, Gebauer F. UNR/CSDE1 Drives a Post-transcriptional Program to Promote Melanoma Invasion and Metastasis. Cancer Cell 2016; 30:694-707. [PMID: 27908735 DOI: 10.1016/j.ccell.2016.10.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 06/13/2016] [Accepted: 10/03/2016] [Indexed: 12/11/2022]
Abstract
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination. Key pro-oncogenic targets of UNR included VIM and RAC1, as validated by loss- and gain-of-function studies. Our results identify UNR as an oncogenic modulator of melanoma progression, unravel the underlying molecular mechanisms, and identify potential targets for this therapeutically challenging malignancy.
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Affiliation(s)
- Laurence Wurth
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Panagiotis Papasaikas
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Olmeda
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Nadine Bley
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Guadalupe T Calvo
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Santiago Guerrero
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Daniela Cerezo-Wallis
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Martinez-Useros
- Translational Oncology Division, Oncohealth Institute - Health Research Institute - University Hospital "Fundacion Jimenez Diaz", 28040 Madrid, Spain
| | - María García-Fernández
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Stefan Hüttelmaier
- Section Molecular Cell Biology, Institute of Molecular Medicine (IMM), Martin-Luther-University (MLU), 06120 Halle, Germany
| | - Maria S Soengas
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
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Li J, Tian H, Yang J, Gong Z. Long Noncoding RNAs Regulate Cell Growth, Proliferation, and Apoptosis. DNA Cell Biol 2016; 35:459-70. [PMID: 27213978 DOI: 10.1089/dna.2015.3187] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The revolutionary findings in nonprotein-coding part of human genome analysis have revealed a large number of RNA transcripts longer than 200 nucleotides that lack coding protein function, termed long noncoding RNAs (lncRNAs). Recently, accumulating shreds of evidence suggest that lncRNAs are widely distributed in human genome and deeply involved in cellular activities such as cell growth, proliferation, and apoptosis. Generally, lncRNAs regulate cell behaviors by targeting cell cycle-associated cyclins, cyclin-dependent kinases (CDKs), and/or CDK inhibitors. Specifically, lncRNAs serve as scaffolds or guides for chromatin-modifying complexes and act as signals in response to DNA damage. In addition, lncRNAs function as protein decoys and microRNA decoys, as well as interveners in cell division by modulating oncogenes and/or tumor suppressors. In this review, we mainly focus on the current understanding of the molecular mechanisms, how lncRNAs influence cellular processes and cancer progression. Finally, we also prospect the limitations of lncRNAs in cell behaviors and the novel roles of lncRNAs in epigenetic regulations.
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Affiliation(s)
- Jingqiu Li
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Haihua Tian
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China .,3 Department of Laboratory Medicine, Ningbo Kangning Hospital , Ningbo, China
| | - Jie Yang
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Zhaohui Gong
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
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Abstract
The daily production of up to 1011 erythrocytes is tightly controlled to maintain the number of erythrocytes in peripheral blood between narrow boundaries. Availability of growth factors and nutrients, particularly iron, control the proliferation and survival of precursor cells partly through control of mRNA translation. General translation initiation mechanisms can selectively control translation of transcripts that carry specific structures in the UTRs. This selective mRNA translation is an important layer of gene expression regulation in erythropoiesis. Ribosome profiling is a recently developed high throughput sequencing technique for global mapping of translation initiation sites across the transcriptome. Here we describe what is known about control of mRNA translation in erythropoiesis and how ribosome profiling will help to further our knowledge. Ribosome footprinting will give insight in transcript-specific translation at codon resolution, which is of great value to understand many cellular processes during erythropoiesis. It will be of particular interest to understand responses to iron availability and reactive oxygen species (ROS), which affects translation initiation of transcripts harbouring upstream ORFs (uORF) and potential alternative downstream ORFs (aORF).
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Ren D, Li H, Li R, Sun J, Guo P, Han H, Yang Y, Li J. Novel insight into MALAT-1 in cancer: Therapeutic targets and clinical applications. Oncol Lett 2016; 11:1621-1630. [PMID: 26998053 DOI: 10.3892/ol.2016.4138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023] Open
Abstract
Long non-protein-coding RNAs (lncRNAs) are emerging as important gene expression regulators that are linked to various biological processes at the post-transcriptional and transcriptional levels. lncRNAs are known to be important in cell proliferation, cell differentiation, apoptosis and metastasis. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), a novel lncRNA, is highly conserved amongst mammals. In addition, it has been considered to act as an oncogene, depending on the tumor system. An increasing number of studies have indicated that MALAT-1 may be detected in certain types of human tumors, including lung and bladder cancer and hepatocellular carcinoma. MALAT-1 silencing may be an effective therapeutic approach against tumors. The present study reviews the current knowledge on the functional role of MALAT-1 in the control of various cancers.
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Affiliation(s)
- Danyang Ren
- Pharmaceutical Preparation Section, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Huiying Li
- Pharmaceutical Preparation Section, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Renqiu Li
- Pharmaceutical Preparation Section, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Jianming Sun
- Pharmaceutical Preparation Section, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Pin Guo
- Pharmaceutical Preparation Section, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Huiyun Han
- Pharmaceutical Preparation Section, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Yuehuang Yang
- Department of Hematology, Children's Hospital of Kunming Medical University, Kunming, Yunnan 650034, P.R. China
| | - Jun Li
- Department of Pharmacy, Anhui Medical University, Hefei, Anhui 230032, P.R. China
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Benegiamo G, Brown SA, Panda S. RNA Dynamics in the Control of Circadian Rhythm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:107-22. [PMID: 27256384 DOI: 10.1007/978-3-319-29073-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The circadian oscillator is based on transcription-translation feedback loops that generate 24 h oscillations in gene expression. Although circadian regulation of mRNA expression at the transcriptional level is one of the most important steps for the generation of circadian rhythms within the cell, multiple lines of evidence point to a disconnect between transcript oscillation and protein oscillation. This can be explained by regulatory RNA-binding proteins acting on the nascent transcripts to modulate their processing, export, translation and degradation rates. In this chapter we will review what is known about the different steps involved in circadian gene expression from transcription initiation to mRNA stability and translation efficiency. The role of ribonucleoprotein particles in the generation of rhythmic gene expression is only starting to be elucidated, but it is likely that they cooperate with the basal transcriptional machinery to help to maintain the precision of the clock under diverse cellular and environmental conditions.
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Affiliation(s)
- Giorgia Benegiamo
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Satchidananda Panda
- Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA.
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40
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Abstract
Protein-RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes to host defense against pathogens. In this chapter we present the computational approach catRAPID to predict protein-RNA interactions and discuss how it could be used to find trends in ribonucleoprotein networks. We envisage that the combination of computational and experimental approaches will be crucial to unravel the role of coding and noncoding RNAs in protein networks.
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Abstract
Unr (upstream of N-ras) is a post-transcriptional regulator of gene expression, essential for mammalian development and mutated in many human cancers. The expression of unr is itself regulated at many levels; transcription of unr, which also affects expression of the downstream N-ras gene, is tissue and developmental stage-dependent and is repressed by c-Myc and Max (Myc associated factor X). Alternative splicing gives rise to six transcript variants, which include three different 5′-UTRs. The transcripts are further diversified by the use of three alternative polyadenylation signals, which governs whether AU-rich instability elements are present in the 3′-UTR or not. Translation of at least some unr transcripts can occur by internal initiation and is regulated in a cell-cycle-dependent manner; binding of PTB (polypyrimidine tract-binding protein) and Unr to the 5′-UTR inhibits translation, but these are displaced by heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNPC1/C2) during mitosis to stimulate translation. Finally, Unr is post-translationally modified by phosphorylation and lysine acetylation, although it is not yet known how these modifications affect Unr activity.
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Cieniková Z, Jayne S, Damberger FF, Allain FHT, Maris C. Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing. RNA (NEW YORK, N.Y.) 2015; 21:1931-42. [PMID: 26370582 PMCID: PMC4604433 DOI: 10.1261/rna.052373.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/21/2015] [Indexed: 05/20/2023]
Abstract
The human hnRNP C is a ubiquitous cellular protein involved in mRNA maturation. Recently, we have shown that this protein specifically recognizes uridine (U) pentamers through its single RNA recognition motif (RRM). However, a large fraction of natural RNA targets of hnRNP C consists of much longer contiguous uridine stretches. To understand how these extended sites are recognized, we studied the binding of the RRM to U-tracts of 8-11 bases. In vivo investigation of internal translation activation of unr (upstream of N-ras) mRNA indicates that the conservation of the entire hnRNP C binding site, UC(U)8, is required for hnRNP C-dependent IRES activation. The assays further suggest a synergistic interplay between hnRNP C monomers, dependent on the protein's ability to oligomerize. In vitro spectroscopic and thermodynamic analyses show that isolated RRMs bind to (U)11 oligomers as dimers. Structural modeling of a ternary double-RRM/RNA complex indicates additionally that two RRM copies can be accommodated on the canonical sequence UC(U)8. The proposed tandem RRM binding is in very good agreement with the transcriptome-wide recognition of extended U-tracts by full-length hnRNP C, which displays a cross-linking pattern consistent with a positively cooperative RRM dimer binding model.
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Affiliation(s)
- Zuzana Cieniková
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Sandrine Jayne
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Fred Franz Damberger
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Christophe Maris
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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Yang B, Hu P, Lin X, Han W, Zhu L, Tan X, Ye F, Wang G, Wu F, Yin B, Bao Z, Jiang T, Yuan J, Qiang B, Peng X. PTBP1 induces ADAR1 p110 isoform expression through IRES-like dependent translation control and influences cell proliferation in gliomas. Cell Mol Life Sci 2015; 72:4383-97. [PMID: 26047657 PMCID: PMC11114032 DOI: 10.1007/s00018-015-1938-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 12/27/2022]
Abstract
Internal ribosomal entry site (IRES)-mediated translation initiation is constitutively activated during stress conditions such as tumorigenesis and hypoxia. The RNA editing enzyme ADAR1 plays an important role in physiology and pathology. Initially, we found that the ADAR1 p150 or p110 transcript levels were decreased in glioma cells compared with normal astrocyte cells. In contrast, protein levels of ADAR1 p110 were significantly upregulated in glioma tissues and cells. This expression pattern indicated translationally controlled regulation. We identified an 885-nt sequence that was located between AUG1 and AUG2 within the ADAR1 mRNA that exhibited IRES-like activity. Furthermore, we confirmed that the translational mode of ADAR1 p110 was mediated by PTBP1 in glioma cells. The protein levels of PTBP1 and ADAR1 were cooperatively expressed in glioma tissues and cells. Knocking down ADAR1 p110 significantly decreased cell proliferation in three types of glioma cells (T98G, U87MG and A172). The removal of a minimal IRES-like sequence in a p150-overexpression construct could effectively abolish p110 induction and resulted in the slight suppression of cell proliferation compared with ADAR1-p150 overexpression in siPTBP1-treated T98G cells. In summary, our study revealed a mechanism whereby ADAR1 p110 can be activated by PTBP1 through an IRES-like element in glioma cells, and ADAR1 is essential for the maintenance of gliomagenesis.
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Affiliation(s)
- Bin Yang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
- The State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and National Center of Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 102300, People's Republic of China
| | - Peishan Hu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Xihua Lin
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Wei Han
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Liyuan Zhu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Xiaochao Tan
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Fei Ye
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Guanzhou Wang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Fan Wu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Bin Yin
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, People's Republic of China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, People's Republic of China
| | - Jiangang Yuan
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China
| | - Boqin Qiang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China.
| | - Xiaozhong Peng
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, People's Republic of China.
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Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD. Regulation of mRNA translation during mitosis. eLife 2015; 4. [PMID: 26305499 PMCID: PMC4548207 DOI: 10.7554/elife.07957] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/02/2015] [Indexed: 12/21/2022] Open
Abstract
Passage through mitosis is driven by precisely-timed changes in transcriptional regulation and protein degradation. However, the importance of translational regulation during mitosis remains poorly understood. Here, using ribosome profiling, we find both a global translational repression and identified ∼200 mRNAs that undergo specific translational regulation at mitotic entry. In contrast, few changes in mRNA abundance are observed, indicating that regulation of translation is the primary mechanism of modulating protein expression during mitosis. Interestingly, 91% of the mRNAs that undergo gene-specific regulation in mitosis are translationally repressed, rather than activated. One of the most pronounced translationally-repressed genes is Emi1, an inhibitor of the anaphase promoting complex (APC) which is degraded during mitosis. We show that full APC activation requires translational repression of Emi1 in addition to its degradation. These results identify gene-specific translational repression as a means of controlling the mitotic proteome, which may complement post-translational mechanisms for inactivating protein function. DOI:http://dx.doi.org/10.7554/eLife.07957.001 The human body contains billions of cells, most of which formed via a process called mitosis in which a single cell divides to produce two new daughter cells. Actively dividing cells pass through a series of events (or phases) that are collectively known as the cell cycle. These phases allow the cell to grow in size, copy its genetic material, and then make preparations for cell division before taking the final decision to divide. Many proteins are involved in regulating the cell cycle and each protein has a particular role in specific phases. The levels of these proteins in cells may change during the cycle, which is often crucial to allow the cell to progress to the next phase. For example, cells need a group of proteins called the anaphase-promoting complex (or APC for short) to destroy other specific proteins at the end of mitosis. Another way in which the amount of protein in a cell can be adjusted is by controlling how much new protein is made during a process known as translation. During this process, a molecule called a messenger RNA (mRNA)—which contains information copied from a particular gene—is used as a template to assemble a new protein. However, it is not clear whether regulation of translation is involved in control of the cell division. Tanenbaum et al. now address this question using a technique called ribosome profiling to measure the translation of individual mRNA molecules. The experiments analysed the changes in protein production before, during and after mitosis. The overall level of translation of all the mRNAs was about 35% lower during mitosis. However, some mRNAs in particular experienced a very large reduction in the level of translation (between three- and ten-fold less than the levels before mitosis). One example of an mRNA whose translation is turned off in mitosis is the mRNA that makes a protein called Emi1. It is known from previous work that Emi1 inhibits the activity of the APC. Therefore, Emi1 needs to be inactivated in mitosis so that the APC can become active and promote progression to the next phase of the cell cycle. It was previously shown that Emi1 is destroyed during mitosis to allow the APC to operate. Tanenbaum et al. found that translation of the Emi1 mRNA must also be suppressed during mitosis in order to keep Emi1 protein levels very low and allow the APC to become fully active. These findings uncover a new role for the control of protein production in regulating the cell cycle. The next challenge will be to find out whether suppression of translation is also used in other biological systems where proteins need to be rapidly inactivated. DOI:http://dx.doi.org/10.7554/eLife.07957.002
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Affiliation(s)
- Marvin E Tanenbaum
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Noam Stern-Ginossar
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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Abstract
Unr (upstream of N-ras) is a eukaryotic RNA-binding protein that has a number of roles in the post-transcriptional regulation of gene expression. Originally identified as an activator of internal initiation of picornavirus translation, it has since been shown to act as an activator and inhibitor of cellular translation and as a positive and negative regulator of mRNA stability, regulating cellular processes such as mitosis and apoptosis. The different post-transcriptional functions of Unr depend on the identity of its mRNA and protein partners and can vary with cell type and changing cellular conditions. Recent high-throughput analyses of RNA–protein interactions indicate that Unr binds to a large subset of cellular mRNAs, suggesting that Unr may play a wider role in translational responses to cellular signals than previously thought.
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Dechtawewat T, Songprakhon P, Limjindaporn T, Puttikhunt C, Kasinrerk W, Saitornuang S, Yenchitsomanus PT, Noisakran S. Role of human heterogeneous nuclear ribonucleoprotein C1/C2 in dengue virus replication. Virol J 2015; 12:14. [PMID: 25890165 PMCID: PMC4351676 DOI: 10.1186/s12985-014-0219-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/27/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Host and viral proteins are involved in dengue virus (DENV) replication. Heterogeneous ribonucleoprotein (hnRNP) C1/C2 are abundant host cellular proteins that exhibit RNA binding activity and play important roles in the replication of positive-strand RNA viruses such as poliovirus and hepatitis C virus. hnRNP C1/C2 have previously been shown to interact with vimentin and viral NS1 in DENV-infected cells; however, their functional role in DENV replication is not clearly understood. In the present study, we investigated the role of hnRNP C1/C2 in DENV replication by using an in vitro model of DENV infection in a hepatocyte cell line (Huh7) and siRNA-mediated knockdown of hnRNP C1/C2. METHODS Huh7 cells were transfected with hnRNP C1/C2-specific siRNA or irrelevant siRNA (control) followed by infection with DENV. Mock and DENV-infected knockdown cells were processed for immunoprecipitation using hnRNP C1/C2-specific antibody or their isotype-matched control antibody. The immunoprecipitated samples were subjected to RNA extraction and reverse transcriptase polymerase chain reaction (RT-PCR) for detection of DENV RNA. In addition, the knockdown cells harvested at varying time points after the infection were assessed for cell viability, cell proliferation, percentage of DENV infection, amount of viral RNA, and viral E and NS1 expression. Culture supernatants were subjected to focus forming unit assays to determine titers of infectious DENV. DENV luciferase reporter assay was also set up to determine viral translation. RESULTS Immunoprecipitation with the anti-hnRNP C1/C2 antibody and subsequent RT-PCR revealed the presence of DENV RNA in the immunoprecipitated complex containing hnRNP C1/C2 proteins. Transfection with hnRNP C1/C2-specific siRNA resulted in a significant reduction of hnRNP C1/C2 mRNA and protein levels but did not induce cell death during DENV infection. The reduced hnRNP C1/C2 expression decreased the percentage of DENV antigen-positive cells as well as the amount of DENV RNA and the relative levels of DENV E and NS1 proteins; however, it had no direct effect on DENV translation. In addition, a significant reduction of DENV titers was observed in the supernatant from DENV-infected cells following the knockdown of hnRNP C1/C2. CONCLUSIONS Our findings suggest that hnRNP C1/C2 is involved in DENV replication at the stage of viral RNA synthesis.
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Affiliation(s)
- Thanyaporn Dechtawewat
- Division of Molecular Medicine, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Pucharee Songprakhon
- Division of Molecular Medicine, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Thawornchai Limjindaporn
- Department of Anatomy, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Chunya Puttikhunt
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, 10700, Thailand.
- Division of Dengue Hemorrhagic Fever Research Unit, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Watchara Kasinrerk
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Chiang Mai, 50200, Thailand.
| | - Sawanan Saitornuang
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, 10700, Thailand.
- Division of Dengue Hemorrhagic Fever Research Unit, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Sansanee Noisakran
- Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, 10700, Thailand.
- Division of Dengue Hemorrhagic Fever Research Unit, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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Zhang C, Zhang M, Wu Q, Peng J, Ruan Y, Gu J. Hepsin inhibits CDK11p58 IRES activity by suppressing unr expression and eIF-2α phosphorylation in prostate cancer. Cell Signal 2015; 27:789-97. [PMID: 25576733 DOI: 10.1016/j.cellsig.2014.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/31/2014] [Indexed: 11/29/2022]
Abstract
Hepsin is a type II transmembrane serine protease frequently overexpressed in prostate cancer (PCa). However, the role of hepsin in PCa remains unclear. In this study, we found that hepsin inhibited the internal ribosome entry site (IRES) activity and expression of CDK11p58, which is associated with cell cycle progression and pro-apoptotic signaling in PCa. Hepsin suppressed CDK11p58 IRES activity in PCa by modulating unr expression and eIF-2α phosphorylation. Further studies revealed that hepsin inhibited the expression of unr by directly binding to unr IRES element and suppressing its activity, and also repressed eIF-2α phosphorylation through down-regulating the expression and phosphorylation of general control non-derepressible-2 (GCN2). Taken together, our data suggest a novel role of hepsin in regulating CDK11p58 IRES activity, and imply that hepsin may act on the machinery of translation to modulate cell cycle progression and survival in PCa cells.
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Affiliation(s)
- Chunyi Zhang
- Gene Research Center, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Mingming Zhang
- Gene Research Center, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qingyu Wu
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Jianhao Peng
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Yuanyuan Ruan
- Gene Research Center, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Jianxin Gu
- Gene Research Center, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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48
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Sharathchandra A, Lal R, Khan D, Das S. Annexin A2 and PSF proteins interact with p53 IRES and regulate translation of p53 mRNA. RNA Biol 2014; 9:1429-39. [DOI: 10.4161/rna.22707] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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49
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Cieniková Z, Damberger FF, Hall J, Allain FHT, Maris C. Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif. J Am Chem Soc 2014; 136:14536-44. [PMID: 25216038 DOI: 10.1021/ja507690d] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HnRNP C is a ubiquitous RNA regulatory factor and the principal constituent of the nuclear hnRNP core particle. The protein contains one amino-terminal RNA recognition motif (RRM) known to bind uridine (U)-rich sequences. This work provides a molecular and mechanistic understanding of this interaction. We solved the solution structures of the RRM in complex with poly(U) oligomers of five and seven nucleotides. The five binding pockets of RRM recognize uridines with an unusual 5'-to-3' gradient of base selectivity. The target recognition is therefore strongly sensitive to base clustering, explaining the preference for contiguous uridine tracts. Using a novel approach integrating the structurally derived recognition consensus of the RRM with a thermodynamic description of its multi-register binding, we modeled the saturation of cellular uridine tracts by this protein. The binding pattern is remarkably consistent with the experimentally observed transcriptome-wide cross-link distribution of the full-length hnRNP C on short uridine tracts. This result re-establishes the RRM as the primary RNA-binding domain of the hnRNP C tetramer and provides a proof of concept for interpreting high-throughput interaction data using structural approaches.
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Affiliation(s)
- Zuzana Cieniková
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich , 8093 Zürich, Switzerland
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Sharathchandra A, Katoch A, Das S. IRES mediated translational regulation of p53 isoforms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:131-9. [PMID: 24343861 DOI: 10.1002/wrna.1202] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 09/14/2013] [Accepted: 09/21/2013] [Indexed: 01/08/2023]
Abstract
p53 is a well known tumor suppressor protein that plays a critical role in cell cycle arrest and apoptosis. It has several isoforms which are produced by transcriptional and posttranscriptional regulatory mechanisms. p53 mRNA has been demonstrated to be translated into two isoforms, full-length p53 (FL-p53) and a truncated isoform ΔN-p53 by the use of alternative translation initiation sites. The mechanism of translation regulation of these two isoforms was further elucidated by the discovery of IRES elements in the p53 mRNA. These two IRESs were shown to regulate the translation of p53 and ΔN-p53 in a distinct cell-cycle phase-dependent manner. This review focuses on the current understanding of the regulation of p53 IRES mediated translation and the role of cis and trans acting factors that influence expression of p53 isoforms.
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