1
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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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Zhou Y, Ray PS, Zhu J, Stein F, Rettel M, Sekaran T, Sahadevan S, Perez-Perri JI, Roth EK, Myklebost O, Meza-Zepeda LA, von Deimling A, Fu C, Brosig AN, Boye K, Nathrath M, Blattmann C, Lehner B, Hentze MW, Kulozik AE. Systematic analysis of RNA-binding proteins identifies targetable therapeutic vulnerabilities in osteosarcoma. Nat Commun 2024; 15:2810. [PMID: 38561347 PMCID: PMC10984982 DOI: 10.1038/s41467-024-47031-y] [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: 01/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Osteosarcoma is the most common primary malignant bone tumor with a strong tendency to metastasize, limiting the prognosis of affected patients. Genomic, epigenomic and transcriptomic analyses have demonstrated the exquisite molecular complexity of this tumor, but have not sufficiently defined the underlying mechanisms or identified promising therapeutic targets. To systematically explore RNA-protein interactions relevant to OS, we define the RNA interactomes together with the full proteome and the transcriptome of cells from five malignant bone tumors (four osteosarcomata and one malignant giant cell tumor of the bone) and from normal mesenchymal stem cells and osteoblasts. These analyses uncover both systematic changes of the RNA-binding activities of defined RNA-binding proteins common to all osteosarcomata and individual alterations that are observed in only a subset of tumors. Functional analyses reveal a particular vulnerability of these tumors to translation inhibition and a positive feedback loop involving the RBP IGF2BP3 and the transcription factor Myc which affects cellular translation and OS cell viability. Our results thus provide insight into potentially clinically relevant RNA-binding protein-dependent mechanisms of osteosarcoma.
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Affiliation(s)
- Yang Zhou
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Partho Sarothi Ray
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jianguo Zhu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Sudeep Sahadevan
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Eva K Roth
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ola Myklebost
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Genomics Core Facility, Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Chuli Fu
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annika N Brosig
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Michaela Nathrath
- Department of Pediatrics and Children's Cancer Research Center, Technical University of Munich, School of Medicine, Munich, Germany
- Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Claudia Blattmann
- Department of Pediatric Oncology, Hematology and Immunology, Olga Hospital, Stuttgart, Germany
| | - Burkhard Lehner
- Department of Orthopaedics, Trauma Surgery and Paraplegiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit (MMPU), Heidelberg University and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany.
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3
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Ascanelli C, Dahir R, Wilson CH. Manipulating Myc for reparative regeneration. Front Cell Dev Biol 2024; 12:1357589. [PMID: 38577503 PMCID: PMC10991803 DOI: 10.3389/fcell.2024.1357589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases.
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Affiliation(s)
| | | | - Catherine H. Wilson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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4
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Fuentes Y, Olguín V, López-Ulloa B, Mendonça D, Ramos H, Abdalla A, Guajardo-Contreras G, Niu M, Rojas-Araya B, Mouland A, López-Lastra M. Heterogeneous nuclear ribonucleoprotein K promotes cap-independent translation initiation of retroviral mRNAs. Nucleic Acids Res 2024; 52:2625-2647. [PMID: 38165048 PMCID: PMC10954487 DOI: 10.1093/nar/gkad1221] [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: 04/25/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024] Open
Abstract
Translation initiation of the human immunodeficiency virus-type 1 (HIV-1) genomic mRNA (vRNA) is cap-dependent or mediated by an internal ribosome entry site (IRES). The HIV-1 IRES requires IRES-transacting factors (ITAFs) for function. In this study, we evaluated the role of the heterogeneous nuclear ribonucleoprotein K (hnRNPK) as a potential ITAF for the HIV-1 IRES. In HIV-1-expressing cells, the depletion of hnRNPK reduced HIV-1 vRNA translation. Furthermore, both the depletion and overexpression of hnRNPK modulated HIV-1 IRES activity. Phosphorylations and protein arginine methyltransferase 1 (PRMT1)-induced asymmetrical dimethylation (aDMA) of hnRNPK strongly impacted the protein's ability to promote the activity of the HIV-1 IRES. We also show that hnRNPK acts as an ITAF for the human T cell lymphotropic virus-type 1 (HTLV-1) IRES, present in the 5'UTR of the viral sense mRNA, but not for the IRES present in the antisense spliced transcript encoding the HTLV-1 basic leucine zipper protein (sHBZ). This study provides evidence for a novel role of the host hnRNPK as an ITAF that stimulates IRES-mediated translation initiation for the retroviruses HIV-1 and HTLV-1.
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Affiliation(s)
- Yazmín Fuentes
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Brenda López-Ulloa
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Dafne Mendonça
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Hade Ramos
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Ana Luiza Abdalla
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Gabriel Guajardo-Contreras
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Meijuan Niu
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
| | - Barbara Rojas-Araya
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute at the Jewish General Hospital, Montréal, Quebec H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
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5
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Rahn K, Abdallah AT, Gan L, Herbrich S, Sonntag R, Benitez O, Malaney P, Zhang X, Rodriguez AG, Brottem J, Marx G, Brümmendorf TH, Ostareck DH, Ostareck-Lederer A, Crysandt M, Post SM, Naarmann-de Vries IS. Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1). BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195004. [PMID: 38008244 DOI: 10.1016/j.bbagrm.2023.195004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Deletions on the long arm of chromosome 9 (del(9q)) are recurrent abnormalities in about 2 % of acute myeloid leukemia cases, which usually involve HNRNPK and are frequently associated with other known aberrations. Based on an Hnrnpk haploinsufficient mouse model, a recent study demonstrated a function of hnRNP K in pathogenesis of myeloid malignancies via the regulation of cellular proliferation and myeloid differentiation programs. Here, we provide evidence that reduced hnRNP K expression results in the dysregulated expression of C/EBPα and additional transcription factors. CyTOF analysis revealed monocytic skewing with increased levels of mature myeloid cells. To explore the role of hnRNP K during normal and pathological myeloid differentiation in humans, we characterized hnRNP K-interacting RNAs in human AML cell lines. Notably, RNA-sequencing revealed several mRNAs encoding key transcription factors involved in the regulation of myeloid differentiation as targets of hnRNP K. We showed that specific sequence motifs confer the interaction of SPI1 and CEBPA 5' and 3'UTRs with hnRNP K. The siRNA mediated reduction of hnRNP K in human AML cells resulted in an increase of PU.1 and C/EBPα that is most pronounced for the p30 isoform. The combinatorial treatment with the inducer of myeloid differentiation valproic acid resulted in increased C/EBPα expression and myeloid differentiation. Together, our results indicate that hnRNP K post-transcriptionally regulates the expression of myeloid master transcription factors. These novel findings can inaugurate novel options for targeted treatment of AML del(9q) by modulation of hnRNP K function.
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Affiliation(s)
- Kerstin Rahn
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research (IZKF) Aachen, RWTH Aachen University, Germany; Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Lin Gan
- Interdisciplinary Center for Clinical Research (IZKF) Aachen, RWTH Aachen University, Germany
| | - Shelley Herbrich
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roland Sonntag
- Department of Internal Medicine III, University Hospital RWTH Aachen University, Aachen, Germany
| | - Oscar Benitez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prerna Malaney
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaorui Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashely G Rodriguez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared Brottem
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gernot Marx
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Dirk H Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany
| | - Antje Ostareck-Lederer
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany
| | - Martina Crysandt
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Sean M Post
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Isabel S Naarmann-de Vries
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany; Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany.
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6
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Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [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: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
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7
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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8
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Yeh DW, Zhao X, Siddique HR, Zheng M, Choi HY, Machida T, Narayanan P, Kou Y, Punj V, Tahara SM, Feldman DE, Chen L, Machida K. MSI2 promotes translation of multiple IRES-containing oncogenes and virus to induce self-renewal of tumor initiating stem-like cells. Cell Death Discov 2023; 9:141. [PMID: 37117191 PMCID: PMC10147607 DOI: 10.1038/s41420-023-01427-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/30/2023] Open
Abstract
RNA-binding protein Musashi 2 (MSI2) is elevated in several cancers and is linked to poor prognosis. Here, we tested if MSI2 promotes MYC and viral mRNA translation to induce self-renewal via an internal ribosome entry sequence (IRES). We performed RIP-seq using anti-MSI2 antibody in tumor-initiating stem-like cells (TICs). MSI2 binds the internal ribosome entry site (IRES)-containing oncogene mRNAs including MYC, JUN and VEGFA as well as HCV IRES to increase their synthesis and promote self-renewal and tumor-initiation at the post-transcriptional level. MSI2 binds a lncRNA to interfere with processing of a miRNA that reduced MYC translation in basal conditions. Deregulation of this integrated MSI2-lncRNA-MYC regulatory loop drives self-renewal and tumorigenesis through increased IRES-dependent translation of MYC mRNA. Overexpression of MSI2 in TICs promoted their self-renewal and tumor-initiation properties. Inhibition of MSI2-RNA binding reduced HCV IRES activity, viral replication and liver hyperplasia in humanized mice predisposed by virus infection and alcohol high-cholesterol high-fat diet. Together MSI2, integrating the MYC oncogenic pathway, can be employed as a therapeutic target in the treatment of HCC patients. A hypothetical model shows that MSI2 binds and activates cap-independent translation of MYC, c-JUN mRNA and HCV through MSI2-binding to Internal Ribosome Entry Sites (IRES) resulting in upregulated MYC, c-JUN and viral protein synthesis and subsequent liver oncogenesis. Inhibitor of the interaction between MYC IRES and MSI2 reduces liver hyperplasia, viral mRNA translation and tumor formation.
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Affiliation(s)
- Da-Wei Yeh
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Xuyao Zhao
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Hifzur R Siddique
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, 202002, India
| | - Mengmei Zheng
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Hye Yeon Choi
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Tatsuya Machida
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Padmini Narayanan
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Yi Kou
- Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, USA
| | - Vasu Punj
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033, USA
| | - Stanley M Tahara
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Douglas E Feldman
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Lin Chen
- Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, USA
| | - Keigo Machida
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA.
- Southern California Research Center for ALPD and Cirrhosis, Los Angeles, 90033, USA.
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9
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Xu C, Li B, Yu N, Yao B, Wang F, Mei Y. The c-Myc targeting hnRNPAB promotes lung adenocarcinoma cell proliferation via stabilization of CDK4 mRNA. Int J Biochem Cell Biol 2023; 156:106372. [PMID: 36657708 DOI: 10.1016/j.biocel.2023.106372] [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: 11/25/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The c-Myc oncoprotein plays a pivotal role in tumorigenesis. The deregulated expression of c-Myc has been linked to a variety of human cancers including lung adenocarcinoma. The oncogenic function of c-Myc has been largely attributed to its intrinsic nature as a transcription factor. Here we reported the RNA binding protein hnRNPAB as a direct transcriptional target of c-Myc by performing quantitative real-time polymerase chain reaction (qRT-PCR), western blot, chromatin immunoprecipitation (ChIP), and luciferase reporter analyses. Flow cytometry, colony formation, and RNA immunoprecipitation (RIP) assays were used to investigate the role of hnRNPAB in lung adenocarcinoma cell proliferation, as well as the underlying mechanism. HnRNPAB was functionally shown to promote lung adenocarcinoma cell proliferation by accelerating G1/S cell cycle progression. Mechanistically, hnRNPAB interacted with and stabilized CDK4 mRNA, thereby increasing CDK4 expression. Moreover, hnRNPAB was able to promote G1/S cell cycle progression and cell proliferation via the regulation of CDK4. HnRNPAB was also revealed as a mediator of the promoting effect of c-Myc on cell proliferation. Together, these findings demonstrate that hnRNPAB is an important regulator of lung adenocarcinoma cell proliferation. They also add new insights into the mechanisms of how c-Myc promotes tumorigenesis.
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Affiliation(s)
- Chen Xu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bingyan Li
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ning Yu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bo Yao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fang Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Yide Mei
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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10
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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11
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The Role of RNA-Binding Proteins in Hematological Malignancies. Int J Mol Sci 2022; 23:ijms23179552. [PMID: 36076951 PMCID: PMC9455611 DOI: 10.3390/ijms23179552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Hematological malignancies comprise a plethora of different neoplasms, such as leukemia, lymphoma, and myeloma, plus a myriad of dysplasia, such as myelodysplastic syndromes or anemias. Despite all the advances in patient care and the development of new therapies, some of these malignancies remain incurable, mainly due to resistance and refractoriness to treatment. Therefore, there is an unmet clinical need to identify new biomarkers and potential therapeutic targets that play a role in treatment resistance and contribute to the poor outcomes of these tumors. RNA-binding proteins (RBPs) are a diverse class of proteins that interact with transcripts and noncoding RNAs and are involved in every step of the post-transcriptional processing of transcripts. Dysregulation of RBPs has been associated with the development of hematological malignancies, making them potential valuable biomarkers and potential therapeutic targets. Although a number of dysregulated RBPs have been identified in hematological malignancies, there is a critical need to understand the biology underlying their contribution to pathology, such as the spatiotemporal context and molecular mechanisms involved. In this review, we emphasize the importance of deciphering the regulatory mechanisms of RBPs to pinpoint novel therapeutic targets that could drive or contribute to hematological malignancy biology.
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12
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Chen Y, Qin H, Zheng L. Research progress on RNA−binding proteins in breast cancer. Front Oncol 2022; 12:974523. [PMID: 36059653 PMCID: PMC9433872 DOI: 10.3389/fonc.2022.974523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common malignancy in women and has a high incidence rate and mortality. Abnormal regulation of gene expression plays an important role in breast cancer occurrence and development. RNA-binding proteins (RBPs) are one kind of the key regulators for gene expression. By interacting with RNA, RBPs are widely involved in RNA cutting, transport, editing, intracellular localization, and translation regulation. RBPs are important during breast cancer occurrence and progression by engaging in many aspects, like proliferation, migration, invasion, and stemness. Therefore, comprehensively understanding the role of RBPs in breast cancer progression can facilitate early diagnosis, timely treatment, and long-term survival and quality of life of breast cancer patients.
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Affiliation(s)
- Ying Chen
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Hai Qin
- Department of Clinical Laboratory, Guizhou Provincial Orthopedic Hospital, Guiyang, China
- *Correspondence: Lufeng Zheng, ; Hai Qin,
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
- *Correspondence: Lufeng Zheng, ; Hai Qin,
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13
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Yi Q, Deng Z, Yue J, He J, Xiong J, Sun W, Sun W. RNA binding proteins in osteoarthritis. Front Cell Dev Biol 2022; 10:954376. [PMID: 36003144 PMCID: PMC9393224 DOI: 10.3389/fcell.2022.954376] [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: 05/27/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Osteoarthritis (OA) is a common chronic degenerative joint disease worldwide. The pathological features of OA are the erosion of articular cartilage, subchondral bone sclerosis, synovitis, and metabolic disorder. Its progression is characterized by aberrant expression of genes involved in inflammation, proliferation, and metabolism of chondrocytes. Effective therapeutic strategies are limited, as mechanisms underlying OA pathophysiology remain unclear. Significant research efforts are ongoing to elucidate the complex molecular mechanisms underlying OA focused on gene transcription. However, posttranscriptional alterations also play significant function in inflammation and metabolic changes related diseases. RNA binding proteins (RBPs) have been recognized as important regulators in posttranscriptional regulation. RBPs regulate RNA subcellular localization, stability, and translational efficiency by binding to their target mRNAs, thereby controlling their protein expression. However, their role in OA is less clear. Identifying RBPs in OA is of great importance to better understand OA pathophysiology and to figure out potential targets for OA treatment. Hence, in this manuscript, we summarize the recent knowledge on the role of dysregulated RBPs in OA and hope it will provide new insight for OA study and targeted treatment.
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Affiliation(s)
- Qian Yi
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Zhenhan Deng
- Department of Sports Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Jiaji Yue
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
| | - Jinglong He
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
| | - Jianyi Xiong
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
| | - Wei Sun
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- *Correspondence: Wei Sun, ; Weichao Sun,
| | - Weichao Sun
- Department of Bone and Joint Surgery, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- The Central Laboratory, Shenzhen Second People’s Hospital (The First Affiliated Hospital of Shenzhen University), Shenzhen, China
- *Correspondence: Wei Sun, ; Weichao Sun,
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14
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Zheng Y, Zhou Z, Wei R, Xiao C, Zhang H, Fan T, Zheng B, Li C, He J. The RNA-binding protein PCBP1 represses lung adenocarcinoma progression by stabilizing DKK1 mRNA and subsequently downregulating β-catenin. J Transl Med 2022; 20:343. [PMID: 35907982 PMCID: PMC9338556 DOI: 10.1186/s12967-022-03552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/24/2022] [Indexed: 12/02/2022] Open
Abstract
Background PolyC-RNA-binding protein 1 (PCBP1) functions as a tumour suppressor and RNA regulator that is downregulated in human cancers. Here, we aimed to reveal the biological function of PCBP1 in lung adenocarcinoma (LUAD). Methods First, PCBP1 was identified as an important biomarker that maintains LUAD through The Cancer Genome Atlas (TCGA) project screening and confirmed by immunohistochemistry and qPCR. Via colony formation, CCK8, IncuCyte cell proliferation, wound healing and Transwell assays, we confirmed that PCBP1 was closely related to the proliferation and migration of LUAD cells. The downstream gene DKK1 was discovered by RNA sequencing of PCBP1 knockdown cells. The underlying mechanisms were further investigated using western blot, qPCR, RIP, RNA pulldown and mRNA stability assays. Results We demonstrate that PCBP1 is downregulated in LUAD tumour tissues. The reduction in PCBP1 promotes the proliferation, migration and invasion of LUAD in vitro and in vivo. Mechanistically, the RNA-binding protein PCBP1 represses LUAD by stabilizing DKK1 mRNA. Subsequently, decreased expression of the DKK1 protein relieves the inhibitory effect on the Wnt/β-catenin signalling pathway. Taken together, these results show that PCBP1 acts as a tumour suppressor gene, inhibiting the tumorigenesis of LUAD. Conclusions We found that PCBP1 inhibits LUAD development by upregulating DKK1 to inactivate the Wnt/β-catenin pathway. Our findings highlight the potential of PCBP1 as a promising therapeutic target. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03552-y.
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Affiliation(s)
- Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ran Wei
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun 2022; 13:3881. [PMID: 35794096 PMCID: PMC9259584 DOI: 10.1038/s41467-022-31355-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractWhile survival has improved for Burkitt lymphoma patients, potential differences in outcome between pediatric and adult patients remain unclear. In both age groups, survival remains poor at relapse. Therefore, we conducted a comparative study in a large pediatric cohort, including 191 cases and 97 samples from adults. While TP53 and CCND3 mutation frequencies are not age related, samples from pediatric patients showed a higher frequency of mutations in ID3, DDX3X, ARID1A and SMARCA4, while several genes such as BCL2 and YY1AP1 are almost exclusively mutated in adult patients. An unbiased analysis reveals a transition of the mutational profile between 25 and 40 years of age. Survival analysis in the pediatric cohort confirms that TP53 mutations are significantly associated with higher incidence of relapse (25 ± 4% versus 6 ± 2%, p-value 0.0002). This identifies a promising molecular marker for relapse incidence in pediatric BL which will be used in future clinical trials.
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16
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Zhao H, Wei Z, Shen G, Chen Y, Hao X, Li S, Wang R. Poly(rC)-binding proteins as pleiotropic regulators in hematopoiesis and hematological malignancy. Front Oncol 2022; 12:1045797. [PMID: 36452487 PMCID: PMC9701828 DOI: 10.3389/fonc.2022.1045797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(rC)-binding proteins (PCBPs), a defined subfamily of RNA binding proteins, are characterized by their high affinity and sequence-specific interaction with poly-cytosine (poly-C). The PCBP family comprises five members, including hnRNP K and PCBP1-4. These proteins share a relatively similar structure motif, with triple hnRNP K homology (KH) domains responsible for recognizing and combining C-rich regions of mRNA and single- and double-stranded DNA. Numerous studies have indicated that PCBPs play a prominent role in hematopoietic cell growth, differentiation, and tumorigenesis at multiple levels of regulation. Herein, we summarized the currently available literature regarding the structural and functional divergence of various PCBP family members. Furthermore, we focused on their roles in normal hematopoiesis, particularly in erythropoiesis. More importantly, we also discussed and highlighted their involvement in carcinogenesis, including leukemia and lymphoma, aiming to clarify the pleiotropic roles and molecular mechanisms in the hematopoietic compartment.
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Affiliation(s)
- Huijuan Zhao
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Ziqing Wei
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Guomin Shen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Yixiang Chen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Xueqin Hao
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Sanqiang Li
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Rong Wang
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
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17
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DNA-methylation-induced silencing of DIO3OS drives non-small cell lung cancer progression via activating hnRNPK-MYC-CDC25A axis. MOLECULAR THERAPY-ONCOLYTICS 2021; 23:205-219. [PMID: 34761103 PMCID: PMC8551476 DOI: 10.1016/j.omto.2021.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/24/2021] [Indexed: 11/22/2022]
Abstract
DNA methylation is a class of epigenetic modification manner, which is responsible for the inactivation of various tumor suppressors. Recently, long non-coding RNAs (lncRNAs) were revealed to be implicated in a variety of malignancies, including non-small cell lung cancer (NSCLC). However, the contributions of lncRNAs to DNA-methylation-induced oncogenic effects in NSCLC remain largely unknown. In this study, we identified a DNA-methylation-repressed lncRNA DIO3 opposite strand upstream RNA (DIO3OS) in NSCLC. DIO3OS is downregulated in NSCLC, and its low expression is related to poor prognosis. Ectopic expression of DIO3OS repressed NSCLC cell growth and motility and promoted NSCLC cell apoptosis in vitro. DIO3OS also repressed NSCLC tumorigenesis and metastasis in vivo. DIO3OS knockdown exhibited opposite biological effects. DIO3OS competitively bound heterogeneous nuclear ribonucleoprotein K (hnRNPK), repressed the binding of hnRNPK to MYC DNA and MYC mRNA, reduced the promoting roles of hnRNPK on MYC transcription and translation, led to the repression of MYC transcription and translation, and therefore remarkably decreased the expression of MYC and CDC25A, a downstream target of MYC. Additionally, depletion of hnRNPK blocked the tumor-suppressive roles of DIO3OS in NSCLC. In conclusion, these findings identified DIO3OS as an important protective factor against NSCLC via modulating hnRNPK-MYC-CDC25A axis.
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18
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Janecki DM, Swiatkowska A, Szpotkowska J, Urbanowicz A, Kabacińska M, Szpotkowski K, Ciesiołka J. Poly(C)-binding Protein 2 Regulates the p53 Expression via Interactions with the 5'-Terminal Region of p53 mRNA. Int J Mol Sci 2021; 22:ijms222413306. [PMID: 34948101 PMCID: PMC8708005 DOI: 10.3390/ijms222413306] [Citation(s) in RCA: 4] [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: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indicate the potential involvement of PCBP2 in cap-independent translation of p53 mRNA especially occurring under stress conditions. It has been postulated that the PCBP2 protein is engaged in the enhancement of p53 mRNA stability, probably via interacting with its 3′ end. Our data show that under stress conditions PCBP2 also modulates p53 translation through binding to the 5′ terminus of p53 mRNA. Thus PCBP2 emerges as a double-function factor in the p53 expression.
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19
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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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20
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MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome. Noncoding RNA 2021; 7:ncrna7040061. [PMID: 34698276 PMCID: PMC8544657 DOI: 10.3390/ncrna7040061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Complete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroSalmon GitHub repository provides all results. RNAHybrid and sRNAtoolbox tools predicted the MREs. UTRscan and the Teiresias algorithm predicted other 3′UTR cis-acting motifs, both known vertebrate motifs and putative novel motifs. MicroSalmon provides search programs to retrieve all FL-transcripts targeted by a miRNA (median number 1487), all miRNAs targeting an FL-transcript (median number 27), and other cis-acting motifs. As thousands of FL-transcripts may be targets of each miRNA, additional experimental strategies are necessary to reduce the likely true and relevant targets to a number that may be functionally validated. Low-complexity motifs known to affect mRNA decay in vertebrates were over-represented. Many of these were enriched in the terminal end, while purine- or pyrimidine-rich motifs with unknown functions were enriched immediately downstream of the stop codon. Furthermore, several novel complex motifs were over-represented, indicating conservation and putative function. In conclusion, MicroSalmon is an extensive and useful, searchable resource for study of Atlantic salmon transcript regulation by miRNAs and cis-acting 3′UTR motifs.
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21
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Strand E, Hollås H, Sakya SA, Romanyuk S, Saraste MEV, Grindheim AK, Patil SS, Vedeler A. Annexin A2 binds the internal ribosomal entry site of c- myc mRNA and regulates its translation. RNA Biol 2021; 18:337-354. [PMID: 34346292 PMCID: PMC8677036 DOI: 10.1080/15476286.2021.1947648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The expression and localization of the oncoprotein c-Myc is highly regulated at the level of transcription, mRNA transport, translation, as well as stability of the protein. We previously showed that Annexin A2 (AnxA2) binds to a specific localization element in the 3'untranslated region (UTR) of c-myc mRNA and is involved in its localization to the perinuclear region. In the present study, we demonstrate that AnxA2 binds in a Ca2+-dependent manner to the internal ribosomal entry site (IRES) containing two pseudo-knots in the 5´UTR of the c-myc mRNA. Here, we employ an in vitro rabbit reticulocyte lysate system with chimeric c-myc reporter mRNAs to demonstrate that binding of AnxA2 to the c-myc IRES modulates the expression of c-Myc. Notably, we show that low levels of AnxA2 appear to increase, while high levels of AnxA2 inhibits translation of the chimeric mRNA. However, when both the AnxA2-binding site and the ribosomal docking site in the c-myc IRES are deleted, AnxA2 has no effect on the translation of the reporter mRNA. Forskolin-treatment of PC12 cells results in upregulation of Ser25 phosphorylated AnxA2 expression while c-Myc expression is down-regulated. The effect of forskolin on c-Myc expression and the level of Ser25 phosphorylated AnxA2 was abolished in the presence of EGTA. These findings indicate that AnxA2 regulates both the transport and subsequent translation of the c-myc mRNA, possibly by silencing the mRNA during its transport. They also suggest that AnxA2 act as a switch to turn off the c-myc IRES activity in the presence of calcium.Abbreviations: AnxA2, Annexin A2; β2--µglob, β2-microglobulin; cpm, counts per minute; hnRNP, heterogenous nuclear ribonucleoprotein; IRES, internal ribosomal entry site; ITAF, IRES trans-acting factor; MM, multiple myeloma; PABP, poly(A)-binding protein; PCBP, poly(rC) binding protein; PSF, PTB-associated splicing factor; PTB, polypyrimidine tract binding protein; RRL, rabbit reticulocyte lysate; UTR, untranslated region; YB, Y-box binding protein.
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Affiliation(s)
- Elin Strand
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hanne Hollås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Siri Aastedatter Sakya
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Norway
| | - Sofya Romanyuk
- Department of Biomedicine, University of Bergen, Bergen, Norway.,City Hospital №40, St. Petersburg, Russia
| | - Mikko E V Saraste
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Quality Control Unit, Thermo Fisher Scientific - Life Technologies, Lillestrøm, Norway
| | | | | | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Bergen, Norway
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22
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Padovani KS, Goto RN, Fugio LB, Garcia CB, Alves VM, Brassesco MS, Greene LJ, Rego EM, Leopoldino AM. Crosstalk between hnRNP K and SET in ATRA-induced differentiation in acute promyelocytic leukemia. FEBS Open Bio 2021; 11:2019-2032. [PMID: 34058077 PMCID: PMC8255839 DOI: 10.1002/2211-5463.13210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/16/2021] [Accepted: 05/28/2021] [Indexed: 11/18/2022] Open
Abstract
HnRNP K protein is a heterogeneous nuclear ribonucleoprotein which has been proposed to be involved in the leukemogenesis of acute promyelocytic leukemia (APL), as well as in differentiation induced by all‐trans retinoic acid (ATRA). We previously demonstrated a connection between SET and hnRNP K function in head and neck squamous cell carcinoma (HNSCC) cells related to splicing processing. The objective of this study was to characterize the participation of hnRNP K and SET proteins in ATRA‐induced differentiation in APL. We observed higher (5‐ to 40‐fold) levels of hnRNP K and SET mRNA in APL patients at the diagnosis phase compared with induction and maintenance phases. hnRNP K knockdown using short‐hairpin RNA led to cell death in ATRA‐sensitive NB4 and resistant NB4‐R2 cells by apoptosis with SET cleavage. In addition, hnRNP K knockdown increased granulocytic differentiation in APL cells, mainly in NB4‐R2 with ATRA. hnRNP K knockdown had an effect similar to that of treatment with U0126 (an meiosis‐specific serine/threonine protein kinase/ERK inhibitor), mainly in NB4‐R2 cells. SET knockdown in APL cells revealed that apoptosis induction in cells with hnRNP K knockdown occurred by SET cleavage rather than by reduction in SET protein. Transplantation of NB4‐R2 cells into nude mice confirmed that arsenic trioxide (ATO) combined with U0126 has higher potential against tumor progression when compared to ATO. Therefore, hnRNP K/SET and ERK are potential therapeutic targets for both antineoplastic leukemia therapy and relapsed APL patients with ATRA resistance.
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Affiliation(s)
- Karina Stringhetta Padovani
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.,CEPID-FAPESP, Center for Cell Based Therapy, Regional Blood Center of Ribeirão, Preto, Brazil
| | - Renata Nishida Goto
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Lais Brigliadori Fugio
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Cristiana Bernadelli Garcia
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Vani Maria Alves
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, School of Medicine of Ribeirão Preto-FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Maria Sol Brassesco
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Brazil
| | - Lewis Joel Greene
- CEPID-FAPESP, Center for Cell Based Therapy, Regional Blood Center of Ribeirão, Preto, Brazil.,Department of Cellular and Molecular Biology and Pathogenic Bioagents, School of Medicine of Ribeirão Preto-FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Eduardo Magalhães Rego
- CEPID-FAPESP, Center for Cell Based Therapy, Regional Blood Center of Ribeirão, Preto, Brazil.,Department of Internal Medicine, School of Medicine of Ribeirão Preto-FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Andréia Machado Leopoldino
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.,CEPID-FAPESP, Center for Cell Based Therapy, Regional Blood Center of Ribeirão, Preto, Brazil
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23
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Yuan C, Chen M, Cai X. Advances in poly(rC)-binding protein 2: Structure, molecular function, and roles in cancer. Biomed Pharmacother 2021; 139:111719. [PMID: 34233389 DOI: 10.1016/j.biopha.2021.111719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Poly(rC)-binding protein 2 (PCBP2) is an RNA-binding protein that is characterized by its ability to interact with poly(C) with high affinity in a sequence-specific manner. PCBP2 contains three K homology domains, which are consensus RNA-binding domains that play a role in recognizing and combining with RNA and DNA. The specific structure and localization of PCBP2 lay the foundation for its multiple roles in transcriptional, posttranscriptional, and translational processes, even in iron metabolism. Numerous studies have indicated that PCBP2 expression is increased in many cancer types. PCBP2 is considered as an oncogene that promotes tumorigenesis, development of cancer cells, and metastasis. Here, we summarized the current evidence regarding PCBP2 in the proliferation, migration, invasion of cancer cells, and drug resistance, aiming to clarify the molecular mechanisms of PCBP2 in cancer. Results from this review suggest that an in-depth study of PCBP2 in cancer may provide novel biomarkers for prognostic or therapeutic purposes.
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Affiliation(s)
- Chendong Yuan
- Department of Vascular Surgery, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, China.
| | - Mingxiang Chen
- Department of Cardiovascular surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, Yubei 401120, China.
| | - Xiaolu Cai
- Department of Oncological Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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24
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Malaney P, Velasco-Estevez M, Aguilar-Garrido P, Aitken MJL, Chan LE, Zhang X, Post SM, Gallardo M. The Eµ-hnRNP K Murine Model of Lymphoma: Novel Insights into the Role of hnRNP K in B-Cell Malignancies. Front Immunol 2021; 12:634584. [PMID: 33912162 PMCID: PMC8072109 DOI: 10.3389/fimmu.2021.634584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 01/18/2023] Open
Abstract
B-cell lymphomas are one of the most biologically and molecularly heterogeneous group of malignancies. The inherent complexity of this cancer subtype necessitates the development of appropriate animal model systems to characterize the disease with the ultimate objective of identifying effective therapies. In this article, we discuss a new driver of B-cell lymphomas - hnRNP K (heterogenous nuclear ribonucleoprotein K)-an RNA-binding protein. We introduce the Eµ-Hnrnpk mouse model, a murine model characterized by hnRNP K overexpression in B cells, which develops B-cell lymphomas with high penetrance. Molecular analysis of the disease developed in this model reveals an upregulation of the c-Myc oncogene via post-transcriptional and translational mechanisms underscoring the impact of non-genomic MYC activation in B-cell lymphomas. Finally, the transplantability of the disease developed in Eµ-Hnrnpk mice makes it a valuable pre-clinical platform for the assessment of novel therapeutics.
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MESH Headings
- Animals
- Animals, Genetically Modified
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Heterogeneous-Nuclear Ribonucleoprotein K/genetics
- Heterogeneous-Nuclear Ribonucleoprotein K/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Phenotype
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Up-Regulation
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Affiliation(s)
- Prerna Malaney
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Marisa J. L. Aitken
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Lauren E. Chan
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaorui Zhang
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Sean M. Post
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Miguel Gallardo
- H12O–CNIO Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
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25
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Wang S, Han C, Liu T, Ma Z, Qiu M, Wang J, You Q, Zheng X, Xu W, Xia W, Xu Y, Hu J, Xu L, Yin R. FAM83H-AS1 is a noncoding oncogenic driver and therapeutic target of lung adenocarcinoma. Clin Transl Med 2021; 11:e316. [PMID: 33634993 PMCID: PMC7882096 DOI: 10.1002/ctm2.316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Little is known about noncoding oncogenes of lung adenocarcinoma (LUAD), and these potential drivers might provide novel therapeutic targets. METHODS Since abnormally overexpression of oncogenic drivers is induced by genomic variation, we here utilized genomic, transcriptomic, and clinical prognosis data of The Cancer Genome Atlas (TCGA) LUAD datasets to discover novel drivers from long noncoding RNAs. We further used zebrafish models to validate the biological function of candidates in vivo. The full length of FAM83H-AS1 was obtained by rapid amplification of the cDNA ends assay. RNA pull-down, RNA immunoprecipitation, quantitative mass spectrometry, and RNA sequencing assays were conducted to explore the potential mechanisms. Additionally, we used CRISPR interference (CRISPRi) method and patient-derived tumor xenograft (PDTX) model to evaluate the therapeutic potential of targeting FAM83H-AS1. RESULTS The results suggest that FAM83H-AS1 is a potential oncogenic driver due to chromosome 8q24 amplification. Upregulation of FAM83H-AS1 results in poor prognosis of LUAD patients in both Jiangsu Cancer Hospital (JSCH) and TCGA cohorts. Functional assays revealed that FAM83H-AS1 promotes malignant progression and inhibits apoptosis. Mechanistically, FAM83H-AS1 binds HNRNPK to enhance the translation of antiapoptotic oncogenes RAB8B and RAB14. Experiments using CRISPRi-mediated xenografts and PDTX models indicated that targeting FAM83H-AS1 inhibited LUAD progression in vivo. CONCLUSIONS Our work demonstrates that FAM83H-AS1 is a noncoding oncogenic driver that inhibits LUAD apoptosis via the FAM83H-AS1-HNRNPK-RAB8B/RAB14 axis, which highlights the importance and potential roles that FAM83H-AS1 may serve as a novel therapeutic target for LUAD.
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Affiliation(s)
- Siwei Wang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Chencheng Han
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Tongyan Liu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Department of Science and technologyNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Zhifei Ma
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Mantang Qiu
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
| | - Jie Wang
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Department of Science and technologyNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Biobank of Lung CancerJiangsu Biobank of Clinical ResourcesNanjingChina
| | - Qingjun You
- Department of Thoracic SurgeryThe Affiliated Hospital of Jiangnan UniversityWuxiChina
| | - Xiufen Zheng
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Weizhang Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Wenjia Xia
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Youtao Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Jingwen Hu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer ResearchNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Department of Science and technologyNanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer ResearchNanjingChina
- Biobank of Lung CancerJiangsu Biobank of Clinical ResourcesNanjingChina
- Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
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26
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Liu J, Yuan C, Guo T, Wang F, Zeng Y, Ding X, Lu Z, Renqing D, Zhang H, Xu X, Yue Y, Sun X, Niu C, Zhuoga D, Yang B. Genetic signatures of high-altitude adaptation and geographic distribution in Tibetan sheep. Sci Rep 2020; 10:18332. [PMID: 33110149 PMCID: PMC7591910 DOI: 10.1038/s41598-020-75428-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022] Open
Abstract
Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. However, the genetic mechanism regulating the multiple biological processes driving adaptive responses remains unclear. In this study, we applied a selective sweep analysis by combing 1% top values of Fst and ZHp on both altitude and geographic subpopulations (APS) in 636 indigenous Tibetan sheep breeds. Results show that 37 genes were identified within overlapped genomic regions regarding Fst significantly associated with APS. Out of the 37 genes, we found that 8, 3 and 6 genes at chromosomes (chr.) 13, 23 and 27, respectively, were identified in the genomic regions with 1% top values of ZHp. We further analyzed the INDEL variation of 6 genes at chr.27 (X chromosome) in APS together with corresponding orthologs of 6 genes in Capra, Pantholops, and Bos Taurus. We found that an INDEL was located within 5′UTR region of HAG1 gene. This INDEL of HAG1 was strongly associated with the variation of APS, which was further confirmed by qPCR. Sheep breeds carrying “C-INDEL” of HAG1 have significantly greater body weight, shear amount, corpuscular hemoglobin and globulin levels, but lower body height, than those carrying “CA-INDEL” of HAG1. We concluded that “C-INDEL” variation of HAG1 gene confers better hypoxia tolerance in the highlands of Tibetan and explains well geographic distributions in this population. These results contribute to our understanding of adaptive responses to altitude and geographic adaptation in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.
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Affiliation(s)
- Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China. .,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Fan Wang
- China Agricultural Veterinarian Biology Science and Technology Co. Ltd, Xujiaping, Lanzhou, China
| | - Yufeng Zeng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Xuezhi Ding
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Dingkao Renqing
- Animal Husbandry Science and Research Institute of Gannan Tibet Autonomous Prefecture in China, Hezuo, China
| | - Hao Zhang
- Pizhou Agricultural and Rural Bureau of Jiangsu Province, Parkway Street, Pizhou, China
| | - Xilan Xu
- Pizhou Animal Health Supervision Institute of Jiangsu Province, Xizhong Street, Pizhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Xiaoping Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China
| | - Deqing Zhuoga
- Institute of Livestock Research, Tibet Academy of Agriculture and Animal Science, Lhasa, 850000, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China. .,Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Jiangouyan Street, Lanzhou, China.
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27
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Zhang X, Di C, Chen Y, Wang J, Su R, Huang G, Xu C, Chen X, Long F, Yang H, Zhang H. Multilevel regulation and molecular mechanism of poly (rC)-binding protein 1 in cancer. FASEB J 2020; 34:15647-15658. [PMID: 33058239 DOI: 10.1096/fj.202000911r] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/02/2020] [Accepted: 09/15/2020] [Indexed: 01/07/2023]
Abstract
Poly (rC)-binding protein 1 (PCBP1), an RNA- or DNA-binding protein with a relative molecular weight of 38 kDa, which is characterized by downregulation in many cancer types. Numerous cases have indicated that PCBP1 could be considered as a tumor suppressor to inhibit tumorigenesis, development, and metastasis. In the current review, we described the multilevel regulatory roles of PCBP1, including gene transcription, alternative splicing, and translation of many cancer-related genes. Additionally, we also provided a brief overview about the inhibitory effect of PCBP1 on most common tumors. More importantly, we summarized the current research status about PCBP1 in hypoxic microenvironment, autophagy, apoptosis, and chemotherapy of cancer cells, aiming to clarify the molecular mechanisms of PCBP1 in cancer. Taken together, in-depth study of PCBP1 in cancer may provide new ideas for cancer therapy.
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Affiliation(s)
- Xuetian Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Cuixia Di
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhong Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Ruowei Su
- The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Guomin Huang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Caipeng Xu
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Long
- Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Hongying Yang
- School of Radiation Medicine and Protection, Medical College of Soochow, Soochow, China
| | - Hong Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, China
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28
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Wang X, Guo Q, Wang H, Yuan X, Wang B, Lobie PE, Zhu T, Tan S, Wu Z. PCBP2 Posttranscriptional Modifications Induce Breast Cancer Progression via Upregulation of UFD1 and NT5E. Mol Cancer Res 2020; 19:86-98. [PMID: 33037085 DOI: 10.1158/1541-7786.mcr-20-0390] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/27/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
It is commonly accepted that cellular protein levels are primarily determined by mRNA levels. However, discordance between protein and mRNA expression has been implicated in many pathologic conditions including oncogenesis. The mechanisms involved in this discordance are complicated and far from understood. In this study, it was observed that the expression levels of poly(C) binding protein 2 (PCBP2) mRNA and protein were diametric in breast normal and cancer cell lines, paraffin-embedded and fresh tissue specimens, consistent with data from The Cancer Genome Atlas and the Clinical Proteomic Tumor Analysis Consortium. Moreover, PCBP2 protein expression was significantly associated with disease progression and poor outcome in patients with breast cancer. Depletion of PCBP2 protein inhibited cell proliferation, colony formation, migration, invasion, and in vivo tumor growth and metastasis. Forced expression of PCBP2 exhibited the opposite effect. Mechanistically, it was demonstrated that PCBP2 3' untranslated region (3'UTR) was subject to alternative splicing and polyadenylation (APA) in breast cancer tissues and cell lines. Non-full-length 3'UTR PCBP2 transcripts yielded more protein than the full-length 3'UTR transcripts and enhanced the oncogenic and metastatic capacities of human breast cancer cells. Furthermore, UFD1 and NT5E were identified as genes downstream of PCBP2. PCBP2 promoted oncogenicity of breast cancer cells via upregulation of the expression of UFD1 and NT5E by direct binding to their 3'UTR-B portions. IMPLICATIONS: Findings demonstrate that APA of PCBP2 3'UTR contributes to its increased expression with subsequent promotion of breast cancer progression by regulating UFD1 and NT5E. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/1/86/F1.large.jpg.
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Affiliation(s)
- Xiaonan Wang
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
- Laboratory of Pathogenic Microbiology and Immunology, Anhui Medical University, Hefei, Anhui, China
| | - Qianying Guo
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Hao Wang
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Xiaodong Yuan
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Bijun Wang
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Peter E Lobie
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School and Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Tao Zhu
- Laboratory of Molecular Tumor Pathology, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China.
| | - Sheng Tan
- Laboratory of Molecular Tumor Pathology, School of Life Science, University of Science and Technology of China, Hefei, Anhui, China.
| | - Zhengsheng Wu
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China.
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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29
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Wang H, Zhu Y, Hu L, Li Y, Liu G, Xia T, Xiong D, Luo Y, Liu B, An Y, Li M, Huang Y, Zhong Q, Zeng M. Internal Ribosome Entry Sites Mediate Cap-Independent Translation of Bmi1 in Nasopharyngeal Carcinoma. Front Oncol 2020; 10:1678. [PMID: 33014838 PMCID: PMC7506037 DOI: 10.3389/fonc.2020.01678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 07/29/2020] [Indexed: 01/03/2023] Open
Abstract
Bmi1 is overexpressed in multiple human cancers. We previously reported the oncogenic function and the transcription regulation mechanisms of Bmi1 in nasopharyngeal carcinoma (NPC). In this study, we observed that the mRNA and the protein levels of Bmi1 were strictly inconsistent in NPC cell lines and cancer tissues. The inhibitors of proteasome and lysosome could not enhance the protein level of Bmi1, indicating that Bmi1 may be post-transcriptionally regulated. The IRESite analysis showed that there were two potential internal ribosome entry sites (IRESs) in the 5'-untranslated region (5'-UTR) of Bmi1. The luciferase assay demonstrated that the 5'-UTR of Bmi1 has IRES activity, which may mediate cap-independent translation. The IRES activity of the Bmi1 5'-UTR was significantly reduced after the mutation of the two IRES elements. Taken together, these results suggested that the IRES elements mediating translation is a novel post-transcriptional regulation mechanism of Bmi1.
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Affiliation(s)
- Hongbo Wang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yunjia Zhu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lijuan Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Peking University People's Hospital, Peking University Institute of Hematology, Beijing, China
| | - Yangyang Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Guihong Liu
- Tungwah Hospital of Sun Yat-sen University, Dongguan, China
| | - Tianliang Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xiong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Laboratory Medicine, Luohu District People's Hospital, Shenzhen, China
| | - Yiling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Binliu Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu An
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Manzhi Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuehua Huang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
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Swiatkowska A, Dutkiewicz M, Machtel P, Janecki DM, Kabacinska M, Żydowicz-Machtel P, Ciesiołka J. Regulation of the p53 expression profile by hnRNP K under stress conditions. RNA Biol 2020; 17:1402-1415. [PMID: 32449427 DOI: 10.1080/15476286.2020.1771944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The p53 protein is one of the transcription factors responsible for cell cycle regulation and prevention of cancer development. Its expression is regulated at the transcriptional, translational and post-translational levels. Recent years of research have shown that the 5' terminus of p53 mRNA plays an important role in this regulation. This region seems to be a docking platform for proteins involved in p53 expression, particularly under stress conditions. Here, we applied RNA-centric affinity chromatography to search for proteins that bind to the 5' terminus of p53 mRNA and thus may be able to regulate the p53 expression profile. We found heterogeneous nuclear ribonucleoprotein K, hnRNP K, to be one of the top candidates. Binding of hnRNP K to the 5'-terminal region of p53 mRNA was confirmed in vitro. We demonstrated that changes in the hnRNP K level in the cell strongly affected the p53 expression profile under various stress conditions. Downregulation or overexpression of hnRNP K caused a decrease or an increase in the p53 mRNA amount, respectively, pointing to the transcriptional mode of expression regulation. However, when hnRNP K was overexpressed under endoplasmic reticulum stress and the p53 amount has elevated no changes in the p53 mRNA level were detected suggesting translational regulation of p53 expression. Our findings have shown that hnRNP K is not only a mutual partner of p53 in the transcriptional activation of target genes under stress conditions but it also acts as a regulator of p53 expression at the transcriptional and potentially translational levels.
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Affiliation(s)
- Agata Swiatkowska
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Mariola Dutkiewicz
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Piotr Machtel
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Damian M Janecki
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | - Martyna Kabacinska
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
| | | | - Jerzy Ciesiołka
- Polish Academy of Sciences, Institute of Bioorganic Chemistry , Poznan, Poland
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31
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RNA-Binding Proteins in Acute Leukemias. Int J Mol Sci 2020; 21:ijms21103409. [PMID: 32408494 PMCID: PMC7279408 DOI: 10.3390/ijms21103409] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 12/12/2022] Open
Abstract
Acute leukemias are genetic diseases caused by translocations or mutations, which dysregulate hematopoiesis towards malignant transformation. However, the molecular mode of action is highly versatile and ranges from direct transcriptional to post-transcriptional control, which includes RNA-binding proteins (RBPs) as crucial regulators of cell fate. RBPs coordinate RNA dynamics, including subcellular localization, translational efficiency and metabolism, by binding to their target messenger RNAs (mRNAs), thereby controlling the expression of the encoded proteins. In view of the growing interest in these regulators, this review summarizes recent research regarding the most influential RBPs relevant in acute leukemias in particular. The reported RBPs, either dysregulated or as components of fusion proteins, are described with respect to their functional domains, the pathways they affect, and clinical aspects associated with their dysregulation or altered functions.
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32
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Good AL, Stoffers DA. Stress-Induced Translational Regulation Mediated by RNA Binding Proteins: Key Links to β-Cell Failure in Diabetes. Diabetes 2020; 69:499-507. [PMID: 32198193 PMCID: PMC7085242 DOI: 10.2337/dbi18-0068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
In type 2 diabetes, β-cells endure various forms of cellular stress, including oxidative stress and endoplasmic reticulum stress, secondary to increased demand for insulin production and extracellular perturbations, including hyperglycemia. Chronic exposure to stress causes impaired insulin secretion, apoptosis, and loss of cell identity, and a combination of these processes leads to β-cell failure and severe hyperglycemia. Therefore, a better understanding of the molecular mechanisms underlying stress responses in β-cells promises to reveal new therapeutic opportunities for type 2 diabetes. In this perspective, we discuss posttranscriptional control of gene expression as a critical, but underappreciated, layer of regulation with broad importance during stress responses. Specifically, regulation of mRNA translation occurs pervasively during stress to activate gene expression programs; however, the convenience of RNA sequencing has caused translational regulation to be overlooked compared with transcriptional controls. We highlight the role of RNA binding proteins in shaping selective translational regulation during stress and the mechanisms underlying this level of regulation. A growing body of evidence indicates that RNA binding proteins control an array of processes in β-cells, including the synthesis and secretion of insulin. Therefore, systematic evaluations of translational regulation and the upstream factors shaping this level of regulation are critical areas of investigation to expand our understanding of β-cell failure in type 2 diabetes.
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Affiliation(s)
- Austin L Good
- Institute for Diabetes, Obesity, and Metabolism and Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Doris A Stoffers
- Institute for Diabetes, Obesity, and Metabolism and Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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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
Graphical 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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34
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Gallardo M, Malaney P, Aitken MJL, Zhang X, Link TM, Shah V, Alybayev S, Wu MH, Pageon LR, Ma H, Jacamo R, Yu L, Xu-Monette ZY, Steinman H, Lee HJ, Sarbassov D, Rapado I, Barton MC, Martinez-Lopez J, Bueso-Ramos C, Young KH, Post SM. Uncovering the Role of RNA-Binding Protein hnRNP K in B-Cell Lymphomas. J Natl Cancer Inst 2020; 112:95-106. [PMID: 31077320 PMCID: PMC7489062 DOI: 10.1093/jnci/djz078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 03/22/2019] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is an RNA-binding protein that is aberrantly expressed in cancers. We and others have previously shown that reduced hnRNP K expression downmodulates tumor-suppressive programs. However, overexpression of hnRNP K is the more commonly observed clinical phenomenon, yet its functional consequences and clinical significance remain unknown. METHODS Clinical implications of hnRNP K overexpression were examined through immunohistochemistry on samples from patients with diffuse large B-cell lymphoma who did not harbor MYC alterations (n = 75). A novel transgenic mouse model that overexpresses hnRNP K specifically in B cells was generated to directly examine the role of hnRNP K overexpression in mice (three transgenic lines). Molecular consequences of hnRNP K overexpression were determined through proteomics, formaldehyde-RNA-immunoprecipitation sequencing, and biochemical assays. Therapeutic response to BET-bromodomain inhibition in the context of hnRNP K overexpression was evaluated in vitro and in vivo (n = 3 per group). All statistical tests were two-sided. RESULTS hnRNP K is overexpressed in diffuse large B-cell lymphoma patients without MYC genomic alterations. This overexpression is associated with dismal overall survival and progression-free survival (P < .001). Overexpression of hnRNP K in transgenic mice resulted in the development of lymphomas and reduced survival (P < .001 for all transgenic lines; Line 171[n = 30]: hazard ratio [HR] = 64.23, 95% confidence interval [CI] = 26.1 to 158.0; Line 173 [n = 31]: HR = 25.27, 95% CI = 10.3 to 62.1; Line 177 [n = 25]: HR = 119.5, 95% CI = 42.7 to 334.2, compared with wild-type mice). Clinical samples, mouse models, global screening assays, and biochemical studies revealed that hnRNP K's oncogenic potential stems from its ability to posttranscriptionally and translationally regulate MYC. Consequently, Hnrnpk overexpression renders cells sensitive to BET-bromodomain-inhibition in both in vitro and transplantation models, which represents a strategy for mitigating hnRNP K-mediated c-Myc activation in patients. CONCLUSION Our findings indicate that hnRNP K is a bona fide oncogene when overexpressed and represents a novel mechanism for c-Myc activation in the absence of MYC lesions.
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Affiliation(s)
- Miguel Gallardo
- Department of Leukemia
- H12O-CNIO Haematological Malignancies Clinical Research Unit, Clinical Research Programme, CNIO, Madrid, Spain
| | | | - Marisa J L Aitken
- Department of Leukemia
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
| | | | | | - Vrutant Shah
- Department of Epigenetics and Molecular Carcinogenesis
| | | | | | | | | | | | - Li Yu
- Department of Hematopathology
| | | | | | - Hun Ju Lee
- Department of Lymphoma and Myeloma The University of Texas, MD Anderson Cancer Center, Houston, TX
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35
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Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA (NEW YORK, N.Y.) 2019; 25:1337-1352. [PMID: 31296583 PMCID: PMC6800478 DOI: 10.1261/rna.072157.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/27/2019] [Indexed: 05/10/2023]
Abstract
Proteins bind mRNA through their entire life cycle from transcription to degradation. We analyzed c-Myc mRNA protein interactors in vivo using the HyPR-MS method to capture the crosslinked mRNA by hybridization and then analyzed the bound proteins using mass spectrometry proteomics. Using HyPR-MS, 229 c-Myc mRNA-binding proteins were identified, confirming previously proposed interactors, suggesting new interactors, and providing information related to the roles and pathways known to involve c-Myc. We performed structural and functional analysis of these proteins and validated our findings with a combination of RIP-qPCR experiments, in vitro results released in past studies, publicly available RIP- and eCLIP-seq data, and results from software tools for predicting RNA-protein interactions.
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Affiliation(s)
- Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Naples 80138, Italy
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples 80131, Italy
| | - Maisie I Steinbrink
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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36
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Wang Z, Qiu H, He J, Liu L, Xue W, Fox A, Tickner J, Xu J. The emerging roles of hnRNPK. J Cell Physiol 2019; 235:1995-2008. [PMID: 31538344 DOI: 10.1002/jcp.29186] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an DNA/RNA-binding protein and regulates a wide range of biological processes and disease pathogenesis. It contains 3 K-homologous (KH) domains, which are conserved in other RNA-binding proteins, mediate nucleic acid binding activity, and function as an enhancer or repressor of gene transcription. Phosphorylation of the protein alters its regulatory function, which also enables the protein to serve as a docking platform for the signal transduction proteins. In terms of the function of hnRNPK, it is central to many cellular events, including long noncoding RNA (lncRNA) regulation, cancer development and bone homoeostasis. Many studies have identified hnRNPK as an oncogene, where it is overexpressed in cancer tissues compared with the nonneoplastic tissues and its expression level is related to the prognosis of different types of host malignancies. However, hnRNPK has also been identified as a tumour suppressor, as it is important for the activation of the p53/p21 pathway. Recently, the protein is also found to be exclusively related to the regulation of paraspeckles and lncRNAs such as Neat1, Lncenc1 and Xist. Interestingly, hnRNPK has been found to associate with the Kabuki-like syndrome and Au-Kline syndrome with prominent skeletal abnormalities. In vitro study revealed that the hnRNPK protein is essential for the formation of osteoclast, in line with its importance in the skeletal system.
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Affiliation(s)
- Ziyi Wang
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Heng Qiu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jianbo He
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Langxia Liu
- Key laboratory of functional protein research of Guangdong higher education institutes, Institute of life and health engineering, Jinan University, Guangzhou, China
| | - Wei Xue
- Department of Biomedical Engineering, Jinan University, Guangzhou, China
| | - Archa Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Jennifer Tickner
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jiake Xu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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37
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García-Cárdenas JM, Guerrero S, López-Cortés A, Armendáriz-Castillo I, Guevara-Ramírez P, Pérez-Villa A, Yumiceba V, Zambrano AK, Leone PE, Paz-y-Miño C. Post-transcriptional Regulation of Colorectal Cancer: A Focus on RNA-Binding Proteins. Front Mol Biosci 2019; 6:65. [PMID: 31440515 PMCID: PMC6693420 DOI: 10.3389/fmolb.2019.00065] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/23/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a major health problem with an estimated 1. 8 million new cases worldwide. To date, most CRC studies have focused on DNA-related aberrations, leaving post-transcriptional processes under-studied. However, post-transcriptional alterations have been shown to play a significant part in the maintenance of cancer features. RNA binding proteins (RBPs) are uprising as critical regulators of every cancer hallmark, yet little is known regarding the underlying mechanisms and key downstream oncogenic targets. Currently, more than a thousand RBPs have been discovered in humans and only a few have been implicated in the carcinogenic process and even much less in CRC. Identification of cancer-related RBPs is of great interest to better understand CRC biology and potentially unveil new targets for cancer therapy and prognostic biomarkers. In this work, we reviewed all RBPs which have a role in CRC, including their control by microRNAs, xenograft studies and their clinical implications.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - César Paz-y-Miño
- Facultad de Ciencias de la Salud Eugenio Espejo, Centro de Investigación Genética y Genómica, Universidad UTE, Quito, Ecuador
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38
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Nazarov IB, Bakhmet EI, Tomilin AN. KH-Domain Poly(C)-Binding Proteins as Versatile Regulators of Multiple Biological Processes. BIOCHEMISTRY (MOSCOW) 2019; 84:205-219. [PMID: 31221059 DOI: 10.1134/s0006297919030039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Five known members of the family of KH-domain poly(C)-binding proteins (Pcbp1-4, hnRNP-K) have an unusually broad spectrum of cellular functions that include regulation of gene transcription, regulation of pre-mRNA processing, splicing, mRNA stability, translational silencing and enhancement, the control of iron turnover, and many others. Mechanistically, these proteins act via nucleic acid binding and protein-protein interactions. Through performing these multiple tasks, the KH-domain poly(C)-binding family members are involved in a wide variety of biological processes such as embryonic development, cell differentiation, and cancer. Deregulation of KH-domain protein expression is frequently associated with severe developmental defects and neoplasia. This review summarizes progress in studies of the KH-domain proteins made over past two decades. The review also reports our recent finding implying an involvement of the KH-factor Pcbp1 into control of transition from naïve to primed pluripotency cell state.
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Affiliation(s)
- I B Nazarov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - E I Bakhmet
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - A N Tomilin
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
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39
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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40
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UNR/ CSDE1 Expression Is Critical to Maintain Invasive Phenotype of Colorectal Cancer through Regulation of c-MYC and Epithelial-to-Mesenchymal Transition. J Clin Med 2019; 8:jcm8040560. [PMID: 31027221 PMCID: PMC6517883 DOI: 10.3390/jcm8040560] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/11/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
CSDE1 (cold shock domain containing E1) gene is located upstream of the N-RAS locus, and codes for an RNA-binding protein named Upstream of N-Ras (UNR). In cancer, CSDE1 has been shown to regulate c-Fos, c-Myc, Pten, Rac1, or Vimentin. UNR/CSDE1 has been studied in breast, melanoma, pancreatic and prostate cancer. Then, the aim of this study is to evaluate the role of CSDE1/UNR in colorectal cancer progression and maintenance of aggressive phenotype. We firstly evaluated UNR/CSDE1 expression in human colon cancer derived cell lines and patient samples. Subsequently, we performed functional experiments by UNR/CSDE1 downregulation. We also evaluated UNR/CSDE1 prognostic relevance in two independent sets of patients. Not only was UNR/CSDE1 expression higher in tumor samples compared to untransformed samples, but also in colonospheres and metastatic origin cell lines than their parental and primary cell lines, respectively. Downregulation of UNR/CSDE1 reduced cell viability and migration throughout a restrain of epithelial-to-mesenchymal transition and increases sensitivity to apoptosis. Interestingly, high UNR/CSDE1 expression was associated with poor prognosis and correlated positively with c-MYC expression in colorectal cancer samples and cell lines. Here, we show for the first time compelling data reporting the oncogenic role of UNR/CSDE1 in human colorectal cancer.
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41
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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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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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43
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Lindquist JA, Mertens PR. Cold shock proteins: from cellular mechanisms to pathophysiology and disease. Cell Commun Signal 2018; 16:63. [PMID: 30257675 PMCID: PMC6158828 DOI: 10.1186/s12964-018-0274-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
Cold shock proteins are multifunctional RNA/DNA binding proteins, characterized by the presence of one or more cold shock domains. In humans, the best characterized members of this family are denoted Y-box binding proteins, such as Y-box binding protein-1 (YB-1). Biological activities range from the regulation of transcription, splicing and translation, to the orchestration of exosomal RNA content. Indeed, the secretion of YB-1 from cells via exosomes has opened the door to further potent activities. Evidence links a skewed cold shock protein expression pattern with cancer and inflammatory diseases. In this review the evidence for a causative involvement of cold shock proteins in disease development and progression is summarized. Furthermore, the potential application of cold shock proteins for diagnostics and as targets for therapy is elucidated.
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Affiliation(s)
- Jonathan A Lindquist
- Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany
| | - Peter R Mertens
- Clinic for Nephrology and Hypertension, Diabetology and Endocrinology, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44, 39120, Magdeburg, Germany.
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44
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Daskalaki W, Wardelmann E, Port M, Stock K, Steinestel J, Huss S, Sperveslage J, Steinestel K, Eder S. Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma. Int J Mol Med 2018; 42:3269-3277. [PMID: 30272263 PMCID: PMC6202084 DOI: 10.3892/ijmm.2018.3898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/14/2018] [Indexed: 12/17/2022] Open
Abstract
Ionizing radiation (IR) is frequently applied in the treatment of rectal adenocarcinoma, however, there is marked variance in the response to radiochemotherapy between individual tumors. In our previous investigations, it was shown that the overexpression of heterogeneous nuclear ribonucleoprotein K (hnRNP K) confers radioresistance to malignant melanoma and colorectal carcinoma (CRC) in vitro, however, the underlying mechanism remains to be elucidated. As hnRNP K, a p53 binding partner and cofactor for the transcriptional activation of p53 target genes, is overexpressed in CRC, the present study investigated the possible radioprotective effect of the hnRNP K/p53-induced upregulation of p21 (also known as WAF1/CIP1) in rectal adenocarcinoma. Immunohistochemistry was performed for hnRNP K, p53 and p21 in a series of 68 consecutive cases of rectal adenocarcinoma with full molecular characterization following radiochemo-therapy and 14 corresponding pre-therapeutic biopsies, and the results were correlated with clinicopathological characteristics and the percentage of vital tumor cells following therapy. In addition, pathway analyses, protein immunoprecipitation, western immunoblotting and immunofluorescence microscopy were performed to identify dysregulated kinase signaling and hnRNP K targets upon exposure of CRC cells to IR. Although the fraction of vital tumor cells upon neoadjuvant therapy was significantly higher in hnRNP K/p21-positive tumors (P=0.0047 and P=0.0223, Students’ t-test), no significant association was found between the protein expression levels of hnRNP K, p53 and p21 (P>0.05, χ2 test). Irradiation enhanced apoptotic pathway activation via p53/CHK2 phosphorylation and poly (ADP-ribose) polymerase cleavage, and induced the overexpression and interaction of hnRNP K and p53. However, p53 Ser15-phosphorylation was independent of the presence of hnRNP K, and there was no measurable effect of hnRNP K on the expression of p21 in vitro. Taken together, the results of the present study support a radioprotective role for hnRNP K, which may be mediated through an interaction with p53, however, this effect appears to be independent of the hnRNP K/p53-induced upregulation of p21 in rectal adenocarcinoma.
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Affiliation(s)
- Wassiliki Daskalaki
- Gerhard‑Domagk‑Institute of Pathology, University Hospital Münster, D‑48149 Münster, Germany
| | - Eva Wardelmann
- Gerhard‑Domagk‑Institute of Pathology, University Hospital Münster, D‑48149 Münster, Germany
| | - Matthias Port
- Bundeswehr Institute of Radiobiology Affiliated to The University of Ulm, D‑80937 Munich, Germany
| | - Katharina Stock
- Gerhard‑Domagk‑Institute of Pathology, University Hospital Münster, D‑48149 Münster, Germany
| | - Julie Steinestel
- Department of Urology, University Hospital Münster, D‑48149 Münster, Germany
| | - Sebastian Huss
- Gerhard‑Domagk‑Institute of Pathology, University Hospital Münster, D‑48149 Münster, Germany
| | - Jan Sperveslage
- Gerhard‑Domagk‑Institute of Pathology, University Hospital Münster, D‑48149 Münster, Germany
| | - Konrad Steinestel
- Gerhard‑Domagk‑Institute of Pathology, University Hospital Münster, D‑48149 Münster, Germany
| | - Stefan Eder
- Bundeswehr Institute of Radiobiology Affiliated to The University of Ulm, D‑80937 Munich, Germany
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45
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Shi H, Li H, Yuan R, Guan W, Zhang X, Zhang S, Zhang W, Tong F, Li L, Song Z, Wang C, Yang S, Wang H. PCBP1 depletion promotes tumorigenesis through attenuation of p27 Kip1 mRNA stability and translation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:187. [PMID: 30086790 PMCID: PMC6081911 DOI: 10.1186/s13046-018-0840-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 11/10/2022]
Abstract
Background Poly C Binding Protein 1 (PCBP1) is an RNA-binding protein that binds and regulates translational activity of subsets of cellular mRNAs. Depletion of PCBP1 is implicated in various carcinomas, but the underlying mechanism in tumorigenesis remains elusive. Methods We performed a transcriptome-wide screen to identify novel bounding mRNA of PCBP1. The bind regions between PCBP1 with target mRNA were investigated by using point mutation and luciferase assay. Cell proliferation, cell cycle, tumorigenesis and cell apoptosis were also evaluated in ovary and colon cancer cell lines. The mechanism that PCBP1 affects p27 was analyzed by mRNA stability and ribosome profiling assays. We analyzed PCBP1 and p27 expression in ovary, colon and renal tumor samples and adjacent non-tumor tissues using RT-PCR, Western Blotting and immunohistochemistry. The prognostic significance of PCBP1 and p27 also analyzed using online databases. Results We identified cell cycle inhibitor p27Kip1 (p27) as a novel PCBP1-bound transcript. We then demonstrated that binding of PCBP1 to p27 3’UTR via its KH1 domain mainly stabilizes p27 mRNA, while enhances its translation to fuel p27 expression, prior to p27 protein degradation. The upregulated p27 consequently inhibits cell proliferation, cell cycle progression and tumorigenesis, whereas promotes cell apoptosis under paclitaxel treatment. Conversely, knockdown of PCBP1 in turn compromises p27 mRNA stability, leading to lower p27 level and tumorigenesis in vivo. Moreover, forced depletion of p27 counteracts the tumor suppressive ability of PCBP1 in the same PCBP1 over-expressing cells. Physiologically, we showed that decreases of both p27 mRNA and its protein expressions are well correlated to PCBP1 depletion in ovary, colon and renal tumor samples, independent of the p27 ubiquitin ligase Skp2 level. Correlation of PCBP1 with p27 is also found in the tamoxifen, doxorubincin and lapatinib resistant breast cancer cells of GEO database. Conclusion Our results thereby indicate that loss of PCBP1 expression firstly attenuates p27 expression at post-transcriptional level, and subsequently promotes carcinogenesis. PCBP1 could be used as a diagnostic marker to cancer patients. Electronic supplementary material The online version of this article (10.1186/s13046-018-0840-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongshun Shi
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Hui Li
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Ronghua Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, China
| | - Wen Guan
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Xiaomei Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Shaoyang Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Wenliang Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Fang Tong
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Li Li
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Zhihong Song
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Changwei Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shulan Yang
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.
| | - Haihe Wang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China. .,Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China.
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46
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Kim JK, Kim I, Choi K, Choi JH, Kim E, Lee HY, Park J, Kim Yoon S. Poly(rC) binding protein 2 acts as a negative regulator of IRES-mediated translation of Hr mRNA. Exp Mol Med 2018; 50:e441. [PMID: 29422543 PMCID: PMC5903819 DOI: 10.1038/emm.2017.262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/16/2017] [Accepted: 08/26/2017] [Indexed: 12/21/2022] Open
Abstract
During the hair follicle (HF) cycle, HR protein expression is not concordant with the presence of the Hr mRNA transcript, suggesting an elaborate regulation of Hr gene expression. Here we present evidence that the 5' untranslated region (UTR) of the Hr gene has internal ribosome entry site (IRES) activity and this activity is regulated by the binding of poly (rC) binding protein 2 (PCBP2) to Hr mRNA. Overexpression and knockdown of PCBP2 resulted in a decrease in Hr 5' UTR IRES activity and an increase in HR protein expression without changing mRNA levels. We also found that this regulation was disrupted in a mutant Hr 5' UTR that has a mutation responsible for Marie Unna hereditary hypotrichosis (MUHH) in both mice and humans. These findings suggest that Hr mRNA expression is regulated at the post-transcriptional level via IRES-mediated translation control through interaction with PCPB2, but not in MUHH.
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Affiliation(s)
- Jeong-Ki Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Injung Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Keonwoo Choi
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Jee-Hyun Choi
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Eunmin Kim
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Hwa-Young Lee
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Jongkeun Park
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
| | - Sungjoo Kim Yoon
- Department of Medical Lifesciences, The Catholic University of Korea, Seoul, Korea
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47
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Li D, Wang X, Mei H, Fang E, Ye L, Song H, Yang F, Li H, Huang K, Zheng L, Tong Q. Long Noncoding RNA pancEts-1 Promotes Neuroblastoma Progression through hnRNPK-Mediated β-Catenin Stabilization. Cancer Res 2018; 78:1169-1183. [PMID: 29311158 DOI: 10.1158/0008-5472.can-17-2295] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/02/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) play essential roles in tumor progression. However, the functions of lncRNAs in the tumorigenesis and aggressiveness of neuroblastoma still remain to be determined. Here, we report the identification of lncRNA pancEts-1 as a novel driver of neuroblastoma progression by using a public microarray dataset. LncRNA pancEts-1 promoted the growth, invasion, and metastasis of neuroblastoma cells in vitro and in vivo Mechanistically, pancEts-1 bound to hnRNPK to facilitate its physical interaction with β-catenin, whereas hnRNPK stabilized the β-catenin by inhibiting proteasome-mediated degradation, resulting in transcriptional alteration of target genes associated with neuroblastoma progression. Both pancEts-1 and hnRNPK were upregulated in clinical neuroblastoma tissues, and were associated with unfavorable outcome of patients. Overall, our results define an oncogenic role of pancEts-1 in neuroblastoma progression through hnRNPK-mediated β-catenin stabilization, with potential implications for the clinical therapeutics of neuroblastoma.Significance: These findings reveal the oncogenic functions of a long noncoding RNA in neuroblastoma progression, offering a potential target for clinical therapeutics. Cancer Res; 78(5); 1169-83. ©2018 AACR.
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Affiliation(s)
- Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Xiaojing Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Hong Mei
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Erhu Fang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Lin Ye
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Huajie Song
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Feng Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Huanhuan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Kai Huang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Liduan Zheng
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China.
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China.
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R. China
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Gritsenko AA, Weingarten-Gabbay S, Elias-Kirma S, Nir R, de Ridder D, Segal E. Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity. PLoS Comput Biol 2017; 13:e1005734. [PMID: 28922394 PMCID: PMC5630158 DOI: 10.1371/journal.pcbi.1005734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/06/2017] [Accepted: 08/22/2017] [Indexed: 01/25/2023] Open
Abstract
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be involved in this process. However due to the small number of IRESs known, there have been no systematic investigations of the determinants of IRES activity. With the recent discovery of thousands of novel IRESs in human and viruses, the next challenge is to decipher the sequence determinants of IRES activity. We present the first in-depth computational analysis of a large body of IRESs, exploring RNA sequence features predictive of IRES activity. We identified predictive k-mer features resembling IRES trans-acting factor (ITAF) binding motifs across human and viral IRESs, and found that their effect on expression depends on their sequence, number and position. Our results also suggest that the architecture of retroviral IRESs differs from that of other viruses, presumably due to their exposure to the nuclear environment. Finally, we measured IRES activity of synthetically designed sequences to confirm our prediction of increasing activity as a function of the number of short IRES elements.
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Affiliation(s)
- Alexey A. Gritsenko
- The Delft Bioinformatics Laboratory, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Platform Green Synthetic Biology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Elias-Kirma
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ronit Nir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dick de Ridder
- The Delft Bioinformatics Laboratory, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
- Platform Green Synthetic Biology, Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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49
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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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50
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Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 462] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
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Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
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