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Ribosome biogenesis: An emerging druggable pathway for cancer therapeutics. Biochem Pharmacol 2018; 159:74-81. [PMID: 30468711 DOI: 10.1016/j.bcp.2018.11.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/16/2018] [Indexed: 01/05/2023]
Abstract
Ribosomes are nanomachines essential for protein production in all living cells. Ribosome synthesis increases in cancer cells to cope with a rise in protein synthesis and sustain unrestricted growth. This increase in ribosome biogenesis is reflected by severe morphological alterations of the nucleolus, the cell compartment where the initial steps of ribosome biogenesis take place. Ribosome biogenesis has recently emerged as an effective target in cancer therapy, and several compounds that inhibit ribosome production or function, killing preferentially cancer cells, have entered clinical trials. Recent research indicates that cells express heterogeneous populations of ribosomes and that the composition of ribosomes may play a key role in tumorigenesis, exposing novel therapeutic opportunities. Here, we review recent data demonstrating that ribosome biogenesis is a promising druggable pathway in cancer therapy, and discuss future research perspectives.
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2
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Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1477. [PMID: 29726113 PMCID: PMC6002909 DOI: 10.1002/wrna.1477] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]
Abstract
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
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3
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Prosser KE, Leung AWY, Harrypersad S, Lewis AR, Bally MB, Walsby CJ. Transition Metal Ions Promote the Bioavailability of Hydrophobic Therapeutics: Cu and Zn Interactions with RNA Polymerase I Inhibitor CX5461. Chemistry 2018; 24:6334-6338. [PMID: 29490115 DOI: 10.1002/chem.201800289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Indexed: 01/27/2023]
Abstract
Low aqueous solubility is a major barrier to the clinical application of otherwise promising drug candidates. We demonstrate that this issue can be resolved in medicinal molecules containing potential ligating groups, through the addition of labile transition-metal ions. Incubation of the chemotherapeutic CX5461 with Cu2+ or Zn2+ enables solubilization at neutral pH but does not affect intrinsic cytotoxicity. Spectroscopic and computational studies demonstrate that this arises from coordination to the pyrazine functionality of CX5461 and may involve bidentate coordination at physiological pH.
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Affiliation(s)
- Kathleen E Prosser
- Department of Chemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC, V5A 1S6, Canada
| | - Ada W Y Leung
- Department of Experimental Therapeutics, British Columbia Cancer Agency, 675 West 10th Ave, Vancouver, BC, V5Z 4E6, Canada
| | - Shane Harrypersad
- Department of Chemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC, V5A 1S6, Canada
| | - Andrew R Lewis
- Department of Chemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC, V5A 1S6, Canada
| | - Marcel B Bally
- Department of Experimental Therapeutics, British Columbia Cancer Agency, 675 West 10th Ave, Vancouver, BC, V5Z 4E6, Canada
| | - Charles J Walsby
- Department of Chemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC, V5A 1S6, Canada
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4
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Marcel V, Catez F, Berger CM, Perrial E, Plesa A, Thomas X, Mattei E, Hayette S, Saintigny P, Bouvet P, Diaz JJ, Dumontet C. Expression Profiling of Ribosome Biogenesis Factors Reveals Nucleolin as a Novel Potential Marker to Predict Outcome in AML Patients. PLoS One 2017; 12:e0170160. [PMID: 28103300 PMCID: PMC5245884 DOI: 10.1371/journal.pone.0170160] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/30/2016] [Indexed: 01/20/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease. Prognosis is mainly influenced by patient age at diagnosis and cytogenetic alterations, two of the main factors currently used in AML patient risk stratification. However, additional criteria are required to improve the current risk classification and better adapt patient care. In neoplastic cells, ribosome biogenesis is increased to sustain the high proliferation rate and ribosome composition is altered to modulate specific gene expression driving tumorigenesis. Here, we investigated the usage of ribosome biogenesis factors as clinical markers in adult patients with AML. We showed that nucleoli, the nucleus compartments where ribosome production takes place, are modified in AML by analyzing a panel of AML and healthy donor cells using immunofluorescence staining. Using four AML series, including the TCGA dataset, altogether representing a total of about 270 samples, we showed that not all factors involved in ribosome biogenesis have clinical values although ribosome biogenesis is increased in AML. Interestingly, we identified the regulator of ribosome production nucleolin (NCL) as over-expressed in AML blasts. Moreover, we found in two series that high NCL mRNA expression level was associated with a poor overall survival, particular in elderly patients. Multivariate analyses taking into account age and cytogenetic risk indicated that NCL expression in blast cells is an independent marker of reduced survival. Our study identifies NCL as a potential novel prognostic factor in AML. Altogether, our results suggest that the ribosome biogenesis pathway may be of interest as clinical markers in AML.
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MESH Headings
- Adolescent
- Adult
- Age Factors
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Case-Control Studies
- Child
- Child, Preschool
- Female
- Gene Expression Profiling
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Male
- Middle Aged
- Nuclear Proteins/genetics
- Phosphoproteins/genetics
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- RNA-Binding Proteins/genetics
- Ribosomes/genetics
- Ribosomes/metabolism
- Up-Regulation
- Young Adult
- Nucleolin
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Affiliation(s)
- Virginie Marcel
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Nuclear domains and pathologies team, Cancer Cell Plasticity Department, Lyon, France
| | - Frédéric Catez
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Nuclear domains and pathologies team, Cancer Cell Plasticity Department, Lyon, France
| | - Caroline M. Berger
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Nuclear domains and pathologies team, Cancer Cell Plasticity Department, Lyon, France
| | - Emeline Perrial
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Anticancer antibodies team, Immunity, Microenvironment and Virus Department, Lyon, France
| | - Adriana Plesa
- Department of Biology, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Xavier Thomas
- Department of Hematology, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Eve Mattei
- Department of Biology, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Sandrine Hayette
- Department of Biology, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Pierre Saintigny
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Department of Medecine, Centre Léon Bérard, Lyon, France
| | - Philippe Bouvet
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Nuclear domains and pathologies team, Cancer Cell Plasticity Department, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Jacques Diaz
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Nuclear domains and pathologies team, Cancer Cell Plasticity Department, Lyon, France
| | - Charles Dumontet
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
- Université Lyon 1, Lyon, France
- Anticancer antibodies team, Immunity, Microenvironment and Virus Department, Lyon, France
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5
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Neben CL, Lay FD, Mao X, Tuzon CT, Merrill AE. Ribosome biogenesis is dynamically regulated during osteoblast differentiation. Gene 2016; 612:29-35. [PMID: 27847259 DOI: 10.1016/j.gene.2016.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 01/19/2023]
Abstract
Changes in ribosome biogenesis are tightly linked to cell growth, proliferation, and differentiation. The rate of ribosome biogenesis is established by RNA Pol I-mediated transcription of ribosomal RNA (rRNA). Thus, rRNA gene transcription is a key determinant of cell behavior. Here, we show that ribosome biogenesis is dynamically regulated during osteoblast differentiation. Upon osteoinduction, osteoprogenitor cells transiently silence a subset of rRNA genes through a reversible mechanism that is initiated through biphasic nucleolar depletion of UBF1 and then RNA Pol I. Nucleolar depletion of UBF1 is coincident with an increase in the number of silent but transcriptionally permissible rRNA genes. This increase in the number of silent rRNA genes reduces levels of ribosome biogenesis and subsequently, protein synthesis. Together these findings demonstrate that fluctuations in rRNA gene transcription are determined by nucleolar occupancy of UBF1 and closely coordinated with the early events necessary for acquisition of the osteoblast cell fate.
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Affiliation(s)
- Cynthia L Neben
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Fides D Lay
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Xiaojing Mao
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Creighton T Tuzon
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States
| | - Amy E Merrill
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, United States; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, United States.
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The importance of being (slightly) modified: The role of rRNA editing on gene expression control and its connections with cancer. Biochim Biophys Acta Rev Cancer 2016; 1866:330-338. [PMID: 27815156 DOI: 10.1016/j.bbcan.2016.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/12/2016] [Accepted: 10/30/2016] [Indexed: 12/22/2022]
Abstract
In human ribosomal RNAs, over 200 residues are modified by specific, RNA-driven enzymatic complexes or stand-alone, RNA-independent enzymes. In most cases, modification sites are placed in specific positions within important functional areas of the ribosome. Some evidence indicates that the altered control in ribosomal RNA modifications may affect ribosomal function during mRNA translation. Here we provide an overview of the connections linking ribosomal RNA modifications to ribosome function, and suggest how aberrant modifications may affect the control of the expression of key cancer genes, thus contributing to tumor development. In addition, the future perspectives in this field are discussed.
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7
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Krogh N, Jansson MD, Häfner SJ, Tehler D, Birkedal U, Christensen-Dalsgaard M, Lund AH, Nielsen H. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Res 2016; 44:7884-95. [PMID: 27257078 PMCID: PMC5027482 DOI: 10.1093/nar/gkw482] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/16/2016] [Accepted: 05/19/2016] [Indexed: 01/05/2023] Open
Abstract
Ribose methylation is one of the two most abundant modifications in human ribosomal RNA and is believed to be important for ribosome biogenesis, mRNA selectivity and translational fidelity. We have applied RiboMeth-seq to rRNA from HeLa cells for ribosome-wide, quantitative mapping of 2'-O-Me sites and obtained a comprehensive set of 106 sites, including two novel sites, and with plausible box C/D guide RNAs assigned to all but three sites. We find approximately two-thirds of the sites to be fully methylated and the remainder to be fractionally modified in support of ribosome heterogeneity at the level of RNA modifications. A comparison to HCT116 cells reveals similar 2'-O-Me profiles with distinct differences at several sites. This study constitutes the first comprehensive mapping of 2'-O-Me sites in human rRNA using a high throughput sequencing approach. It establishes the existence of a core of constitutively methylated positions and a subset of variable, potentially regulatory positions, and paves the way for experimental analyses of the role of variations in rRNA methylation under different physiological or pathological settings.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark
| | - Martin D Jansson
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Sophia J Häfner
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Disa Tehler
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Ulf Birkedal
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark
| | | | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark
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8
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Goudarzi KM, Lindström MS. Role of ribosomal protein mutations in tumor development (Review). Int J Oncol 2016; 48:1313-24. [PMID: 26892688 PMCID: PMC4777597 DOI: 10.3892/ijo.2016.3387] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/07/2016] [Indexed: 12/16/2022] Open
Abstract
Ribosomes are cellular machines essential for protein synthesis. The biogenesis of ribosomes is a highly complex and energy consuming process that initiates in the nucleolus. Recently, a series of studies applying whole-exome or whole-genome sequencing techniques have led to the discovery of ribosomal protein gene mutations in different cancer types. Mutations in ribosomal protein genes have for example been found in endometrial cancer (RPL22), T-cell acute lymphoblastic leukemia (RPL10, RPL5 and RPL11), chronic lymphocytic leukemia (RPS15), colorectal cancer (RPS20), and glioma (RPL5). Moreover, patients suffering from Diamond-Blackfan anemia, a bone marrow failure syndrome caused by mutant ribosomal proteins are also at higher risk for developing leukemia, or solid tumors. Different experimental models indicate potential mechanisms whereby ribosomal proteins may initiate cancer development. In particular, deregulation of the p53 tumor suppressor network and altered mRNA translation are mechanisms likely to be involved. We envisage that changes in expression and the occurrence of ribosomal protein gene mutations play important roles in cancer development. Ribosome biology constitutes a re-emerging vital area of basic and translational cancer research.
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Affiliation(s)
- Kaveh M Goudarzi
- Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, CCK R8:05, Karolinska University Hospital in Solna, Stockholm, Sweden
| | - Mikael S Lindström
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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9
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In vitro translation in a hybrid cell free lysate with exogenous cellular ribosomes. Biochem J 2015; 467:387-98. [PMID: 25628018 DOI: 10.1042/bj20141498] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cell free protein synthesis systems (CFPS) have been widely used to express proteins and to explore the pathways of gene expression. In the present manuscript, we describe the design of a novel adaptable hybrid in vitro translation system which is assembled with ribosomes isolated from many different origins. We first show that this hybrid system exhibits all important features such as efficiency, sensitivity, reproducibility and the ability to translate specialized mRNAs in less than 1 h. In addition, the unique design of this cell free assay makes it highly adaptable to utilize ribosomes isolated from many different organs, tissues or cell types.
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10
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Marcel V, Catez F, Diaz JJ. p53, a translational regulator: contribution to its tumour-suppressor activity. Oncogene 2015; 34:5513-23. [DOI: 10.1038/onc.2015.25] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 12/14/2022]
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