1
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Hwang SP, Denicourt C. The impact of ribosome biogenesis in cancer: from proliferation to metastasis. NAR Cancer 2024; 6:zcae017. [PMID: 38633862 PMCID: PMC11023387 DOI: 10.1093/narcan/zcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The dysregulation of ribosome biogenesis is a hallmark of cancer, facilitating the adaptation to altered translational demands essential for various aspects of tumor progression. This review explores the intricate interplay between ribosome biogenesis and cancer development, highlighting dynamic regulation orchestrated by key oncogenic signaling pathways. Recent studies reveal the multifaceted roles of ribosomes, extending beyond protein factories to include regulatory functions in mRNA translation. Dysregulated ribosome biogenesis not only hampers precise control of global protein production and proliferation but also influences processes such as the maintenance of stem cell-like properties and epithelial-mesenchymal transition, contributing to cancer progression. Interference with ribosome biogenesis, notably through RNA Pol I inhibition, elicits a stress response marked by nucleolar integrity loss, and subsequent G1-cell cycle arrest or cell death. These findings suggest that cancer cells may rely on heightened RNA Pol I transcription, rendering ribosomal RNA synthesis a potential therapeutic vulnerability. The review further explores targeting ribosome biogenesis vulnerabilities as a promising strategy to disrupt global ribosome production, presenting therapeutic opportunities for cancer treatment.
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Affiliation(s)
- Sseu-Pei Hwang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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2
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van den Akker GGH, Chabronova A, Housmans BAC, van der Vloet L, Surtel DAM, Cremers A, Marchand V, Motorin Y, Caron MMJ, Peffers MJ, Welting TJM. TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes. Int J Mol Sci 2024; 25:5031. [PMID: 38732249 PMCID: PMC11084827 DOI: 10.3390/ijms25095031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribosome activity. Dual luciferase reporter assays were used to assess ribosomal modus. Ribosomal RNA expression and processing were determined by RT-qPCR, while RiboMethSeq and HydraPsiSeq were used to determine rRNA modification profiles. Label-free protein quantification of total cell lysates, isolated ribosomes and secreted proteins was done by LC-MS/MS. A three-day TGF-β2 stimulation induced total protein synthesis in SW1353 chondrocytic cells and human articular chondrocytes. Specifically, TGF-β2 induced cap-mediated protein synthesis, while IRES-mediated translation was not (P53 IRES) or little affected (CrPv IGR and HCV IRES). Three rRNA post-transcriptional modifications (PTMs) were affected by TGF-β2 stimulation (18S-Gm1447 downregulated, 18S-ψ1177 and 28S-ψ4598 upregulated). Proteomic analysis of isolated ribosomes revealed increased interaction with eIF2 and tRNA ligases and decreased association of eIF4A3 and heterogeneous nuclear ribonucleoprotein (HNRNP)s. In addition, thirteen core ribosomal proteins were more present in ribosomes from TGF-β2 stimulated cells, albeit with a modest fold change. A prolonged stimulation of chondrocytic cells with TGF-β2 induced ribosome activity and changed the mode of translation. These functional changes could be coupled to alterations in accessory proteins in the ribosomal proteome.
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Affiliation(s)
- Guus G. H. van den Akker
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Alzbeta Chabronova
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Bas A. C. Housmans
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Laura van der Vloet
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Don A. M. Surtel
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Andy Cremers
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Virginie Marchand
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
| | - Yuri Motorin
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
- UMR7365 IMoPA, CNRS, Université de Lorraine, BioPole, F54000 Nancy, France
| | - Marjolein M. J. Caron
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Mandy J. Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Tim J. M. Welting
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center +, 6229 HX Maastricht, The Netherlands
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3
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Huo M, Rai SK, Nakatsu K, Deng Y, Jijiwa M. Subverting the Canon: Novel Cancer-Promoting Functions and Mechanisms for snoRNAs. Int J Mol Sci 2024; 25:2923. [PMID: 38474168 PMCID: PMC10932220 DOI: 10.3390/ijms25052923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) constitute a class of intron-derived non-coding RNAs ranging from 60 to 300 nucleotides. Canonically localized in the nucleolus, snoRNAs play a pivotal role in RNA modifications and pre-ribosomal RNA processing. Based on the types of modifications they involve, such as methylation and pseudouridylation, they are classified into two main families-box C/D and H/ACA snoRNAs. Recent investigations have revealed the unconventional synthesis and biogenesis strategies of snoRNAs, indicating their more profound roles in pathogenesis than previously envisioned. This review consolidates recent discoveries surrounding snoRNAs and provides insights into their mechanistic roles in cancer. It explores the intricate interactions of snoRNAs within signaling pathways and speculates on potential therapeutic solutions emerging from snoRNA research. In addition, it presents recent findings on the long non-coding small nucleolar RNA host gene (lncSNHG), a subset of long non-coding RNAs (lncRNAs), which are the transcripts of parental SNHGs that generate snoRNA. The nucleolus, the functional epicenter of snoRNAs, is also discussed. Through a deconstruction of the pathways driving snoRNA-induced oncogenesis, this review aims to serve as a roadmap to guide future research in the nuanced field of snoRNA-cancer interactions and inspire potential snoRNA-related cancer therapies.
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Affiliation(s)
- Matthew Huo
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA;
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
| | - Sudhir Kumar Rai
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
| | - Ken Nakatsu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
| | - Mayumi Jijiwa
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA; (S.K.R.); (K.N.)
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Zacchini F, Barozzi C, Venturi G, Montanaro L. How snoRNAs can contribute to cancer at multiple levels. NAR Cancer 2024; 6:zcae005. [PMID: 38406265 PMCID: PMC10894041 DOI: 10.1093/narcan/zcae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
snoRNAs are a class of non-coding RNAs known to guide site specifically RNA modifications such as 2'-O-methylation and pseudouridylation. Recent results regarding snoRNA alterations in cancer has been made available and suggest their potential evaluation as diagnostic and prognostic biomarkers. A large part of these data, however, was not consistently confirmed and failed to provide mechanistic insights on the contribution of altered snoRNA expression to the neoplastic process. Here, we aim to critically review the available literature on snoRNA in cancer focusing on the studies elucidating the functional consequences of their deregulation. Beyond the canonical guide function in RNA processing and modification we also considered additional roles in which snoRNA, in various forms and through different modalities, are involved and that have been recently reported.
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Affiliation(s)
- Federico Zacchini
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Lorenzo Montanaro
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
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5
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Chabronova A, van den Akker G, Housmans BAC, Caron MMJ, Cremers A, Surtel DAM, Peffers MJ, van Rhijn LW, Marchand V, Motorin Y, Welting TJM. Depletion of SNORA33 Abolishes ψ of 28S-U4966 and Affects the Ribosome Translational Apparatus. Int J Mol Sci 2023; 24:12578. [PMID: 37628759 PMCID: PMC10454564 DOI: 10.3390/ijms241612578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Eukaryotic ribosomes are complex molecular nanomachines translating genetic information from mRNAs into proteins. There is natural heterogeneity in ribosome composition. The pseudouridylation (ψ) of ribosomal RNAs (rRNAs) is one of the key sources of ribosome heterogeneity. Nevertheless, the functional consequences of ψ-based ribosome heterogeneity and its relevance for human disease are yet to be understood. Using HydraPsiSeq and a chronic disease model of non-osteoarthritic primary human articular chondrocytes exposed to osteoarthritic synovial fluid, we demonstrated that the disease microenvironment is capable of instigating site-specific changes in rRNA ψ profiles. To investigate one of the identified differential rRNA ψ sites (28S-ψ4966), we generated SNORA22 and SNORA33 KO SW1353 cell pools using LentiCRISPRv2/Cas9 and evaluated the ribosome translational capacity by 35S-Met/Cys incorporation, assessed the mode of translation initiation and ribosomal fidelity using dual luciferase reporters, and assessed cellular and ribosomal proteomes by LC-MS/MS. We uncovered that the depletion of SNORA33, but not SNORA22, reduced 28S-ψ4966 levels. The resulting loss of 28S-ψ4966 affected ribosomal protein composition and function and led to specific changes in the cellular proteome. Overall, our pioneering findings demonstrate that cells dynamically respond to disease-relevant changes in their environment by altering their rRNA pseudouridylation profiles, with consequences for ribosome function and the cellular proteome relevant to human disease.
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Affiliation(s)
- Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Guus van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Bas A. C. Housmans
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Marjolein M. J. Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Don A. M. Surtel
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Mandy J. Peffers
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L8 7TX, UK
| | - Lodewijk W. van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
| | - Virginie Marchand
- UAR2008 IBSLor CNRS-INSERM-Université de Lorraine, F54000 Nancy, France
| | - Yuri Motorin
- UAR2008 IBSLor CNRS-INSERM-Université de Lorraine, F54000 Nancy, France
- UMR7365 IMOPA, CNRS-Université de Lorraine, F54000 Nancy, France
| | - Tim J. M. Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 HX Maastricht, The Netherlands; (A.C.); (B.A.C.H.)
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
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6
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Matsuura-Suzuki E, Toh H, Iwasaki S. Human-rabbit Hybrid Translation System to Explore the Function of Modified Ribosomes. Bio Protoc 2023; 13:e4714. [PMID: 37456340 PMCID: PMC10339341 DOI: 10.21769/bioprotoc.4714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/15/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
In vitro translation systems are a useful biochemical tool to research translational regulation. Although the preparation of translation-competent cell extracts from mammals has often been a challenge, the commercially available rabbit reticulocyte lysate (RRL) is an exception. However, its valid use, investigating the mechanism of translation machinery such as ribosomes in RRL, presents an analytic hurdle. To overcome this issue, the hybrid translation system, which is based on the supplementation of purified human ribosomes into ribosome-depleted RRL, has been developed. Here, we describe the step-by-step protocol of this system to study translation driven by ribosomes lacking post-translational modifications of the ribosomal protein. Moreover, we combined this approach with a previously developed reporter mRNA to assess the processivity of translation elongation. This protocol could be used to study the potency of heterologous ribosomes.
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Affiliation(s)
- Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
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Zhu J, Mao S, Zhen N, Zhu G, Bian Z, Xie Y, Tang X, Ding M, Wu H, Ma J, Zhu Y, Sun F, Pan Q. SNORA14A inhibits hepatoblastoma cell proliferation by regulating SDHB-mediated succinate metabolism. Cell Death Dis 2023; 9:36. [PMID: 36717552 PMCID: PMC9886955 DOI: 10.1038/s41420-023-01325-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/31/2023]
Abstract
Hepatoblastoma (HB) is the most common paediatric liver malignancy. Dysregulation of small nucleolar RNAs (snoRNAs) is a critical inducer of tumour initiation and progression. However, the association between snoRNAs and HB remains unknown. Here, we conducted snoRNA expression profiling in HB by snoRNA sequencing and identified a decreased level of SNORA14A, a box H/ACA snoRNA, in HB tissues. Low expression of SNORA14A was correlated with PRETEXT stage and metastasis in patients. Functionally, overexpression of SNORA14A suppressed HB cell proliferation and triggered cell apoptosis and G2/M phase arrest. Mechanistically, SNORA14A overexpression promoted the processing and maturation of the 18 S ribosomal RNA (rRNA) precursor to increase succinate dehydrogenase subunit B (SDHB) protein levels. In accordance with SNORA14A downregulation, SDHB protein expression was significantly reduced in HB tissues and cells, accompanied by abnormal accumulation of succinate. Overexpression of SDHB showed antiproliferative and proapoptotic effects and the capacity to induce G2/M phase arrest, while succinate dose-dependently stimulated HB cell growth. Furthermore, the inhibition of SNORA14A in HB malignant phenotypes was mediated by SDHB upregulation-induced reduction of cellular succinate levels. Therefore, the SNORA14A/18 S rRNA/SDHB axis suppresses HB progression by preventing cellular accumulation of the oncometabolite succinate and provides promising prognostic biomarkers and novel therapeutic targets for HB.
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Affiliation(s)
- Jiabei Zhu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China
| | - Siwei Mao
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China
| | - Ni Zhen
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Guoqing Zhu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhixuan Bian
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yi Xie
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Xiaochen Tang
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Miao Ding
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Han Wu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Ji Ma
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yizhun Zhu
- grid.259384.10000 0000 8945 4455State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, 999078 China
| | - Fenyong Sun
- grid.412538.90000 0004 0527 0050Department of Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, 200072 China
| | - Qiuhui Pan
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China ,grid.415626.20000 0004 4903 1529Sanya Women and Children’s Hospital Managed by Shanghai Children’s Medical Center, Sanya, 572000 China
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Naarmann-de Vries IS, Zorbas C, Lemsara A, Piechotta M, Ernst FGM, Wacheul L, Lafontaine DLJ, Dieterich C. Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2. RNA Biol 2023; 20:652-665. [PMID: 37635368 PMCID: PMC10464549 DOI: 10.1080/15476286.2023.2248752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
Ribosomal RNAs are decorated by numerous post-transcriptional modifications whose exact roles in ribosome biogenesis, function, and human pathophysiology remain largely unknown. Here, we report a targeted direct rRNA sequencing approach involving a substrate selection step and demonstrate its suitability to identify differential modification sites in combination with the JACUSA2 software. We compared JACUSA2 to other tools designed for RNA modification detection and show that JACUSA2 outperforms other software with regard to detection of base modifications such as methylation, acetylation and aminocarboxypropylation. To illustrate its widespread usability, we applied our method to a collection of CRISPR-Cas9 engineered colon carcinoma cells lacking specific enzymatic activities responsible for particular rRNA modifications and systematically compared them to isogenic wild-type RNAs. Besides the numerous 2'-O methylated riboses and pseudouridylated residues, our approach was suitable to reliably identify differential base methylation and acetylation events. Importantly, our method does not require any prior knowledge of modification sites or the need to train complex models. We further report for the first time detection of human rRNA modifications by direct RNA-sequencing on Flongle flow cells, the smallest-scale nanopore flow cell available to date. The use of these smaller flow cells reduces RNA input requirements, making our workflow suitable for the analysis of samples with limited availability and clinical work.
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Affiliation(s)
- Isabel S. Naarmann-de Vries
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christiane Zorbas
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Amina Lemsara
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Piechotta
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix G. M. Ernst
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Ludivine Wacheul
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Denis L. J. Lafontaine
- RNA Molecular Biology, Université libre de Bruxelles (ULB), Fonds de la Recherche Scientifique (F.R.S./FNRS), Gosselies, Belgium
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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9
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Nagpal N, Tai AK, Nandakumar J, Agarwal S. Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13. Nucleic Acids Res 2022; 50:9413-9425. [PMID: 36018809 PMCID: PMC9458449 DOI: 10.1093/nar/gkac706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in DKC1 (encoding dyskerin) cause telomere diseases including dyskeratosis congenita (DC) by decreasing steady-state levels of TERC, the non-coding RNA component of telomerase. How DKC1 mutations variably impact numerous other snoRNAs remains unclear, which is a barrier to understanding disease mechanisms in DC beyond impaired telomere maintenance. Here, using DC patient iPSCs, we show that mutations in the dyskerin N-terminal extension domain (NTE) dysregulate scaRNA13. In iPSCs carrying the del37L NTE mutation or engineered to carry NTE mutations via CRISPR/Cas9, but not in those with C-terminal mutations, we found scaRNA13 transcripts with aberrant 3' extensions, as seen when the exoribonuclease PARN is mutated in DC. Biogenesis of scaRNA13 was rescued by repair of the del37L DKC1 mutation by genome-editing, or genetic or pharmacological inactivation of the polymerase PAPD5, which counteracts PARN. Inspection of the human telomerase cryo-EM structure revealed that in addition to mediating intermolecular dyskerin interactions, the NTE interacts with terminal residues of the associated snoRNA, indicating a role for this domain in 3' end definition. Our results provide mechanistic insights into the interplay of dyskerin and the PARN/PAPD5 axis in the biogenesis and accumulation of snoRNAs beyond TERC, broadening our understanding of ncRNA dysregulation in human diseases.
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Affiliation(s)
- Neha Nagpal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children's Hospital; Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; Department of Pediatrics, Harvard Medical School; Manton Center for Orphan Disease Research; Harvard Initiative in RNA Medicine; Boston, MA, USA
| | - Albert K Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
- Data Intensive Studies Center, Tufts University, Medford, MA, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Suneet Agarwal
- To whom correspondence should be addressed. Tel: +1 617 919 4610; Fax: +1 617 919 3359;
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10
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Zacchini F, Venturi G, De Sanctis V, Bertorelli R, Ceccarelli C, Santini D, Taffurelli M, Penzo M, Treré D, Inga A, Dassi E, Montanaro L. Human dyskerin binds to cytoplasmic H/ACA-box-containing transcripts affecting nuclear hormone receptor dependence. Genome Biol 2022; 23:177. [PMID: 35996163 PMCID: PMC9394076 DOI: 10.1186/s13059-022-02746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/11/2022] [Indexed: 12/05/2022] Open
Abstract
Background Dyskerin is a nuclear protein involved in H/ACA box snoRNA-guided uridine modification of RNA. In humans, its defective function is associated with cancer development and induces specific post-transcriptional alterations of gene expression. In this study, we seek to unbiasedly identify mRNAs regulated by dyskerin in human breast cancer-derived cells. Results We find that dyskerin depletion affects the expression and the association with polysomes of selected mRNA isoforms characterized by the retention of H/ACA box snoRNA-containing introns. These snoRNA retaining transcripts (snoRTs) are bound by dyskerin in the cytoplasm in the form of shorter 3′ snoRT fragments. We then characterize the whole cytoplasmic dyskerin RNA interactome and find both H/ACA box snoRTs and protein-coding transcripts which may be targeted by the snoRTs’ guide properties. Since a fraction of these protein-coding transcripts is involved in the nuclear hormone receptor binding, we test to see if this specific activity is affected by dyskerin. Obtained results indicate that dyskerin dysregulation may alter the dependence on nuclear hormone receptor ligands in breast cancer cells. These results are paralleled by consistent observations on the outcome of primary breast cancer patients stratified according to their tumor hormonal status. Accordingly, experiments in nude mice show that the reduction of dyskerin levels in estrogen-dependent cells favors xenograft development in the absence of estrogen supplementation. Conclusions Our work suggests a cytoplasmic function for dyskerin which could affect mRNA post-transcriptional networks relevant for nuclear hormone receptor functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02746-3.
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Affiliation(s)
- Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Giulia Venturi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Veronica De Sanctis
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Roberto Bertorelli
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Claudio Ceccarelli
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Unità Operativa di Anatomia e Istologia Patologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Donatella Santini
- Unità Operativa di Anatomia e Istologia Patologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Mario Taffurelli
- Unità Operativa di Chirurgia Senologica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy.,Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy
| | - Marianna Penzo
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Centro di Ricerca Biomedica Applicata - CRBA, Università̀ di Bologna, Policlinico di Sant'Orsola, I-40138, Bologna, Italy
| | - Davide Treré
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy.,Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy
| | - Alberto Inga
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Erik Dassi
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università di Trento, I-38123, Trento, Italy
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum - Università di Bologna, I-40138, Bologna, Italy. .,Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138, Bologna, Italy.
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11
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Steinbusch MMF, van den Akker GGH, Cremers A, Witlox AMA, Staal HM, Peffers MJ, van Rhijn LW, Caron MMJ, Welting TJM. Adaptation of the protein translational apparatus during ATDC5 chondrogenic differentiation. Noncoding RNA Res 2022; 7:55-65. [PMID: 35261930 PMCID: PMC8881200 DOI: 10.1016/j.ncrna.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 11/05/2022] Open
Abstract
Introduction Ribosome biogenesis is integrated with many cellular processes including proliferation, differentiation and oncogenic events. Chondrogenic proliferation and differentiation require a high cellular translational capacity to facilitate cartilaginous extracellular matrix production. We here investigated the expression dynamics of factors involved in ribosome biogenesis during in vitro chondrogenic differentiation and determined whether protein translation capacity adapts to different phases of chondrogenic differentiation. Materials SnoRNA expression during ATDC5 differentiation was analyzed by RNA sequencing of samples acquired from day 0 (progenitor stage), 7 (chondrogenic stage) and day 14 (hypertrophic stage). RT-qPCR was used to determine expression of fibrillarin, dyskerin, UBF-1, Sox9, Col2a1, Runx2, Col10a1 mRNAs and 18S, 5.8S and 28S rRNAs. Protein expression of fibrillarin, dyskerin and UBF-1 was determined by immunoblotting. Ribosomal RNA content per cell was determined by calculating rRNA RT-qPCR signals relative to DNA content (SYBR Green assay). Total protein translational activity was evaluated with a puromycilation assay and polysome profiling. Results As a result of initiation of chondrogenic differentiation (Δt0-t7), 21 snoRNAs were differentially expressed (DE). Hypertrophic differentiation caused DE of 23 snoRNAs (Δt7-t14) and 43 when t0 was compared to t14. DE snoRNAs, amongst others, target nucleotide modifications in the 28S rRNA peptidyl transferase center and the 18S rRNA decoding center. UBF-1, fibrillarin and dyskerin expression increased as function of differentiation and displayed highest fold induction at day 5-6 in differentiation. Ribosomal RNA content per cell was significantly increased at day 7, but not at day 14 in differentiation. Similar dynamics in translational capacity and monosomal ribosome fraction were observed during differentiation. Conclusion The expression of a great number of ribosome biogenesis factors is altered during chondrogenic differentiation of ATDC5 cells, which is accompanied by significant changes in cellular translational activity. This elucidation of ribosome biogenesis dynamics in chondrogenic differentiation models enables the further understanding of the role of ribosome biogenesis and activity during chondrocyte cell commitment and their roles in human skeletal development diseases.
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Affiliation(s)
- Mandy M F Steinbusch
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Guus G H van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Adhiambo M A Witlox
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Heleen M Staal
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Mandy J Peffers
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, L7 8TX, Liverpool, United Kingdom
| | - Lodewijk W van Rhijn
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Marjolein M J Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands.,Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, the Netherlands
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12
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Maiello D, Varone M, Vicidomini R, Belli V, Rosa MD, Dama P, Furia M, Turano M. Dyskerin Downregulation Can Induce ER Stress and Promote Autophagy via AKT-mTOR Signaling Deregulation. Biomedicines 2022; 10:1092. [PMID: 35625829 PMCID: PMC9138296 DOI: 10.3390/biomedicines10051092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/05/2023] Open
Abstract
Dyskerin is an evolutionarily conserved nucleolar protein implicated in a wide range of fundamental biological roles, including telomere maintenance and ribosome biogenesis. Germline mutations of DKC1, the human gene encoding dyskerin, cause the hereditary disorders known as X-linked dyskeratosis congenita (X-DC). Moreover, dyskerin is upregulated in several cancers. Due to the pleiotropic functions of dyskerin, the X-DC clinical features overlap with those of both telomeropathies and ribosomopathies. In this paper, we evaluate the telomerase-independent effects of dyskerin depletion on cellular physiology by using inducible DCK1 knockdown. This system allows the downregulation of DKC1 expression within a short timeframe. We report that, in these cellular systems, dyskerin depletion induces the accumulation of unfolded/misfolded proteins in the endoplasmic reticulum, which in turn induces the activation of the PERK branch of the unfolded protein response. We also demonstrate that the PERK-eIF2a-ATF4-CHOP signaling pathway, activated by dyskerin downregulation, triggers a functional autophagic flux through the inhibition of the PI3K/AKT/mTOR pathway. By revealing a novel unpredicted connection between the loss of dyskerin, autophagy and UPR, our results establish a firm link between the lowering of dyskerin levels and the activation of the ER stress response, that plays a key role in the pathogenesis of several diseases.
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13
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Xue C, Chu Q, Zheng Q, Jiang S, Bao Z, Su Y, Lu J, Li L. Role of main RNA modifications in cancer: N 6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct Target Ther 2022; 7:142. [PMID: 35484099 DOI: 10.1038/s41392-022-01003-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied several common RNA modifications, such as N6-methyladenosine, 5-methylcytosine, and pseudouridine. The deposition and roles of these modifications in coding and noncoding RNAs are summarized in detail. Based on the RNA modification background, this review summarized the expression, function, and underlying molecular mechanism of these modifications and their regulators in cancer and further discussed the role of some existing small-molecule inhibitors. More in-depth studies on RNA modification and cancer are needed to broaden the understanding of epigenetics and cancer diagnosis, treatment, and prognosis.
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14
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Cerneckis J, Cui Q, He C, Yi C, Shi Y. Decoding pseudouridine: an emerging target for therapeutic development. Trends Pharmacol Sci 2022; 43:522-535. [DOI: 10.1016/j.tips.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 03/22/2022] [Indexed: 01/18/2023]
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15
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Therizols G, Bash-Imam Z, Panthu B, Machon C, Vincent A, Ripoll J, Nait-Slimane S, Chalabi-Dchar M, Gaucherot A, Garcia M, Laforêts F, Marcel V, Boubaker-Vitre J, Monet MA, Bouclier C, Vanbelle C, Souahlia G, Berthel E, Albaret MA, Mertani HC, Prudhomme M, Bertrand M, David A, Saurin JC, Bouvet P, Rivals E, Ohlmann T, Guitton J, Dalla Venezia N, Pannequin J, Catez F, Diaz JJ. Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance. Nat Commun 2022; 13:173. [PMID: 35013311 PMCID: PMC8748862 DOI: 10.1038/s41467-021-27847-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Mechanisms of drug-tolerance remain poorly understood and have been linked to genomic but also to non-genomic processes. 5-fluorouracil (5-FU), the most widely used chemotherapy in oncology is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the production of fluorinated ribosomes exhibiting altered translational activities. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs depending on the nature of their 5'-untranslated region. As a result, we find that sustained translation of IGF-1R mRNA, which encodes one of the most potent cell survival effectors, promotes the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that "man-made" fluorinated ribosomes favor the drug-tolerant cellular phenotype by promoting translation of survival genes.
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MESH Headings
- Antimetabolites, Antineoplastic/pharmacology
- Cell Line, Tumor
- Cell Survival/drug effects
- Colorectal Neoplasms/drug therapy
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/pathology
- DNA Replication
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Drug Resistance, Neoplasm/genetics
- Drug Tolerance/genetics
- Fluorouracil/pharmacology
- HCT116 Cells
- Halogenation
- Humans
- Protein Biosynthesis/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Receptor, IGF Type 1/agonists
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/metabolism
- Ribosomes/drug effects
- Ribosomes/genetics
- Ribosomes/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Gabriel Therizols
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Zeina Bash-Imam
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Baptiste Panthu
- CIRI-Inserm U1111, Ecole Normale Supérieure de Lyon, Lyon, F-693643, France
- Inserm U1060, CARMEN, F-69310, Pierre Bénite, France
| | - Christelle Machon
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Laboratoire de chimie analytique, Faculté de pharmacie de Lyon, 8 avenue Rockefeller, F-69373, Lyon, France
- Laboratoire de biochimie et de pharmaco-toxicologie, Centre hospitalier Lyon-Sud - HCL, F-69495, Pierre Bénite, France
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Julie Ripoll
- LIRMM, UMR 5506, University of Montpellier, CNRS, Montpellier, France
| | - Sophie Nait-Slimane
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Mounira Chalabi-Dchar
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Angéline Gaucherot
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Maxime Garcia
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Florian Laforêts
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | | | - Marie-Ambre Monet
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | | | - Christophe Vanbelle
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Guillaume Souahlia
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Elise Berthel
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Marie Alexandra Albaret
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Department of Translational Research and Innovation, Centre Léon Bérard, 69373, Lyon, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | - Michel Prudhomme
- Department of Digestive Surgery, CHU Nimes, Univ Montpellier, Nimes, France
| | - Martin Bertrand
- Department of Digestive Surgery, CHU Nimes, Univ Montpellier, Nimes, France
| | - Alexandre David
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, France
- IRMB-PPC, Univ Montpellier, INSERM, CHU Montpellier, CNRS, Montpellier, France
| | - Jean-Christophe Saurin
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Department of Endoscopy and Gastroenterology, Pavillon L, Edouard Herriot Hospital, Lyon, France
| | - Philippe Bouvet
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Eric Rivals
- LIRMM, UMR 5506, University of Montpellier, CNRS, Montpellier, France
- Institut Français de Bioinformatique, CNRS UMS 3601, Évry, France
| | - Théophile Ohlmann
- CIRI-Inserm U1111, Ecole Normale Supérieure de Lyon, Lyon, F-693643, France
| | - Jérôme Guitton
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
- Laboratoire de biochimie et de pharmaco-toxicologie, Centre hospitalier Lyon-Sud - HCL, F-69495, Pierre Bénite, France
- Laboratoire de toxicologie, Faculté de pharmacie de Lyon, Université de Lyon, 8 avenue Rockefeller, F-69373, Lyon, France
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France
- Centre Léon Bérard, F-69008, Lyon, France
- Université de Lyon 1, F-69000, Lyon, France
| | | | - Frédéric Catez
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France.
- Centre Léon Bérard, F-69008, Lyon, France.
- Université de Lyon 1, F-69000, Lyon, France.
- Institut Convergence PLAsCAN, F-69373, Lyon, France.
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000, Lyon, France.
- Centre Léon Bérard, F-69008, Lyon, France.
- Université de Lyon 1, F-69000, Lyon, France.
- Institut Convergence PLAsCAN, F-69373, Lyon, France.
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Bussotti G, Piel L, Pescher P, Domagalska MA, Rajan KS, Cohen-Chalamish S, Doniger T, Hiregange DG, Myler PJ, Unger R, Michaeli S, Späth GF. Genome instability drives epistatic adaptation in the human pathogen Leishmania. Proc Natl Acad Sci U S A 2021; 118:e2113744118. [PMID: 34903666 DOI: 10.1073/pnas.2113744118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/25/2023] Open
Abstract
Chromosome and gene copy number variations often correlate with the evolution of microbial and cancer drug resistance, thus causing important human mortality. How genome instability is harnessed to generate beneficial phenotypes and how deleterious gene dosage effects are compensated remain open questions. The protist pathogen Leishmania exploits genome instability to regulate expression via gene dosage changes. Using these parasites as a unique model system, we uncover complex epistatic interactions between gene copy number variations and compensatory transcriptomic responses as key processes that harness genome instability for adaptive evolution in Leishmania. Our results propose a model of eukaryotic fitness gain that may be broadly applicable to pathogenic fungi or tumor cells known to exploit genome instability for adaptation. How genome instability is harnessed for fitness gain despite its potential deleterious effects is largely elusive. An ideal system to address this important open question is provided by the protozoan pathogen Leishmania, which exploits frequent variations in chromosome and gene copy number to regulate expression levels. Using ecological genomics and experimental evolution approaches, we provide evidence that Leishmania adaptation relies on epistatic interactions between functionally associated gene copy number variations in pathways driving fitness gain in a given environment. We further uncover posttranscriptional regulation as a key mechanism that compensates for deleterious gene dosage effects and provides phenotypic robustness to genetically heterogenous parasite populations. Finally, we correlate dynamic variations in small nucleolar RNA (snoRNA) gene dosage with changes in ribosomal RNA 2′-O-methylation and pseudouridylation, suggesting translational control as an additional layer of parasite adaptation. Leishmania genome instability is thus harnessed for fitness gain by genome-dependent variations in gene expression and genome-independent compensatory mechanisms. This allows for polyclonal adaptation and maintenance of genetic heterogeneity despite strong selective pressure. The epistatic adaptation described here needs to be considered in Leishmania epidemiology and biomarker discovery and may be relevant to other fast-evolving eukaryotic cells that exploit genome instability for adaptation, such as fungal pathogens or cancer.
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Gueiderikh A, Maczkowiak-Chartois F, Rosselli F. A new frontier in Fanconi anemia: From DNA repair to ribosome biogenesis. Blood Rev 2021; 52:100904. [PMID: 34750031 DOI: 10.1016/j.blre.2021.100904] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 12/27/2022]
Abstract
Described by Guido Fanconi almost 100 years ago, Fanconi anemia (FA) is a rare genetic disease characterized by developmental abnormalities, bone marrow failure (BMF) and cancer predisposition. The proteins encoded by FA-mutated genes (FANC proteins) and assembled in the so-called FANC/BRCA pathway have key functions in DNA repair and replication safeguarding, which loss leads to chromosome structural aberrancies. Therefore, since the 1980s, FA has been considered a genomic instability and chromosome fragility syndrome. However, recent findings have demonstrated new and unexpected roles of FANC proteins in nucleolar homeostasis and ribosome biogenesis, the alteration of which impacts cellular proteostasis. Here, we review the different cellular, biochemical and molecular anomalies associated with the loss of function of FANC proteins and discuss how these anomalies contribute to BMF by comparing FA to other major inherited BMF syndromes. Our aim is to determine the extent to which alterations in the DNA damage response in FA contribute to BMF compared to the consequences of the loss of function of the FANC/BRCA pathway on the other roles of the pathway.
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Affiliation(s)
- Anna Gueiderikh
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Frédérique Maczkowiak-Chartois
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Filippo Rosselli
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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19
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Chalabi-Dchar M, Fenouil T, Machon C, Vincent A, Catez F, Marcel V, Mertani HC, Saurin JC, Bouvet P, Guitton J, Venezia ND, Diaz JJ. A novel view on an old drug, 5-fluorouracil: an unexpected RNA modifier with intriguing impact on cancer cell fate. NAR Cancer 2021; 3:zcab032. [PMID: 34409299 PMCID: PMC8364333 DOI: 10.1093/narcan/zcab032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/01/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
5-Fluorouracil (5-FU) is a chemotherapeutic drug widely used to treat patients with solid tumours, such as colorectal and pancreatic cancers. Colorectal cancer (CRC) is the second leading cause of cancer-related death and half of patients experience tumour recurrence. Used for over 60 years, 5-FU was long thought to exert its cytotoxic effects by altering DNA metabolism. However, 5-FU mode of action is more complex than previously anticipated since 5-FU is an extrinsic source of RNA modifications through its ability to be incorporated into most classes of RNA. In particular, a recent report highlighted that, by its integration into the most abundant RNA, namely ribosomal RNA (rRNA), 5-FU creates fluorinated active ribosomes and induces translational reprogramming. Here, we review the historical knowledge of 5-FU mode of action and discuss progress in the field of 5-FU-induced RNA modifications. The case of rRNA, the essential component of ribosome and translational activity, and the plasticity of which was recently associated with cancer, is highlighted. We propose that translational reprogramming, induced by 5-FU integration in ribosomes, contributes to 5-FU-driven cell plasticity and ultimately to relapse.
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Affiliation(s)
- Mounira Chalabi-Dchar
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Tanguy Fenouil
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Christelle Machon
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Anne Vincent
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Jean-Christophe Saurin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Philippe Bouvet
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Jérôme Guitton
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Nicole Dalla Venezia
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France
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Babaian A, Rothe K, Girodat D, Minia I, Djondovic S, Milek M, Spencer Miko SE, Wieden HJ, Landthaler M, Morin GB, Mager DL. Loss of m 1acp 3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Cell Rep 2020; 31:107611. [PMID: 32375039 DOI: 10.1016/j.celrep.2020.107611] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/03/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
The ribosome is an RNA-protein complex that is essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We identify a cancer-specific single-nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of patients with colorectal carcinoma (CRC) and present across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m1acp3Ψ), a >1-billion-years-conserved RNA modification at the peptidyl decoding site of the ribosome. A subset of CRC tumors we call hypo-m1acp3Ψ shows sub-stoichiometric m1acp3Ψ modification, unlike normal control tissues. An m1acp3Ψ knockout model and hypo-m1acp3Ψ patient tumors share a translational signature characterized by highly abundant ribosomal proteins. Thus, m1acp3Ψ-deficient rRNA forms an uncharacterized class of "onco-ribosome" which may serve as a chemotherapeutic target for treating cancer patients.
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van den Akker GGH, Zacchini F, Housmans BAC, van der Vloet L, Caron MMJ, Montanaro L, Welting TJM. Current Practice in Bicistronic IRES Reporter Use: A Systematic Review. Int J Mol Sci 2021; 22:5193. [PMID: 34068921 PMCID: PMC8156625 DOI: 10.3390/ijms22105193] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994-2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.
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Affiliation(s)
- Guus Gijsbertus Hubert van den Akker
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Federico Zacchini
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
| | - Bas Adrianus Catharina Housmans
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Laura van der Vloet
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Marjolein Maria Johanna Caron
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
- Programma Dipartimentale in Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Tim Johannes Maria Welting
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
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22
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Malfatti MC, Antoniali G, Codrich M, Tell G. Coping with RNA damage with a focus on APE1, a BER enzyme at the crossroad between DNA damage repair and RNA processing/decay. DNA Repair (Amst) 2021; 104:103133. [PMID: 34049077 DOI: 10.1016/j.dnarep.2021.103133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/17/2022]
Abstract
Interest in RNA damage as a novel threat associated with several human pathologies is rapidly increasing. Knowledge on damaged RNA recognition, repair, processing and decay is still scanty. Interestingly, in the last few years, more and more evidence put a bridge between DNA damage repair enzymes and the RNA world. The Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) was firstly identified as a crucial enzyme of the base excision repair (BER) pathway preserving genome stability toward non-distorting DNA lesion-induced damages. Later, an unsuspected role of APE1 in controlling gene expression was discovered and its pivotal involvement in several human pathologies, ranging from tumor progression to neurodegenerative diseases, has emerged. Recent novel findings indicate a role of APE1 in RNA metabolism, particularly in processing activities of damaged (abasic and oxidized) RNA and in the regulation of oncogenic microRNAs (miRNAs). Even though the role of miRNAs in human pathologies is well-known, the mechanisms underlying their quality control are still totally unexplored. A detailed knowledge of damaged RNA decay processes in human cells is crucial in order to understand the molecular processes involved in multiple pathologies. This cutting-edge perspective article will highlight these emerging aspects of damaged RNA processing and decay, focusing the attention on the involvement of APE1 in RNA world.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
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Nombela P, Miguel-López B, Blanco S. The role of m 6A, m 5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities. Mol Cancer 2021; 20:18. [PMID: 33461542 PMCID: PMC7812662 DOI: 10.1186/s12943-020-01263-w] [Citation(s) in RCA: 236] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.
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Affiliation(s)
- Paz Nombela
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007, Salamanca, Spain. .,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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Alnafakh R, Saretzki G, Midgley A, Flynn J, Kamal AM, Dobson L, Natarajan P, Stringfellow H, Martin-Hirsch P, DeCruze SB, Coupland SE, Hapangama DK. Aberrant Dyskerin Expression Is Related to Proliferation and Poor Survival in Endometrial Cancer. Cancers (Basel) 2021; 13:cancers13020273. [PMID: 33450922 PMCID: PMC7828388 DOI: 10.3390/cancers13020273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Telomeres are the protective caps at the ends of chromosomes, and they are maintained by an enzyme called telomerase. Telomerase activity allows rapid reproduction of the cells (proliferation) of the lining of the womb (endometrium). Telomerase levels are high in cancers in general, including in endometrial cancer. Dyskerin is one of the main components of the telomerase enzyme. While the other main components of telomerase have been studied in endometrial cancer, there are no previous studies on dyskerin in the endometrium. Our study shows that dyskerin levels are significantly lower in endometrial cancer and levels are linked to the survival of women. Experimentally increasing dyskerin protein in endometrial cells in the laboratory reduces the rate of cell proliferation. Consequently, we propose that dyskerin may be a regulator of endometrial cancer cell proliferation, and further studies are required to test if it can be targeted to develop new therapies for endometrial cancer. Abstract Dyskerin is a core-component of the telomerase holo-enzyme, which elongates telomeres. Telomerase is involved in endometrial epithelial cell proliferation. Most endometrial cancers (ECs) have high telomerase activity; however, dyskerin expression in human healthy endometrium or in endometrial pathologies has not been investigated yet. We aimed to examine the expression, prognostic relevance, and functional role of dyskerin in human EC. Endometrial samples from a cohort of 175 women were examined with immunohistochemistry, immunoblotting, and qPCR. The EC cells were transfected with Myc-DDK-DKC1 plasmid and the effect of dyskerin overexpression on EC cell proliferation was assessed by flow cytometry. Human endometrium expresses dyskerin (DKC1) and dyskerin protein levels are significantly reduced in ECs when compared with healthy postmenopausal endometrium. Low dyskerin immunoscores were potentially associated with worse outcomes, suggesting a possible prognostic relevance. Cancer Genome Atlas (TCGA) ECs dataset (n = 589) was also interrogated. The TCGA dataset further confirmed changes in DKC1 expression in EC with prognostic significance. Transient dyskerin overexpression had a negative effect on EC cell proliferation. Our data demonstrates a role for dyskerin in normal endometrium for the first time and confirms aberrant expression with possible prognostic relevance in EC. Interventions aimed at modulating dyskerin levels may provide novel therapeutic options in EC.
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Affiliation(s)
- Rafah Alnafakh
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Department of Pathology, Al-Hilla Teaching Hospital, Babil, Iraq
| | - Gabriele Saretzki
- Biosciences Institute, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne NE4 5PL, UK;
| | - Angela Midgley
- Experimental Arthritis Treatment Centre for Children, Institute in the Park, Department of Women’s and Children’s Health, University of Liverpool, Liverpool L12 2AP, UK;
| | | | - Areege M. Kamal
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Pathology Department, Oncology Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - Lucy Dobson
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
| | - Purushothaman Natarajan
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
| | - Helen Stringfellow
- Lancashire Teaching Hospital NHS Trust, Preston PR2 9HT, UK; (H.S.); (P.M.-H.)
| | | | - Shandya B. DeCruze
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
| | - Sarah E. Coupland
- Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, UK;
| | - Dharani K. Hapangama
- Liverpool Women’s Hospital NHS Foundation Trust, Member of Liverpool Health Partners, Liverpool L8 7SS, UK; (R.A.); (L.D.); (P.N.); (S.B.D.)
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Member of Liverpool Health Partners, Liverpool L8 7SS, UK;
- Correspondence:
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25
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Nagpal N, Agarwal S. Telomerase RNA processing: Implications for human health and disease. Stem Cells 2020; 38:10.1002/stem.3270. [PMID: 32875693 PMCID: PMC7917152 DOI: 10.1002/stem.3270] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/11/2020] [Indexed: 11/11/2022]
Abstract
Telomeres are composed of repetitive DNA sequences that are replenished by the enzyme telomerase to maintain the self-renewal capacity of stem cells. The RNA component of human telomerase (TERC) is the essential template for repeat addition by the telomerase reverse transcriptase (TERT), and also serves as a scaffold for several factors comprising the telomerase ribonucleoprotein (RNP). Unique features of TERC regulation and function have been informed not only through biochemical studies but also through human genetics. Disease-causing mutations impact TERC biogenesis at several levels including RNA transcription, post-transcriptional processing, folding, RNP assembly, and trafficking. Defects in TERC reduce telomerase activity and impair telomere maintenance, thereby causing a spectrum of degenerative diseases called telomere biology disorders (TBDs). Deciphering mechanisms of TERC dysregulation have led to a broader understanding of noncoding RNA biology, and more recently points to new therapeutic strategies for TBDs. In this review, we summarize over two decades of work revealing mechanisms of human telomerase RNA biogenesis, and how its disruption causes human diseases.
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Affiliation(s)
- Neha Nagpal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Initiative for RNA Medicine and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Boston, Massachusetts
| | - Suneet Agarwal
- Division of Hematology/Oncology and Stem Cell Program, Boston Children’s Hospital, Boston, Massachusetts
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Initiative for RNA Medicine and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Boston, Massachusetts
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26
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Lezzerini M, Penzo M, O'Donohue MF, Marques Dos Santos Vieira C, Saby M, Elfrink HL, Diets IJ, Hesse AM, Couté Y, Gastou M, Nin-Velez A, Nikkels PGJ, Olson AN, Zonneveld-Huijssoon E, Jongmans MCJ, Zhang G, van Weeghel M, Houtkooper RH, Wlodarski MW, Kuiper RP, Bierings MB, van der Werff Ten Bosch J, Leblanc T, Montanaro L, Dinman JD, Da Costa L, Gleizes PE, MacInnes AW. Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism. Nucleic Acids Res 2020; 48:770-787. [PMID: 31799629 PMCID: PMC6954397 DOI: 10.1093/nar/gkz1042] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5′UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5′UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5′UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts.
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Affiliation(s)
- Marco Lezzerini
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marianna Penzo
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale and Centro di Ricerca Biomedica Applicata (CRBA), Policlinico Universitario di S. Orsola, Università di Bologna,Via Massarenti 9, 40138 Bologna, Italy
| | - Marie-Françoise O'Donohue
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | | | - Manon Saby
- INSERM UMR S1134, F-75015, Paris, France
| | - Hyung L Elfrink
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Core Facility Metabolomics, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne-Marie Hesse
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Marc Gastou
- Paris University, Paris, France.,Laboratory of Excellence for Red Cell, LABEX GR-Ex, F-75015, Paris, France.,Institute Gustave Roussy, Inserm unit U1170, F-94800 Villejuif, France
| | - Alexandra Nin-Velez
- Department of Comparative Biology and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Peter G J Nikkels
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.,Princess Maxima Center for Pediatric Oncology and Utrecht University Children's Hospital, Utrecht, The Netherlands
| | - GuangJun Zhang
- Department of Comparative Biology and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Michel van Weeghel
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Core Facility Metabolomics, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcin W Wlodarski
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, D-79106 Freiburg, Germany.,St. Jude's Children Research Hospital, Memphis, TN, USA
| | - Roland P Kuiper
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
| | - Marc B Bierings
- Princess Maxima Center for Pediatric Oncology and Utrecht University Children's Hospital, Utrecht, The Netherlands
| | | | - Thierry Leblanc
- Pediatric Hematology/Oncology Service, Robert Debré Hospital, F-75019 Paris, France
| | - Lorenzo Montanaro
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale and Centro di Ricerca Biomedica Applicata (CRBA), Policlinico Universitario di S. Orsola, Università di Bologna,Via Massarenti 9, 40138 Bologna, Italy
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Lydie Da Costa
- INSERM UMR S1134, F-75015, Paris, France.,Paris University, Paris, France.,Laboratory of Excellence for Red Cell, LABEX GR-Ex, F-75015, Paris, France.,Hematology Lab, Robert Debré Hospital, F-75019 Paris, France
| | - Pierre-Emmanuel Gleizes
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Alyson W MacInnes
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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27
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Penzo M, Clima R, Trerè D, Montanaro L. Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types. Cells 2020; 9:E387. [PMID: 32046192 DOI: 10.3390/cells9020387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs involved in RNA modification and processing. Approximately half of the so far identified snoRNA genes map within the intronic regions of host genes, and their expression, as well as the expression of their host genes, is dependent on transcript splicing and maturation. Growing evidence indicates that mutations and/or deregulations that affect snoRNAs, as well as host genes, play a significant role in oncogenesis. Among the possible factors underlying snoRNA/host gene expression deregulation is copy number alteration (CNA). We analyzed the data available in The Cancer Genome Atlas database, relative to CNA and expression of 295 snoRNA/host gene couples in 10 cancer types, to understand whether the genetic or expression alteration of snoRNAs and their matched host genes would have overlapping trends. Our results show that, counterintuitively, copy number and expression alterations of snoRNAs and matched host genes are not necessarily coupled. In addition, some snoRNA/host genes are mutated and overexpressed recurrently in multiple cancer types. Our findings suggest that the differential contribution to cancer development of both snoRNAs and host genes should always be considered, and that snoRNAs and their host genes may contribute to cancer development in conjunction or independently.
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28
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Heissenberger C, Liendl L, Nagelreiter F, Gonskikh Y, Yang G, Stelzer EM, Krammer TL, Micutkova L, Vogt S, Kreil DP, Sekot G, Siena E, Poser I, Harreither E, Linder A, Ehret V, Helbich TH, Grillari-Voglauer R, Jansen-Dürr P, Koš M, Polacek N, Grillari J, Schosserer M. Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth. Nucleic Acids Res 2019; 47:11807-11825. [PMID: 31722427 PMCID: PMC7145617 DOI: 10.1093/nar/gkz1043] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 09/27/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022] Open
Abstract
Modifications of ribosomal RNA expand the nucleotide repertoire and thereby contribute to ribosome heterogeneity and translational regulation of gene expression. One particular m5C modification of 25S ribosomal RNA, which is introduced by Rcm1p, was previously shown to modulate stress responses and lifespan in yeast and other small organisms. Here, we report that NSUN5 is the functional orthologue of Rcm1p, introducing m5C3782 into human and m5C3438 into mouse 28S ribosomal RNA. Haploinsufficiency of the NSUN5 gene in fibroblasts from William Beuren syndrome patients causes partial loss of this modification. The N-terminal domain of NSUN5 is required for targeting to nucleoli, while two evolutionary highly conserved cysteines mediate catalysis. Phenotypic consequences of NSUN5 deficiency in mammalian cells include decreased proliferation and size, which can be attributed to a reduction in total protein synthesis by altered ribosomes. Strikingly, Nsun5 knockout in mice causes decreased body weight and lean mass without alterations in food intake, as well as a trend towards reduced protein synthesis in several tissues. Together, our findings emphasize the importance of single RNA modifications for ribosome function and normal cellular and organismal physiology.
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Affiliation(s)
- Clemens Heissenberger
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Lisa Liendl
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Fabian Nagelreiter
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Yulia Gonskikh
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Guohuan Yang
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Elena M Stelzer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Teresa L Krammer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Lucia Micutkova
- Institute for Biomedical Aging Research, University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Vogt
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - David P Kreil
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Gerhard Sekot
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Emilio Siena
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eva Harreither
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Angela Linder
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Viktoria Ehret
- Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Preclinical Imaging Laboratory, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas H Helbich
- Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Preclinical Imaging Laboratory, Medical University of Vienna, 1090 Vienna, Austria
| | - Regina Grillari-Voglauer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin Koš
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Johannes Grillari
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
- Christian Doppler Laboratory on Biotechnology of Skin Aging, 1190 Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, 1200 Vienna, Austria
| | - Markus Schosserer
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria
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29
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Alupei MC, Maity P, Esser PR, Krikki I, Tuorto F, Parlato R, Penzo M, Schelling A, Laugel V, Montanaro L, Scharffetter-Kochanek K, Iben S. Loss of Proteostasis Is a Pathomechanism in Cockayne Syndrome. Cell Rep 2019; 23:1612-1619. [PMID: 29742419 DOI: 10.1016/j.celrep.2018.04.041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/02/2018] [Accepted: 04/09/2018] [Indexed: 01/04/2023] Open
Abstract
Retarded growth and neurodegeneration are hallmarks of the premature aging disease Cockayne syndrome (CS). Cockayne syndrome proteins take part in the key step of ribosomal biogenesis, transcription of RNA polymerase I. Here, we identify a mechanism originating from a disturbed RNA polymerase I transcription that impacts translational fidelity of the ribosomes and consequently produces misfolded proteins. In cells from CS patients, the misfolded proteins are oxidized by the elevated reactive oxygen species (ROS) and provoke an unfolded protein response that represses RNA polymerase I transcription. This pathomechanism can be disrupted by the addition of pharmacological chaperones, suggesting a treatment strategy for CS. Additionally, this loss of proteostasis was not observed in mouse models of CS.
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Affiliation(s)
- Marius Costel Alupei
- Clinic of Dermatology and Allergic Diseases, University Medical Center, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Pallab Maity
- Clinic of Dermatology and Allergic Diseases, University Medical Center, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Philipp Ralf Esser
- Allergy Research Group, Department of Dermatology, University Medical Center Freiburg, Faculty of Medicine, 79104 Freiburg, Germany
| | - Ioanna Krikki
- Clinic of Dermatology and Allergic Diseases, University Medical Center, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Rosanna Parlato
- Institute of Applied Physiology, Ulm University, 89081 Ulm, Germany; Institute of Anatomy and Medical Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Marianna Penzo
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Adrian Schelling
- Clinic of Dermatology and Allergic Diseases, University Medical Center, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Vincent Laugel
- Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, 67000 Strasbourg, France
| | - Lorenzo Montanaro
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Università di Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Karin Scharffetter-Kochanek
- Clinic of Dermatology and Allergic Diseases, University Medical Center, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Sebastian Iben
- Clinic of Dermatology and Allergic Diseases, University Medical Center, Albert-Einstein Allee 23, 89081 Ulm, Germany.
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30
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Belli V, Matrone N, Sagliocchi S, Incarnato R, Conte A, Pizzo E, Turano M, Angrisani A, Furia M. A dynamic link between H/ACA snoRNP components and cytoplasmic stress granules. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2019; 1866:118529. [DOI: 10.1016/j.bbamcr.2019.118529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/08/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023]
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31
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Kelly EK, Czekay DP, Kothe U. Base-pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar ribonucleoproteins. RNA 2019; 25:1393-1404. [PMID: 31311819 PMCID: PMC6800473 DOI: 10.1261/rna.071043.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/11/2019] [Indexed: 05/04/2023]
Abstract
H/ACA small nucleolar ribonucleoproteins (snoRNPs) pseudouridylate RNA in eukaryotes and archaea. They target many RNAs site-specifically through base-pairing interactions between H/ACA guide and substrate RNA. Besides ribosomal RNA (rRNA) and small nuclear RNA (snRNA), H/ACA snoRNPs are thought to also modify messenger RNA (mRNA) with potential impacts on gene expression. However, the base pairing between known target RNAs and H/ACA guide RNAs varies widely in nature, and therefore the rules governing substrate RNA selection are still not fully understood. To provide quantitative insight into substrate RNA recognition, we systematically altered the sequence of a substrate RNA target by the Saccharomyces cerevisiae H/ACA guide RNA snR34. Time courses measuring pseudouridine formation revealed a gradual decrease in the initial velocity of pseudouridylation upon reducing the number of base pairs between substrate and guide RNA. Changing or inserting nucleotides close to the target uridine severely impairs pseudouridine formation. Interestingly, filter binding experiments show that all substrate RNA variants bind to H/ACA snoRNPs with nanomolar affinity. Next, we showed that binding of inactive, near-cognate RNAs to H/ACA snoRNPs does not inhibit their activity for cognate RNAs, presumably because near-cognate RNAs dissociate rapidly. We discuss that the modulation of initial velocities by the base-pairing strength might affect the order and efficiency of pseudouridylation in rRNA during ribosome biogenesis. Moreover, the binding of H/ACA snoRNPs to near-cognate RNAs may be a mechanism to search for cognate target sites. Together, our data provide critical information to aid in the prediction of productive H/ACA guide-substrate RNA pairs.
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Affiliation(s)
- Erin K Kelly
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Dominic P Czekay
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Ute Kothe
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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32
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Taoka M, Nobe Y, Yamaki Y, Sato K, Ishikawa H, Izumikawa K, Yamauchi Y, Hirota K, Nakayama H, Takahashi N, Isobe T. Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res 2019; 46:9289-9298. [PMID: 30202881 PMCID: PMC6182160 DOI: 10.1093/nar/gky811] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023] Open
Abstract
During ribosome biogenesis, ribosomal RNAs acquire various chemical modifications that ensure the fidelity of translation, and dysregulation of the modification processes can cause proteome changes as observed in cancer and inherited human disorders. Here, we report the complete chemical modifications of all RNAs of the human 80S ribosome as determined with quantitative mass spectrometry. We assigned 228 sites with 14 different post-transcriptional modifications, most of which are located in functional regions of the ribosome. All modifications detected are typical of eukaryotic ribosomal RNAs, and no human-specific modifications were observed, in contrast to a recently reported cryo-electron microscopy analysis. While human ribosomal RNAs appeared to have little polymorphism regarding the post-transcriptional modifications, we found that pseudouridylation at two specific sites in 28S ribosomal RNA are significantly reduced in ribosomes of patients with familial dyskeratosis congenita, a genetic disease caused by a point mutation in the pseudouridine synthase gene DKC1. The landscape of the entire epitranscriptomic ribosomal RNA modifications provides a firm basis for understanding ribosome function and dysfunction associated with human disease.
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Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuka Yamaki
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ko Sato
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hideaki Ishikawa
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Keiichi Izumikawa
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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33
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Dalla Venezia N, Vincent A, Marcel V, Catez F, Diaz JJ. Emerging Role of Eukaryote Ribosomes in Translational Control. Int J Mol Sci 2019; 20:E1226. [PMID: 30862090 DOI: 10.3390/ijms20051226] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/15/2022] Open
Abstract
Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently that ribosomes themselves could contribute to this regulation. Indeed, though it is well-known that the translational efficiency of the cell is linked to ribosome abundance, studies recently demonstrated that the composition of the ribosome could alter translation of specific mRNAs. Evidences suggest that according to the status, environment, development, or pathological conditions, cells produce different populations of ribosomes which differ in their ribosomal protein and/or RNA composition. Those observations gave rise to the concept of "specialized ribosomes", which proposes that a unique ribosome composition determines the translational activity of this ribosome. The current review will present how technological advances have participated in the emergence of this concept, and to which extent the literature sustains this concept today.
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34
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Abstract
Multifaceted relations link ribosome biogenesis to cancer. Ribosome biogenesis takes place in the nucleolus. Clarifying the mechanisms involved in this nucleolar function and its relationship with cell proliferation: (1) allowed the understanding of the reasons for the nucleolar changes in cancer cells and their exploitation in tumor pathology, (2) defined the importance of the inhibition of ribosome biogenesis in cancer chemotherapy and (3) focused the attention on alterations of ribosome biogenesis in the pathogenesis of cancer. This review summarizes the research milestones regarding these relevant relationships between ribosome biogenesis and cancer. The structure and function of the nucleolus will also be briefly described.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Davide Treré
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
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Catez F, Dalla Venezia N, Marcel V, Zorbas C, Lafontaine DLJ, Diaz JJ. Ribosome biogenesis: An emerging druggable pathway for cancer therapeutics. Biochem Pharmacol 2019; 159:74-81. [PMID: 30468711 DOI: 10.1016/j.bcp.2018.11.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Monaco PL, Marcel V, Diaz JJ, Catez F. 2'-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation? Biomolecules 2018; 8:E106. [PMID: 30282949 DOI: 10.3390/biom8040106] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2′-O-methylation (2′-O-Me). 2′-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2′-O-Me to the translational capacity of ribosomes has been established. Yet, how 2′-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2′-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population. Moreover, recent advances in ribosome structure analysis and in vitro translation assays have proven, for the first time, that 2′-O-Me contributes to regulating protein synthesis. This review highlights the recent data exploring the impact of 2′-O-Me on ribosome structure and function, and the emerging idea that the rRNA epitranscriptome is involved in translational control.
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Quan Wang J, Di Yang M, Chen X, Wang Y, Zeng Chen L, Cheng X, Hua Liu X. Discovery of new chromen-4-one derivatives as telomerase inhibitors through regulating expression of dyskerin. J Enzyme Inhib Med Chem 2018; 33:1199-1211. [PMID: 30132373 PMCID: PMC6104605 DOI: 10.1080/14756366.2018.1466881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A series of new trimethoxyphenyl-4H-chromen derivatives as telomerase inhibitors through regulation dyskerin were designed and synthesised. The anticancer activity assay in vitro showed that compound 5i 3-(4-(4-isonicotinoylpiperazin-1-yl)butoxy)-5,7-dimethoxy-2-(3,4,5-trimethoxyphenyl)-4H-chromen-4-one exhibited high activity against Hela, SMMC-7721, SGC-7901, U87 and HepG2 cell lines. Compound 5i also showed potent inhibitory activity against telomerase. The further results confirmed this title compound could significantly improve pathological changes induced rat hepatic tumor in vivo. Preliminary mechanisms showed that compound 5i inhibited telomerase activity through decrease expression of dyskerin.
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Affiliation(s)
- Jie Quan Wang
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China
| | - Meng Di Yang
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China
| | - Xing Chen
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China
| | - Yang Wang
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China
| | - Liu Zeng Chen
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China
| | - Xiu Cheng
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China
| | - Xin Hua Liu
- a School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases , Anhui Institute of Innovative Drugs, Anhui Medical University , Hefei , P. R. China.,b School of Material Science Chemical Engineering , ChuZhou University , ChuZhou , P. R. China
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Penzo M, Montanaro L. Turning Uridines around: Role of rRNA Pseudouridylation in Ribosome Biogenesis and Ribosomal Function. Biomolecules 2018; 8:E38. [PMID: 29874862 DOI: 10.3390/biom8020038] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 01/09/2023] Open
Abstract
Ribosomal RNA (rRNA) is extensively edited through base methylation and acetylation, 2'-O-ribose methylation and uridine isomerization. In human rRNA, 95 uridines are predicted to by modified to pseudouridine by ribonucleoprotein complexes sharing four core proteins and differing for a RNA sequence guiding the complex to specific residues to be modified. Most pseudouridylation sites are placed within functionally important ribosomal domains and can influence ribosomal functional features. Information obtained so far only partially explained the degree of regulation and the consequences of pseudouridylation on ribosomal structure and function in different physiological and pathological conditions. This short review focuses on the available evidence in this topic, highlighting open questions in the field and perspectives that the development of emerging techniques is offering.
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Panthu B, Ohlmann T, Perrier J, Schlattner U, Jalinot P, Elena-Herrmann B, Rautureau GJP. Cell-Free Protein Synthesis Enhancement from Real-Time NMR Metabolite Kinetics: Redirecting Energy Fluxes in Hybrid RRL Systems. ACS Synth Biol 2018; 7:218-226. [PMID: 28915016 DOI: 10.1021/acssynbio.7b00280] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A counterintuitive cell-free protein synthesis (CFPS) strategy, based on reducing the ribosomal fraction in rabbit reticulocyte lysate (RRL), triggers the development of hybrid systems composed of RRL ribosome-free supernatant complemented with ribosomes from different mammalian cell-types. Hybrid RRL systems maintain translational properties of the original ribosome cell types, and deliver protein expression levels similar to RRL. Here, we show that persistent ribosome-associated metabolic activity consuming ATP is a major obstacle for maximal protein yield. We provide a detailed picture of hybrid CFPS systems energetic metabolism based on real-time nuclear magnetic resonance (NMR) investigation of metabolites kinetics. We demonstrate that protein synthesis capacity has an upper limit at native ribosome concentration and that lower amounts of the ribosomal fraction optimize energy fluxes toward protein translation, consequently increasing CFPS yield. These results provide a rationalized strategy for further mammalian CFPS developments and reveal the potential of real-time NMR metabolism phenotyping for optimization of cell-free protein expression systems.
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Affiliation(s)
- Baptiste Panthu
- Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Théophile Ohlmann
- CIRI, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ. Lyon, F-69007 Lyon, France
| | - Johan Perrier
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Uwe Schlattner
- Univ. Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble cedex, France
| | - Pierre Jalinot
- Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Bénédicte Elena-Herrmann
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Gilles J. P. Rautureau
- Univ. Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
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40
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Nakamoto MA, Lovejoy AF, Cygan AM, Boothroyd JC. mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii. RNA 2017; 23:1834-1849. [PMID: 28851751 PMCID: PMC5689004 DOI: 10.1261/rna.062794.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/18/2017] [Indexed: 05/09/2023]
Abstract
RNA contains over 100 modified nucleotides that are created post-transcriptionally, among which pseudouridine (Ψ) is one of the most abundant. Although it was one of the first modifications discovered, the biological role of this modification is still not fully understood. Recently, we reported that a pseudouridine synthase (TgPUS1) is necessary for differentiation of the single-celled eukaryotic parasite Toxoplasma gondii from active to chronic infection. To better understand the biological role of pseudouridylation, we report here gel-based and deep-sequencing methods to identify TgPUS1-dependent Ψ's in Toxoplasma RNA, and the use of TgPUS1 mutants to examine the effect of this modification on mRNAs. In addition to identifying conserved sites of pseudouridylation in Toxoplasma rRNA, tRNA, and snRNA, we also report extensive pseudouridylation of Toxoplasma mRNAs, with the Ψ's being relatively depleted in the 3'-UTR but enriched at position 1 of codons. We show that many Ψ's in tRNA and mRNA are dependent on the action of TgPUS1 and that TgPUS1-dependent mRNA Ψ's are enriched in developmentally regulated transcripts. RNA-seq data obtained from wild-type and TgPUS1-mutant parasites shows that genes containing a TgPUS1-dependent Ψ are relatively more abundant in mutant parasites, while pulse/chase labeling of RNA with 4-thiouracil shows that mRNAs containing TgPUS1-dependent Ψ have a modest but statistically significant increase in half-life in the mutant parasites. These data are some of the first evidence suggesting that mRNA Ψ's play an important biological role.
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Affiliation(s)
- Margaret A Nakamoto
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander F Lovejoy
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alicja M Cygan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John C Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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Erales J, Marchand V, Panthu B, Gillot S, Belin S, Ghayad SE, Garcia M, Laforêts F, Marcel V, Baudin-Baillieu A, Bertin P, Couté Y, Adrait A, Meyer M, Therizols G, Yusupov M, Namy O, Ohlmann T, Motorin Y, Catez F, Diaz JJ. Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes. Proc Natl Acad Sci U S A 2017; 114:12934-9. [PMID: 29158377 DOI: 10.1073/pnas.1707674114] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.
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42
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Penzo M, Guerrieri AN, Zacchini F, Treré D, Montanaro L. RNA Pseudouridylation in Physiology and Medicine: For Better and for Worse. Genes (Basel) 2017; 8:E301. [PMID: 29104216 DOI: 10.3390/genes8110301] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022] Open
Abstract
Pseudouridine is the most abundant modification found in RNA. Today, thanks to next-generation sequencing techniques used in the detection of RNA modifications, pseudouridylation sites have been described in most eukaryotic RNA classes. In the present review, we will first consider the available information on the functional roles of pseudouridine(s) in different RNA species. We will then focus on how alterations in the pseudouridylation process may be connected with a series of human pathologies, including inherited disorders, cancer, diabetes, and viral infections. Finally, we will discuss how the availability of novel technical approaches are likely to increase the knowledge in this field.
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Henras AK, Plisson-Chastang C, Humbert O, Romeo Y, Henry Y. Synthesis, Function, and Heterogeneity of snoRNA-Guided Posttranscriptional Nucleoside Modifications in Eukaryotic Ribosomal RNAs. Enzymes 2017; 41:169-213. [PMID: 28601222 DOI: 10.1016/bs.enz.2017.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosomal RNAs contain numerous 2'-O-methylated nucleosides and pseudouridines. Methylation of the 2' oxygen of ribose moieties and isomerization of uridines into pseudouridines are catalyzed by C/D and H/ACA small nucleolar ribonucleoprotein particles, respectively. We review the composition, structure, and mode of action of archaeal and eukaryotic C/D and H/ACA particles. Most rRNA modifications cluster in functionally crucial regions of the rRNAs, suggesting they play important roles in translation. Some of these modifications promote global translation efficiency or modulate translation fidelity. Strikingly, recent quantitative nucleoside modification profiling methods have revealed that a subset of modification sites is not always fully modified. The finding of such ribosome heterogeneity is in line with the concept of specialized ribosomes that could preferentially translate specific mRNAs. This emerging concept is supported by findings that some human diseases are caused by defects in the rRNA modification machinery correlated with a significant alteration of IRES-dependent translation.
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Romeo
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France.
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Penzo M, Galbiati A, Treré D, Montanaro L. 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; 1866:330-8. [PMID: 27815156 DOI: 10.1016/j.bbcan.2016.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [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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45
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Penzo M, Carnicelli D, Montanaro L, Brigotti M. A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes. Nat Protoc 2016; 11:1309-25. [PMID: 27336708 DOI: 10.1038/nprot.2016.072] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe a cell-free translation system for evaluating the activity of ribosomes stringently purified from human cells. This system is based on in vitro reconstitution of the cellular translation machinery, in which a ribosome-free rabbit reticulocyte lysate (RRL) is reassembled with human ribosomes and in vitro-transcribed reporter mRNAs. The protocol describes the preparation of the RRL-derived fractions, purification of ribosomes devoid of detectable nonribosomal-associated factors, and assembly of the reactions to evaluate ribosomal translational efficiency and fidelity using appropriate reporter transcripts. The whole procedure can be completed in ∼2.5 d (plus 2 weeks for RRL preparation and cell expansion time). This protocol can be applied to study intrinsic functional properties (cis-acting element-mediated translation initiation or translational fidelity) of ribosome populations from different sources (including nonhuman origin). It is therefore useful for the characterization of ribosomal function in ribosomopathies and cancer, and it will be applicable in the emerging fields of ribosome diversity and specialized ribosomes.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Domenica Carnicelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Maurizio Brigotti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
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46
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Li X, Ma S, Yi C. Pseudouridine: the fifth RNA nucleotide with renewed interests. Curr Opin Chem Biol 2016; 33:108-16. [PMID: 27348156 DOI: 10.1016/j.cbpa.2016.06.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 12/23/2022]
Abstract
More than 100 different types of chemical modifications to RNA have been documented so far. Historically, most of these modifications were found in rRNA, tRNA and snRNA; recently, new methods aided by high-throughput sequencing have enabled identification of chemical modifications to mRNA, leading to the emerging field of 'RNA epigenetics'. One such example is pseudouridine, which has long been known as a RNA modification in abundant non-coding RNA (ncRNA) and has recently been found to be present in mRNAas well. This review first summarizes biogenesis and known functions of pseudouridine in ncRNAs. We then focus on progress in pseudouridine detection, especially the chemical-assisted, transcriptome-wide sequencing tools that revealed the dynamic nature of mRNA pseudouridylation. Such enabling tools are expected to facilitate future functional studies of pseudouridine.
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Affiliation(s)
- Xiaoyu Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shiqing Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PR China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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47
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Sbarrato T, Horvilleur E, Pöyry T, Hill K, Chaplin LC, Spriggs RV, Stoneley M, Wilson L, Jayne S, Vulliamy T, Beck D, Dokal I, Dyer MJS, Yeomans AM, Packham G, Bushell M, Wagner SD, Willis AE. A ribosome-related signature in peripheral blood CLL B cells is linked to reduced survival following treatment. Cell Death Dis 2016; 7:e2249. [PMID: 27253413 PMCID: PMC5143378 DOI: 10.1038/cddis.2016.148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/14/2023]
Abstract
We have used polysome profiling coupled to microarray analysis to examine the translatome of a panel of peripheral blood (PB) B cells isolated from 34 chronic lymphocytic leukaemia (CLL) patients. We have identified a ‘ribosome-related' signature in CLL patients with mRNAs encoding for ribosomal proteins and factors that modify ribosomal RNA, e.g. DKC1 (which encodes dyskerin, a pseudouridine synthase), showing reduced polysomal association and decreased expression of the corresponding proteins. Our data suggest a general impact of dyskerin dysregulation on the translational apparatus in CLL and importantly patients with low dyskerin levels have a significantly shorter period of overall survival following treatment. Thus, translational dysregulation of dyskerin could constitute a mechanism by which the CLL PB B cells acquire an aggressive phenotype and thus have a major role in oncogenesis.
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Affiliation(s)
- T Sbarrato
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - E Horvilleur
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - T Pöyry
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - K Hill
- The Babraham Institute, Babraham, Cambridge, UK
| | - L C Chaplin
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - R V Spriggs
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - M Stoneley
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - L Wilson
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - S Jayne
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - T Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AT, UK
| | - D Beck
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - I Dokal
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AT, UK
| | - M J S Dyer
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - A M Yeomans
- Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - G Packham
- Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Bushell
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - S D Wagner
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - A E Willis
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
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48
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Abstract
The primary function of ribosomes is to decode mRNAs into polypeptide chains; however, this description is overly simplistic. Accumulating evidence shows that ribosomes themselves can affect the relative efficiency with which various mRNAs are translated and indicates that these effects can be modulated by ribosome heterogeneity. The notion that ribosomes have regulatory capabilities was elaborated more than a decade ago in the ribosome filter hypothesis. Various lines of evidence support this idea and have shown that the translation of some mRNAs is affected by discrete binding interactions with rRNA or ribosomal proteins. Recent work from our laboratory has demonstrated that base-pairing of the Hepatitis C Virus (HCV) internal ribosome entry site (IRES) to 18S rRNA is required for IRES function, but only in the context of more complex ribosomal interactions. The HCV IRES provides an example of the ribosome filter that involves multiple binding interactions between mRNAs and ribosomal subunits.
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Affiliation(s)
- Vincent P Mauro
- a Promosome, LLC , San Diego , CA , USA.,b The Scripps Research Institute , La Jolla , CA , USA
| | - Daiki Matsuda
- b The Scripps Research Institute , La Jolla , CA , USA
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