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Shi X, Zhang Y, Wang Y, Wang J, Gao Y, Wang R, Wang L, Xiong M, Cao Y, Ou N, Liu Q, Ma H, Cai J, Chen H. The tRNA Gm18 methyltransferase TARBP1 promotes hepatocellular carcinoma progression via metabolic reprogramming of glutamine. Cell Death Differ 2024:10.1038/s41418-024-01323-4. [PMID: 38867004 DOI: 10.1038/s41418-024-01323-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Cancer cells rely on metabolic reprogramming to sustain the prodigious energetic requirements for rapid growth and proliferation. Glutamine metabolism is frequently dysregulated in cancers and is being exploited as a potential therapeutic target. Using CRISPR/Cas9 interference (CRISPRi) screening, we identified TARBP1 (TAR (HIV-1) RNA Binding Protein 1) as a critical regulator involved in glutamine reliance of cancer cell. Consistent with this discovery, TARBP1 amplification and overexpression are frequently observed in various cancers. Knockout of TARBP1 significantly suppresses cell proliferation, colony formation and xenograft tumor growth. Mechanistically, TARBP1 selectively methylates and stabilizes a small subset of tRNAs, which promotes efficient protein synthesis of glutamine transporter-ASCT2 (also known as SLC1A5) and glutamine import to fuel the growth of cancer cell. Moreover, we found that the gene expression of TARBP1 and ASCT2 are upregulated in combination in clinical cohorts and their upregulation is associated with unfavorable prognosis of HCC (hepatocellular carcinoma). Taken together, this study reveals the unexpected role of TARBP1 in coordinating the tRNA availability and glutamine uptake during HCC progression and provides a potential target for tumor therapy.
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Affiliation(s)
- Xiaoyan Shi
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yangyi Zhang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuci Wang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jie Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China
| | - Yang Gao
- Department of Ultrasound, West China Hospital, Sichuan University, Chengdu, 610041, China
- College of Polymer Science and Engineering, Med-X Center for Materials, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Ruiqi Wang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liyong Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China
| | - Minggang Xiong
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Yanlan Cao
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ningjing Ou
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences; Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou, 510640, China.
| | - Honghui Ma
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China.
- Shenzhen Ruipuxun Academy for Stem Cell & Regenerative Medicine, Shenzhen, China.
| | - Jiabin Cai
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China.
| | - Hao Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
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El-Hachem N, Leclercq M, Susaeta Ruiz M, Vanleyssem R, Shostak K, Körner PR, Capron C, Martin-Morales L, Roncarati P, Lavergne A, Blomme A, Turchetto S, Goffin E, Thandapani P, Tarassov I, Nguyen L, Pirotte B, Chariot A, Marine JC, Herfs M, Rapino F, Agami R, Close P. Valine aminoacyl-tRNA synthetase promotes therapy resistance in melanoma. Nat Cell Biol 2024:10.1038/s41556-024-01439-2. [PMID: 38849541 DOI: 10.1038/s41556-024-01439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/12/2024] [Indexed: 06/09/2024]
Abstract
Transfer RNA dynamics contribute to cancer development through regulation of codon-specific messenger RNA translation. Specific aminoacyl-tRNA synthetases can either promote or suppress tumourigenesis. Here we show that valine aminoacyl-tRNA synthetase (VARS) is a key player in the codon-biased translation reprogramming induced by resistance to targeted (MAPK) therapy in melanoma. The proteome rewiring in patient-derived MAPK therapy-resistant melanoma is biased towards the usage of valine and coincides with the upregulation of valine cognate tRNAs and of VARS expression and activity. Strikingly, VARS knockdown re-sensitizes MAPK-therapy-resistant patient-derived melanoma in vitro and in vivo. Mechanistically, VARS regulates the messenger RNA translation of valine-enriched transcripts, among which hydroxyacyl-CoA dehydrogenase mRNA encodes for a key enzyme in fatty acid oxidation. Resistant melanoma cultures rely on fatty acid oxidation and hydroxyacyl-CoA dehydrogenase for their survival upon MAPK treatment. Together, our data demonstrate that VARS may represent an attractive therapeutic target for the treatment of therapy-resistant melanoma.
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Affiliation(s)
- Najla El-Hachem
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Marine Leclercq
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Miguel Susaeta Ruiz
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Raphael Vanleyssem
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Kateryna Shostak
- Laboratory of Cancer Biology, GIGA Institute, University of Liège, Liège, Belgium
| | - Pierre-René Körner
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Coralie Capron
- Laboratory of Cancer Stemness, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Patrick Roncarati
- Laboratory of Experimental Pathology, GIGA Institute, University of Liège, Liège, Belgium
| | - Arnaud Lavergne
- Bioinformatics platform, GIGA Institute, University of Liège, Liège, Belgium
| | - Arnaud Blomme
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Silvia Turchetto
- Laboratory of Molecular Regulation of Neurogenesis, GIGA Institute, University of Liège, Liège, Belgium
| | - Eric Goffin
- Center for Interdisciplinary Research on Medicines-Laboratory of Medicinal Chemistry, University of Liège, Liège, Belgium
| | - Palaniraja Thandapani
- Department of Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, USA
| | - Ivan Tarassov
- UMR 7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg/CNRS, Strasbourg, France
| | - Laurent Nguyen
- Laboratory of Molecular Regulation of Neurogenesis, GIGA Institute, University of Liège, Liège, Belgium
- WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Bernard Pirotte
- Center for Interdisciplinary Research on Medicines-Laboratory of Medicinal Chemistry, University of Liège, Liège, Belgium
| | - Alain Chariot
- Laboratory of Cancer Biology, GIGA Institute, University of Liège, Liège, Belgium
- WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA Institute, University of Liège, Liège, Belgium
| | - Francesca Rapino
- Laboratory of Cancer Stemness, GIGA Institute, University of Liège, Liège, Belgium
- WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Erasmus MC, Department of Genetics, Rotterdam University, Rotterdam, The Netherlands
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium.
- WELBIO department, WEL Research Institute, Wavre, Belgium.
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3
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Rojas J, Hose J, Auguste Dutcher H, Place M, Wolters JF, Hittinger CT, Gasch AP. Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588778. [PMID: 38645209 PMCID: PMC11030387 DOI: 10.1101/2024.04.09.588778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will only be maintained if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74-94% of the variance in aneuploid strains' growth rates is explained by the additive cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of snoRNAs and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.
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Affiliation(s)
- Julie Rojas
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John F Wolters
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
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4
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Cabrelle C, Giorgi FM, Mercatelli D. Quantitative and qualitative detection of tRNAs, tRNA halves and tRFs in human cancer samples: Molecular grounds for biomarker development and clinical perspectives. Gene 2024; 898:148097. [PMID: 38128792 DOI: 10.1016/j.gene.2023.148097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs playing a central role during protein synthesis. Besides translation, growing evidence suggests that in many contexts, precursor or mature tRNAs can also be processed into smaller fragments playing many non-canonical regulatory roles in different biological pathways with oncogenic relevance. Depending on the source, these molecules can be classified as tRNA halves (also known as tiRNAs) or tRNA-derived fragments (tRFs), and furtherly divided into 5'-tRNA and 3'-tRNA halves, or tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, respectively. Unlike DNA and mRNA, high-throughput sequencing of tRNAs is challenging, because of technical limitations of currently developed sequencing methods. In recent years, different sequencing approaches have been proposed allowing the quantification and identification of an increasing number of tRNA fragments with critical functions in distinct physiological and pathophysiological processes. In the present review, we discussed pros and cons of recent advances in different sequencing methods, also introducing the expanding repertoire of bioinformatics tool and resources specifically focused on tRNA research and discussing current issues in the study of these small RNA molecules. Furthermore, we discussed the potential value of tRNA fragments as diagnostic and prognostic biomarkers for different types of cancers.
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Affiliation(s)
- Chiara Cabrelle
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
| | | | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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5
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Padhiar NH, Katneni U, Komar AA, Motorin Y, Kimchi-Sarfaty C. Advances in methods for tRNA sequencing and quantification. Trends Genet 2024; 40:276-290. [PMID: 38123442 DOI: 10.1016/j.tig.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023]
Abstract
In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.
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Affiliation(s)
- Nigam H Padhiar
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Anton A Komar
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR 2008, IBSLor UMR 7365 IMoPA, Nancy, France.
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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6
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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7
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Shi Y, Feng Y, Wang Q, Dong G, Xia W, Jiang F. The Role of tRNA-Centered Translational Regulatory Mechanisms in Cancer. Cancers (Basel) 2023; 16:77. [PMID: 38201505 PMCID: PMC10778012 DOI: 10.3390/cancers16010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. While numerous factors have been identified as contributing to the development of malignancy, our understanding of the mechanisms involved remains limited. Early cancer detection and the development of effective treatments are therefore critical areas of research. One class of molecules that play a crucial role in the transmission of genetic information are transfer RNAs (tRNAs), which are the most abundant RNA molecules in the human transcriptome. Dysregulated synthesis of tRNAs directly results in translation disorders and diseases, including cancer. Moreover, various types of tRNA modifications and the enzymes responsible for these modifications have been implicated in tumor biology. Furthermore, alterations in tRNA modification can impact tRNA stability, and impaired stability can prompt the cleavage of tRNAs into smaller fragments known as tRNA fragments (tRFs). Initially believed to be random byproducts lacking any physiological function, tRFs have now been redefined as non-coding RNA molecules with distinct roles in regulating RNA stability, translation, target gene expression, and other biological processes. In this review, we present recent findings on translational regulatory models centered around tRNAs in tumors, providing a deeper understanding of tumorigenesis and suggesting new directions for cancer treatment.
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Affiliation(s)
- Yuanjian Shi
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Qinglin Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
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Lin YH, Chen CW, Cheng HC, Liu CJ, Chung ST, Hsieh MC, Tseng PL, Tsai WH, Wu TS, Lai MD, Shih CL, Yen MC, Fang WK, Chang WT. Inhibition of lncRNA RPPH1 activity decreases tumor proliferation and metastasis through down-regulation of inflammation-related oncogenes. Am J Transl Res 2023; 15:6701-6717. [PMID: 38186977 PMCID: PMC10767529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/13/2023] [Indexed: 01/09/2024]
Abstract
OBJECTIVE Ribonuclease P RNA component H1 (RPPH1) is a long non-coding RNA (lncRNA) associated with cancer progression. Higher RPPH1 expression in breast and cervical cancer samples than that in normal tissues were observed through the lncRNASNP2 database; therefore, silencing RPPH1 expression might be a potential strategy for cancer treatments, even though RPPH1 is also an RNA subunit of ribonuclease P involved in processing transfer RNA (tRNA) precursors and the effect of RPPH1 knockdown is not yet fully understood. METHODS Differentially expressed genes (DEGs) were identified through RNA sequencing in each shRNA-transfected RPPH1 knockdown MDA-MB-231, RPPH1 knockdown HeLa cell, and respective control cells, then the gene ontology enrichment analysis was performed by IPA and MetaCore database according to these DEGs, with further in vitro experiments validating the effect of RPPH1 silencing in MDA-MB-231 and HeLa cells. RESULTS Hundreds of down-regulated DEGs were identified in RPPH1 knockdown MDA-MB-231 and HeLa cells while bioinformatics analysis revealed that these genes were involved in pathways related to immune response and cancerogenesis. Compared to mock- and vector-transfected cells, the production of mature tRNAs, cell proliferation and migration capacity were inhibited in RPPH1-silenced HeLa and MDA-MB-231 cells. Additionally, RPPH1 knockdown promoted G1 cell cycle arrest mainly through the down-regulation of cyclin D1, although glycolytic pathways were only affected in RPPH1 knockdown HeLa cells but not MDA-MB-231 cells. CONCLUSION This study demonstrated that knockdown RPPH1 affected tRNA production, cell proliferation and metabolism. Our findings might provide insight into the role of RPPH1 in tumor development.
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Affiliation(s)
- Yuan-Ho Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Chih-Wei Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
- Department of Surgery, Chi Mei Medical CenterTainan 710, Taiwan
- Department of Occupational Safety and Health/Institute of Industrial Safety and Disaster Prevention, College of Sustainable Environment, Chia Nan University of Pharmacy and ScienceTainan 717, Taiwan
| | - Hung-Chi Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Chun-Jhih Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Sheng-Ting Chung
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Meng-Che Hsieh
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Po-Lin Tseng
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung UniversityTaoyuan 302, Taiwan
| | - Wen-Hui Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
- Department of Pediatrics, Chi Mei Foundation Medical CenterTainan 710, Taiwan
- Graduate Institute of Medical Sciences, College of Health Sciences, Chang Jung Christian UniversityTainan 711, Taiwan
| | - Tian-Shung Wu
- School of Pharmacy, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Ming-Derg Lai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
| | - Chia-Lung Shih
- Clinical Research Center, Ditmanson Medical Foundation Chia-Yi Christian HospitalChiayi 600, Taiwan
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiung 807, Taiwan
| | - Wen-Kuei Fang
- Department of Neurosurgery, Ditmanson Medical Foundation Chia-Yi Christian HospitalChiayi 600, Taiwan
| | - Wen-Tsan Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung UniversityTainan 701, Taiwan
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9
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Nakano Y, Gamper H, McGuigan H, Maharjan S, Sun Z, Krishnan K, Yigit E, Li NS, Piccirilli JA, Kleiner R, Nichols N, Hou YM. Genome-Wide Profiling of tRNA Using an Unexplored Reverse Transcriptase with High Processivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569604. [PMID: 38106225 PMCID: PMC10723452 DOI: 10.1101/2023.12.09.569604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.
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10
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Palacios-Pérez M, José MV. A Proposal of the Ur-RNAome. Genes (Basel) 2023; 14:2158. [PMID: 38136981 PMCID: PMC10743229 DOI: 10.3390/genes14122158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
It is widely accepted that the earliest RNA molecules were folded into hairpins or mini-helixes. Herein, we depict the 2D and 3D conformations of those earliest RNA molecules with only RNY triplets, which Eigen proposed as the primeval genetic code. We selected 26 species (13 bacteria and 13 archaea). We found that the free energy of RNY hairpins was consistently lower than that of their corresponding shuffled controls. We found traces of the three ribosomal RNAs (16S, 23S, and 5S), tRNAs, 6S RNA, and the RNA moieties of RNase P and the signal recognition particle. Nevertheless, at this stage of evolution there was no genetic code (as seen in the absence of the peptidyl transferase centre and any vestiges of the anti-Shine-Dalgarno sequence). Interestingly, we detected the anticodons of both glycine (GCC) and threonine (GGU) in the hairpins of proto-tRNA.
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Affiliation(s)
- Miryam Palacios-Pérez
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Network of Researchers on the Chemical Emergence of Life (NoRCEL), Leeds LS7 3RB, UK
- NoRCEL’s Latin America Hub, 113 Philosophy Hall, University of California, Berkeley, CA 94720, USA
| | - Marco V. José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Network of Researchers on the Chemical Emergence of Life (NoRCEL), Leeds LS7 3RB, UK
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11
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Wu EY, Landry L. Conserved spatiotemporal expression landscape of dominant tRNA genes in human and mouse. Biochem Biophys Res Commun 2023; 681:173-179. [PMID: 37776749 DOI: 10.1016/j.bbrc.2023.09.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023]
Abstract
Transfer RNAs are integral for protein synthesis and the interpretation of the information contained in DNA. To date, a few methods, including custom microarrays and custom targeted sequencing, have been used to quantify tRNA. However, methods using available RNA-sequencing data have not yet been reported. We created a bioinformatics pipeline to quantify the highly expressed tRNAs in RNA-Seq effectively, demonstrated by the preserved ratio of the expression levels of two massively duplicated tRNAAla genes in mouse. Using this quantification, we examined the tRNA expression with relation to tissue type and developmental stage in both human and mouse. Heart exhibited the highest overall tRNA expression for both human and mouse. Furthermore, tRNA expression grew to a peak before decreasing steadily with developmental stage, a trend that was conserved in both human and mouse. The two mitochondrial tRNA genes, tRNASer(TCA)(m) and tRNALeu(TTA)(m), which partly contribute to these trends, have been attributed to various human diseases. The tissue-specific high expression of tRNAGln(CAG) and tRNAGln(CAA) in human brains, especially in hindbrain and cerebellum, suggests their important roles in neurological disorders. In summary, our approach revealed conserved spatiotemporal expression of highly expressed tRNAs in both human and mouse. Our method can be applied to other RNA-Seq data to examine the roles of these tRNAs in different human diseases or scientific studies.
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Affiliation(s)
- Evan Y Wu
- Memphis University School, 6191 Park Ave, Memphis, TN, 38119, USA.
| | - Laura Landry
- Memphis University School, 6191 Park Ave, Memphis, TN, 38119, USA.
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12
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Yu NJ, Dai W, Li A, He M, Kleiner RE. Cell type-specific translational regulation by human DUS enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565399. [PMID: 37965204 PMCID: PMC10635104 DOI: 10.1101/2023.11.03.565399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Dihydrouridine is an abundant and conserved modified nucleoside present on tRNA, but characterization and functional studies of modification sites and associated DUS writer enzymes in mammals is lacking. Here we use a chemical probing strategy, RNABPP-PS, to identify 5-chlorouridine as an activity-based probe for human DUS enzymes. We map D modifications using RNA-protein crosslinking and chemical transformation and mutational profiling to reveal D modification sites on human tRNAs. Further, we knock out individual DUS genes in two human cell lines to investigate regulation of tRNA expression levels and codon-specific translation. We show that whereas D modifications are present across most tRNA species, loss of D only perturbs the translational function of a subset of tRNAs in a cell type-specific manner. Our work provides powerful chemical strategies for investigating D and DUS enzymes in diverse biological systems and provides insight into the role of a ubiquitous tRNA modification in translational regulation.
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13
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Jia W, Yuan J, Li S, Cheng B. The role of dysregulated mRNA translation machinery in cancer pathogenesis and therapeutic value of ribosome-inactivating proteins. Biochim Biophys Acta Rev Cancer 2023; 1878:189018. [PMID: 37944831 DOI: 10.1016/j.bbcan.2023.189018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/17/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Dysregulated protein synthesis is a hallmark of tumors. mRNA translation reprogramming contributes to tumorigenesis, which is fueled by abnormalities in ribosome formation, tRNA abundance and modification, and translation factors. Not only malignant cells but also stromal cells within tumor microenvironment can undergo transformation toward tumorigenic phenotypes during translational reprogramming. Ribosome-inactivating proteins (RIPs) have garnered interests for their ability to selectively inhibit protein synthesis and suppress tumor growth. This review summarizes the role of dysregulated translation machinery in tumor development and explores the potential of RIPs in cancer treatment.
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Affiliation(s)
- Wentao Jia
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China
| | - Jiaying Yuan
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China
| | - Shu Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201900, China.
| | - Binbin Cheng
- Oncology Department of Traditional Chinese Medicine, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China; Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai 200043, China.
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14
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Pinzaru AM, Tavazoie SF. Transfer RNAs as dynamic and critical regulators of cancer progression. Nat Rev Cancer 2023; 23:746-761. [PMID: 37814109 DOI: 10.1038/s41568-023-00611-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 10/11/2023]
Abstract
Transfer RNAs (tRNAs) have been historically viewed as non-dynamic adaptors that decode the genetic code into proteins. Recent work has uncovered dynamic regulatory roles for these fascinating molecules. Advances in tRNA detection methods have revealed that specific tRNAs can become modulated upon DNA copy number and chromatin alterations and can also be perturbed by oncogenic signalling and transcriptional regulators in cancer cells or the tumour microenvironment. Such alterations in the levels of specific tRNAs have been shown to causally impact cancer progression, including metastasis. Moreover, sequencing methods have identified tRNA-derived small RNAs that influence various aspects of cancer progression, such as cell proliferation and invasion, and could serve as diagnostic and prognostic biomarkers or putative therapeutic targets in various cancers. Finally, there is accumulating evidence, including from genetic models, that specific tRNA synthetases - the enzymes responsible for charging tRNAs with amino acids - can either promote or suppress tumour formation. In this Review, we provide an overview of how deregulation of tRNAs influences cancer formation and progression.
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Affiliation(s)
- Alexandra M Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
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15
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Dai H, Yang X, Sheng X, Wang Y, Zhang S, Zhang X, Hu L, Zhang Z, Dong X, Yin W, Yao L, Lu J. XPOT Disruption Suppresses TNBC Growth through Inhibition of Specific tRNA Nuclear Exportation and TTC19 Expression to Induce Cytokinesis Failure. Int J Biol Sci 2023; 19:5319-5336. [PMID: 37928256 PMCID: PMC10620816 DOI: 10.7150/ijbs.85006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/08/2023] [Indexed: 11/07/2023] Open
Abstract
Transfer RNAs (tRNAs) impact the development and progression of various cancers, but how individual tRNAs are modulated during triple-negative breast cancer (TNBC) progression remains poorly understood. Here, we found that XPOT (Exportin-T), a nuclear export protein receptor of tRNAs, is associated with poor prognosis in breast cancer and directly orchestrates the nuclear export of a subset of tRNAs, subsequently promoting protein synthesis and proliferation of human TNBC cells. XPOT knockdown inhibited TNBC cell proliferation in vitro, and RNA-seq indicated that XPOT is involved in the completion of cytokinesis in TNBC cells. High-throughput sequencing of tRNA revealed that XPOT specifically influenced a subset of tRNA isodecoders involved in nucleocytoplasmic trafficking, including tRNA-Ala-AGC-10-1. Through codon preferential analysis and protein mass spectrometry, we found that XPOT preferentially transported nuclear tRNA-Ala-AGC-10-1 to the cytoplasm, driving the translation of TPR Repeat Protein 19 (TTC19). TTC19 is also indispensable for cytokinesis and proliferation of TNBC cells. Altogether, these findings provide a novel regulatory translation mechanism for preferential tRNA isodecoder nucleocytoplasmic transport through XPOT, which coordinates the spatial location of specific tRNA and the translation of mRNA to facilitate TNBC proliferation and progression. Targeting XPOT may be a novel therapeutic strategy for treating TNBC.
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Affiliation(s)
- Huijuan Dai
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Xiaomei Yang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xiaonan Sheng
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Yaohui Wang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Shan Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xueli Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Lipeng Hu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhigang Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xinrui Dong
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Wenjin Yin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Linli Yao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jinsong Lu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
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16
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Anastassiadis T, Köhrer C. Ushering in the era of tRNA medicines. J Biol Chem 2023; 299:105246. [PMID: 37703991 PMCID: PMC10583094 DOI: 10.1016/j.jbc.2023.105246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
Long viewed as an intermediary in protein translation, there is a growing awareness that tRNAs are capable of myriad other biological functions linked to human health and disease. These emerging roles could be tapped to leverage tRNAs as diagnostic biomarkers, therapeutic targets, or even as novel medicines. Furthermore, the growing array of tRNA-derived fragments, which modulate an increasingly broad spectrum of cellular pathways, is expanding this opportunity. Together, these molecules offer drug developers the chance to modulate the impact of mutations and to alter cell homeostasis. Moreover, because a single therapeutic tRNA can facilitate readthrough of a genetic mutation shared across multiple genes, such medicines afford the opportunity to define patient populations not based on their clinical presentation or mutated gene but rather on the mutation itself. This approach could potentially transform the treatment of patients with rare and ultrarare diseases. In this review, we explore the diverse biology of tRNA and its fragments, examining the past and present challenges to provide a comprehensive understanding of the molecules and their therapeutic potential.
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17
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Butterfield SP, Sizer RE, Rand E, White RJ. Selection of tRNA Genes in Human Breast Tumours Varies Substantially between Individuals. Cancers (Basel) 2023; 15:3576. [PMID: 37509247 PMCID: PMC10377016 DOI: 10.3390/cancers15143576] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Abnormally elevated expression of tRNA is a common feature of breast tumours. Rather than a uniform increase in all tRNAs, some are deregulated more strongly than others. Elevation of particular tRNAs has been associated with poor prognosis for patients, and experimental models have demonstrated the ability of some tRNAs to promote proliferation or metastasis. Each tRNA isoacceptor is encoded redundantly by multiple genes, which are commonly dispersed across several chromosomes. An unanswered question is whether the consistently high expression of a tRNA in a cancer type reflects the consistent activation of the same members of a gene family, or whether different family members are activated from one patient to the next. To address this question, we interrogated ChIP-seq data to determine which tRNA genes were active in individual breast tumours. This revealed that distinct sets of tRNA genes become activated in individual cancers, whereas there is much less variation in the expression patterns of families. Several pathways have been described that are likely to contribute to increases in tRNA gene transcription in breast tumours, but none of these can adequately explain the observed variation in the choice of genes between tumours. Current models may therefore lack at least one level of regulation.
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Affiliation(s)
| | - Rebecca E Sizer
- Department of Biology, University of York, York YO10 5DD, UK
| | - Emma Rand
- Department of Biology, University of York, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, University of York, York YO10 5DD, UK
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18
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U A, Viswam P, Kattupalli D, Eppurathu Vasudevan S. Elucidation of transfer RNAs as stress regulating agents and the experimental strategies to conceive the functional role of tRNA-derived fragments in plants. Crit Rev Biotechnol 2023; 43:275-292. [PMID: 35382663 DOI: 10.1080/07388551.2022.2026288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In plants, the transfer RNAs (tRNAs) exhibit their profound influence in orchestrating diverse physiological activities like cell growth, development, and response to several surrounding stimuli. The tRNAs, which were known to restrict their function solely in deciphering the codons, are now emerging as frontline defenders in stress biology. The plants that are constantly confronted with a huge panoply of stresses rely on tRNA-mediated stress regulation by altering the tRNA abundance, curbing the transport of tRNAs, fragmenting the mature tRNAs during stress. Among them, the studies on the generation of transfer RNA-derived fragments (tRFs) and their biological implication in stress response have attained huge interest. In plants, the tRFs hold stable expression patterns and regulate biological functions under diverse environmental conditions. In this review, we discuss the fate of plant tRNAs upon stress and thereafter how the tRFs are metamorphosed into sharp ammunition to wrestle with stress. We also address the various methods developed to date for uncovering the role of tRFs and their function in plants.
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Affiliation(s)
- Aswathi U
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Pooja Viswam
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Divya Kattupalli
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
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19
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Scheepbouwer C, Aparicio-Puerta E, Gomez-Martin C, Verschueren H, van Eijndhoven M, Wedekind LE, Giannoukakos S, Hijmering N, Gasparotto L, van der Galien HT, van Rijn RS, Aronica E, Kibbelaar R, Heine VM, Wesseling P, Noske DP, Vandertop WP, de Jong D, Pegtel DM, Hackenberg M, Wurdinger T, Gerber A, Koppers-Lalic D. ALL-tRNAseq enables robust tRNA profiling in tissue samples. Genes Dev 2023; 37:243-257. [PMID: 36810209 PMCID: PMC10111867 DOI: 10.1101/gad.350233.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/26/2023] [Indexed: 02/23/2023]
Abstract
Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.
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Affiliation(s)
- Chantal Scheepbouwer
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands;
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | | | - Cristina Gomez-Martin
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Heleen Verschueren
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Monique van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Laurine E Wedekind
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Stavros Giannoukakos
- Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain
| | - Nathalie Hijmering
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Lisa Gasparotto
- Department of Child and Adolescent Psychiatry, Emma Children's Hospital, Amsterdam UMC, Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Hilde T van der Galien
- Department of Hematology, Medical Center Leeuwarden, 8934 AD Leeuwarden, the Netherlands
- HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands
| | - Roos S van Rijn
- Department of Hematology, Medical Center Leeuwarden, 8934 AD Leeuwarden, the Netherlands
- HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC location University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Robby Kibbelaar
- HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands
- Department of Pathology, Pathology Friesland, 8917 EN Leeuwarden, the Netherlands
| | - Vivi M Heine
- Department of Child and Adolescent Psychiatry, Emma Children's Hospital, Amsterdam UMC, Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, University Medical Center Utrecht, 3584 CS Utrecht, the Netherlands
| | - David P Noske
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - W Peter Vandertop
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Daphne de Jong
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - D Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain
| | - Tom Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Danijela Koppers-Lalic
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands;
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
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20
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Clusan L, Percevault F, Jullion E, Le Goff P, Tiffoche C, Fernandez-Calero T, Métivier R, Marin M, Pakdel F, Michel D, Flouriot G. Codon adaptation by synonymous mutations impacts the functional properties of the estrogen receptor-alpha protein in breast cancer cells. Mol Oncol 2023. [PMID: 36808875 DOI: 10.1002/1878-0261.13399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Oestrogen receptor-alpha (ERα) positivity is intimately associated with the development of hormone-dependent breast cancers. A major challenge in the treatment of these cancers is to understand and overcome the mechanisms of endocrine resistance. Recently, two distinct translation programmes using specific transfer RNA (tRNA) repertoires and codon usage frequencies were evidenced during cell proliferation and differentiation. Considering the phenotype switch of cancer cells to more proliferating and less-differentiated states, we can speculate that the changes in the tRNA pool and codon usage that likely occur make the ERα coding sequence no longer adapted, impacting translational rate, co-translational folding and the resulting functional properties of the protein. To verify this hypothesis, we generated an ERα synonymous coding sequence whose codon usage was optimized to the frequencies observed in genes expressed specifically in proliferating cells and then investigated the functional properties of the encoded receptor. We demonstrate that such a codon adaptation restores ERα activities to levels observed in differentiated cells, including: (a) an enhanced contribution exerted by transactivation function 1 (AF1) in ERα transcriptional activity; (b) enhanced interactions with nuclear receptor corepressor 1 and 2 [NCoR1 and NCoR2 (also known as SMRT) respectively], promoting repressive capability; and (c) reduced interactions with SRC proto-oncogene, non-receptor tyrosine kinase (Src) and phosphoinositide 3-kinase (PI3K) p85 kinases, inhibiting MAPK and AKT signalling pathway.
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Affiliation(s)
- Léa Clusan
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Frederic Percevault
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Emmanuelle Jullion
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Pascale Le Goff
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Christophe Tiffoche
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Tamara Fernandez-Calero
- Departamento de Ciencias Exactas Y Naturales, Universidad Catolica del Uruguay, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur Montevideo, Uruguay
| | - Raphaël Métivier
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Monica Marin
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Farzad Pakdel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Denis Michel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Gilles Flouriot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
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21
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Kochavi A, Lovecchio D, Faller WJ, Agami R. Proteome diversification by mRNA translation in cancer. Mol Cell 2023; 83:469-480. [PMID: 36521491 DOI: 10.1016/j.molcel.2022.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis and is well known to be altered by oncogenes to promote cancer development. This distorted mRNA translation is accompanied by the vulnerability of cancer to inhibitors of key mRNA translation components. Novel studies also suggest that these alternations could be utilized for immunotherapy. Ribosome heterogeneity and alternative responses to nutrient shortages, which aid cancer growth and spread, are proposed to elicit aberrant protein production but may also result in previously unidentified therapeutic targets, such as the presentation of cancer-specific peptides at the surface of cancer cells (neoepitopes). This review will assess the driving forces in tRNA and ribosome function that underlie proteome diversification due to alterations in mRNA translation in cancer cells.
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Affiliation(s)
- Adva Kochavi
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Domenica Lovecchio
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands; Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.
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22
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Koffler-Brill T, Noy Y, Avraham KB. The long and short: Non-coding RNAs in the mammalian inner ear. Hear Res 2023; 428:108666. [PMID: 36566643 PMCID: PMC9883734 DOI: 10.1016/j.heares.2022.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 10/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Non-coding RNAs (ncRNAs) play a critical role in the entire body, and their mis-regulation is often associated with disease. In parallel with the advances in high-throughput sequencing technologies, there is a great deal of focus on this broad class of RNAs. Although these molecules are not translated into proteins, they are now well established as significant regulatory components in many biological pathways and pathological conditions. ncRNAs can be roughly divided into two main sub-groups based on the length of the transcript, with both the small and long non-coding RNAs having diverse regulatory functions. The smaller length group includes ribosomal RNAs (rRNA), transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), microRNAs (miRNA), small interfering RNAs (siRNA), and PIWI-associated RNAs (piRNA). The longer length group includes linear long non-coding RNAs (lncRNA) and circular RNAs (circRNA). This review is designed to present the different classes of small and long ncRNA molecules and describe some of their known roles in physiological and pathological conditions, as well as methods used to assess the validity and function of miRNAs and lncRNAs, with a focus on their role and functions in the inner ear, hearing and deafness.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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23
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Ye Y, Liu M, Wu F, Ou S, Wang W, Fei J, Xie F, Bai L. TRMT6 promotes hepatocellular carcinoma progression through the PI3K/AKT signaling pathway. Eur J Med Res 2023; 28:48. [PMID: 36707905 PMCID: PMC9881333 DOI: 10.1186/s40001-022-00951-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/14/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma is one of the most common and deadly cancers. The aim of this study was to elucidate the role of tRNA methyltransferase 6 (TRMT6) during HCC progression. METHODS The role of TRMT6 in the progression and prognosis of HCC was confirmed by analysis of online databases and clinical human samples. The effects of up-regulation or down-regulation of TRMT6 on HCC cell proliferation and PI3K/AKT pathway-related protein expressions were verified. The molecular mechanism was investigated in vivo by constructing subcutaneous xenograft tumor model. RESULTS TRMT6 was overexpressed in HCC tissues and associated with Tumour-Node-Metastasis (TNM) stage, primary tumor (T) and regional lymph node (N) classification. TRMT6 expressions in HCC cell lines were higher than that in normal liver cell. TRMT6 overexpression can promote HCC cell proliferation, increase the number of S phase cells. Interference with TRMT6 reduced the PI3K/AKT pathway-related protein expressions, and was reversed by the addition of IGF1. Interference with TRMT6 inhibited tumor growth in vivo and was related to PI3K/AKT pathway. CONCLUSIONS Overexpression of TRMT6 promote HCC cell proliferation in vivo and in vitro through PI3K/AKT/mTOR axis, which provides a potential choice for the treatment of HCC in clinical practice.
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Affiliation(s)
- Yanqing Ye
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China ,grid.452437.3Department of Gastroenterology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000 Jiangxi People’s Republic of China
| | - Maosheng Liu
- grid.452437.3Department of Gastroenterology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000 Jiangxi People’s Republic of China
| | - Fengfei Wu
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Shiyu Ou
- grid.460075.0Department of Gastroenterology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, 545005 Guangxi People’s Republic of China
| | - Weidong Wang
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Jieying Fei
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Fang Xie
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
| | - Lan Bai
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515 Guangdong People’s Republic of China
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Guo X, Su M. The Origin of Translation: Bridging the Nucleotides and Peptides. Int J Mol Sci 2022; 24:ijms24010197. [PMID: 36613641 PMCID: PMC9820756 DOI: 10.3390/ijms24010197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To reveal how the translation emerged in the prebiotic context, we start with the structure and dissection of tRNA, followed by the theory and hypothesis of tRNA and amino acid recognition. Last, we review how amino acids assemble on the tRNA and further form peptides. Understanding the origin of life will also promote our knowledge of artificial living systems.
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Affiliation(s)
- Xuyuan Guo
- School of Genetics and Microbiology, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, D02 PN40 Dublin, Ireland
| | - Meng Su
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Correspondence:
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25
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Two isoleucyl tRNAs that decode synonymous codons divergently regulate breast cancer metastatic growth by controlling translation of proliferation-regulating genes. NATURE CANCER 2022; 3:1484-1497. [PMID: 36510010 DOI: 10.1038/s43018-022-00469-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
The human genome contains 61 codons encoding 20 amino acids. Synonymous codons representing a given amino acid are decoded by a set of transfer RNAs (tRNAs) called isoacceptors. We report the surprising observation that two isoacceptor tRNAs that decode synonymous codons become modulated in opposing directions during breast cancer progression. Specifically, tRNAIleUAU became upregulated, whereas tRNAIleGAU became repressed as breast cancer cells attained enhanced metastatic capacity. Functionally, tRNAIleUAU promoted and tRNAIleGAU suppressed metastatic colonization in mouse xenograft models. These tRNAs mediated opposing effects on codon-dependent translation of growth-promoting genes, consistent with genomic enrichment or depletion of their cognate codons in mitotic genes. Our findings uncover a specific isoacceptor tRNA pair that act in opposition, divergently impacting growth-regulating genes and a disease phenotype. Degeneracy of the genetic code can thus be biologically exploited by human cancer cells via tRNA isoacceptor shifts that causally facilitate the transition toward a growth-promoting state.
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26
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The POLR3G Subunit of Human RNA Polymerase III Regulates Tumorigenesis and Metastasis in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14235732. [PMID: 36497214 PMCID: PMC9735567 DOI: 10.3390/cancers14235732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes short untranslated RNAs that contribute to the regulation of gene expression. Two isoforms of human Pol III have been described that differ by the presence of the POLR3G/RPC32α or POLR3GL/RPC32β subunits. POLR3G was found to be expressed in embryonic stem cells and at least a subset of transformed cells, whereas POLR3GL shows a ubiquitous expression pattern. Here, we demonstrate that POLR3G is specifically overexpressed in clinical samples of triple-negative breast cancer (TNBC) but not in other molecular subtypes of breast cancer. POLR3G KO in the MDA-MB231 TNBC cell line dramatically reduces anchorage-independent growth and invasive capabilities in vitro. In addition, the POLR3G KO impairs tumor growth and metastasis formation of orthotopic xenografts in mice. Moreover, KO of POLR3G induces expression of the pioneer transcription factor FOXA1 and androgen receptor. In contrast, the POLR3G KO neither alters proliferation nor the expression of epithelial-mesenchymal transition marker genes. These data demonstrate that POLR3G expression is required for TNBC tumor growth, invasiveness and dissemination and that its deletion affects triple-negative breast cancer-specific gene expression.
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27
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Jacobs RQ, Fuller KB, Cooper SL, Carter ZI, Laiho M, Lucius AL, Schneider DA. RNA Polymerase I Is Uniquely Vulnerable to the Small-Molecule Inhibitor BMH-21. Cancers (Basel) 2022; 14:5544. [PMID: 36428638 PMCID: PMC9688676 DOI: 10.3390/cancers14225544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer cells require robust ribosome biogenesis to maintain rapid cell growth during tumorigenesis. Because RNA polymerase I (Pol I) transcription of the ribosomal DNA (rDNA) is the first and rate-limiting step of ribosome biogenesis, it has emerged as a promising anti-cancer target. Over the last decade, novel cancer therapeutics targeting Pol I have progressed to clinical trials. BMH-21 is a first-in-class small molecule that inhibits Pol I transcription and represses cancer cell growth. Several recent studies have uncovered key mechanisms by which BMH-21 inhibits ribosome biosynthesis but the selectivity of BMH-21 for Pol I has not been directly measured. Here, we quantify the effects of BMH-21 on Pol I, RNA polymerase II (Pol II), and RNA polymerase III (Pol III) in vitro using purified components. We found that BMH-21 directly impairs nucleotide addition by Pol I, with no or modest effect on Pols II and III, respectively. Additionally, we found that BMH-21 does not affect the stability of any of the Pols' elongation complexes. These data demonstrate that BMH-21 directly exploits unique vulnerabilities of Pol I.
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Affiliation(s)
- Ruth Q. Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kaila B. Fuller
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephanie L. Cooper
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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28
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Dysfunctional tRNA reprogramming and codon-biased translation in cancer. Trends Mol Med 2022; 28:964-978. [PMID: 36241532 PMCID: PMC10071289 DOI: 10.1016/j.molmed.2022.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/20/2022] [Accepted: 09/12/2022] [Indexed: 12/17/2022]
Abstract
Many cancers hijack translation to increase the synthesis of tumor-driving proteins, the messenger mRNAs of which have specific codon usage patterns. Termed 'codon-biased translation' and originally identified in stress response regulation, this mechanism is supported by diverse studies demonstrating how the 50 RNA modifications of the epitranscriptome, specific tRNAs, and codon-biased mRNAs are used by oncogenic programs to promote proliferation and chemoresistance. The epitranscriptome writers METTL1-WDR4, Elongator complex protein (ELP)1-6, CTU1-2, and ALKBH8-TRM112 illustrate the principal mechanism of codon-biased translation, with gene amplifications, increased RNA modifications, and enhanced tRNA stability promoting cancer proliferation. Furthermore, systems-level analyses of 34 tRNA writers and 493 tRNA genes highlight the theme of tRNA epitranscriptome dysregulation in many cancers and identify candidate tRNA writers, tRNA modifications, and tRNA molecules as drivers of pathological codon-biased translation.
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Abstract
tRNAs are key adaptor molecules that decipher the genetic code during translation of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously expressed housekeeping molecules, awareness is now growing that tRNA-encoding genes display tissue-specific and cell type-specific patterns of expression, and that tRNA gene expression and function are both dynamically regulated by post-transcriptional RNA modifications. Moreover, dysregulation of tRNAs, mediated by alterations in either their abundance or function, can have deleterious consequences that contribute to several distinct human diseases, including neurological disorders and cancer. Accumulating evidence shows that reprogramming of mRNA translation through altered tRNA activity can drive pathological processes in a codon-dependent manner. This Review considers the emerging evidence in support of the precise control of functional tRNA levels as an important regulatory mechanism that coordinates mRNA translation and protein expression in physiological cell homeostasis, and highlights key examples of human diseases that are linked directly to tRNA dysregulation.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Siegal
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Harvard University, Boston, MA, USA.
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30
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A miR-34a-guided, tRNA iMet-derived, piR_019752-like fragment (tRiMetF31) suppresses migration and angiogenesis of breast cancer cells via targeting PFKFB3. Cell Death Dis 2022; 8:355. [PMID: 35961977 PMCID: PMC9374763 DOI: 10.1038/s41420-022-01054-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/12/2022] [Accepted: 05/03/2022] [Indexed: 12/01/2022]
Abstract
Although we recently demonstrated that miR-34a directly targets tRNAiMet precursors via Argonaute 2 (AGO2)-mediated cleavage, consequently attenuating the proliferation of breast cancer cells, whether tRNAiMet fragments derived from this cleavage influence breast tumor angiogenesis remains unknown. Here, using small-RNA-Seq, we identified a tRNAiMet-derived, piR_019752-like 31-nt fragment tRiMetF31 in breast cancer cells expressing miR-34a. Bioinformatic analysis predicted 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) as a potential target of tRiMrtF31, which was validated by luciferase assay. tRiMetF31 was downregulated, whereas PFKFB3 was overexpressed in cancer cell lines. Overexpression of tRiMetF31 profoundly inhibited the migration and angiogenesis of two breast cancer cell lines while slightly inducing apoptosis. Conversely, knockdown of tRiMetF31 restored PFKFB3-driven angiogenesis. miR-34a was downregulated, whereas tRNAiMet and PFKFB3 were upregulated in breast cancer, and elevated PFKFB3 significantly correlated with metastasis. Our findings demonstrate that tRiMetF31 profoundly suppresses angiogenesis by silencing PFKFB3, presenting a novel target for therapeutic intervention in breast cancer.
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31
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The Aminoacyl-tRNA Synthetase and tRNA Expression Levels Are Deregulated in Cancer and Correlate Independently with Patient Survival. Curr Issues Mol Biol 2022; 44:3001-3017. [PMID: 35877431 PMCID: PMC9324904 DOI: 10.3390/cimb44070207] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes that load amino acids to their cognate tRNA molecules. The expression of certain ARSs and tRNAs has been shown to be deregulated in cancer, presumably to accommodate elevated protein synthesis requirements. In this work, the expression of cytoplasmic ARSs and tRNAs in ten TCGA cancers has been systematically examined. ARSs were found to be mostly upregulated in tumours and their upregulation often correlated with worse patient survival. tRNAs were found to be either upregulated or downregulated in tumours and their expression sometimes correlated to worse survival outcomes. However, although the expression of most ARSs and tRNAs was deregulated in tumours when compared to healthy adjacent tissues, only in a few cases, and independently, did it correlate to patient survival. These data point to the general uncoupling of concomitant ARS and tRNA expression deregulation and patient survival, highlighting the different ARS and tRNA requirements in cancers.
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32
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Miller JB, Meurs TE, Hodgman MW, Song B, Miller KN, Ebbert MTW, Kauwe JSK, Ridge PG. The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface. NAR Genom Bioinform 2022; 4:lqac039. [PMID: 35664804 PMCID: PMC9155233 DOI: 10.1093/nargab/lqac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/01/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Ramp sequences occur when the average translational efficiency of codons near the 5′ end of highly expressed genes is significantly lower than the rest of the gene sequence, which counterintuitively increases translational efficiency by decreasing downstream ribosomal collisions. Here, we show that the relative codon adaptiveness within different tissues changes the existence of a ramp sequence without altering the underlying genetic code. We present the first comprehensive analysis of tissue and cell type-specific ramp sequences and report 3108 genes with ramp sequences that change between tissues and cell types, which corresponds with increased gene expression within those tissues and cells. The Ramp Atlas (https://ramps.byu.edu/) allows researchers to query precomputed ramp sequences in 18 388 genes across 62 tissues and 66 cell types and calculate tissue-specific ramp sequences from user-uploaded FASTA files through an intuitive web interface. We used The Ramp Atlas to identify seven SARS-CoV-2 genes and seven human SARS-CoV-2 entry factor genes with tissue-specific ramp sequences that may help explain viral proliferation within those tissues. We anticipate that The Ramp Atlas will facilitate personalized and creative tissue-specific ramp sequence analyses for both human and viral genes that will increase our ability to utilize this often-overlooked regulatory region.
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Affiliation(s)
- Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Taylor E Meurs
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Matthew W Hodgman
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Benjamin Song
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kyle N Miller
- Department of Computer Science, Utah Valley University, Orem, UT 84058, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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33
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Gupta T, Malkin MG, Huang S. tRNA Function and Dysregulation in Cancer. Front Cell Dev Biol 2022; 10:886642. [PMID: 35721477 PMCID: PMC9198291 DOI: 10.3389/fcell.2022.886642] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA (tRNA) is a central component of protein synthesis and plays important roles in epigenetic regulation of gene expression in tumors. tRNAs are also involved in many cell processes including cell proliferation, cell signaling pathways and stress response, implicating a role in tumorigenesis and cancer progression. The complex role of tRNA in cell regulation implies that an understanding of tRNA function and dysregulation can be used to develop treatments for many cancers including breast cancer, colon cancer, and glioblastoma. Moreover, tRNA modifications including methylation are necessary for tRNA folding, stability, and function. In response to certain stress conditions, tRNAs can be cleaved in half to form tiRNAs, or even shorter tRNA fragments (tRF). tRNA structure and modifications, tiRNA induction of stress granule formation, and tRF regulation of gene expression through the repression of translation can all impact a cell’s fate. This review focuses on how these functions of tRNAs, tiRNA, and tRFs can lead to tumor development and progression. Further studies focusing on the specific pathways of tRNA regulation could help identify tRNA biomarkers and therapeutic targets, which might prevent and treat cancers.
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Affiliation(s)
- Tania Gupta
- Virginia Commonwealth University, Richmond, VA, United States
| | - Mark G. Malkin
- Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Suyun Huang
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Suyun Huang,
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34
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Malcolm JR, Leese NK, Lamond-Warner PI, Brackenbury WJ, White RJ. Widespread association of ERα with RMRP and tRNA genes in MCF-7 cells and breast cancers. Gene X 2022; 821:146280. [PMID: 35143945 PMCID: PMC8942118 DOI: 10.1016/j.gene.2022.146280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/04/2022] Open
Abstract
Estrogen receptor (ER) interacts with hundreds of tRNA genes (tDNAs) in MCF-7 cells. Hundreds of tDNAs are also targeted in primary breast tumours and metastases. Canonical estrogen response element is not found near top tDNA targets of ER. ER also targets non-coding breast cancer driver gene RMRP. ER also targets RN7SL1 gene that promotes breast cancer progression.
tRNA gene transcription by RNA polymerase III (Pol III) is a tightly regulated process, but dysregulated Pol III transcription is widely observed in cancers. Approximately 75% of all breast cancers are positive for expression of Estrogen Receptor alpha (ERα), which acts as a key driver of disease. MCF-7 cells rapidly upregulate tRNA gene transcription in response to estrogen and ChIP-PCR demonstrated ERα enrichment at tRNALeu and 5S rRNA genes in this breast cancer cell line. While these data implicate the ERα as a Pol III transcriptional regulator, how widespread this regulation is across the 631 tRNA genes has yet to be revealed. Through analyses of ERα ChIP-seq datasets, we show that ERα interacts with hundreds of tRNA genes, not only in MCF-7 cells, but also in primary human breast tumours and distant metastases. The extent of ERα association with tRNA genes varies between breast cancer cell lines and does not correlate with levels of ERα binding to its canonical target gene GREB1. Amongst other Pol III-transcribed genes, ERα is consistently enriched at the long non-coding RNA gene RMRP, a positive regulator of cell cycle progression that is subject to focal amplification in tumours. Another Pol III template targeted by ERα is the RN7SL1 gene, which is strongly implicated in breast cancer pathology by inducing inflammatory responses in tumours. Our data indicate that Pol III-transcribed non-coding genes should be added to the list of ERα targets in breast cancer.
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Affiliation(s)
- Jodie R Malcolm
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | - Natasha K Leese
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | | | - William J Brackenbury
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom
| | - Robert J White
- Department of Biology, The University of York, Heslington Road, YO10 5DD, United Kingdom.
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Santos M, Fidalgo A, Varanda AS, Soares AR, Almeida GM, Martins D, Mendes N, Oliveira C, Santos MAS. Upregulation of tRNA-Ser-AGA-2-1 Promotes Malignant Behavior in Normal Bronchial Cells. Front Mol Biosci 2022; 9:809985. [PMID: 35586191 PMCID: PMC9108184 DOI: 10.3389/fmolb.2022.809985] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/30/2022] [Indexed: 11/25/2022] Open
Abstract
Serine tRNAs (tRNASer) are frequently overexpressed in tumors and associated with poor prognosis and increased risk of recurrence in breast cancer. Impairment of tRNA biogenesis and abundance also impacts proteome homeostasis, and activates protein quality control systems. Herein, we aimed at testing whether increasing tRNASer abundance could foster tumor establishment through activation of the UPR. In order to do so, firstly we confirmed that the expression of tRNA-Ser-AGA-2-1 [hereafter tRNASer(AGA)] was upregulated by 1.79-fold in Stage I NSCLC tumors when compared to normal adjacent tissue. To study the impact of tRNASer(AGA) in early stage tumorigenesis, we induced its upregulation in a non-tumoral bronchial cell line, BEAS-2B. Upregulation of this tRNA increased cellular proliferation and protein synthesis rate, driven by eIF2α dephosphorylation and ATF4 activation downstream of PERK signaling. Futhermore, tRNASer(AGA) enhanced transformation potential in vitro, and promoted the establishment of slow growing tumors with aggressive features in nude mice. Our work highlights the importance of studying tRNA deregulation on early stage tumorigenesis, as they may be potential malignancy and aggressiveness biomarkers.
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Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Raquel Soares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela M. Almeida
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department Pathology, Medical Faculty of Porto, Porto, Portugal
| | - Diana Martins
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
| | - Nuno Mendes
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal
- Department Pathology, Medical Faculty of Porto, Porto, Portugal
- *Correspondence: Carla Oliveira, ; Manuel A. S. Santos,
| | - Manuel A. S. Santos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
- *Correspondence: Carla Oliveira, ; Manuel A. S. Santos,
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Codon optimality-mediated mRNA degradation: Linking translational elongation to mRNA stability. Mol Cell 2022; 82:1467-1476. [PMID: 35452615 PMCID: PMC10111967 DOI: 10.1016/j.molcel.2022.03.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/21/2023]
Abstract
Messenger RNA (mRNA) translation by the ribosome represents the final step of a complicated molecular dance from DNA to protein. Although classically considered a decipherer that translates a 64-word genetic code into a proteome of astonishing complexity, the ribosome can also shape the transcriptome by controlling mRNA stability. Recent work has discovered that the ribosome is an arbiter of the general mRNA degradation pathway, wherein the ribosome transit rate serves as a major determinant of transcript half-lives. Specifically, members of the degradation complex sense ribosome translocation rates as a function of ribosome elongation rates. Central to this notion is the concept of codon optimality: although all codons impact translation rates, some are deciphered quickly, whereas others cause ribosome hesitation as a consequence of relative cognate tRNA concentration. These transient pauses induce a unique ribosome conformational state that is probed by the deadenylase complex, thereby inducing an orchestrated set of events that enhance both poly(A) shortening and cap removal. Together, these data imply that the coding region of an mRNA not only encodes for protein content but also impacts protein levels through determining the transcript's fate.
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Kovalski JR, Kuzuoglu‐Ozturk D, Ruggero D. Protein synthesis control in cancer: selectivity and therapeutic targeting. EMBO J 2022; 41:e109823. [PMID: 35315941 PMCID: PMC9016353 DOI: 10.15252/embj.2021109823] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.
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Affiliation(s)
- Joanna R Kovalski
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Duygu Kuzuoglu‐Ozturk
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
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38
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Goldkamp AK, Li Y, Rivera RM, Hagen DE. Characterization of tRNA expression profiles in large offspring syndrome. BMC Genomics 2022; 23:273. [PMID: 35392796 PMCID: PMC8988405 DOI: 10.1186/s12864-022-08496-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Assisted Reproductive Technologies (ART) use can increase the risk of congenital overgrowth syndromes, such as large offspring syndrome (LOS) in ruminants. Epigenetic variations are known to influence gene expression and differentially methylated regions (DMRs) were previously determined to be associated with LOS in cattle. We observed DMRs overlapping tRNA clusters which could affect tRNA abundance and be associated with tissue specificity or overgrowth. Variations in tRNA expression have been identified in several disease pathways suggesting an important role in the regulation of biological processes. Understanding the role of tRNA expression in cattle offers an opportunity to reveal mechanisms of regulation at the translational level. We analyzed tRNA expression in the skeletal muscle and liver tissues of day 105 artificial insemination-conceived, ART-conceived with a normal body weight, and ART-conceived bovine fetuses with a body weight above the 97th percentile compared to Control-AI. Results Despite the centrality of tRNAs to translation, in silico predictions have revealed dramatic differences in the number of tRNA genes between humans and cattle (597 vs 1,659). Consistent with reports in human, only a fraction of predicted tRNA genes are expressed. We detected the expression of 474 and 487 bovine tRNA genes in the muscle and liver with the remainder being unexpressed. 193 and 198 unique tRNA sequences were expressed in all treatment groups within muscle and liver respectively. In addition, an average of 193 tRNA sequences were expressed within the same treatment group in different tissues. Some tRNA isodecoders were differentially expressed between treatment groups. In the skeletal muscle and liver, we categorized 11 tRNA isoacceptors with undetected expression as well as an isodecoder that was unexpressed in the liver (SerGGA). Our results identified variation in the proportion of tRNA gene copies expressed between tissues and differences in the highest contributing tRNA anticodon within an amino acid family due to treatment and tissue type. Out of all amino acid families, roughly half of the most highly expressed tRNA isoacceptors correlated to their most frequent codon in the bovine genome. Conclusion Although the number of bovine tRNA genes is nearly triple of that of the tRNA genes in human, there is a shared occurrence of transcriptionally inactive tRNA genes in both species. We detected differential expression of tRNA genes as well as tissue- and treatment- specific tRNA transcripts with unique sequence variations that could modulate translation during protein homeostasis or cellular stress, and give rise to regulatory products targeting genes related to overgrowth in the skeletal muscle and/or tumor development in the liver of LOS individuals. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could increase the likelihood of mistranslation or mRNA degradation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08496-7.
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Affiliation(s)
- Anna K Goldkamp
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yahan Li
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Rocio M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
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Leucyl-tRNA synthetase is a tumour suppressor in breast cancer and regulates codon-dependent translation dynamics. Nat Cell Biol 2022; 24:307-315. [PMID: 35288656 PMCID: PMC8977047 DOI: 10.1038/s41556-022-00856-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/27/2022] [Indexed: 12/17/2022]
Abstract
Tumourigenesis and cancer progression require enhanced global protein translation1–3. Such enhanced translation is caused by oncogenic and tumour suppressive events that drive the synthesis and activity of translational machinery4,5. Here we report the surprising observation that leucyl-tRNA synthetase (LARS) becomes repressed during mammary cell transformation and in human breast cancer. Monoallelic genetic deletion of LARS in mouse mammary glands enhanced breast cancer tumour formation and proliferation. LARS repression reduced the abundance of select leucine tRNA isoacceptors, leading to impaired leucine codon-dependent translation of growth suppressive genes including epithelial membrane protein 3 (EMP3) and gamma-glutamyltransferase 5 (GGT5). Our findings uncover a tumour suppressive tRNA synthetase and reveal that dynamic repression of a specific tRNA synthetase—along with its downstream cognate tRNAs—elicits a downstream codon-biased translational gene network response that enhances breast tumour formation and growth.
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Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis. Proc Natl Acad Sci U S A 2022; 119:e2119529119. [PMID: 35238631 PMCID: PMC8915964 DOI: 10.1073/pnas.2119529119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Understanding and treating neurological disorders are global priorities. Some of these diseases are engendered by mutations that cause defects in the cellular synthesis of transfer RNAs (tRNAs), which function as adapter molecules that translate messenger RNAs into proteins. During tRNA biogenesis, ribonuclease P catalyzes removal of the transcribed sequence upstream of the mature tRNA. Here, we focus on a cytoplasmic tRNAArgUCU that is expressed specifically in neurons and, when harboring a particular point mutation, contributes to neurodegeneration in mice. Our results suggest that this mutation favors stable alternative structures that are not cleaved by mouse ribonuclease P and motivate a paradigm that may help to understand the molecular basis for disease-associated mutations in other tRNAs. n-Tr20 is a neuron-specific, cytoplasmic transfer RNAArgUCU (tRNAArgUCU) isodecoder that affects seizure susceptibility, neuronal excitability, and translation signaling in mice. In addition, the C50U substitution in n-Tr20 (n-Tr20C50U), which is found in the widely used C57BL/6J (B6J) inbred mouse line, contributes to neurodegeneration by epistatic interactions with mutations in Gtpbp1 or Gtpbp2, two factors that rescue ribosomal stalling. The brains of B6J mice have high levels of immature and low levels of mature n-Tr20C50U, implicating defective tRNA biogenesis as the basis for neuronal dysfunction, a hypothesis tested in this study. We demonstrate that partially purified mouse brain ribonuclease P, the endonuclease responsible for 5′ maturation of tRNAs, exhibits at 1 mM magnesium a 20-fold lower apparent cleavage rate for processing the n-Tr20C50U precursor than the wild-type precursor. Thermal denaturation studies unexpectedly revealed that substituting the native C50-G64 base pair with the U50-G64 wobble pair in n-Tr20C50U increased the Tm by as much as 8 °C, with the magnitude of the change dependent on [Mg2+]. Moreover, results from thermal denaturation, native gel electrophoresis, 1H nuclear magnetic resonance spectroscopy, and kinetic studies collectively support the presence of stable alternative folds for n-Tr20C50U that may also be sampled transiently and in low abundance by the wild-type tRNA. These findings suggest that mutation-driven restructuring could foster nonnative folds and that conformational toggling of tRNAs poses an intrinsic risk for dysfunction when point mutations selectively stabilize nonnative states. This model may be applicable for understanding the molecular basis of other diseases that are associated with tRNA mutations.
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Zhang C, Zhao H, Song X, Wang J, Zhao S, Deng H, He L, Zhou X, Yin X, Zhang K, Zhang Y, Wu Z, Chen Q, Du J, Yu D, Zhang S, Deng W. Transcription factor GATA4 drives RNA polymerase III-directed transcription and transformed cell proliferation through a filamin A/GATA4/SP1 pathway. J Biol Chem 2022; 298:101581. [PMID: 35038452 PMCID: PMC8857480 DOI: 10.1016/j.jbc.2022.101581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 11/27/2022] Open
Abstract
RNA polymerase III (pol III) products play fundamental roles in a variety of cellular processes, including protein synthesis and cancer cell proliferation. In addition, dysregulation of pol III-directed transcription closely correlates with tumorigenesis. It is therefore of interest to identify novel pathways or factors governing pol III-directed transcription. Here, we show that transcription factor (TF) GATA binding protein 4 (GATA4) expression in SaOS2 cells was stimulated by the silencing of filamin A (FLNA), a repressor of pol III-directed transcription, suggesting that GATA4 is potentially associated with the regulation of pol III-directed transcription. Indeed, we show that GATA4 expression positively correlates with pol III-mediated transcription and tumor cell proliferation. Mechanistically, we found that GATA4 depletion inhibits the occupancies of the pol III transcription machinery factors at the loci of pol III target genes by reducing expression of both TFIIIB subunit TFIIB-related factor 1 and TFIIIC subunit general transcription factor 3C subunit 2 (GTF3C2). GATA4 has been shown to activate specificity factor 1 (Sp1) gene transcription by binding to the Sp1 gene promoter, and Sp1 has been confirmed to activate pol III gene transcription by directly binding to both Brf1 and Gtf3c2 gene promoters. Thus, the findings from this study suggest that GATA4 links FLNA and Sp1 signaling to form an FLNA/GATA4/Sp1 axis to modulate pol III-directed transcription and transformed cell proliferation. Taken together, these results provide novel insights into the regulatory mechanism of pol III-directed transcription.
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Affiliation(s)
- Cheng Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Houliang Zhao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaoye Song
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Juan Wang
- School of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, China
| | - Shasha Zhao
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Huan Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Liu He
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiangyu Zhou
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaomei Yin
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kewei Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yue Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Zhongyu Wu
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Qiyue Chen
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Jiannan Du
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Deen Yu
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shihua Zhang
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China.
| | - Wensheng Deng
- School of Life Science and Health, Wuhan University of Science and Technology, Wuhan, China.
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Chen L, Xu W, Liu K, Jiang Z, Han Y, Jin H, Zhang L, Shen W, Jia S, Sun Q, Meng A. 5' Half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos. SCIENCE ADVANCES 2021; 7:eabh0494. [PMID: 34797706 PMCID: PMC8604414 DOI: 10.1126/sciadv.abh0494] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
5′tRFls are small transfer RNA (tRNA) fragments derived from 5′ half of mature tRNAs. However, it is unknown whether 5′tRFls could feed back to regulate tRNA biogenesis. Here, we show that 5′tRFlGly/GCC and 5′tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5′tRFlGly/GCC and 5′tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5′tRFlGly/GCC or 5′tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels, respectively, and causes embryonic lethality that is efficiently rescued by coinjection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5′tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5′tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA gene transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.
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Affiliation(s)
- Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kunpeng Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Jiang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Han
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongbin Jin
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Guangzhou Laboratory, Guangzhou 510320, Guangdong Province, China
- Corresponding author.
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Chen M, Long Q, Borrie MS, Sun H, Zhang C, Yang H, Shi D, Gartenberg MR, Deng W. Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells. PLoS Genet 2021; 17:e1009899. [PMID: 34793452 PMCID: PMC8639082 DOI: 10.1371/journal.pgen.1009899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/02/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
The robust proliferation of cancer cells requires vastly elevated levels of protein synthesis, which relies on a steady supply of aminoacylated tRNAs. Delivery of tRNAs to the cytoplasm is a highly regulated process, but the machinery for tRNA nuclear export is not fully elucidated. In this study, using a live cell imaging strategy that visualizes nascent transcripts from a specific tRNA gene in yeast, we identified the nuclear basket proteins Mlp1 and Mlp2, two homologs of the human TPR protein, as regulators of tRNA export. TPR expression is significantly increased in lung cancer tissues and correlated with poor prognosis. Consistently, knockdown of TPR inhibits tRNA nuclear export, protein synthesis and cell growth in lung cancer cell lines. We further show that NXF1, a well-known mRNA nuclear export factor, associates with tRNAs and mediates their transport through nuclear pores. Collectively, our findings uncover a conserved mechanism that regulates nuclear export of tRNAs, which is a limiting step in protein synthesis in eukaryotes.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Qian Long
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Haohui Sun
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Changlin Zhang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Han Yang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Dingbo Shi
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- The Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
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Gillen SL, Waldron JA, Bushell M. Codon optimality in cancer. Oncogene 2021; 40:6309-6320. [PMID: 34584217 PMCID: PMC8585667 DOI: 10.1038/s41388-021-02022-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022]
Abstract
A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are encoded by multiple codons, the nucleotide sequence of a coding region can vary dramatically without altering the polypeptide sequence of the encoded protein. Although mutations that do not alter the final amino acid sequence are often thought of as silent/synonymous, these can still have dramatic effects on protein output. Because each codon has a distinct translation elongation rate and can differentially impact mRNA stability, each codon has a different degree of 'optimality' for protein synthesis. Recent data demonstrates that the codon preference of a transcriptome matches the abundance of tRNAs within the cell and that this supply and demand between tRNAs and mRNAs varies between different cell types. The largest observed distinction is between mRNAs encoding proteins associated with proliferation or differentiation. Nevertheless, precisely how codon optimality and tRNA expression levels regulate cell fate decisions and their role in malignancy is not fully understood. This review describes the current mechanistic understanding on codon optimality, its role in malignancy and discusses the potential to target codon optimality therapeutically in the context of cancer.
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Affiliation(s)
- Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK, G61 1QH.
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Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
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Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
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Kumari K, Groza P, Aguilo F. Regulatory roles of RNA modifications in breast cancer. NAR Cancer 2021; 3:zcab036. [PMID: 34541538 PMCID: PMC8445368 DOI: 10.1093/narcan/zcab036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
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Affiliation(s)
- Kanchan Kumari
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
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Fabbri L, Chakraborty A, Robert C, Vagner S. The plasticity of mRNA translation during cancer progression and therapy resistance. Nat Rev Cancer 2021; 21:558-577. [PMID: 34341537 DOI: 10.1038/s41568-021-00380-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/14/2021] [Indexed: 02/07/2023]
Abstract
Translational control of mRNAs during gene expression allows cells to promptly and dynamically adapt to a variety of stimuli, including in neoplasia in response to aberrant oncogenic signalling (for example, PI3K-AKT-mTOR, RAS-MAPK and MYC) and microenvironmental stress such as low oxygen and nutrient supply. Such translational rewiring allows rapid, specific changes in the cell proteome that shape specific cancer phenotypes to promote cancer onset, progression and resistance to anticancer therapies. In this Review, we illustrate the plasticity of mRNA translation. We first highlight the diverse mechanisms by which it is regulated, including by translation factors (for example, eukaryotic initiation factor 4F (eIF4F) and eIF2), RNA-binding proteins, tRNAs and ribosomal RNAs that are modulated in response to aberrant intracellular pathways or microenvironmental stress. We then describe how translational control can influence tumour behaviour by impacting on the phenotypic plasticity of cancer cells as well as on components of the tumour microenvironment. Finally, we highlight the role of mRNA translation in the cellular response to anticancer therapies and its promise as a key therapeutic target.
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Affiliation(s)
- Lucilla Fabbri
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France
| | - Alina Chakraborty
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, Kremlin-Bicêtre, France
- Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer, Orsay, France.
- Dermato-Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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Orellana EA, Liu Q, Yankova E, Pirouz M, De Braekeleer E, Zhang W, Lim J, Aspris D, Sendinc E, Garyfallos DA, Gu M, Ali R, Gutierrez A, Mikutis S, Bernardes GJL, Fischer ES, Bradley A, Vassiliou GS, Slack FJ, Tzelepis K, Gregory RI. METTL1-mediated m 7G modification of Arg-TCT tRNA drives oncogenic transformation. Mol Cell 2021; 81:3323-3338.e14. [PMID: 34352207 PMCID: PMC8380730 DOI: 10.1016/j.molcel.2021.06.031] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 02/02/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023]
Abstract
The emerging "epitranscriptomics" field is providing insights into the biological and pathological roles of different RNA modifications. The RNA methyltransferase METTL1 catalyzes N7-methylguanosine (m7G) modification of tRNAs. Here we find METTL1 is frequently amplified and overexpressed in cancers and is associated with poor patient survival. METTL1 depletion causes decreased abundance of m7G-modified tRNAs and altered cell cycle and inhibits oncogenicity. Conversely, METTL1 overexpression induces oncogenic cell transformation and cancer. Mechanistically, we find increased abundance of m7G-modified tRNAs, in particular Arg-TCT-4-1, and increased translation of mRNAs, including cell cycle regulators that are enriched in the corresponding AGA codon. Accordingly, Arg-TCT expression is elevated in many tumor types and is associated with patient survival, and strikingly, overexpression of this individual tRNA induces oncogenic transformation. Thus, METTL1-mediated tRNA modification drives oncogenic transformation through a remodeling of the mRNA "translatome" to increase expression of growth-promoting proteins and represents a promising anti-cancer target.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eliza Yankova
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Storm Therapeutics Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Wencai Zhang
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jihoon Lim
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - Erdem Sendinc
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dimitrios A Garyfallos
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Muxin Gu
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Raja Ali
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sigitas Mikutis
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Allan Bradley
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Frank J Slack
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Konstantinos Tzelepis
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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Ma J, Han H, Huang Y, Yang C, Zheng S, Cai T, Bi J, Huang X, Liu R, Huang L, Luo Y, Li W, Lin S. METTL1/WDR4 mediated m 7G tRNA modifications and m 7G codon usage promote mRNA translation and lung cancer progression. Mol Ther 2021; 29:3422-3435. [PMID: 34371184 DOI: 10.1016/j.ymthe.2021.08.005] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 06/14/2021] [Accepted: 07/20/2021] [Indexed: 11/29/2022] Open
Abstract
Mis-regulated epigenetic modifications in RNAs are associated with human cancers. The transfer RNAs (tRNAs) are the most heavily modified RNA species in cells, however, little is known about the functions of tRNA modifications in cancers. In this study, we uncovered that the expression levels of tRNA N7-methylguanosine (m7G) methyltransferase complex components METTL1 and WDR4 are significantly elevated in human lung cancer samples and negatively associated with patient prognosis. Impaired m7G tRNA modification upon METTL1/WDR4 depletion resulted in decreased cell proliferation, colony formation, cell invasion and impaired tumorigenic capacities of lung cancer cells in vitro and in vivo. Moreover, gain-of-function and mutagenesis experiments revealed that METTL1 promoted lung cancer growth and invasion through regulation of m7G tRNA modifications. Profiling of tRNA methylation and mRNA translation revealed that highly translated mRNAs have higher frequencies of m7G tRNA decoded codons and knockdown of METTL1 resulted in decreased translation of mRNAs with higher frequencies of m7G tRNA codons, suggesting that tRNA modifications and codon usage play essential function in mRNA translation regulation. Our data uncovered novel insights on mRNA translation regulation through tRNA modifications and the corresponding mRNA codon compositions in lung cancer, providing new molecular basis underlying lung cancer progression.
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Affiliation(s)
- Jieyi Ma
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080; Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Hui Han
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Ying Huang
- Department of Pediatrics, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Chunlong Yang
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Siyi Zheng
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Tiancai Cai
- Xiamen special service convalescent center, Xiamen, China 361005
| | - Jiong Bi
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Xiaohui Huang
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Ruiming Liu
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Libin Huang
- Department of Pediatrics, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Yifeng Luo
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China 510080.
| | - Wen Li
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080.
| | - Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China 510060.
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50
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Lata E, Choquet K, Sagliocco F, Brais B, Bernard G, Teichmann M. RNA Polymerase III Subunit Mutations in Genetic Diseases. Front Mol Biosci 2021; 8:696438. [PMID: 34395528 PMCID: PMC8362101 DOI: 10.3389/fmolb.2021.696438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes small untranslated RNAs such as 5S ribosomal RNA, transfer RNAs, and U6 small nuclear RNA. Because of the functions of these RNAs, Pol III transcription is best known for its essential contribution to RNA maturation and translation. Surprisingly, it was discovered in the last decade that various inherited mutations in genes encoding nine distinct subunits of Pol III cause tissue-specific diseases rather than a general failure of all vital functions. Mutations in the POLR3A, POLR3C, POLR3E and POLR3F subunits are associated with susceptibility to varicella zoster virus-induced encephalitis and pneumonitis. In addition, an ever-increasing number of distinct mutations in the POLR3A, POLR3B, POLR1C and POLR3K subunits cause a spectrum of neurodegenerative diseases, which includes most notably hypomyelinating leukodystrophy. Furthermore, other rare diseases are also associated with mutations in genes encoding subunits of Pol III (POLR3H, POLR3GL) and the BRF1 component of the TFIIIB transcription initiation factor. Although the causal relationship between these mutations and disease development is widely accepted, the exact molecular mechanisms underlying disease pathogenesis remain enigmatic. Here, we review the current knowledge on the functional impact of specific mutations, possible Pol III-related disease-causing mechanisms, and animal models that may help to better understand the links between Pol III mutations and disease.
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Affiliation(s)
- Elisabeth Lata
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Karine Choquet
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Francis Sagliocco
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
| | - Bernard Brais
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Geneviève Bernard
- Departments of Neurology and Neurosurgery, Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Martin Teichmann
- Bordeaux University, Inserm U 1212, CNRS UMR 5320, ARNA laboratory, Bordeaux, France
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