1
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Ghashghaei M, Liu Y, Ettles J, Bombaci G, Ramkumar N, Liu Z, Escano L, Miko SS, Kim Y, Waldron JA, Do K, MacPherson K, Yuen KA, Taibi T, Yue M, Arsalan A, Jin Z, Edin G, Karsan A, Morin GB, Kuchenbauer F, Perna F, Bushell M, Vu LP. Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis. Nat Commun 2024; 15:2340. [PMID: 38491013 PMCID: PMC10943099 DOI: 10.1038/s41467-024-46665-2] [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: 09/05/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
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Affiliation(s)
- Maryam Ghashghaei
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Yilin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, Canada
| | - James Ettles
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Giuseppe Bombaci
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
| | - Niveditha Ramkumar
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zongmin Liu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Leo Escano
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Sandra Spencer Miko
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Yerin Kim
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Bioinformatics program, University of British Columbia, Vancouver, Canada
| | - Joseph A Waldron
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kim Do
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Katie A Yuen
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Thilelli Taibi
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Marty Yue
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aaremish Arsalan
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zhen Jin
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Glenn Edin
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aly Karsan
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Gregg B Morin
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Florian Kuchenbauer
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Fabiana Perna
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffit Cancer Center, Tampa, FL, USA
| | - Martin Bushell
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ly P Vu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada.
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2
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Rao Y, Ahmed N, Pritchard J, O'Brien EP. Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. BMC Bioinformatics 2023; 24:462. [PMID: 38062391 PMCID: PMC10704839 DOI: 10.1186/s12859-023-05521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations might be enriched in cancer has been explored in several recent studies. However, none of these studies control for all three types of mutational heterogeneity (patient, histology, and gene) that are known to affect the accurate identification of non-synonymous cancer-associated genes. Our goal is to adopt the current standard for non-synonymous mutations in an investigation of synonymous mutations. RESULTS Here, we create an algorithm, MutSigCVsyn, an adaptation of MutSigCV, to identify cancer-associated genes that are enriched for synonymous mutations based on a non-coding background model that takes into account the mutational heterogeneity across these levels. Using MutSigCVsyn, we first analyzed 2572 cancer whole-genome samples from the Pan-cancer Analysis of Whole Genomes (PCAWG) to identify non-synonymous cancer drivers as a quality control. Indicative of the algorithm accuracy we find that 58.6% of these candidate genes were also found in Cancer Census Gene (CGC) list, and 66.2% were found within the PCAWG cancer driver list. We then applied it to identify 30 putative cancer-associated genes that are enriched for synonymous mutations within the same samples. One of the promising gene candidates is the B cell lymphoma 2 (BCL-2) gene. BCL-2 regulates apoptosis by antagonizing the action of proapoptotic BCL-2 family member proteins. The synonymous mutations in BCL2 are enriched in its anti-apoptotic domain and likely play a role in cancer cell proliferation. CONCLUSION Our study introduces MutSigCVsyn, an algorithm that accounts for mutational heterogeneity at patient, histology, and gene levels, to identify cancer-associated genes that are enriched for synonymous mutations using whole genome sequencing data. We identified 30 putative candidate genes that will benefit from future experimental studies on the role of synonymous mutations in cancer biology.
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Affiliation(s)
- Yiyun Rao
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Nabeel Ahmed
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
- Moderna, Inc., Cambridge, USA
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA.
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3
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Abouelwafa M, Ibrahim TM, El-Hadidi MS, Mahnashi MH, Owaidah AY, Saeedi NH, Attia HG, Georrge JJ, Mostafa A. Using CADD tools to inhibit the overexpressed genes FAP, FN1, and MMP1 by repurposing ginsenoside C and Rg1 as a treatment for oral cancer. Front Mol Biosci 2023; 10:1248885. [PMID: 37936719 PMCID: PMC10627001 DOI: 10.3389/fmolb.2023.1248885] [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: 06/27/2023] [Accepted: 08/11/2023] [Indexed: 11/09/2023] Open
Abstract
Oral cancer is one of the most common cancer types. Many factors can express certain genes that cause the proliferation of oral tissues. Overexpressed genes were detected in oral cancer patients; three were highly impacted. FAP, FN1, and MMP1 were the targeted genes that showed inhibition results in silico by ginsenoside C and Rg1. Approved drugs were retrieved from the DrugBank database. The docking scores show an excellent interaction between the ligands and the targeted macromolecules. Further molecular dynamics simulations showed the binding stability of the proposed natural products. This work recommends repurposing ginsenoside C and Rg1 as potential binders for the selected targets and endorses future experimental validation for the treatment of oral cancer.
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Affiliation(s)
- Manal Abouelwafa
- Department of Bioinformatics, Christ College, Rajkot, Gujarat, India
| | - Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- Bioinformatics Group, Center for Informatics Sciences, School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Mohamed S. El-Hadidi
- Bioinformatics Group, Center for Informatics Sciences, School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Mater H. Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Amani Y. Owaidah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Nizar H. Saeedi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Hany G. Attia
- Department of Pharmacognosy, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - John J. Georrge
- Department of Bioinformatics, University of North Bengal, West Bengal, India
| | - Amany Mostafa
- Nanomedicine and Tissue Engineering Laboratory, Medical Research Centre of Excellence, National Research Centre (NRC), Cairo, Egypt
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4
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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5
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Jassim A, Rahrmann EP, Simons BD, Gilbertson RJ. Cancers make their own luck: theories of cancer origins. Nat Rev Cancer 2023; 23:710-724. [PMID: 37488363 DOI: 10.1038/s41568-023-00602-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Cancer has been a leading cause of death for decades. This dismal statistic has increased efforts to prevent the disease or to detect it early, when treatment is less invasive, relatively inexpensive and more likely to cure. But precisely how tissues are transformed continues to provoke controversy and debate, hindering cancer prevention and early intervention strategies. Various theories of cancer origins have emerged, including the suggestion that it is 'bad luck': the inevitable consequence of random mutations in proliferating stem cells. In this Review, we discuss the principal theories of cancer origins and the relative importance of the factors that underpin them. The body of available evidence suggests that developing and ageing tissues 'walk a tightrope', retaining adequate levels of cell plasticity to generate and maintain tissues while avoiding overstepping into transformation. Rather than viewing cancer as 'bad luck', understanding the complex choreography of cell intrinsic and extrinsic factors that characterize transformation holds promise to discover effective new ways to prevent, detect and stop cancer before it becomes incurable.
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Affiliation(s)
- Amir Jassim
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Eric P Rahrmann
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ben D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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6
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Bonner ER, Dawood A, Gordish-Dressman H, Eze A, Bhattacharya S, Yadavilli S, Mueller S, Waszak SM, Nazarian J. Pan-cancer atlas of somatic core and linker histone mutations. NPJ Genom Med 2023; 8:23. [PMID: 37640703 PMCID: PMC10462747 DOI: 10.1038/s41525-023-00367-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
Recent genomic data points to a growing role for somatic mutations altering core histone and linker histone-encoding genes in cancer. However, the prevalence and the clinical and biological implications of histone gene mutations in malignant tumors remain incompletely defined. To address these knowledge gaps, we analyzed somatic mutations in 88 linker and core histone genes across 12,743 tumors from pediatric, adolescent and young adult (AYA), and adult cancer patients. We established a pan-cancer histone mutation atlas contextualized by patient age, survival outcome, and tumor location. Overall, 11% of tumors harbored somatic histone mutations, with the highest rates observed among chondrosarcoma (67%), pediatric high-grade glioma (pHGG, >60%), and lymphoma (>30%). Previously unreported histone mutations were discovered in pHGG and other pediatric brain tumors, extending the spectrum of histone gene alterations associated with these cancers. Histone mutation status predicted patient survival outcome in tumor entities including adrenocortical carcinoma. Recurrent pan-cancer histone mutation hotspots were defined and shown to converge on evolutionarily conserved and functional residues. Moreover, we studied histone gene mutations in 1700 pan-cancer cell lines to validate the prevalence and spectrum of histone mutations seen in primary tumors and derived histone-associated drug response profiles, revealing candidate drugs targeting histone mutant cancer cells. This study presents the first-of-its-kind atlas of both core and linker histone mutations across pediatric, AYA, and adult cancers, providing a framework by which specific cancers may be redefined in the context of histone and chromatin alterations.
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Affiliation(s)
- Erin R Bonner
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Adam Dawood
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | | | - Augustine Eze
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Sridevi Yadavilli
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Department of Oncology, University Children's Hospital Zürich, Zürich, Switzerland
| | - Sebastian M Waszak
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Oncology, University Children's Hospital Zürich, Zürich, Switzerland.
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7
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Ras protein abundance correlates with Ras isoform mutation patterns in cancer. Oncogene 2023; 42:1224-1232. [PMID: 36864243 PMCID: PMC10079525 DOI: 10.1038/s41388-023-02638-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023]
Abstract
Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.
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8
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Benisty H, Hernandez-Alias X, Weber M, Anglada-Girotto M, Mantica F, Radusky L, Senger G, Calvet F, Weghorn D, Irimia M, Schaefer MH, Serrano L. Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Cell Syst 2023; 14:312-323.e3. [PMID: 36889307 DOI: 10.1016/j.cels.2023.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/11/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
Codon usage influences gene expression distinctly depending on the cell context. Yet, the importance of codon bias in the simultaneous turnover of specific groups of protein-coding genes remains to be investigated. Here, we find that genes enriched in A/T-ending codons are expressed more coordinately in general and across tissues and development than those enriched in G/C-ending codons. tRNA abundance measurements indicate that this coordination is linked to the expression changes of tRNA isoacceptors reading A/T-ending codons. Genes with similar codon composition are more likely to be part of the same protein complex, especially for genes with A/T-ending codons. The codon preferences of genes with A/T-ending codons are conserved among mammals and other vertebrates. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.
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Affiliation(s)
- Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marc Weber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Federica Mantica
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Gökçe Senger
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Donate Weghorn
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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9
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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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10
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Ran X, Xiao J, Cheng F, Wang T, Teng H, Sun Z. Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality. Comput Struct Biotechnol J 2022; 20:3567-3580. [PMID: 35860410 PMCID: PMC9287186 DOI: 10.1016/j.csbj.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/22/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022] Open
Abstract
Developed tissue-specific codon optimality in 29 human tissues. Applied these to analyze synonymous mutations in ∼10,000 tumor and normal samples. Synonymous mutations frequently increase optimal codons in most cancer types. Synonymous mutations frequently increase optimal codons cell cycle-related genes. Frequency of optimal codon gain relates to proliferation, DDR deficiency, and survival.
Codon optimality has been demonstrated to be an important determinant of mRNA stability and expression levels in multiple model organisms and human cell lines. However, tissue-specific codon optimality has not been developed to investigate how codon optimality is usually perturbed by somatic synonymous mutations in human cancers. Here, we determined tissue-specific codon optimality in 29 human tissues based on mRNA expression data from the Genotype-Tissue Expression project. We found that optimal codons were associated with differentiation, whereas non-optimal codons were correlated with proliferation. Furthermore, codons biased toward differentiation displayed greater tissue specificity in codon optimality, and the tissue specificity of codon optimality was primarily present in amino acids with high degeneracy of the genetic code. By applying tissue-specific codon optimality to somatic synonymous mutations in 8532 tumor samples across 24 cancer types and to those in 416 normal cells across six human tissues, we found that synonymous mutations frequently increased optimal codons in tumor cells and cancer-related genes (e.g., genes involved in cell cycle). Furthermore, an elevated frequency of optimal codon gain was found to promote tumor cell proliferation in three cancer types characterized by DNA damage repair deficiency and could act as a prognostic biomarker for patients with triple-negative breast cancer. In summary, this study profiled tissue-specific codon optimality in human tissues, revealed alterations in codon optimality caused by synonymous mutations in human cancers, and highlighted the non-negligible role of optimal codon gain in tumorigenesis and therapeutics.
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Affiliation(s)
- Xia Ran
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyuan Xiao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Fang Cheng
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
| | - Huajing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
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11
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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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12
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KRAS-related long noncoding RNAs in human cancers. Cancer Gene Ther 2022; 29:418-427. [PMID: 34489556 PMCID: PMC9113938 DOI: 10.1038/s41417-021-00381-x] [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: 03/17/2021] [Revised: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
KRAS is one of the most widely prevalent proto-oncogenes in human cancers. The constitutively active KRAS oncoprotein contributes to both tumor onset and cancer development by promoting cell proliferation and anchorage-independent growth in a MAPK pathway-dependent manner. The expression of microRNAs (miRNAs) and the KRAS oncogene are known to be dysregulated in various cancers, while long noncoding RNAs (lncRNAs) can act as regulators of the miRNAs targeting KRAS oncogene in different cancers and have gradually become a focus of research in recent years. In this review article, we summarize recent advances in the research on lncRNAs that have sponging effects on KRAS-targeting miRNAs as crucial mediators of KRAS expression in different cell types and organs. A deeper understanding of lncRNA function in KRAS-driven cancers is of major fundamental importance and will provide a valuable clinical tool for the diagnosis, prognosis, and eventual treatment of cancers.
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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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Iriarte A, Lamolle G, Musto H. Codon Usage Bias: An Endless Tale. J Mol Evol 2021; 89:589-593. [PMID: 34383106 DOI: 10.1007/s00239-021-10027-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
Since the genetic code is degenerate, several codons are translated to the same amino acid. Although these triplets were historically considered to be "synonymous" and therefore expected to be used at rather equal frequencies in all genomes, we now know that this is not the case. Indeed, since several coding sequences were obtained in the late '70s and early '80s in the last century, coming from either the same or different species, it was evident that (a) each genome, taken globally, displayed different codon usage patterns, which means that different genomes display a particular global codon usage table when all genes are considered together, and (b) there is a strong intragenomic diversity: in other words, within a given species the codon usage pattern can (and usually do) differ greatly among genes in the same genome. These different patterns were attributed to two main factors: first, the mutational bias characteristic of each genome, which determines that GC- poor species display a general bias towards A/T codons while the reverse is true for GC- rich species. Second, the differences in codon usage among genes from the same species are due to natural selection acting at the level of translation, in such a way that highly expressed genes tend to use codons that match with the most abundant isoacceptor tRNAs. Thus, these genes are translated at a highest rate, which in turn leads to avoid the limiting factor in translation which is the number of available ribosomes per cell. Although these explanations are still valid, new factors are almost constantly postulated to affect codon usage. In this mini review, we shall try to summarize them.
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Affiliation(s)
- Andrés Iriarte
- Laboratorio de Genómica Evolutiva, Depto. de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay.,Laboratorio de Biología Computacional, Depto. de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, 11600, Montevideo, Uruguay
| | - Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Depto. de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Depto. de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay.
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Meyer D, Kames J, Bar H, Komar AA, Alexaki A, Ibla J, Hunt RC, Santana-Quintero LV, Golikov A, DiCuccio M, Kimchi-Sarfaty C. Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage. Genome Med 2021; 13:122. [PMID: 34321100 PMCID: PMC8317675 DOI: 10.1186/s13073-021-00935-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gene expression is highly variable across tissues of multi-cellular organisms, influencing the codon usage of the tissue-specific transcriptome. Cancer disrupts the gene expression pattern of healthy tissue resulting in altered codon usage preferences. The topic of codon usage changes as they relate to codon demand, and tRNA supply in cancer is of growing interest. METHODS We analyzed transcriptome-weighted codon and codon pair usage based on The Cancer Genome Atlas (TCGA) RNA-seq data from 6427 solid tumor samples and 632 normal tissue samples. This dataset represents 32 cancer types affecting 11 distinct tissues. Our analysis focused on tissues that give rise to multiple solid tumor types and cancer types that are present in multiple tissues. RESULTS We identified distinct patterns of synonymous codon usage changes for different cancer types affecting the same tissue. For example, a substantial increase in GGT-glycine was observed in invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), and mixed invasive ductal and lobular carcinoma (IDLC) of the breast. Change in synonymous codon preference favoring GGT correlated with change in synonymous codon preference against GGC in IDC and IDLC, but not in ILC. Furthermore, we examined the codon usage changes between paired healthy/tumor tissue from the same patient. Using clinical data from TCGA, we conducted a survival analysis of patients based on the degree of change between healthy and tumor-specific codon usage, revealing an association between larger changes and increased mortality. We have also created a database that contains cancer-specific codon and codon pair usage data for cancer types derived from TCGA, which represents a comprehensive tool for codon-usage-oriented cancer research. CONCLUSIONS Based on data from TCGA, we have highlighted tumor type-specific signatures of codon and codon pair usage. Paired data revealed variable changes to codon usage patterns, which must be considered when designing personalized cancer treatments. The associated database, CancerCoCoPUTs, represents a comprehensive resource for codon and codon pair usage in cancer and is available at https://dnahive.fda.gov/review/cancercocoputs/ . These findings are important to understand the relationship between tRNA supply and codon demand in cancer states and could help guide the development of new cancer therapeutics.
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Affiliation(s)
- Douglas Meyer
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Jacob Kames
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT, USA
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
| | - Aikaterini Alexaki
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Juan Ibla
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan C Hunt
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Luis V Santana-Quintero
- High-performance Integrated Virtual Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Anton Golikov
- High-performance Integrated Virtual Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Michael DiCuccio
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA.
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