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Dumas L, Shin S, Rigaud Q, Cargnello M, Hernández-Suárez B, Herviou P, Saint-Laurent N, Leduc M, Le Gall M, Monchaud D, Dassi E, Cammas A, Millevoi S. RNA G-quadruplexes control mitochondria-localized mRNA translation and energy metabolism. Nat Commun 2025; 16:3292. [PMID: 40195294 PMCID: PMC11977240 DOI: 10.1038/s41467-025-58118-5] [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: 08/18/2022] [Accepted: 03/12/2025] [Indexed: 04/09/2025] Open
Abstract
Cancer cells rely on mitochondria for their bioenergetic supply and macromolecule synthesis. Central to mitochondrial function is the regulation of mitochondrial protein synthesis, which primarily depends on the cytoplasmic translation of nuclear-encoded mitochondrial mRNAs whose protein products are imported into mitochondria. Despite the growing evidence that mitochondrial protein synthesis contributes to the onset and progression of cancer, and can thus offer new opportunities for cancer therapy, knowledge of the underlying molecular mechanisms remains limited. Here, we show that RNA G-quadruplexes (RG4s) regulate mitochondrial function by modulating cytoplasmic mRNA translation of nuclear-encoded mitochondrial proteins. Our data support a model whereby the RG4 folding dynamics, under the control of oncogenic signaling and modulated by small molecule ligands or RG4-binding proteins, modifies mitochondria-localized cytoplasmic protein synthesis. Ultimately, this impairs mitochondrial functions, affecting energy metabolism and consequently cancer cell proliferation.
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Affiliation(s)
- Leïla Dumas
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Sauyeun Shin
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Quentin Rigaud
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Marie Cargnello
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Beatriz Hernández-Suárez
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Pauline Herviou
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Nathalie Saint-Laurent
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Marjorie Leduc
- Proteom'IC facility, Université Paris Cité, CNRS, INSERM Institut Cochin, Paris, France
| | - Morgane Le Gall
- Proteom'IC facility, Université Paris Cité, CNRS, INSERM Institut Cochin, Paris, France
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), UBFC Dijon CNRS UMR6302, Dijon, France
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, TN, Italy.
| | - Anne Cammas
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France.
| | - Stefania Millevoi
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Equipe Labellisée Fondation ARC, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France.
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2
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Sun C, Xu X, Chen Z, Zhou F, Wang W, Chen J, Sun M, Wang F, Jiang L, Ji M, Liu S, Xu J, He M, Su B, Liu X, Gao Y, Wei H, Li J, Wang X, Zhao M, Yu J, Ma Y. Selective translational control by PABPC1 phase separation regulates blast crisis and therapy resistance in chronic myeloid leukaemia. Nat Cell Biol 2025; 27:683-695. [PMID: 40102686 DOI: 10.1038/s41556-024-01607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 12/23/2024] [Indexed: 03/20/2025]
Abstract
Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukaemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten patients with CML. Accumulating evidence suggests that translational control is crucial for cancer progression. Our high-throughput CRISPR-Cas9 screening identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML progression in the BC stage. PABPC1 preferentially improved the translation efficiency of multiple leukaemogenic mRNAs with long and highly structured 5' untranslated regions by forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, with minimal effects on normal haematopoiesis. Moreover, we identified two PABPC1 inhibitors that inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identifies PABPC1 as a selective translation enhancing factor in CML-BC, with its genetic or pharmacological inhibition overcoming TKI resistance and suppressed BC progression.
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MESH Headings
- Blast Crisis/genetics
- Blast Crisis/pathology
- Blast Crisis/metabolism
- Blast Crisis/drug therapy
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Animals
- Drug Resistance, Neoplasm/genetics
- Protein Kinase Inhibitors/pharmacology
- Mice
- Poly(A)-Binding Protein I/genetics
- Poly(A)-Binding Protein I/metabolism
- Poly(A)-Binding Protein I/antagonists & inhibitors
- Protein Biosynthesis/drug effects
- Cell Proliferation/drug effects
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Cell Line, Tumor
- Gene Expression Regulation, Leukemic
- Female
- Phase Separation
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Affiliation(s)
- Chenguang Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Xi Xu
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhongyang Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fanqi Zhou
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wen Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Junzhu Chen
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Mengyao Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fang Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Linjia Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ming Ji
- Institute of Materia Medica and Peking Union Medical College, Chinese Academy of Medical Sciences, Tianjin, China
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiayue Xu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Manman He
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bowei Su
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoling Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingdai Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Hui Wei
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jian Li
- Department of Hematology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoshuang Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China.
- State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| | - Meng Zhao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China.
- Key Laboratory of Stem Cells and Tissue Engineering (Ministry of Education), Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China.
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China.
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Klapp V, Gumustekin O, Paggetti J, Moussay E, Largeot A. Assessment of translation rate in leukemic cells and immune cells of the microenvironment by OPP protein synthesis assay. Methods Cell Biol 2024; 189:1-21. [PMID: 39393878 DOI: 10.1016/bs.mcb.2024.06.006] [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] [Indexed: 10/13/2024]
Abstract
Despite being tightly regulated, messenger RNA (mRNA) translation, a manner in which cells control expression of genes and rapidly respond to stimuli, is highly dysfunctional and plastic in pathologies including cancer. Conversely, the investigation of molecular mechanisms whereby mRNA translation becomes aberrant in cancer, as well as inhibition thereof, become critical in developing novel therapeutic approaches. More specifically, in malignancies such as chronic lymphocytic leukemia in which aberrant global and transcript specific translation has been linked with poorer patient outcomes, targeting translation is a relevant approach, with various translation inhibitors under development. Here we elaborate on a protein synthesis assay by flow cytometry, O-propargyl-puromycin, demonstrating global mRNA translation rate with a variety of different applications including cell lines, primary cells or co-culture systems in vitro. This method provides a comprehensive tool in quantifying the rate of global mRNA translation in cancer cells, as well as that of the tumor microenvironment cells, or in response to inhibitory therapeutic agents while offering the possibility to simultaneously assess other cellular markers.
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Affiliation(s)
- Vanessa Klapp
- Tumor Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ozgu Gumustekin
- Tumor Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jerome Paggetti
- Tumor Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Etienne Moussay
- Tumor Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anne Largeot
- Tumor Stroma Interactions Group, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg.
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4
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Reimão-Pinto MM, Castillo-Hair SM, Seelig G, Schier AF. The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568470. [PMID: 38045294 PMCID: PMC10690280 DOI: 10.1101/2023.11.23.568470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The 5' UTRs of mRNAs are critical for translation regulation, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR is sufficient to confer temporal dynamics to translation initiation, and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, DaniO5P, revealed a combined role for 5' UTR length, translation initiation site context, upstream AUGs and sequence motifs on in vivo ribosome recruitment. DaniO5P predicts the activities of 5' UTR isoforms and indicates that modulating 5' UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5' UTR-based translation regulation in early vertebrate development and lays the foundation for identifying the underlying molecular effectors.
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Affiliation(s)
| | - Sebastian M Castillo-Hair
- Department of Electrical & Computer Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Alex F Schier
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington 98195, United States
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