1
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Cao X, Zhang Y, Ding Y, Wan Y. Identification of RNA structures and their roles in RNA functions. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00748-6. [PMID: 38926530 DOI: 10.1038/s41580-024-00748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The development of high-throughput RNA structure profiling methods in the past decade has greatly facilitated our ability to map and characterize different aspects of RNA structures transcriptome-wide in cell populations, single cells and single molecules. The resulting high-resolution data have provided insights into the static and dynamic nature of RNA structures, revealing their complexity as they perform their respective functions in the cell. In this Review, we discuss recent technical advances in the determination of RNA structures, and the roles of RNA structures in RNA biogenesis and functions, including in transcription, processing, translation, degradation, localization and RNA structure-dependent condensates. We also discuss the current understanding of how RNA structures could guide drug design for treating genetic diseases and battling pathogenic viruses, and highlight existing challenges and future directions in RNA structure research.
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Affiliation(s)
- Xinang Cao
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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2
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Volegova MP, Brown LE, Banerjee U, Dries R, Sharma B, Kennedy A, Porco JA, George RE. The MYCN 5' UTR as a therapeutic target in neuroblastoma. Cell Rep 2024; 43:114134. [PMID: 38662542 PMCID: PMC11284644 DOI: 10.1016/j.celrep.2024.114134] [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: 07/27/2023] [Revised: 02/07/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Tumor MYCN amplification is seen in high-risk neuroblastoma, yet direct targeting of this oncogenic transcription factor has been challenging. Here, we take advantage of the dependence of MYCN-amplified neuroblastoma cells on increased protein synthesis to inhibit the activity of eukaryotic translation initiation factor 4A1 (eIF4A1) using an amidino-rocaglate, CMLD012824. Consistent with the role of this RNA helicase in resolving structural barriers in 5' untranslated regions (UTRs), CMLD012824 increased eIF4A1 affinity for polypurine-rich 5' UTRs, including that of the MYCN and associated transcripts with critical roles in cell proliferation. CMLD012824-mediated clamping of eIF4A1 spanned the full lengths of mRNAs, while translational inhibition was mediated through 5' UTR binding in a cap-dependent and -independent manner. Finally, CMLD012824 led to growth inhibition in MYCN-amplified neuroblastoma models without generalized toxicity. Our studies highlight the key role of eIF4A1 in MYCN-amplified neuroblastoma and demonstrate the therapeutic potential of disrupting its function.
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Affiliation(s)
- Marina P Volegova
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lauren E Brown
- Boston University, Center for Molecular Discovery (BU-CMD), Boston, MA, USA; Boston University, Department of Chemistry, Boston, MA, USA
| | - Ushashi Banerjee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ruben Dries
- Boston University School of Medicine, Computational Biomedicine, Boston, MA, USA
| | - Bandana Sharma
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alyssa Kennedy
- Boston Children's Cancer and Blood Disorders Center, Pediatric Hematology/Oncology, Boston, MA, USA
| | - John A Porco
- Boston University, Center for Molecular Discovery (BU-CMD), Boston, MA, USA; Boston University, Department of Chemistry, Boston, MA, USA
| | - Rani E George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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3
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Shichino Y, Yamaguchi T, Kashiwagi K, Mito M, Takahashi M, Ito T, Ingolia NT, Kuba K, Iwasaki S. eIF4A1 enhances LARP1-mediated translational repression during mTORC1 inhibition. Nat Struct Mol Biol 2024:10.1038/s41594-024-01321-7. [PMID: 38773334 DOI: 10.1038/s41594-024-01321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/18/2024] [Indexed: 05/23/2024]
Abstract
Eukaryotic translation initiation factor (eIF)4A-a DEAD-box RNA-binding protein-plays an essential role in translation initiation. Recent reports have suggested helicase-dependent and helicase-independent functions for eIF4A, but the multifaceted roles of eIF4A have not been fully explored. Here we show that eIF4A1 enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA pulldown followed by sequencing revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTORC1 inhibition. This selective interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that deletion of EIF4A1 attenuated the translational repression of TOP mRNAs upon mTORC1 inactivation. Moreover, eIF4A1 increases the interaction between TOP mRNAs and LARP1 and, thus, ensures stronger translational repression upon mTORC1 inhibition. Our data show the multimodality of eIF4A1 in modulating protein synthesis through an inhibitory binding partner and provide a unique example of the repressive role of a universal translational activator.
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Affiliation(s)
- Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kazuhiro Kashiwagi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Mari Takahashi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University Graduate School of Medicine, Akita, Japan
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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4
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Huang J, Zhang L, Yang R, Yao L, Gou J, Cao D, Pan Z, Li D, Pan Y, Zhang W. Eukaryotic translation initiation factor 4A1 in the pathogenesis and treatment of cancers. Front Mol Biosci 2023; 10:1289650. [PMID: 38028556 PMCID: PMC10666758 DOI: 10.3389/fmolb.2023.1289650] [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: 09/06/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Abnormal translate regulation is an important phenomenon in cancer initiation and progression. Eukaryotic translation initiation factor 4A1 (eIF4A1) protein is an ATP-dependent Ribonucleic Acid (RNA) helicase, which is essential for translation and has bidirectional RNA unwinders function. In this review, we discuss the levels of expression, regulatory mechanisms and protein functions of eIF4A1 in different human tumors. eIF4A1 is often involved as a target of microRNAs or long non-coding RNAs during the epithelial-mesenchymal transition, associating with the proliferation and metastasis of tumor cells. eIF4A1 protein exhibits the promising biomarker for rapid diagnosis of pre-cancer lesions, histological phenotypes, clinical staging diagnosis and outcome prediction, which provides a novel strategy for precise medical care and target therapy for patients with tumors at the same time, relevant small molecule inhibitors have also been applied in clinical practice, providing reliable theoretical support and clinical basis for the development of this gene target.
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Affiliation(s)
- Jinghong Huang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Lei Zhang
- Clinical Laboratory, First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, China
| | - Rui Yang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Lixia Yao
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Jinming Gou
- Troops of the People’s Liberation Army, Urumqi, Xinjiang, China
| | - Dongdong Cao
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Zeming Pan
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Dongmei Li
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases, School of Medicine, Shihezi University, Shihezi, Xinjiang, China
| | - Yuanming Pan
- Cancer Research Center, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | - Wei Zhang
- Shihezi People’s Hospital, Shihezi, Xinjiang, China
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5
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Zheng B, Chen X, Ling Q, Cheng Q, Ye S. Role and therapeutic potential of DEAD-box RNA helicase family in colorectal cancer. Front Oncol 2023; 13:1278282. [PMID: 38023215 PMCID: PMC10654640 DOI: 10.3389/fonc.2023.1278282] [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: 08/16/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed and the second cancer-related death worldwide, leading to more than 0.9 million deaths every year. Unfortunately, this disease is changing rapidly to a younger age, and in a more advanced stage when diagnosed. The DEAD-box RNA helicase proteins are the largest family of RNA helicases so far. They regulate almost every aspect of RNA physiological processes, including RNA transcription, editing, splicing and transport. Aberrant expression and critical roles of the DEAD-box RNA helicase proteins have been found in CRC. In this review, we first summarize the protein structure, cellular distribution, and diverse biological functions of DEAD-box RNA helicases. Then, we discuss the distinct roles of DEAD-box RNA helicase family in CRC and describe the cellular mechanism of actions based on recent studies, with an aim to provide future strategies for the treatment of CRC.
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Affiliation(s)
- Bichun Zheng
- Department of Anorectal Surgery, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
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6
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Williams AM, Jolley EA, Santiago-Martínez MG, Chan CX, Gutell RR, Ferry JG, Bevilacqua PC. In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans. RNA (NEW YORK, N.Y.) 2023; 29:1610-1620. [PMID: 37491319 PMCID: PMC10578495 DOI: 10.1261/rna.079687.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/24/2023] [Indexed: 07/27/2023]
Abstract
Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date, such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. With archaeal species being diverse and having many similarities to both bacteria and eukaryotes, the archaea domain has the potential to be an evolutionary bridge. In this study, we introduce a method for probing RNA structure in vivo in the archaea domain of life. We investigated the structure of ribosomal RNA (rRNA) from Methanosarcina acetivorans, a well-studied anaerobic archaeal species, grown with either methanol or acetate. After probing the RNA in vivo with dimethyl sulfate (DMS), Structure-seq2 libraries were generated, sequenced, and analyzed. We mapped the reactivity of DMS onto the secondary structure of the ribosome, which we determined independently with comparative analysis, and confirmed the accuracy of DMS probing in M. acetivorans Accessibility of the rRNA to DMS in the two carbon sources was found to be quite similar, although some differences were found. Overall, this study establishes the Structure-seq2 pipeline in the archaea domain of life and informs about ribosomal structure within M. acetivorans.
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Affiliation(s)
- Allison M Williams
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth A Jolley
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072, Australia
| | - Robin R Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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7
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Obermann W, Azri MFD, Konopka L, Schmidt N, Magari F, Sherman J, Silva LMR, Hermosilla C, Ludewig AH, Houhou H, Haeberlein S, Luo MY, Häcker I, Schetelig MF, Grevelding CG, Schroeder FC, Lau GSK, Taubert A, Rodriguez A, Heine A, Yeo TC, Grünweller A, Taroncher-Oldenburg G. Broad anti-pathogen potential of DEAD box RNA helicase eIF4A-targeting rocaglates. Sci Rep 2023; 13:9297. [PMID: 37291191 PMCID: PMC10250355 DOI: 10.1038/s41598-023-35765-6] [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: 11/23/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Inhibition of eukaryotic initiation factor 4A has been proposed as a strategy to fight pathogens. Rocaglates exhibit the highest specificities among eIF4A inhibitors, but their anti-pathogenic potential has not been comprehensively assessed across eukaryotes. In silico analysis of the substitution patterns of six eIF4A1 aa residues critical to rocaglate binding, uncovered 35 variants. Molecular docking of eIF4A:RNA:rocaglate complexes, and in vitro thermal shift assays with select recombinantly expressed eIF4A variants, revealed that sensitivity correlated with low inferred binding energies and high melting temperature shifts. In vitro testing with silvestrol validated predicted resistance in Caenorhabditis elegans and Leishmania amazonensis and predicted sensitivity in Aedes sp., Schistosoma mansoni, Trypanosoma brucei, Plasmodium falciparum, and Toxoplasma gondii. Our analysis further revealed the possibility of targeting important insect, plant, animal, and human pathogens with rocaglates. Finally, our findings might help design novel synthetic rocaglate derivatives or alternative eIF4A inhibitors to fight pathogens.
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Affiliation(s)
- Wiebke Obermann
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | | | - Leonie Konopka
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Nina Schmidt
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Julian Sherman
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Liliana M R Silva
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Carlos Hermosilla
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Andreas H Ludewig
- Boyce Thompson Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Hicham Houhou
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Simone Haeberlein
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mona Yiting Luo
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Irina Häcker
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Marc F Schetelig
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph G Grevelding
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Anja Taubert
- Institute of Parasitology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Ana Rodriguez
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany
| | - Tiong Chia Yeo
- Sarawak Biodiversity Centre, Kuching, Sarawak, Malaysia.
| | - Arnold Grünweller
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marburg, Germany.
| | - Gaspar Taroncher-Oldenburg
- Sarawak Biodiversity Centre, Kuching, Sarawak, Malaysia.
- Gaspar Taroncher Consulting, Philadelphia, PA, USA.
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8
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Schmidt T, Dabrowska A, Waldron JA, Hodge K, Koulouras G, Gabrielsen M, Munro J, Tack DC, Harris G, McGhee E, Scott D, Carlin L, Huang D, Le Quesne J, Zanivan S, Wilczynska A, Bushell M. eIF4A1-dependent mRNAs employ purine-rich 5'UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation. Nucleic Acids Res 2023; 51:1859-1879. [PMID: 36727461 PMCID: PMC9976904 DOI: 10.1093/nar/gkad030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/20/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Altered eIF4A1 activity promotes translation of highly structured, eIF4A1-dependent oncogene mRNAs at root of oncogenic translational programmes. It remains unclear how these mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate their preferential translation. Here, we show that single-stranded RNA sequence motifs specifically activate eIF4A1 unwinding allowing local RNA structural rearrangement and translation of eIF4A1-dependent mRNAs in cells. Our data demonstrate that eIF4A1-dependent mRNAs contain AG-rich motifs within their 5'UTR which specifically activate eIF4A1 unwinding of local RNA structure to facilitate translation. This mode of eIF4A1 regulation is used by mRNAs encoding components of mTORC-signalling and cell cycle progression, and renders these mRNAs particularly sensitive to eIF4A1-inhibition. Mechanistically, we show that binding of eIF4A1 to AG-rich sequences leads to multimerization of eIF4A1 with eIF4A1 subunits performing distinct enzymatic activities. Our structural data suggest that RNA-binding of multimeric eIF4A1 induces conformational changes in the RNA resulting in an optimal positioning of eIF4A1 proximal to the RNA duplex enabling efficient unwinding. Our data proposes a model in which AG-motifs in the 5'UTR of eIF4A1-dependent mRNAs specifically activate eIF4A1, enabling assembly of the helicase-competent multimeric eIF4A1 complex, and positioning these complexes proximal to stable localised RNA structure allowing ribosomal subunit scanning.
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Affiliation(s)
- Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Adrianna Dabrowska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
- Department of Urology, University of California, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Kelly Hodge
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Grigorios Koulouras
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Mads Gabrielsen
- MVLS Structural Biology and Biophysical Characterisation Facility, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - June Munro
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David C Tack
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI 49503, USA
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, UK
| | - Ewan McGhee
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, UK
- ISIS Spallation Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, DidcotOX11 0QX, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington LE12 5RD, UK
| | - Leo M Carlin
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Danny Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
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9
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Jagadeesan SK, Al-gafari M, Wang J, Takallou S, Allard D, Hajikarimlou M, Kazmirchuk TDD, Moteshareie H, Said KB, Nokhbeh R, Smith M, Samanfar B, Golshani A. DBP7 and YRF1-6 Are Involved in Cell Sensitivity to LiCl by Regulating the Translation of PGM2 mRNA. Int J Mol Sci 2023; 24:ijms24021785. [PMID: 36675300 PMCID: PMC9864399 DOI: 10.3390/ijms24021785] [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: 11/15/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023] Open
Abstract
Lithium chloride (LiCl) has been widely researched and utilized as a therapeutic option for bipolar disorder (BD). Several pathways, including cell signaling and signal transduction pathways in mammalian cells, are shown to be regulated by LiCl. LiCl can negatively control the expression and activity of PGM2, a phosphoglucomutase that influences sugar metabolism in yeast. In the presence of galactose, when yeast cells are challenged by LiCl, the phosphoglucomutase activity of PGM2p is decreased, causing an increase in the concentration of toxic galactose metabolism intermediates that result in cell sensitivity. Here, we report that the null yeast mutant strains DBP7∆ and YRF1-6∆ exhibit increased LiCl sensitivity on galactose-containing media. Additionally, we demonstrate that DBP7 and YRF1-6 modulate the translational level of PGM2 mRNA, and the observed alteration in translation seems to be associated with the 5'-untranslated region (UTR) of PGM2 mRNA. Furthermore, we observe that DBP7 and YRF1-6 influence, to varying degrees, the translation of other mRNAs that carry different 5'-UTR secondary structures.
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Affiliation(s)
- Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Houman Moteshareie
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Kamaledin B. Said
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Reza Nokhbeh
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Myron Smith
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence:
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10
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Rubio A, Garland GD, Sfakianos A, Harvey RF, Willis AE. Aberrant protein synthesis and cancer development: The role of canonical eukaryotic initiation, elongation and termination factors in tumorigenesis. Semin Cancer Biol 2022; 86:151-165. [PMID: 35487398 DOI: 10.1016/j.semcancer.2022.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023]
Abstract
In tumourigenesis, oncogenes or dysregulated tumour suppressor genes alter the canonical translation machinery leading to a reprogramming of the translatome that, in turn, promotes the translation of selected mRNAs encoding proteins involved in proliferation and metastasis. It is therefore unsurprising that abnormal expression levels and activities of eukaryotic initiation factors (eIFs), elongation factors (eEFs) or termination factors (eRFs) are associated with poor outcome for patients with a wide range of cancers. In this review we discuss how RNA binding proteins (RBPs) within the canonical translation factor machinery are dysregulated in cancers and how targeting such proteins is leading to new therapeutic avenues.
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Affiliation(s)
- Angela Rubio
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Gavin D Garland
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Aristeidis Sfakianos
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Rd, Cambridge CB2 1QR, UK.
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11
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Shin S, Solorzano J, Liauzun M, Pyronnet S, Bousquet C, Martineau Y. Translational alterations in pancreatic cancer: a central role for the integrated stress response. NAR Cancer 2022; 4:zcac031. [PMID: 36325577 PMCID: PMC9615149 DOI: 10.1093/narcan/zcac031] [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: 07/29/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
mRNA translation is a key mechanism for cancer cell proliferation and stress adaptation. Regulation of this machinery implicates upstream pathways such as PI3K/AKT/mTOR, RAS/MEK/ERK and the integrated stress response (ISR), principally coordinating the translation initiation step. During the last decade, dysregulation of the mRNA translation process in pancreatic cancer has been widely reported, and shown to critically impact on cancer initiation, development and survival. This includes translation dysregulation of mRNAs encoding oncogenes and tumor suppressors. Hence, cancer cells survive a stressful microenvironment through a flexible regulation of translation initiation for rapid adaptation. The ISR pathway has an important role in chemoresistance and shows high potential therapeutic interest. Despite the numerous translational alterations reported in pancreatic cancer, their consequences are greatly underestimated. In this review, we summarize the different translation dysregulations described in pancreatic cancer, which make it invulnerable, as well as the latest drug discoveries bringing a glimmer of hope.
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Affiliation(s)
- Sauyeun Shin
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III Paul Sabatier, ERL5294 CNRS, Toulouse, France,Equipe labellisée Ligue Contre le Cancer
| | - Jacobo Solorzano
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III Paul Sabatier, ERL5294 CNRS, Toulouse, France,Equipe labellisée Ligue Contre le Cancer
| | - Mehdi Liauzun
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III Paul Sabatier, ERL5294 CNRS, Toulouse, France,Equipe labellisée Ligue Contre le Cancer
| | - Stéphane Pyronnet
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III Paul Sabatier, ERL5294 CNRS, Toulouse, France,Equipe labellisée Ligue Contre le Cancer
| | - Corinne Bousquet
- Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM U1037, Université Toulouse III Paul Sabatier, ERL5294 CNRS, Toulouse, France,Equipe labellisée Ligue Contre le Cancer
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12
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Ali ES, Lipońska A, O'Hara BP, Amici DR, Torno MD, Gao P, Asara JM, Yap MNF, Mendillo ML, Ben-Sahra I. The mTORC1-SLC4A7 axis stimulates bicarbonate import to enhance de novo nucleotide synthesis. Mol Cell 2022; 82:3284-3298.e7. [PMID: 35772404 PMCID: PMC9444906 DOI: 10.1016/j.molcel.2022.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/15/2022] [Accepted: 06/07/2022] [Indexed: 12/12/2022]
Abstract
Bicarbonate (HCO3-) ions maintain pH homeostasis in eukaryotic cells and serve as a carbonyl donor to support cellular metabolism. However, whether the abundance of HCO3- is regulated or harnessed to promote cell growth is unknown. The mechanistic target of rapamycin complex 1 (mTORC1) adjusts cellular metabolism to support biomass production and cell growth. We find that mTORC1 stimulates the intracellular transport of HCO3- to promote nucleotide synthesis through the selective translational regulation of the sodium bicarbonate cotransporter SLC4A7. Downstream of mTORC1, SLC4A7 mRNA translation required the S6K-dependent phosphorylation of the translation factor eIF4B. In mTORC1-driven cells, loss of SLC4A7 resulted in reduced cell and tumor growth and decreased flux through de novo purine and pyrimidine synthesis in human cells and tumors without altering the intracellular pH. Thus, mTORC1 signaling, through the control of SLC4A7 expression, harnesses environmental bicarbonate to promote anabolic metabolism, cell biomass, and growth.
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Affiliation(s)
- Eunus S Ali
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Anna Lipońska
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael D Torno
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mee-Ngan F Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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13
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Luo Y, Zhang B, Geng N, Sun S, Song X, Chen J, Zhang H. Insights into the hepatotoxicity of pyrene and 1-chloropyrene using an integrated approach of metabolomics and transcriptomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154637. [PMID: 35307418 DOI: 10.1016/j.scitotenv.2022.154637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The toxicity of pyrene (Pyr) and its chlorinated species have not be comprehensively and clearly elucidated. In this study, an integrated approach of metabolomics and transcriptomics were applied to evaluate the hepatotoxicity of Pyr and 1-chloropyrene (1-Cl-Pyr) at human exposure level, using human L02 hepatocytes. After 24 h exposure to Pyr and 1-Cl-Pyr at 5-500 nM, cell viability was not significantly changed. Transcriptomics results showed that exposure to Pyr and 1-Cl-Pyr at 5 and 50 nM obviously altered the gene expression profiles, but did not significantly induce the expression of genes strongly related to the activation of aryl hydrocarbon receptor (AhR), such as CYP1A1, CYP1B1, AHR, ARNT. Pyr and 1-Cl-Pyr both induced a notable metabolic perturbation to L02 cells. Glycerophospholipid metabolism was found to be the most significantly perturbed pathway after exposure to Pyr and 1-Cl-Pyr, indicating their potential damage to the cell membrane. The other significantly perturbed pathways were identified to be oxidative phosphorylation (OXPHOS), glycolysis, and fatty acid β oxidation, all of which are related to energy production. Exposure to Pyr at 5 and 50 nM induced the up-regulation of fatty acid β oxidation and OXPHOS. The similar result was observed after exposure to 5 nM 1-Cl-Pyr. In contrast, exposure to 50 nM 1-Cl-Pyr induced the down-regulation of OXPHOS by inhibiting the activity of complex I. The obtained results suggested that the modes of action of Pyr and 1-Cl-Pyr on energy production remarkably varied not only with molecular structure change but also with exposure concentration.
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Affiliation(s)
- Yun Luo
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoqin Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ningbo Geng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Shuai Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyao Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jiping Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haijun Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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14
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Wu KL, Huang YC, Wu YY, Chang CY, Chang YY, Chiang HH, Liu LX, Tsai YM, Hung JY. Characterization of the Oncogenic Potential of Eukaryotic Initiation Factor 4A1 in Lung Adenocarcinoma via Cell Cycle Regulation and Immune Microenvironment Reprogramming. BIOLOGY 2022; 11:biology11070975. [PMID: 36101357 PMCID: PMC9311917 DOI: 10.3390/biology11070975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/14/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
Lung adenocarcinoma (LUAD) is a common type of lung cancer. Although the diagnosis and treatment of LUAD have significantly improved in recent decades, the survival for advanced LUAD is still poor. It is necessary to identify more targets for developing potential agents against LUAD. This study explored the dysregulation of translation initiation factors, specifically eukaryotic initiation factors 4A1 (EIF4A1) and EIF4A2, in developing LUAD, as well as their underlying mechanisms. We found that the expression of EIF4A1, but not EIF4A2, was higher in tumor tissue and associated with poor clinical outcomes in LUAD patients. Elevated expression of EIF4H with poor prognosis may potentiate the oncogenic role of EIF4A1. Functional enrichment analysis revealed that upregulation of EIF4A1 was related to cell cycle regulation and DNA repair. The oncogenic effect of EIF4A1 was further elucidated by Gene Set Variation Analysis (GSVA). The GSVA score of the gene set positively correlated with EIF4A1 was higher in tumors and significantly associated with worse survival. In the meantime, gene set enrichment analysis (GSEA) also indicated that elevated EIF4A1 expression in LUAD patients was associated with a decreased infiltration score for immune cells by reducing anticancer immune cell types and recruiting immunosuppressive cells. Consistent with the results, the GSVA score of genes whose expression was negatively correlated with EIF4A1 was lower in the tumor tissue of LUAD cases with worse clinical outcomes and was strongly associated with the disequilibrium of anti-cancer immunity by recruiting anticancer immune cells. Based on the results from the present study, we hypothesize that the dysregulation of EIF4A1 might be involved in the pathophysiology of LUAD development by promoting cancer growth and changing the tumor immune microenvironment. This can be used to develop potential diagnostic biomarkers or therapeutic targets for LUAD.
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Affiliation(s)
- Kuan-Li Wu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (K.-L.W.); (Y.-C.H.); (C.-Y.C.); (L.-X.L.)
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (Y.-Y.C.); (Y.-M.T.)
| | - Yung-Chi Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (K.-L.W.); (Y.-C.H.); (C.-Y.C.); (L.-X.L.)
| | - Yu-Yuan Wu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Chao-Yuan Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (K.-L.W.); (Y.-C.H.); (C.-Y.C.); (L.-X.L.)
- Department of Anatomy, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yung-Yun Chang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (Y.-Y.C.); (Y.-M.T.)
- Division of General Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Hung-Hsing Chiang
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Lian-Xiu Liu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (K.-L.W.); (Y.-C.H.); (C.-Y.C.); (L.-X.L.)
| | - Ying-Ming Tsai
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (Y.-Y.C.); (Y.-M.T.)
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jen-Yu Hung
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; (Y.-Y.C.); (Y.-M.T.)
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-3121101 (ext. 5651)
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15
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Fritz SE, Ranganathan S, Wang CD, Hogg JR. An alternative UPF1 isoform drives conditional remodeling of nonsense-mediated mRNA decay. EMBO J 2022; 41:e108898. [PMID: 35403729 PMCID: PMC9108617 DOI: 10.15252/embj.2021108898] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 12/11/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway monitors translation termination in order to degrade transcripts with premature stop codons and regulate thousands of human genes. Here, we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1LL , enables condition-dependent remodeling of NMD specificity. Previous studies indicate that the extension of a conserved regulatory loop in the UPF1LL helicase core confers a decreased propensity to dissociate from RNA upon ATP hydrolysis relative to UPF1SL , the major UPF1 isoform. Using biochemical and transcriptome-wide approaches, we find that UPF1LL can circumvent the protective RNA binding proteins PTBP1 and hnRNP L to preferentially bind and down-regulate transcripts with long 3'UTRs normally shielded from NMD. Unexpectedly, UPF1LL supports induction of NMD on new populations of substrate mRNAs in response to activation of the integrated stress response and impaired translation efficiency. Thus, while canonical NMD is abolished by moderate translational repression, UPF1LL activity is enhanced, offering the possibility to rapidly rewire NMD specificity in response to cellular stress.
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Affiliation(s)
- Sarah E Fritz
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - Soumya Ranganathan
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - Clara D Wang
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
| | - J Robert Hogg
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMDUSA
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16
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Ferrero-Serrano Á, Sylvia MM, Forstmeier PC, Olson AJ, Ware D, Bevilacqua PC, Assmann SM. Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. Genome Biol 2022; 23:101. [PMID: 35440059 PMCID: PMC9017077 DOI: 10.1186/s13059-022-02656-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.” Results We experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. Conclusion We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02656-4.
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Affiliation(s)
- Ángel Ferrero-Serrano
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Megan M Sylvia
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Peter C Forstmeier
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Andrew J Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Philip C Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA. .,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
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17
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Epigenetic regulation of EIF4A1 through DNA methylation and an oncogenic role of eIF4A1 through BRD2 signaling in prostate cancer. Oncogene 2022; 41:2778-2785. [PMID: 35361883 PMCID: PMC9215223 DOI: 10.1038/s41388-022-02272-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/21/2022] [Accepted: 03/08/2022] [Indexed: 01/10/2023]
Abstract
In prostate cancers, elongation initiation factor 4A1 (eIF4A1) supports an oncogenic translation program and is highly expressed, but its role remains elusive. By use of human specimens and cell models, we addressed the role of eIF4A1 in prostate cancer in vitro and in vivo. EIF4A1 expression, as determined by mRNA and protein levels, was higher in primary prostate cancers relative to normal prostate tissue. Also, for primary prostate cancers, elevated mRNA levels of EIF4A1 correlated with DNA hypomethylation levels in the CpG-rich island of EIF4A1. Using a DNMT3a CRISPR-Cas9-based tool for specific targeting of DNA methylation, we characterized, in human prostate cancer cells, the epigenetic regulation of EIF4A1 transcripts through DNA methylation in the CpG-rich island of EIF4A1. Next, we investigated the oncogenic effect of EIF4A1 on cancer cell proliferation in vitro and tumor growth in vivo. For prostate cancer cells, EIF4A1 heterozygous knockout or knockdown inhibited protein translation and tumor growth. In addition, using RNA immunoprecipitation with RNA sequencing, we discovered the eIF4A1-mediated translational regulation of the oncogene BRD2, which contains the most enriched eIF4A1-binding motifs in its 5’ untranslated region, establishing an eIF4A1-BRD2 axis for oncogenic translation. Finally, we found a positive correlation between expression levels of eIF4A1 and BRD2 in primary prostate cancers. Our results demonstrate, for prostate cancer cells, epigenetic regulation of EIF4A1 transcripts through DNA methylation and an oncogenic roles of eIF4A1 through BRD2 signaling.
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18
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Biswas B, Guemiri R, Cadix M, Labbé CM, Chakraborty A, Dutertre M, Robert C, Vagner S. Differential Effects on the Translation of Immune-Related Alternatively Polyadenylated mRNAs in Melanoma and T Cells by eIF4A Inhibition. Cancers (Basel) 2022; 14:cancers14051177. [PMID: 35267483 PMCID: PMC8909304 DOI: 10.3390/cancers14051177] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Targeting the translation initiation complex eIF4F, which binds the 5' cap of mRNAs, is a promising anti-cancer approach. Silvestrol, a small molecule inhibitor of eIF4A, the RNA helicase component of eIF4F, inhibits the translation of the mRNA encoding the signal transducer and activator of transcription 1 (STAT1) transcription factor, which, in turn, reduces the transcription of the gene encoding one of the major immune checkpoint proteins, i.e., programmed death ligand-1 (PD-L1) in melanoma cells. A large proportion of human genes produce multiple mRNAs differing in their 3'-ends through the use of alternative polyadenylation (APA) sites, which, when located in alternative last exons, can generate protein isoforms, as in the STAT1 gene. Here, we provide evidence that the STAT1α, but not STAT1β protein isoform generated by APA, is required for silvestrol-dependent inhibition of PD-L1 expression in interferon-γ-treated melanoma cells. Using polysome profiling in activated T cells we find that, beyond STAT1, eIF4A inhibition downregulates the translation of some important immune-related mRNAs, such as the ones encoding TIM-3, LAG-3, IDO1, CD27 or CD137, but with little effect on the ones for BTLA and ADAR-1 and no effect on the ones encoding CTLA-4, PD-1 and CD40-L. We next apply RT-qPCR and 3'-seq (RNA-seq focused on mRNA 3' ends) on polysomal RNAs to analyze in a high throughput manner the effect of eIF4A inhibition on the translation of APA isoforms. We identify about 150 genes, including TIM-3, LAG-3, AHNAK and SEMA4D, for which silvestrol differentially inhibits the translation of APA isoforms in T cells. It is therefore crucial to consider 3'-end mRNA heterogeneity in the understanding of the anti-tumor activities of eIF4A inhibitors.
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Affiliation(s)
- Biswendu Biswas
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, 91401 Orsay, France; (B.B.); (M.C.); (C.M.L.); (A.C.); (M.D.)
- Biologie de l’ARN, Signalisation et Cancer, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, 91401 Orsay, France
- Équipe Labellisée Ligue Contre le Cancer, 91401 Orsay, France
- INSERM U981, Gustave Roussy Cancer Campus, 94805 Villejuif, France;
- Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94270 Kremlin-Bicêtre, France
| | - Ramdane Guemiri
- INSERM U981, Gustave Roussy Cancer Campus, 94805 Villejuif, France;
- Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94270 Kremlin-Bicêtre, France
| | - Mandy Cadix
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, 91401 Orsay, France; (B.B.); (M.C.); (C.M.L.); (A.C.); (M.D.)
- Biologie de l’ARN, Signalisation et Cancer, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, 91401 Orsay, France
- Équipe Labellisée Ligue Contre le Cancer, 91401 Orsay, France
| | - Céline M. Labbé
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, 91401 Orsay, France; (B.B.); (M.C.); (C.M.L.); (A.C.); (M.D.)
- Biologie de l’ARN, Signalisation et Cancer, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, 91401 Orsay, France
- Équipe Labellisée Ligue Contre le Cancer, 91401 Orsay, France
| | - Alina Chakraborty
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, 91401 Orsay, France; (B.B.); (M.C.); (C.M.L.); (A.C.); (M.D.)
- Biologie de l’ARN, Signalisation et Cancer, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, 91401 Orsay, France
- Équipe Labellisée Ligue Contre le Cancer, 91401 Orsay, France
| | - Martin Dutertre
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, 91401 Orsay, France; (B.B.); (M.C.); (C.M.L.); (A.C.); (M.D.)
- Biologie de l’ARN, Signalisation et Cancer, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, 91401 Orsay, France
- Équipe Labellisée Ligue Contre le Cancer, 91401 Orsay, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, 94805 Villejuif, France;
- Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94270 Kremlin-Bicêtre, France
- Correspondence: (C.R.); (S.V.)
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, 91401 Orsay, France; (B.B.); (M.C.); (C.M.L.); (A.C.); (M.D.)
- Biologie de l’ARN, Signalisation et Cancer, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, 91401 Orsay, France
- Équipe Labellisée Ligue Contre le Cancer, 91401 Orsay, France
- Correspondence: (C.R.); (S.V.)
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19
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Oertlin C, Watt K, Ristau J, Larsson O. Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:243-268. [PMID: 35119670 DOI: 10.1007/978-1-0716-1920-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
mRNA translation plays a critical role in determining proteome composition. In health, regulation of mRNA translation facilitates rapid gene expression responses to intra- and extracellular signals. Moreover, dysregulated mRNA translation is a common feature in disease states, including neurological disorders and cancer. Yet, most studies of gene expression focus on analysis of mRNA levels, leaving variations in translational efficiencies largely uncharacterized. Here, we outline procedures to identify mRNA-selective alterations in translational efficiencies on a transcriptome-wide scale using the anota2seq package. Anota2seq compares expression data originating from translated mRNA to data from matched total mRNA to identify changes in translated mRNA not paralleled by corresponding changes in total mRNA (interpreted as changes in translational efficiencies impacting protein levels), congruent changes in total and translated mRNA (interpreted as changes in transcription and/or mRNA stability), and changes in total mRNA not paralleled by corresponding alterations in translated mRNA (interpreted as translational buffering). To illustrate the functionality of the anota2seq analysis package, we demonstrate a detailed analysis using a polysome-profiling data set quantified by RNA sequencing, revealing that estrogen receptor α modulates gene expression via a type of translational buffering termed offsetting. Notably, this anota2seq analysis procedure is also applicable to ribosome-profiling (RiboSeq) data sets and can be adapted to a variety of other data types and experimental contexts. Finally, we provide guidance for extending anota2seq analysis to examine associations between untranslated regions and altered translational efficiencies as well as targeted cellular functions to gain insights into mechanisms and phenotypic consequences of altered mRNA translation. Thus, this step-by-step manual allows users to interrogate selective changes in mRNA translation on a transcriptome-wide scale using the Bioconductor package anota2seq.
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Affiliation(s)
- Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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20
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Xue C, Gu X, Li G, Bao Z, Li L. Expression and Functional Roles of Eukaryotic Initiation Factor 4A Family Proteins in Human Cancers. Front Cell Dev Biol 2021; 9:711965. [PMID: 34869305 PMCID: PMC8640450 DOI: 10.3389/fcell.2021.711965] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/05/2021] [Indexed: 01/11/2023] Open
Abstract
The dysregulation of mRNA translation is common in malignancies and may lead to tumorigenesis and progression. Eukaryotic initiation factor 4A (eIF4A) proteins are essential for translation, exhibit bidirectional RNA helicase function, and act as RNA-dependent ATPases. In this review, we explored the predicted structures of the three eIF4A isoforms (eIF4A1, eIF4A2, and eIF4A3), and discussed possible explanations for which function during different translation stages (initiation, mRNA localization, export, and mRNA splicing). These proteins also frequently served as targets of microRNAs (miRNAs) or long noncoding RNAs (lncRNAs) to mediate epithelial-mesenchymal transition (EMT), which was associated with tumor cell invasion and metastasis. To define the differential expression of eIF4A family members, we applied the Tumor Immune Estimation Resource website. We figured out that the eIF4A family genes were differently expressed in specific cancer types. We also found that the level of the eIF4A family genes were associated with abundant immune cells infiltration and tumor purity. The associations between eIF4A proteins and cancer patient clinicopathological features suggested that eIF4A proteins might serve as biomarkers for early tumor diagnosis, histological classification, and clinical grading/staging, providing new tools for precise and individualized cancer treatment.
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Affiliation(s)
- Chen Xue
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ganglei Li
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhengyi Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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21
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Busa VF, Favorov AV, Fertig EJ, Leung AK. Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding. CELL REPORTS METHODS 2021; 1:100088. [PMID: 35474897 PMCID: PMC9017189 DOI: 10.1016/j.crmeth.2021.100088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/23/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022]
Abstract
Molecular interactions at identical transcriptomic locations or at proximal but non-overlapping sites can mediate RNA modification and regulation, necessitating tools to uncover these spatial relationships. We present nearBynding, a flexible algorithm and software pipeline that models spatial correlation between transcriptome-wide tracks from diverse data types. nearBynding can process and correlate interval as well as continuous data and incorporate experimentally derived or in silico predicted transcriptomic tracks. nearBynding offers visualization functions for its statistics to identify colocalizations and adjacent features. We demonstrate the application of nearBynding to correlate RNA-binding protein (RBP) binding preferences with other RBPs, RNA structure, or RNA modification. By cross-correlating RBP binding and RNA structure data, we demonstrate that nearBynding recapitulates known RBP binding to structural motifs and provides biological insights into RBP binding preference of G-quadruplexes. nearBynding is available as an R/Bioconductor package and can run on a personal computer, making correlation of transcriptomic features broadly accessible.
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Affiliation(s)
- Veronica F. Busa
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Alexander V. Favorov
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elana J. Fertig
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21205, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21205, USA
| | - Anthony K.L. Leung
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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22
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Radecki P, Uppuluri R, Deshpande K, Aviran S. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites. RNA Biol 2021; 18:521-536. [PMID: 34606413 PMCID: PMC8677038 DOI: 10.1080/15476286.2021.1971382] [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] [Indexed: 10/31/2022] Open
Abstract
RNA molecules are known to fold into specific structures which often play a central role in their functions and regulation. In silico folding of RNA transcripts, especially when assisted with structure profiling (SP) data, is capable of accurately elucidating relevant structural conformations. However, such methods scale poorly to the swaths of SP data generated by transcriptome-wide experiments, which are becoming more commonplace and advancing our understanding of RNA structure and its regulation at global and local levels. This has created a need for tools capable of rapidly deriving structural assessments from SP data in a scalable manner. One such tool we previously introduced that aims to process such data is patteRNA, a statistical learning algorithm capable of rapidly mining big SP datasets for structural elements. Here, we present a reformulation of patteRNA's pattern recognition scheme that sees significantly improved precision without major compromises to computational overhead. Specifically, we developed a data-driven logistic classifier which interprets patteRNA's statistical characterizations of SP data in addition to local sequence properties as measured with a nearest neighbour thermodynamic model. Application of the classifier to human structurome data reveals a marked association between detected stem-loops and RNA binding protein (RBP) footprints. The results of our application demonstrate that upwards of 30% of RBP footprints occur within loops of stable stem-loop elements. Overall, our work arrives at a rapid and accurate method for automatically detecting families of RNA structure motifs and demonstrates the functional relevance of identifying them transcriptome-wide.
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Affiliation(s)
- Pierce Radecki
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
| | - Rahul Uppuluri
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
| | - Kaustubh Deshpande
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
| | - Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California, Davis, CA, USA
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23
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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24
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Radecki P, Uppuluri R, Aviran S. Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets. NAR Genom Bioinform 2021; 3:lqab073. [PMID: 34447931 PMCID: PMC8384053 DOI: 10.1093/nargab/lqab073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
The functions of RNA are often tied to its structure, hence analyzing structure is of significant interest when studying cellular processes. Recently, large-scale structure probing (SP) studies have enabled assessment of global structure-function relationships via standard data summarizations or local folding. Here, we approach structure quantification from a hairpin-centric perspective where putative hairpins are identified in SP datasets and used as a means to capture local structural effects. This has the advantage of rapid processing of big (e.g. transcriptome-wide) data as RNA folding is circumvented, yet it captures more information than simple data summarizations. We reformulate a statistical learning algorithm we previously developed to significantly improve precision of hairpin detection, then introduce a novel nucleotide-wise measure, termed the hairpin-derived structure level (HDSL), which captures local structuredness by accounting for the presence of likely hairpin elements. Applying HDSL to data from recent studies recapitulates, strengthens and expands on their findings which were obtained by more comprehensive folding algorithms, yet our analyses are orders of magnitude faster. These results demonstrate that hairpin detection is a promising avenue for global and rapid structure-function analysis, furthering our understanding of RNA biology and the principal features which drive biological insights from SP data.
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Affiliation(s)
- Pierce Radecki
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Rahul Uppuluri
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
| | - Sharon Aviran
- Biomedical Engineering Department and Genome Center, University of California at Davis, Davis, CA 95616, USA
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25
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Wilmore S, Rogers-Broadway KR, Taylor J, Lemm E, Fell R, Stevenson FK, Forconi F, Steele AJ, Coldwell M, Packham G, Yeomans A. Targeted inhibition of eIF4A suppresses B-cell receptor-induced translation and expression of MYC and MCL1 in chronic lymphocytic leukemia cells. Cell Mol Life Sci 2021; 78:6337-6349. [PMID: 34398253 PMCID: PMC8429177 DOI: 10.1007/s00018-021-03910-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022]
Abstract
Signaling via the B-cell receptor (BCR) is a key driver and therapeutic target in chronic lymphocytic leukemia (CLL). BCR stimulation of CLL cells induces expression of eIF4A, an initiation factor important for translation of multiple oncoproteins, and reduces expression of PDCD4, a natural inhibitor of eIF4A, suggesting that eIF4A may be a critical nexus controlling protein expression downstream of the BCR in these cells. We, therefore, investigated the effect of eIF4A inhibitors (eIF4Ai) on BCR-induced responses. We demonstrated that eIF4Ai (silvestrol and rocaglamide A) reduced anti-IgM-induced global mRNA translation in CLL cells and also inhibited accumulation of MYC and MCL1, key drivers of proliferation and survival, respectively, without effects on upstream signaling responses (ERK1/2 and AKT phosphorylation). Analysis of normal naïve and non-switched memory B cells, likely counterparts of the two main subsets of CLL, demonstrated that basal RNA translation was higher in memory B cells, but was similarly increased and susceptible to eIF4Ai-mediated inhibition in both. We probed the fate of MYC mRNA in eIF4Ai-treated CLL cells and found that eIF4Ai caused a profound accumulation of MYC mRNA in anti-IgM treated cells. This was mediated by MYC mRNA stabilization and was not observed for MCL1 mRNA. Following drug wash-out, MYC mRNA levels declined but without substantial MYC protein accumulation, indicating that stabilized MYC mRNA remained blocked from translation. In conclusion, BCR-induced regulation of eIF4A may be a critical signal-dependent nexus for therapeutic attack in CLL and other B-cell malignancies, especially those dependent on MYC and/or MCL1.
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MESH Headings
- Antibodies, Anti-Idiotypic/pharmacology
- Benzofurans/pharmacology
- Cells, Cultured
- Eukaryotic Initiation Factor-4A/antagonists & inhibitors
- Eukaryotic Initiation Factor-4A/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/metabolism
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Protein Biosynthesis/drug effects
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA Stability/drug effects
- RNA, Messenger/metabolism
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/drug effects
- Triterpenes/pharmacology
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Affiliation(s)
- Sarah Wilmore
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Karly-Rai Rogers-Broadway
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Joe Taylor
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Elizabeth Lemm
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Rachel Fell
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Freda K Stevenson
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Francesco Forconi
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Andrew J Steele
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Mark Coldwell
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK.
| | - Alison Yeomans
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
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26
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Tyagi V, Parihar V, Singh D, Kapoor S, Kapoor M. The DEAD-box RNA helicase eIF4A1 interacts with the SWI2/SNF2-related chromatin remodelling ATPase DDM1 in the moss Physcomitrella. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140592. [PMID: 33359411 DOI: 10.1016/j.bbapap.2020.140592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/27/2022]
Abstract
eIF4A is a DEAD box containing RNA helicase that plays crucial roles in regulating translation initiation, growth and abiotic stress tolerance in plants. It also functions as an ATP-dependent RNA binding protein to curb granule formation by limiting RNA-RNA interactions that promote RNA condensation and formation of ribonucleoprotein particles in vivo. Helicase activity of eIF4A is known to be dictated by its binding partners. Proteins interacting with eIF4A have been identified across land plants. In monocots a close link between eIF4A regulated processes and DNA methylation in epigenetic regulation of plant development is inferred from interaction between OseIF4A and the de novo methyltransferase OsDRM2 and loss-of-function studies of these genes in Oryza sativa and Brachypodium distachyon. In the moss Physcomitrella patens, eIF4A1 encoded by Pp3c6_1080V3.1 interacts with the heterogeneous nuclear ribonucleoprotein (hnRNP) PpLIF2L1, homolog of which in Arabidopsis regulates transcription of stress-responsive genes. In this study, using different protein-protein interaction methods, targeted gene knockout strategy and quantitative expression analysis we show genetic interaction between PpeIF4A1 and the putative nucleosome remodeler protein PpDDM1 and between PpDDM1 and PpLIF2L1 in vivo. Stress-induced co-expression of PpeIF4A1, PpDDM1 and PpLIF2L1, their roles in salt stress tolerance and differences in subnuclear distribution of PpLIF2L1 in ppeif4a1 cells in comparison to wild type suggest existence of a regulatory network comprising of RNA helicases, chromatin remodelling proteins and hnRNP active in stress-responsive biological processes in P. patens.
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Affiliation(s)
- Vidhi Tyagi
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Vimala Parihar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus Benito Juarez Road, New Delhi 110021, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India.
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27
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Winnard PT, Vesuna F, Raman V. Targeting host DEAD-box RNA helicase DDX3X for treating viral infections. Antiviral Res 2020; 185:104994. [PMID: 33301755 DOI: 10.1016/j.antiviral.2020.104994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
Abstract
DDX3X or DDX3, a member of the DEAD (asp, glu, ala, asp) box RNA helicase family of proteins, is a multifunctional protein, which is usurped by several viruses and is vital to their production. To date, 18 species of virus from 12 genera have been demonstrated to be dependent on DDX3 for virulence. In addition, DDX3 has been shown to function within 7 of 10 subcellular regions that are involved in the metabolism of viruses. As such, due to its direct interaction with viral components across most or all stages of viral life cycles, DDX3 can be considered an excellent host target for pan-antiviral drug therapy and has been reported to be a possible broad-spectrum antiviral target. Along these lines, it has been demonstrated that treatment of virally infected cells with small molecule inhibitors of DDX3 blunts virion productions. On the other hand, DDX3 bolsters an innate immune response and viruses have evolved capacities to sequester or block DDX3, which dampens an innate immune response. Thus, enhancing DDX3 production or co-targeting direct viral products that interfere with DDX3's modulation of innate immunity would also diminish virion production. Here we review the evidence that supports the hypothesis that modulating DDX3's agonistic and antagonistic functions during viral infections could have an important impact on safely and efficiently subduing a broad-spectrum of viral infections.
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Affiliation(s)
- Paul T Winnard
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA
| | - Farhad Vesuna
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA
| | - Venu Raman
- Division of Cancer Imaging Research, The Russell H Morgan Department of Radiology and Radiological Sciences, USA; Department of Oncology, The Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands.
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28
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Steinberger J, Shen L, J Kiniry S, Naineni SK, Cencic R, Amiri M, Aboushawareb SAE, Chu J, Maïga RI, Yachnin BJ, Robert F, Sonenberg N, Baranov PV, Pelletier J. Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5' leader regions. Nucleic Acids Res 2020; 48:9521-9537. [PMID: 32766783 PMCID: PMC7515738 DOI: 10.1093/nar/gkaa662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Hippuristanol (Hipp) is a natural product that selectively inhibits protein synthesis by targeting eukaryotic initiation factor (eIF) 4A, a DEAD-box RNA helicase required for ribosome recruitment to mRNA templates. Hipp binds to the carboxyl-terminal domain of eIF4A, locks it in a closed conformation, and inhibits its RNA binding. The dependencies of mRNAs for eIF4A during initiation is contingent on the degree of secondary structure within their 5′ leader region. Interest in targeting eIF4A therapeutically in cancer and viral-infected settings stems from the dependencies that certain cellular (e.g. pro-oncogenic, pro-survival) and viral mRNAs show towards eIF4A. Using a CRISPR/Cas9-based variomics screen, we identify functional EIF4A1 Hipp-resistant alleles, which in turn allowed us to link the translation-inhibitory and cytotoxic properties of Hipp to eIF4A1 target engagement. Genome-wide translational profiling in the absence or presence of Hipp were undertaken and our validation studies provided insight into the structure-activity relationships of eIF4A-dependent mRNAs. We find that mRNA 5′ leader length, overall secondary structure and cytosine content are defining features of Hipp-dependent mRNAs.
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Affiliation(s)
- Jutta Steinberger
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Leo Shen
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Mehdi Amiri
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | | | - Jennifer Chu
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | | | - Brahm J Yachnin
- Department of Chemistry & Chemical Biology & the Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway 08854, NJ
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada.,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal H3A 1A3, Canada
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada.,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal H3G 1Y6, Canada
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Ritchey LE, Tack DC, Yakhnin H, Jolley EA, Assmann SM, Bevilacqua PC, Babitzke P. Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis. RNA (NEW YORK, N.Y.) 2020; 26:1431-1447. [PMID: 32611709 PMCID: PMC7491331 DOI: 10.1261/rna.075986.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/28/2020] [Indexed: 06/01/2023]
Abstract
RNA structure influences numerous processes in all organisms. In bacteria, these processes include transcription termination and attenuation, small RNA and protein binding, translation initiation, and mRNA stability, and can be regulated via metabolite availability and other stresses. Here we use Structure-seq2 to probe the in vivo RNA structurome of Bacillus subtilis grown in the presence and absence of amino acids. Our results reveal that amino acid starvation results in lower overall dimethyl sulfate (DMS) reactivity of the transcriptome, indicating enhanced protection owing to protein binding or RNA structure. Starvation-induced changes in DMS reactivity correlated inversely with transcript abundance changes. This correlation was particularly pronounced in genes associated with the stringent response and CodY regulons, which are involved in adaptation to nutritional stress, suggesting that RNA structure contributes to transcript abundance change in regulons involved in amino acid metabolism. Structure-seq2 accurately reported on four known amino acid-responsive riboswitches: T-box, SAM, glycine, and lysine riboswitches. Additionally, we discovered a transcription attenuation mechanism that reduces yfmG expression when amino acids are added to the growth medium. We also found that translation of a leader peptide (YfmH) encoded just upstream of yfmG regulates yfmG expression. Our results are consistent with a model in which a slow rate of yfmH translation caused by limitation of the amino acids encoded in YfmH prevents transcription termination in the yfmG leader region by favoring formation of an overlapping antiterminator structure. This novel RNA switch offers a way to simultaneously monitor the levels of multiple amino acids.
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Affiliation(s)
- Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David C Tack
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth A Jolley
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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30
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Identification of Cardiac Glycosides as Novel Inhibitors of eIF4A1-Mediated Translation in Triple-Negative Breast Cancer Cells. Cancers (Basel) 2020; 12:cancers12082169. [PMID: 32759815 PMCID: PMC7465665 DOI: 10.3390/cancers12082169] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
The eukaryotic translation initiation factor 4F complex (eIF4F) is a potential chemotherapeutic target in triple-negative breast cancer (TNBC). This complex regulates cap-dependent translational initiation and consists of three core proteins: eIF4E, eIF4G, and eIF4A1. In this study, we focus on repositioning compounds as novel inhibitors of eIF4A1-mediated translation. In order to accomplish this goal, a modified synthetic reporter assay was established. More specifically, a (CGG)4 motif, which confers eIF4A dependency, was incorporated into the 5'-leader region of a luciferase-tdTomato lentiviral reporter construct. The Prestwick Chemical Library was then screened in multiple TNBC cell lines by measuring the tdTomato fluorescent intensity. We identified several cardiac glycosides as potential inhibitors of eIF4A1-mediated translation. Based on our studies, we find that cardiac glycosides inhibit the expression of eIF4A1. To identify a potential mechanism by which this was occurring, we utilized the Integrative Library of Integrated Network-Based Cellular Signatures (iLINCS). Our pursuits led us to the discovery that cardiac glycosides also decrease levels of c-MYC. Quantitative PCR confirmed that decreases in c-MYC and eIF4A were occurring at the transcriptional level. As such, disruption of the eIF4A1-c-MYC axis may be a viable approach in the treatment of TNBC. The novel combination of rocaglamide A and digoxin exhibited synergistic anti-cancer activity against TNBC cells in vitro. The findings in this study and others are important for formulating potential combination chemotherapies against eIF4A1 in vivo. Thus, drug repositioning may be one classical approach to successfully target eIF4A1 in TNBC patients.
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31
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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32
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Tack DC, Su Z, Yu Y, Bevilacqua PC, Assmann SM. Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis. RNA (NEW YORK, N.Y.) 2020; 26:492-511. [PMID: 31937672 PMCID: PMC7075263 DOI: 10.1261/rna.072850.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5'UTR, CDS, and 3'UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy." Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.
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Affiliation(s)
- David C Tack
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Spectrum Health Office of Research, Grand Rapids, Michigan 49503, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yunqing Yu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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