1
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Quintas A, Harvey RF, Horvilleur E, Garland GD, Schmidt T, Kalmar L, Dezi V, Marini A, Fulton AM, Pöyry TAA, Cole CH, Turner M, Sawarkar R, Chapman MA, Bushell M, Willis AE. Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs. Nucleic Acids Res 2024:gkae767. [PMID: 39225047 DOI: 10.1093/nar/gkae767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/13/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
RNA binding proteins drive proliferation and tumorigenesis by regulating the translation and stability of specific subsets of messenger RNAs (mRNAs). We have investigated the role of eukaryotic initiation factor 4B (eIF4B) in this process and identify 10-fold more RNA binding sites for eIF4B in tumour cells from patients with diffuse large B-cell lymphoma compared to control B cells and, using individual-nucleotide resolution UV cross-linking and immunoprecipitation, find that eIF4B binds the entire length of mRNA transcripts. eIF4B stimulates the helicase activity of eIF4A, thereby promoting the unwinding of RNA structure within the 5' untranslated regions of mRNAs. We have found that, in addition to its well-documented role in mRNA translation, eIF4B additionally interacts with proteins associated with RNA turnover, including UPF1 (up-frameshift protein 1), which plays a key role in histone mRNA degradation at the end of S phase. Consistent with these data, we locate an eIF4B binding site upstream of the stem-loop structure in histone mRNAs and show that decreased eIF4B expression alters histone mRNA turnover and delays cell cycle progression through S phase. Collectively, these data provide insight into how eIF4B promotes tumorigenesis.
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Affiliation(s)
- Ana Quintas
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Robert F Harvey
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Emilie Horvilleur
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Gavin D Garland
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Tobias Schmidt
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lajos Kalmar
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Veronica Dezi
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alberto Marini
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alexander M Fulton
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Tuija A A Pöyry
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Cameron H Cole
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Martin Turner
- Immunology Programme, Babraham Institute, Babraham Science Campus, Cambridgeshire CB22 3AT, UK
| | - Ritwick Sawarkar
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Michael A Chapman
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QW, UK
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2
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Saito H, Handa Y, Chen M, Schneider-Poetsch T, Shichino Y, Takahashi M, Romo D, Yoshida M, Fürstner A, Ito T, Fukuzawa K, Iwasaki S. DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs. Nat Commun 2024; 15:7418. [PMID: 39223140 PMCID: PMC11369270 DOI: 10.1038/s41467-024-51635-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
Small-molecule compounds that elicit mRNA-selective translation repression have attracted interest due to their potential for expansion of druggable space. However, only a limited number of examples have been reported to date. Here, we show that desmethyl desamino pateamine A (DMDA-PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, onto GNG motifs. By systematically comparing multiple eIF4A inhibitors by ribosome profiling, we found that DMDA-PatA has unique mRNA selectivity for translation repression. Unbiased Bind-n-Seq reveals that DMDA-PatA-targeted eIF4A exhibits a preference for GNG motifs in an ATP-independent manner. This unusual RNA binding sterically hinders scanning by 40S ribosomes. A combination of classical molecular dynamics simulations and quantum chemical calculations, and the subsequent development of an inactive DMDA-PatA derivative reveals that the positive charge of the tertiary amine on the trienyl arm induces G selectivity. Moreover, we identified that DDX3, another DEAD-box protein, is an alternative DMDA-PatA target with the same effects on eIF4A. Our results provide an example of the sequence-selective anchoring of RNA-binding proteins and the mRNA-selective inhibition of protein synthesis by small-molecule compounds.
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Grants
- Incentive Research Projects MEXT | RIKEN
- JP23gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23H00095 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP18H05503 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- S10 OD018174 NIH HHS
- R01 GM052964 NIGMS NIH HHS
- JP21H05281 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Pioneering Projects MEXT | RIKEN
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP19H05640 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- R37 GM052964 NIGMS NIH HHS
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- R29 GM052964 NIGMS NIH HHS
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Affiliation(s)
- Hironori Saito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yuma Handa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo, Japan
| | - Mingming Chen
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Mari Takahashi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Daniel Romo
- Department of Chemistry & Biochemistry and Baylor Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, TX, USA
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Office of University Professors, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Alois Fürstner
- Max-Planck-Institut für Kohlenforschung, Mülheim/Ruhr, Germany
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
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3
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Wang Z, Thakare RP, Chitale S, Mishra AK, Goldstein SI, Fan AC, Li R, Zhu LJ, Brown LE, Cencic R, Huang S, Green MR, Pelletier J, Malonia SK, Porco JA. Identification of Rocaglate Acyl Sulfamides as Selective Inhibitors of Glioblastoma Stem Cells. ACS CENTRAL SCIENCE 2024; 10:1640-1656. [PMID: 39220711 PMCID: PMC11363328 DOI: 10.1021/acscentsci.4c01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Glioblastoma (GBM) is the most aggressive and frequently occurring type of malignant brain tumor in adults. The initiation, progression, and recurrence of malignant tumors are known to be driven by a small subpopulation of cells known as tumor-initiating cells or cancer stem cells (CSCs). GBM CSCs play a pivotal role in orchestrating drug resistance and tumor relapse. As a prospective avenue for GBM intervention, the targeted suppression of GBM CSCs holds considerable promise. In this study, we found that rocaglates, compounds which are known to inhibit translation via targeting of the DEAD-box helicase eIF4A, exert a robust, dose-dependent cytotoxic impact on GBM CSCs with minimal killing of nonstem GBM cells. Subsequent optimization identified novel rocaglate derivatives (rocaglate acyl sulfamides or Roc ASFs) that selectively inhibit GBM CSCs with nanomolar EC50 values. Furthermore, comparative evaluation of a lead CSC-optimized Roc ASF across diverse mechanistic and target profiling assays revealed suppressed translation inhibition relative to that of other CSC-selective rocaglates, with enhanced targeting of the DEAD-box helicase DDX3X, a recently identified secondary target of rocaglates. Overall, these findings suggest a promising therapeutic strategy for targeting GBM CSCs.
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Affiliation(s)
- Zihao Wang
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ritesh P. Thakare
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Shalaka Chitale
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Alok K. Mishra
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Stanley I. Goldstein
- Boston
University Target Discovery Laboratory (BU-TDL), Boston, Massachusetts 02215, United States
- Department
of Pharmacology, Physiology, and Biophysics, Boston University, Boston, Massachusetts 02118, United States
| | - Alice C. Fan
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Boston
University Target Discovery Laboratory (BU-TDL), Boston, Massachusetts 02215, United States
| | - Rui Li
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department
of Molecular Medicine and Program in Bioinformatics and Integrative
Biology, University of Massachusetts Chan
Medical School, Worcester, Massachusetts 01605, United States
| | - Lihua Julie Zhu
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department
of Molecular Medicine and Program in Bioinformatics and Integrative
Biology, University of Massachusetts Chan
Medical School, Worcester, Massachusetts 01605, United States
| | - Lauren E. Brown
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Regina Cencic
- Department
of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sidong Huang
- Department
of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael R. Green
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Jerry Pelletier
- Department
of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sunil K. Malonia
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - John A. Porco
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Boston
University Target Discovery Laboratory (BU-TDL), Boston, Massachusetts 02215, United States
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4
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Tomuro K, Mito M, Toh H, Kawamoto N, Miyake T, Chow SYA, Doi M, Ikeuchi Y, Shichino Y, Iwasaki S. Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts. Nat Commun 2024; 15:7061. [PMID: 39187487 PMCID: PMC11347596 DOI: 10.1038/s41467-024-51258-0] [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: 07/09/2023] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05782 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02306 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP24H02307 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP22fk0108570 Japan Agency for Medical Research and Development (AMED)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23H00095 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP22K20765 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K14173 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2178 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- Pioneering Project MEXT | RIKEN
- RIKEN TRIP initiative "TRIP-AGIS" MEXT | RIKEN
- Pioneering Project MEXT | RIKEN
- JPMJBS2418 MEXT | Japan Science and Technology Agency (JST)
- JPMJFR226F MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Kotaro Tomuro
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Hirotaka Toh
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Takahito Miyake
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Masao Doi
- Department of Systems Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyō-ku, Kyoto, 606-8501, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
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5
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Gupta I, Gaykalova DA. Unveiling the role of PIK3R1 in cancer: A comprehensive review of regulatory signaling and therapeutic implications. Semin Cancer Biol 2024; 106-107:58-86. [PMID: 39197810 DOI: 10.1016/j.semcancer.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/11/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024]
Abstract
Phosphoinositide 3-kinase (PI3K) is responsible for phosphorylating phosphoinositides to generate secondary signaling molecules crucial for regulating various cellular processes, including cell growth, survival, and metabolism. The PI3K is a heterodimeric enzyme complex comprising of a catalytic subunit (p110α, p110β, or p110δ) and a regulatory subunit (p85). The binding of the regulatory subunit, p85, with the catalytic subunit, p110, forms an integral component of the PI3K enzyme. PIK3R1 (phosphoinositide-3-kinase regulatory subunit 1) belongs to class IA of the PI3K family. PIK3R1 exhibits structural complexity due to alternative splicing, giving rise to distinct isoforms, prominently p85α and p55α. While the primary p85α isoform comprises multiple domains, including Src homology 3 (SH3) domains, a Breakpoint Cluster Region Homology (BH) domain, and Src homology 2 (SH2) domains (iSH2 and nSH2), the shorter isoform, p55α, lacks certain domains present in p85α. In this review, we will highlight the intricate regulatory mechanisms governing PI3K signaling along with the impact of PIK3R1 alterations on cellular processes. We will further delve into the clinical significance of PIK3R1 mutations in various cancer types and their implications for prognosis and treatment outcomes. Additionally, we will discuss the evolving landscape of targeted therapies aimed at modulating PI3K-associated pathways. Overall, this review will provide insights into the dynamic interplay of PIK3R1 in cancer, fostering advancements in precision medicine and the development of targeted interventions.
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Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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6
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Magari F, Messner H, Salisch F, Schmelzle SM, van Zandbergen G, Fürstner A, Ziebuhr J, Heine A, Müller-Ruttloff C, Grünweller A. Potent anti-coronaviral activity of pateamines and new insights into their mode of action. Heliyon 2024; 10:e33409. [PMID: 39035482 PMCID: PMC11259845 DOI: 10.1016/j.heliyon.2024.e33409] [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: 01/11/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Pateamines, derived from the sponge Mycale hentscheli, function as inhibitors of the RNA helicase eIF4A and exhibit promising antiviral and anticancer properties. eIF4A plays a pivotal role in unwinding stable RNA structures within the 5'-UTR of selected mRNAs, facilitating the binding of the 43S preinitiation complex during translation initiation. Pateamines function by clamping RNA substrates onto the eIF4A surface, effectively preventing eIF4A from carrying out the unwinding step. Rocaglates, a compound class isolated from plants of the genus Aglaia, target the same binding pocket on eIF4A, and based on structural data, a similar mode of action has been proposed for pateamines and rocaglates. In this study, we conducted a detailed characterization of pateamines' binding mode and assessed their antiviral activity against human pathogenic coronaviruses (human coronavirus 229E (HCoV-229E), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)). Our findings reveal significant differences in the binding behavior of pateamines compared to rocaglates when interacting with an eIF4A-RNA complex. We also observed that pateamines do not depend on the presence of a polypurine tract in the RNA substrate for efficient RNA clamping, as it is the case for rocaglates. Most notably, pateamines demonstrate potent antiviral activity against coronaviruses in the low nanomolar range. Consequently, pateamines broaden our toolbox for combating viruses that rely on the host enzyme eIF4A to conduct their viral protein synthesis, indicating a possible future treatment strategy against new or re-emerging pathogenic viruses.
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Affiliation(s)
- Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | - Henri Messner
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | - Florian Salisch
- Institute of Medical Virology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | | | - Ger van Zandbergen
- Division of Immunology, Paul-Ehrlich-Institute, 63225, Langen, Germany
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Alois Fürstner
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim Ruhr, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | | | - Arnold Grünweller
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany
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7
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Zhu X, Zuo Q, Xie X, Chen Z, Wang L, Chang L, Liu Y, Luo J, Fang C, Che L, Zhou X, Yao C, Gong C, Hu D, Zhao W, Zhou Y, Zhu S. Rocaglamide regulates iron homeostasis by suppressing hepcidin expression. Free Radic Biol Med 2024; 219:153-162. [PMID: 38657753 DOI: 10.1016/j.freeradbiomed.2024.04.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
The anemia of inflammation (AI) is characterized by the presence of inflammation and abnormal elevation of hepcidin. Accumulating evidence has proved that Rocaglamide (RocA) was involved in inflammation regulation. Nevertheless, the role of RocA in AI, especially in iron metabolism, has not been investigated, and its underlying mechanism remains elusive. Here, we demonstrated that RocA dramatically suppressed the elevation of hepcidin and ferritin in LPS-treated mice cell line RAW264.7 and peritoneal macrophages. In vivo study showed that RocA can restrain the depletion of serum iron (SI) and transferrin (Tf) saturation caused by LPS. Further investigation showed that RocA suppressed the upregulation of hepcidin mRNA and downregulation of Fpn1 protein expression in the spleen and liver of LPS-treated mice. Mechanistically, this effect was attributed to RocA's ability to inhibit the IL-6/STAT3 pathway, resulting in the suppression of hepcidin mRNA and subsequent increase in Fpn1 and TfR1 expression in LPS-treated macrophages. Moreover, RocA inhibited the elevation of the cellular labile iron pool (LIP) and reactive oxygen species (ROS) induced by LPS in RAW264.7 cells. These findings reveal a pivotal mechanism underlying the roles of RocA in modulating iron homeostasis and also provide a candidate natural product on alleviating AI.
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Affiliation(s)
- Xinyue Zhu
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Quan Zuo
- Natural Product Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Xueting Xie
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Zhongxian Chen
- Natural Product Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Lixin Wang
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Linyue Chang
- Natural Product Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Yangli Liu
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Jiaojiao Luo
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Cheng Fang
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Linlin Che
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Xinyue Zhou
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Chao Yao
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Chenyuan Gong
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China
| | - Dan Hu
- School of Acupuncture, Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, 1200 CaiLun Rd, Shanghai, 201203, PR China
| | - Weimin Zhao
- Natural Product Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China.
| | - Yufu Zhou
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China.
| | - Shiguo Zhu
- Department of Immunology and Pathogenic Biology, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China.
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8
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms. Life Sci Alliance 2024; 7:e202302501. [PMID: 38803235 PMCID: PMC11109482 DOI: 10.26508/lsa.202302501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the developmental transcription factor CCAAT/enhancer-binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This choice between alternative start sites depends on sequence features of the CEBPA transcript, including a regulatory uORF, but the molecular basis is not fully understood. Here, we identify the factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescent reporter coupled with CRISPRi screening. Our screen uncovered a role of the ribosome rescue factor PELOTA (PELO) in promoting the expression of the longer C/EBPα isoform by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin kinase. Our work uncovers further links between ribosome recycling and translation reinitiation that regulate a key transcription factor, with implications for normal hematopoiesis and leukemogenesis.
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Affiliation(s)
- Samantha G Fernandez
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas Ferguson
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Nicholas T Ingolia
- https://ror.org/01an7q238 Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- https://ror.org/01an7q238 Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
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9
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Leśniczak-Staszak M, Pietras P, Ruciński M, Johnston R, Sowiński M, Andrzejewska M, Nowicki M, Gowin E, Lyons SM, Ivanov P, Szaflarski W. Stress granule-mediated sequestration of EGR1 mRNAs correlates with lomustine-induced cell death prevention. J Cell Sci 2024; 137:jcs261825. [PMID: 38940347 PMCID: PMC11234381 DOI: 10.1242/jcs.261825] [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: 11/22/2023] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
Some chemotherapy drugs modulate the formation of stress granules (SGs), which are RNA-containing cytoplasmic foci contributing to stress response pathways. How SGs mechanistically contribute to pro-survival or pro-apoptotic functions must be better defined. The chemotherapy drug lomustine promotes SG formation by activating the stress-sensing eIF2α kinase HRI (encoded by the EIF2AK1 gene). Here, we applied a DNA microarray-based transcriptome analysis to determine the genes modulated by lomustine-induced stress and suggest roles for SGs in this process. We found that the expression of the pro-apoptotic EGR1 gene was specifically regulated in cells upon lomustine treatment. The appearance of EGR1-encoding mRNA in SGs correlated with a decrease in EGR1 mRNA translation. Specifically, EGR1 mRNA was sequestered to SGs upon lomustine treatment, probably preventing its ribosome translation and consequently limiting the degree of apoptosis. Our data support the model where SGs can selectively sequester specific mRNAs in a stress-specific manner, modulate their availability for translation, and thus determine the fate of a stressed cell.
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Affiliation(s)
- Marta Leśniczak-Staszak
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Paulina Pietras
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Marcin Ruciński
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Ryan Johnston
- Department of Biochemistry and Cell Biology, Boston University School of Medicine, Boston, MA 02118, USA
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mateusz Sowiński
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Małgorzata Andrzejewska
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Ewelina Gowin
- Department of Health Promotion, Poznan University of Medical Sciences, Poznań 60-781, Poland
| | - Shawn M. Lyons
- Department of Biochemistry and Cell Biology, Boston University School of Medicine, Boston, MA 02118, USA
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Witold Szaflarski
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznań 60-781, Poland
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10
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Coupe S, Fakhri N. ATP-induced cross-linking of a biomolecular condensate. Biophys J 2024; 123:1356-1366. [PMID: 37480229 PMCID: PMC11163290 DOI: 10.1016/j.bpj.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023] Open
Abstract
DEAD-box helicases are important regulators of biomolecular condensates. However, the mechanisms through which these enzymes affect the dynamics of biomolecular condensates have not been systematically explored. Here, we demonstrate the mechanism by which the mutation of a DEAD-box helicase's catalytic core alters ribonucleoprotein condensate dynamics in the presence of ATP. Through altering RNA length within the system, we are able to attribute the altered biomolecular dynamics and material properties to physical cross-linking of RNA facilitated by the mutant helicase. These results suggest that mutant condensates approach a gel transition when RNA length is increased to lengths comparable to eukaryotic mRNA. Lastly, we show that this cross-linking effect is tunable with ATP concentration, uncovering a system whose RNA mobility and material properties vary with enzyme activity. More generally, these findings point to a fundamental mechanism for modulating condensate dynamics and emergent material properties through nonequilibrium, molecular-scale interactions.
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Affiliation(s)
- Sebastian Coupe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Nikta Fakhri
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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11
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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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12
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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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13
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Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome decision graphs for the representation of eukaryotic RNA translation complexity. Genome Res 2024; 34:530-538. [PMID: 38719470 PMCID: PMC11146595 DOI: 10.1101/gr.278810.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/01/2024] [Indexed: 05/21/2024]
Abstract
The application of ribosome profiling has revealed an unexpected abundance of translation in addition to that responsible for the synthesis of previously annotated protein-coding regions. Multiple short sequences have been found to be translated within single RNA molecules, within both annotated protein-coding and noncoding regions. The biological significance of this translation is a matter of intensive investigation. However, current schematic or annotation-based representations of mRNA translation generally do not account for the apparent multitude of translated regions within the same molecules. They also do not take into account the stochasticity of the process that allows alternative translations of the same RNA molecules by different ribosomes. There is a need for formal representations of mRNA complexity that would enable the analysis of quantitative information on translation and more accurate models for predicting the phenotypic effects of genetic variants affecting translation. To address this, we developed a conceptually novel abstraction that we term ribosome decision graphs (RDGs). RDGs represent translation as multiple ribosome paths through untranslated and translated mRNA segments. We termed the latter "translons." Nondeterministic events, such as initiation, reinitiation, selenocysteine insertion, or ribosomal frameshifting, are then represented as branching points. This representation allows for an adequate representation of eukaryotic translation complexity and focuses on locations critical for translation regulation. We show how RDGs can be used for depicting translated regions and for analyzing genetic variation and quantitative genome-wide data on translation for characterization of regulatory modulators of translation.
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Affiliation(s)
- Jack A S Tierney
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 K8AF, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork T12 K8AF, Ireland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Håkon Tjeldnes
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 K8AF, Ireland
- Computational Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridge, United Kingdom
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Nicola Whiffin
- The Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, NO-5020 Bergen, Norway
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 K8AF, Ireland;
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14
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Goldstein SI, Fan AC, Wang Z, Naineni SK, Lengqvist J, Chernobrovkin A, Garcia-Gutierrez SB, Cencic R, Patel K, Huang S, Brown LE, Emili A, Porco JA. Proteomic Discovery of RNA-Protein Molecular Clamps Using a Thermal Shift Assay with ATP and RNA (TSAR). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590252. [PMID: 38659867 PMCID: PMC11042367 DOI: 10.1101/2024.04.19.590252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Uncompetitive inhibition is an effective strategy for suppressing dysregulated enzymes and their substrates, but discovery of suitable ligands depends on often-unavailable structural knowledge and serendipity. Hence, despite surging interest in mass spectrometry-based target identification, proteomic studies of substrate-dependent target engagement remain sparse. Herein, we describe the Thermal Shift Assay with ATP and RNA (TSAR) as a template for proteome-wide discovery of substrate-dependent ligand binding. Using proteomic thermal shift assays, we show that simple biochemical additives can facilitate detection of target engagement in native cell lysates. We apply our approach to rocaglates, a family of molecules that specifically clamp RNA to eukaryotic translation initiation factor 4A (eIF4A), DEAD-box helicase 3X (DDX3X), and potentially other members of the DEAD-box (DDX) family of RNA helicases. To identify unexpected interactions, we optimized a target class-specific thermal denaturation window and evaluated ATP analog and RNA probe dependencies for key rocaglate-DDX interactions. We report novel DDX targets of the rocaglate clamping spectrum, confirm that DDX3X is a common target of several widely studied analogs, and provide structural insights into divergent DDX3X affinities between synthetic rocaglates. We independently validate novel targets of high-profile rocaglates, including the clinical candidate Zotatifin (eFT226), using limited proteolysis-mass spectrometry and fluorescence polarization experiments. Taken together, our study provides a model for screening uncompetitive inhibitors using a systematic chemical-proteomics approach to uncover actionable DDX targets, clearing a path towards characterization of novel molecular clamps and associated RNA helicase targets.
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Affiliation(s)
- Stanley I. Goldstein
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
- Department of Pharmacology, Physiology, and Biophysics, Boston University, Boston, MA, USA
| | - Alice C. Fan
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Zihao Wang
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Sai K. Naineni
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | | | | | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Kesha Patel
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | | | - Andrew Emili
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - John A. Porco
- BU Target Discovery Laboratory (BU-TDL), Boston University, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
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15
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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16
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González-Sánchez AM, Castellanos-Silva EA, Díaz-Figueroa G, Cate JHD. JUN mRNA translation regulation is mediated by multiple 5' UTR and start codon features. PLoS One 2024; 19:e0299779. [PMID: 38483896 PMCID: PMC10939236 DOI: 10.1371/journal.pone.0299779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Regulation of mRNA translation by eukaryotic initiation factors (eIFs) is crucial for cell survival. In humans, eIF3 stimulates translation of the JUN mRNA which encodes the transcription factor JUN, an oncogenic transcription factor involved in cell cycle progression, apoptosis, and cell proliferation. Previous studies revealed that eIF3 activates translation of the JUN mRNA by interacting with a stem loop in the 5' untranslated region (5' UTR) and with the 5' -7-methylguanosine cap structure. In addition to its interaction site with eIF3, the JUN 5' UTR is nearly one kilobase in length, and has a high degree of secondary structure, high GC content, and an upstream start codon (uAUG). This motivated us to explore the complexity of JUN mRNA translation regulation in human cells. Here we find that JUN translation is regulated in a sequence and structure-dependent manner in regions adjacent to the eIF3-interacting site in the JUN 5' UTR. Furthermore, we identify contributions of an additional initiation factor, eIF4A, in JUN regulation. We show that enhancing the interaction of eIF4A with JUN by using the compound Rocaglamide A (RocA) represses JUN translation. We also find that both the upstream AUG (uAUG) and the main AUG (mAUG) contribute to JUN translation and that they are conserved throughout vertebrates. Our results reveal additional layers of regulation for JUN translation and show the potential of JUN as a model transcript for understanding multiple interacting modes of translation regulation.
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Affiliation(s)
- Angélica M. González-Sánchez
- Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, United States of America
| | - Eimy A. Castellanos-Silva
- Department of Biochemistry and Molecular Biology, University of California, Davis, Davis, CA, United States of America
| | - Gabriela Díaz-Figueroa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
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17
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Apostolopoulos A, Kawamoto N, Chow SYA, Tsuiji H, Ikeuchi Y, Shichino Y, Iwasaki S. dCas13-mediated translational repression for accurate gene silencing in mammalian cells. Nat Commun 2024; 15:2205. [PMID: 38467613 PMCID: PMC10928199 DOI: 10.1038/s41467-024-46412-7] [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: 05/19/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Current gene silencing tools based on RNA interference (RNAi) or, more recently, clustered regularly interspaced short palindromic repeats (CRISPR)‒Cas13 systems have critical drawbacks, such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR‒Cas13). Thus, a more specific method of gene knockdown is needed. Here, we develop CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13). Owing to its tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes during translation initiation and does not affect mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy regardless of the translation initiation mechanism: cap-dependent, internal ribosome entry site (IRES)-dependent, or repeat-associated non-AUG (RAN) translation. Strikingly, genome-wide ribosome profiling reveals the ultrahigh gene silencing specificity of CRISPRδ. Moreover, the fusion of a translational repressor to dCas13 further improves the performance. Our method provides a framework for translational repression-based gene silencing in eukaryotes.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05278 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K07016 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005h0001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- Pioneering Projects MEXT | RIKEN
- Pioneering Projects MEXT | RIKEN
- Exploratory Research Center on Life and Living Systems (ExCELLS), 23EX601
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hitomi Tsuiji
- Education and Research Division of Pharmacy, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi, 464-8650, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
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18
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Brito Querido J, Sokabe M, Díaz-López I, Gordiyenko Y, Fraser CS, Ramakrishnan V. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat Struct Mol Biol 2024; 31:455-464. [PMID: 38287194 PMCID: PMC10948362 DOI: 10.1038/s41594-023-01196-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 11/30/2023] [Indexed: 01/31/2024]
Abstract
Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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19
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Ge W, Ming W, Li Z, Tang Y, Li YN, Yang J, Hao X, Yuan C. Design and Synthesis of Cytotoxic Water-Soluble Rocaglaol Derivatives against HEL Cells by Inhibiting Fli-1. JOURNAL OF NATURAL PRODUCTS 2024; 87:276-285. [PMID: 38253024 DOI: 10.1021/acs.jnatprod.3c00948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Rocaglaol, embedding a cyclopenta[b]benzofuran scaffold, was isolated mainly from the plants of Aglaia and exhibited nanomolar level antitumor activity. However, the drug-like properties of these compounds are poor. To improve the physicochemical properties of rocaglaol, 36 nitrogen-containing phenyl-substituted rocaglaol derivatives were designed and synthesized. These derivatives were tested for the inhibitory effects on three tumor cell lines, HEL, MDA-231, and SW480, using the MTT assay. Among them, 22 derivatives exhibited good cytotoxic activities with IC50 values between 0.11 ± 0.07 and 0.88 ± 0.02 μM. Fourteen derivatives exhibited stronger cytotoxicity than the positive control, adriamycin. In particular, a water-soluble derivative revealed selective cytotoxic effects on HEL cells (IC50 = 0.19 ± 0.01 μM). This compound could induce G1 cell cycle arrest and apoptosis in HEL cells. Western blot assays suggested that the water-soluble derivative could downregulate the expression of the marker proteins of apoptosis, PARP, caspase-3, and caspase-9, thus inducing apoptosis. Further CETSA and Western blot studies implied that this water-soluble derivative might be an inhibitor of friend leukemia integration 1 (Fli-1). This water-soluble derivative may serve as a potential antileukemia agent by suppressing the expression of Fli-1.
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Affiliation(s)
- Wei Ge
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
| | - Weikang Ming
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
| | - Zhenkun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
| | - Yunyan Tang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
| | - Ya-Nan Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
| | - Jue Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
| | - Xiaojiang Hao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Chunmao Yuan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 550025, People's Republic of China
- Natural Products Research Center of Guizhou Province, Guiyang 550014, People's Republic of China
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20
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Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
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21
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Su D, Ding C, Qiu J, Yang G, Wang R, Liu Y, Tao J, Luo W, Weng G, Zhang T. Ribosome profiling: a powerful tool in oncological research. Biomark Res 2024; 12:11. [PMID: 38273337 PMCID: PMC10809610 DOI: 10.1186/s40364-024-00562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.
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Affiliation(s)
- Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Chen Ding
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Gang Yang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College Hospital, Beijing, 100023, P.R. China
| | - Guihu Weng
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P.R. China.
- Key Laboratory of Research in Pancreatic Tumor, Chinese Academy of Medical Sciences, Beijing, 100023, P.R. China.
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22
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Cencic R, Im YK, Naineni SK, Moustafa-Kamal M, Jovanovic P, Sabourin V, Annis MG, Robert F, Schmeing TM, Koromilas A, Paquet M, Teodoro JG, Huang S, Siegel PM, Topisirovic I, Ursini-Siegel J, Pelletier J. A second-generation eIF4A RNA helicase inhibitor exploits translational reprogramming as a vulnerability in triple-negative breast cancer. Proc Natl Acad Sci U S A 2024; 121:e2318093121. [PMID: 38232291 PMCID: PMC10823175 DOI: 10.1073/pnas.2318093121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
In this study, we aimed to address the current limitations of therapies for macro-metastatic triple-negative breast cancer (TNBC) and provide a therapeutic lead that overcomes the high degree of heterogeneity associated with this disease. Specifically, we focused on well-documented but clinically underexploited cancer-fueling perturbations in mRNA translation as a potential therapeutic vulnerability. We therefore developed an orally bioavailable rocaglate-based molecule, MG-002, which hinders ribosome recruitment and scanning via unscheduled and non-productive RNA clamping by the eukaryotic translation initiation factor (eIF) 4A RNA helicase. We demonstrate that MG-002 potently inhibits mRNA translation and primary TNBC tumor growth without causing overt toxicity in mice. Importantly, given that metastatic spread is a major cause of mortality in TNBC, we show that MG-002 attenuates metastasis in pre-clinical models. We report on MG-002, a rocaglate that shows superior properties relative to existing eIF4A inhibitors in pre-clinical models. Our study also paves the way for future clinical trials exploring the potential of MG-002 in TNBC and other oncological indications.
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Affiliation(s)
- Regina Cencic
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Young K. Im
- Lady Davis Institute for Medical Research, Montreal, QCH3T 1E2, Canada
| | - Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Mohamed Moustafa-Kamal
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Predrag Jovanovic
- Lady Davis Institute for Medical Research, Montreal, QCH3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QCH4A 3J1, Canada
| | - Valerie Sabourin
- Lady Davis Institute for Medical Research, Montreal, QCH3T 1E2, Canada
| | - Matthew G. Annis
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Antonis Koromilas
- Lady Davis Institute for Medical Research, Montreal, QCH3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QCH4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QCH4A 3T2, Canada
| | - Marilène Paquet
- Département de pathologie et de microbiologie, Faculté de médecine vétérinaire, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Jose G. Teodoro
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
| | - Peter M. Siegel
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
- Division of Experimental Medicine, McGill University, Montreal, QCH4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QCH4A 3T2, Canada
- Department of Medicine, McGill University, Montreal, QCH4A 3J1, Canada
| | - Ivan Topisirovic
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Lady Davis Institute for Medical Research, Montreal, QCH3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QCH4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QCH4A 3T2, Canada
| | - Josie Ursini-Siegel
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Lady Davis Institute for Medical Research, Montreal, QCH3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QCH4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QCH4A 3T2, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QCH3A 1A3, Canada
- Division of Experimental Medicine, McGill University, Montreal, QCH4A 3J1, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QCH4A 3T2, Canada
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23
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Zhao N, Kabotyanski EB, Saltzman AB, Malovannaya A, Yuan X, Reineke LC, Lieu N, Gao Y, Pedroza DA, Calderon SJ, Smith AJ, Hamor C, Safari K, Savage S, Zhang B, Zhou J, Solis LM, Hilsenbeck SG, Fan C, Perou CM, Rosen JM. Targeting eIF4A triggers an interferon response to synergize with chemotherapy and suppress triple-negative breast cancer. J Clin Invest 2023; 133:e172503. [PMID: 37874652 PMCID: PMC10721161 DOI: 10.1172/jci172503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Protein synthesis is frequently dysregulated in cancer and selective inhibition of mRNA translation represents an attractive cancer therapy. Here, we show that therapeutically targeting the RNA helicase eIF4A with zotatifin, the first-in-class eIF4A inhibitor, exerts pleiotropic effects on both tumor cells and the tumor immune microenvironment in a diverse cohort of syngeneic triple-negative breast cancer (TNBC) mouse models. Zotatifin not only suppresses tumor cell proliferation but also directly repolarizes macrophages toward an M1-like phenotype and inhibits neutrophil infiltration, which sensitizes tumors to immune checkpoint blockade. Mechanistic studies revealed that zotatifin reprograms the tumor translational landscape, inhibits the translation of Sox4 and Fgfr1, and induces an interferon (IFN) response uniformly across models. The induction of an IFN response is partially due to the inhibition of Sox4 translation by zotatifin. A similar induction of IFN-stimulated genes was observed in breast cancer patient biopsies following zotatifin treatment. Surprisingly, zotatifin significantly synergizes with carboplatin to trigger DNA damage and an even heightened IFN response, resulting in T cell-dependent tumor suppression. These studies identified a vulnerability of eIF4A in TNBC, potential pharmacodynamic biomarkers for zotatifin, and provide a rationale for new combination regimens consisting of zotatifin and chemotherapy or immunotherapy as treatments for TNBC.
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Affiliation(s)
- Na Zhao
- Department of Molecular and Cellular Biology
| | | | | | - Anna Malovannaya
- Mass Spectrometry Proteomics Core
- Department of Biochemistry and Molecular Pharmacology, and
| | | | - Lucas C. Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Nadia Lieu
- Department of Molecular and Cellular Biology
| | - Yang Gao
- Department of Molecular and Cellular Biology
| | | | | | | | - Clark Hamor
- Department of Molecular and Cellular Biology
| | - Kazem Safari
- Texas A&M Health Science Center, Houston, Texas, USA
| | - Sara Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jianling Zhou
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Susan G. Hilsenbeck
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
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24
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Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, Suzuki T, Suzuki T. Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell 2023; 186:5517-5535.e24. [PMID: 37992713 DOI: 10.1016/j.cell.2023.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/14/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.
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Affiliation(s)
- Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toru Irie
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kota Ishibashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kimi Wakabayashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
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25
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Shieh AW, Bansal SK, Zuo Z, Wang SH. Transcriptome-wide profiling of acute stress induced changes in ribosome occupancy level using external standards. PLoS One 2023; 18:e0294308. [PMID: 37988379 PMCID: PMC10662766 DOI: 10.1371/journal.pone.0294308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Acute cellular stress is known to induce a global reduction in mRNA translation through suppression of cap dependent translation. Selective translation in response to acute stress has been shown to play important roles in regulating the stress response. However, accurately profiling translational changes transcriptome-wide in response to acute cellular stress has been challenging. Commonly used data normalization methods operate on the assumption that any systematic shifts are experimental artifacts. Consequently, if applied to profiling acute cellular stress-induced mRNA translation changes, these methods are expected to produce biased estimates. To address this issue, we designed, produced, and evaluated a panel of 16 oligomers to serve as external standards for ribosome profiling studies. Using Sodium Arsenite treatment-induced oxidative stress in lymphoblastoid cell lines as a model system, we applied spike-in oligomers as external standards. We found our spike-in oligomers to display a strong linear correlation between the observed and the expected quantification, with small ratio compression at the lower concentration range. Using the expected fold changes constructed from spike-in controls, we found in our dataset that TMM normalization, a popular global scaling normalization approach, produced 87.5% false positives at a significant cutoff that is expected to produce only 10% false positive discoveries. In addition, TMM normalization produced a systematic shift of fold change by 3.25 fold. These results highlight the consequences of applying global scaling approaches to conditions that clearly violate their key assumptions. In contrast, we found RUVg normalization using spike-in oligomers as control genes recapitulated the expected stress induced global reduction of translation and resulted in little, if any, systematic shifts in the expected fold change. Our results clearly demonstrated the utility of our spike-in oligomers, both for constructing expected results as controls and for data normalization.
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Affiliation(s)
- Annie W. Shieh
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Sandeep K. Bansal
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Zhen Zuo
- Baylor College of Medicine, Houston, TX, United States of America
| | - Sidney H. Wang
- Center for Human Genetics, The Brown foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States of America
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26
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González-Sánchez AM, Castellanos-Silva EA, Díaz-Figueroa G, Cate JHD. JUN mRNA Translation Regulation is Mediated by Multiple 5' UTR and Start Codon Features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567602. [PMID: 38014201 PMCID: PMC10680820 DOI: 10.1101/2023.11.17.567602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Regulation of mRNA translation by eukaryotic initiation factors (eIFs) is crucial for cell survival. In humans, eIF3 stimulates translation of the JUN mRNA which encodes the transcription factor JUN, an oncogenic transcription factor involved in cell cycle progression, apoptosis, and cell proliferation. Previous studies revealed that eIF3 activates translation of the JUN mRNA by interacting with a stem loop in the 5' untranslated region (5' UTR) and with the 5'-7-methylguanosine cap structure. In addition to its interaction site with eIF3, the JUN 5' UTR is nearly one kilobase in length, and has a high degree of secondary structure, high GC content, and an upstream start codon (uAUG). This motivated us to explore the complexity of JUN mRNA translation regulation in human cells. Here we find that JUN translation is regulated in a sequence and structure-dependent manner in regions adjacent to the eIF3-interacting site in the JUN 5' UTR. Furthermore, we identify contributions of an additional initiation factor, eIF4A, in JUN regulation. We show that enhancing the interaction of eIF4A with JUN by using the compound Rocaglamide A (RocA) represses JUN translation. We also find that both the upstream AUG (uAUG) and the main AUG (mAUG) contribute to JUN translation and that they are conserved throughout vertebrates. Our results reveal additional layers of regulation for JUN translation and show the potential of JUN as a model transcript for understanding multiple interacting modes of translation regulation.
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Affiliation(s)
| | - Eimy A Castellanos-Silva
- University of California, Davis, Department of Biochemistry and Molecular Biology, Davis, CA, USA
| | - Gabriela Díaz-Figueroa
- University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Jamie H D Cate
- University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA, USA
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27
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Li S, Chen JS, Li X, Bai X, Shi D. MNK, mTOR or eIF4E-selecting the best anti-tumor target for blocking translation initiation. Eur J Med Chem 2023; 260:115781. [PMID: 37669595 DOI: 10.1016/j.ejmech.2023.115781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023]
Abstract
Overexpression of eIF4E is common in patients with various solid tumors and hematologic cancers. As a potential anti-cancer target, eIF4E has attracted extensive attention from researchers. At the same time, mTOR kinases inhibitors and MNK kinases inhibitors, which are directly related to regulation of eIF4E, have been rapidly developed. To explore the optimal anti-cancer targets among MNK, mTOR, and eIF4E, this review provides a detailed classification and description of the anti-cancer activities of promising compounds. In addition, the structures and activities of some dual-target inhibitors are briefly described. By analyzing the different characteristics of the inhibitors, it can be concluded that MNK1/2 and eIF4E/eIF4G interaction inhibitors are superior to mTOR inhibitors. Simultaneous inhibition of MNK and eIF4E/eIF4G interaction may be the most promising anti-cancer method for targeting translation initiation.
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Affiliation(s)
- Shuo Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, PR China.
| | - Jia-Shu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, PR China.
| | - Xiangqian Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, PR China.
| | - Xiaoyi Bai
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, PR China.
| | - Dayong Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, PR China.
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28
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Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV. Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566564. [PMID: 37986835 PMCID: PMC10659439 DOI: 10.1101/2023.11.10.566564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The application of ribosome profiling has revealed an unexpected abundance of translation in addition to that responsible for the synthesis of previously annotated protein-coding regions. Multiple short sequences have been found to be translated within single RNA molecules, both within annotated protein-coding and non-coding regions. The biological significance of this translation is a matter of intensive investigation. However, current schematic or annotation-based representations of mRNA translation generally do not account for the apparent multitude of translated regions within the same molecules. They also do not take into account the stochasticity of the process that allows alternative translations of the same RNA molecules by different ribosomes. There is a need for formal representations of mRNA complexity that would enable the analysis of quantitative information on translation and more accurate models for predicting the phenotypic effects of genetic variants affecting translation. To address this, we developed a conceptually novel abstraction that we term Ribosome Decision Graphs (RDGs). RDGs represent translation as multiple ribosome paths through untranslated and translated mRNA segments. We termed the later 'translons'. Non-deterministic events, such as initiation, re-initiation, selenocysteine insertion or ribosomal frameshifting are then represented as branching points. This representation allows for an adequate representation of eukaryotic translation complexity and focuses on locations critical for translation regulation. We show how RDGs can be used for depicting translated regions, analysis of genetic variation and quantitative genome-wide data on translation for characterisation of regulatory modulators of translation.
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Affiliation(s)
- Jack A S Tierney
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Michał Świrski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Håkon Tjeldnes
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Nicola Whiffin
- The Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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29
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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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30
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Gumilar KE, Chin Y, Ibrahim IH, Tjokroprawiro BA, Yang JY, Zhou M, Gassman NR, Tan M. Heat Shock Factor 1 Inhibition: A Novel Anti-Cancer Strategy with Promise for Precision Oncology. Cancers (Basel) 2023; 15:5167. [PMID: 37958341 PMCID: PMC10649344 DOI: 10.3390/cancers15215167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Heat shock factor 1 (HSF1) is a transcription factor crucial for regulating heat shock response (HSR), one of the significant cellular protective mechanisms. When cells are exposed to proteotoxic stress, HSF1 induces the expression of heat shock proteins (HSPs) to act as chaperones, correcting the protein-folding process and maintaining proteostasis. In addition to its role in HSR, HSF1 is overexpressed in multiple cancer cells, where its activation promotes malignancy and leads to poor prognosis. The mechanisms of HSF1-induced tumorigenesis are complex and involve diverse signaling pathways, dependent on cancer type. With its important roles in tumorigenesis and tumor progression, targeting HSF1 offers a novel cancer treatment strategy. In this article, we examine the basic function of HSF1 and its regulatory mechanisms, focus on the mechanisms involved in HSF1's roles in different cancer types, and examine current HSF1 inhibitors as novel therapeutics to treat cancers.
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Affiliation(s)
- Khanisyah Erza Gumilar
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan (Y.C.); (I.H.I.); (J.-Y.Y.)
- Department of Obstetrics and Gynecology, Faculty of Medicine, Airlangga University, Surabaya 60286, Indonesia;
| | - Yeh Chin
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan (Y.C.); (I.H.I.); (J.-Y.Y.)
| | - Ibrahim Haruna Ibrahim
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan (Y.C.); (I.H.I.); (J.-Y.Y.)
| | - Brahmana A. Tjokroprawiro
- Department of Obstetrics and Gynecology, Faculty of Medicine, Airlangga University, Surabaya 60286, Indonesia;
| | - Jer-Yen Yang
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan (Y.C.); (I.H.I.); (J.-Y.Y.)
| | - Ming Zhou
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha 410013, China;
| | - Natalie R. Gassman
- Department of Pharmacology and Toxicology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Ming Tan
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan (Y.C.); (I.H.I.); (J.-Y.Y.)
- Institute of Biochemistry and Molecular Biology, Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
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31
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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32
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Yabaji SM, Rukhlenko OS, Chatterjee S, Bhattacharya B, Wood E, Kasaikina M, Kholodenko BN, Gimelbrant AA, Kramnik I. Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages. SCIENCE ADVANCES 2023; 9:eadh4119. [PMID: 37756395 PMCID: PMC10530096 DOI: 10.1126/sciadv.adh4119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Understanding cell state transitions and purposefully controlling them to improve therapies is a longstanding challenge in biological research and medicine. Here, we identify a transcriptional signature that distinguishes activated macrophages from the tuberculosis (TB) susceptible and resistant mice. We then apply the cSTAR (cell state transition assessment and regulation) approach to data from screening-by-RNA sequencing to identify chemical perturbations that shift the transcriptional state of tumor necrosis factor (TNF)-activated TB-susceptible macrophages toward that of TB-resistant cells, i.e., prevents their aberrant activation without suppressing beneficial TNF responses. Last, we demonstrate that the compounds identified with this approach enhance the resistance of the TB-susceptible mouse macrophages to virulent Mycobacterium tuberculosis.
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Affiliation(s)
- Shivraj M. Yabaji
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland
| | - Sujoy Chatterjee
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Bidisha Bhattacharya
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Emily Wood
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland
| | - Marina Kasaikina
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
- Pulmonary Center, The Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
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33
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Zhao N, Kabotyanski EB, Saltzman AB, Malovannaya A, Yuan X, Reineke LC, Lieu N, Gao Y, Pedroza DA, Calderon SJ, Smith AJ, Hamor C, Safari K, Savage S, Zhang B, Zhou J, Solis LM, Hilsenbeck SG, Fan C, Perou CM, Rosen JM. Targeting EIF4A triggers an interferon response to synergize with chemotherapy and suppress triple-negative breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559973. [PMID: 37808840 PMCID: PMC10557675 DOI: 10.1101/2023.09.28.559973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Protein synthesis is frequently dysregulated in cancer and selective inhibition of mRNA translation represents an attractive cancer therapy. Here, we show that therapeutically targeting the RNA helicase eIF4A by Zotatifin, the first-in-class eIF4A inhibitor, exerts pleiotropic effects on both tumor cells and the tumor immune microenvironment in a diverse cohort of syngeneic triple-negative breast cancer (TNBC) mouse models. Zotatifin not only suppresses tumor cell proliferation but also directly repolarizes macrophages towards an M1-like phenotype and inhibits neutrophil infiltration, which sensitizes tumors to immune checkpoint blockade. Mechanistic studies revealed that Zotatifin reprograms the tumor translational landscape, inhibits the translation of Sox4 and Fgfr1, and induces an interferon response uniformly across models. The induction of an interferon response is partially due to the inhibition of Sox4 translation by Zotatifin. A similar induction of interferon-stimulated genes was observed in breast cancer patient biopsies following Zotatifin treatment. Surprisingly, Zotatifin significantly synergizes with carboplatin to trigger DNA damage and an even heightened interferon response resulting in T cell-dependent tumor suppression. These studies identified a vulnerability of eIF4A in TNBC, potential pharmacodynamic biomarkers for Zotatifin, and provide a rationale for new combination regimens comprising Zotatifin and chemotherapy or immunotherapy as treatments for TNBC.
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Affiliation(s)
- Na Zhao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Elena B. Kabotyanski
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, Texas, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Xueying Yuan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Lucas C. Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Nadia Lieu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yang Gao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Diego A Pedroza
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Sebastian J Calderon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Alex J Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Clark Hamor
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Kazem Safari
- Texas A&M Health Science Center, Houston, Texas, USA
| | - Sara Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jianling Zhou
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Susan G. Hilsenbeck
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey M. Rosen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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34
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Volegova MP, Hermosillo C, Cate JHD. The Helix-Loop-Helix motif of human EIF3A regulates translation of proliferative cellular mRNAs. PLoS One 2023; 18:e0292080. [PMID: 37768948 PMCID: PMC10538695 DOI: 10.1371/journal.pone.0292080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
Improper regulation of translation initiation, a vital checkpoint of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) is associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiation in vitro. Here we show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, including MYC. We demonstrate that the HLH motif of EIF3A acts specifically on the 5' UTR of MYC mRNA and modulates the function of EIF4A1 on select transcripts during translation initiation. In Ramos lymphoma cell lines, which are dependent on MYC overexpression, mutations in the HLH motif greatly reduce MYC expression, impede proliferation and sensitize cells to anti-cancer compounds. These results reveal the potential of the EIF3A HLH motif in eIF3 as a promising chemotherapeutic target.
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Affiliation(s)
- Marina P. Volegova
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Cynthia Hermosillo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- Department of Chemistry, University of California, Berkeley, CA, United States of America
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
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35
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Sharma C, Kadosh D. Post-transcriptional control of antifungal resistance in human fungal pathogens. Crit Rev Microbiol 2023; 49:469-484. [PMID: 35634915 PMCID: PMC9766424 DOI: 10.1080/1040841x.2022.2080527] [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: 01/12/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 11/03/2022]
Abstract
Global estimates suggest that over 300 million individuals of all ages are affected by serious fungal infections every year, culminating in about 1.7 million deaths. The societal and economic burden on the public health sector due to opportunistic fungal pathogens is quite significant, especially among immunocompromised patients. Despite the high clinical significance of these infectious agents, treatment options are limited with only three major classes of antifungal drugs approved for use. Clinical management of fungal diseases is further compromised by the emergence of antifungal resistant strains. Transcriptional and genetic mechanisms that control drug resistance in human fungal pathogens are well-studied and include drug target alteration, upregulation of drug efflux pumps as well as changes in drug affinity and abundance of target proteins. In this review, we highlight several recently discovered novel post-transcriptional mechanisms that control antifungal resistance, which involve regulation at the translational, post-translational, epigenetic, and mRNA stability levels. The discovery of many of these novel mechanisms has opened new avenues for the development of more effective antifungal treatment strategies and new insights, perspectives, and future directions that will facilitate this process are discussed.
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Affiliation(s)
- Cheshta Sharma
- Department of Microbiology, Immunology and Molecular Genetics University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - David Kadosh
- Department of Microbiology, Immunology and Molecular Genetics University of Texas Health Science Center at San Antonio, San Antonio, TX
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36
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Zhuang Y, Li Z, Xiong S, Sun C, Li B, Wu SA, Lyu J, Shi X, Yang L, Chen Y, Bao Z, Li X, Sun C, Chen Y, Deng H, Li T, Wu Q, Qi L, Huang Y, Yang X, Lin Y. Circadian clocks are modulated by compartmentalized oscillating translation. Cell 2023; 186:3245-3260.e23. [PMID: 37369203 DOI: 10.1016/j.cell.2023.05.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/12/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023]
Abstract
Terrestrial organisms developed circadian rhythms for adaptation to Earth's quasi-24-h rotation. Achieving precise rhythms requires diurnal oscillation of fundamental biological processes, such as rhythmic shifts in the cellular translational landscape; however, regulatory mechanisms underlying rhythmic translation remain elusive. Here, we identified mammalian ATXN2 and ATXN2L as cooperating master regulators of rhythmic translation, through oscillating phase separation in the suprachiasmatic nucleus along circadian cycles. The spatiotemporal oscillating condensates facilitate sequential initiation of multiple cycling processes, from mRNA processing to protein translation, for selective genes including core clock genes. Depleting ATXN2 or 2L induces opposite alterations to the circadian period, whereas the absence of both disrupts translational activation cycles and weakens circadian rhythmicity in mice. Such cellular defect can be rescued by wild type, but not phase-separation-defective ATXN2. Together, we revealed that oscillating translation is regulated by spatiotemporal condensation of two master regulators to achieve precise circadian rhythm in mammals.
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Affiliation(s)
- Yanrong Zhuang
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhiyuan Li
- School of Life Sciences, MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Shiyue Xiong
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chujie Sun
- School of Life Sciences, MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Boya Li
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuangcheng Alivia Wu
- Department of Molecular & Integrative Physiology, Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| | - Jiali Lyu
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiang Shi
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education, National Health Commission of China, Peking University, Beijing 100191, China
| | - Yutong Chen
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhangbin Bao
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Li
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuhanwen Sun
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuling Chen
- School of Life Sciences, MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- School of Life Sciences, MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tingting Li
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Ministry of Education, National Health Commission of China, Peking University, Beijing 100191, China
| | - Qingfeng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Qi
- Department of Molecular & Integrative Physiology, Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| | - Yue Huang
- China National Clinical Research Center for Neurological Diseases and Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China; Phamalology Department, School of Biomedical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Xuerui Yang
- School of Life Sciences, MOE Key Laboratory of Bioinformatics, Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China.
| | - Yi Lin
- State Key Laboratory of Membrane Biology, IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Livingston NM, Kwon J, Valera O, Saba JA, Sinha NK, Reddy P, Nelson B, Wolfe C, Ha T, Green R, Liu J, Wu B. Bursting translation on single mRNAs in live cells. Mol Cell 2023; 83:2276-2289.e11. [PMID: 37329884 PMCID: PMC10330622 DOI: 10.1016/j.molcel.2023.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/27/2023] [Accepted: 05/14/2023] [Indexed: 06/19/2023]
Abstract
Stochasticity has emerged as a mechanism of gene regulation. Much of this so-called "noise" has been attributed to bursting transcription. Although bursting transcription has been studied extensively, the role of stochasticity in translation has not been fully investigated due to the lack of enabling imaging technology. In this study, we developed techniques to track single mRNAs and their translation in live cells for hours, allowing the measurement of previously uncharacterized translation dynamics. We applied genetic and pharmacological perturbations to control translation kinetics and found that, like transcription, translation is not a constitutive process but instead cycles between inactive and active states, or "bursts." However, unlike transcription, which is largely frequency-modulated, complex structures in the 5'-untranslated region alter burst amplitudes. Bursting frequency can be controlled through cap-proximal sequences and trans-acting factors such as eIF4F. We coupled single-molecule imaging with stochastic modeling to quantitatively determine the kinetic parameters of translational bursting.
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Affiliation(s)
- Nathan M Livingston
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jiwoong Kwon
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oliver Valera
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James A Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pranav Reddy
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clara Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jian Liu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Naineni SK, Cencic R, Robert F, Brown LE, Haque M, Scott-Talib J, Sénéchal P, Schmeing TM, Porco JA, Pelletier J. Exploring the targeting spectrum of rocaglates among eIF4A homologs. RNA (NEW YORK, N.Y.) 2023; 29:826-835. [PMID: 36882295 PMCID: PMC10187672 DOI: 10.1261/rna.079318.122] [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: 06/15/2022] [Accepted: 02/16/2023] [Indexed: 05/18/2023]
Abstract
Inhibition of eukaryotic translation initiation through unscheduled RNA clamping of the DEAD-box (DDX) RNA helicases eIF4A1 and eIF4A2 has been documented for pateamine A (PatA) and rocaglates-two structurally different classes of compounds that share overlapping binding sites on eIF4A. Clamping of eIF4A to RNA causes steric blocks that interfere with ribosome binding and scanning, rationalizing the potency of these molecules since not all eIF4A molecules need to be engaged to elicit a biological effect. In addition to targeting translation, PatA and analogs have also been shown to target the eIF4A homolog, eIF4A3-a helicase necessary for exon junction complex (EJC) formation. EJCs are deposited on mRNAs upstream of exon-exon junctions and, when present downstream from premature termination codons (PTCs), participate in nonsense-mediated decay (NMD), a quality control mechanism aimed at preventing the production of dominant-negative or gain-of-function polypeptides from faulty mRNA transcripts. We find that rocaglates can also interact with eIF4A3 to induce RNA clamping. Rocaglates also inhibit EJC-dependent NMD in mammalian cells, but this does not appear to be due to induced eIF4A3-RNA clamping, but rather a secondary consequence of translation inhibition incurred by clamping eIF4A1 and eIF4A2 to mRNA.
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Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - Regina Cencic
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - Lauren E Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Massachusetts 02215, USA
| | - Minza Haque
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | | | - Patrick Sénéchal
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Quebec, H3G 0B1 Canada
| | - John A Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Massachusetts 02215, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Quebec, H3G 1Y6 Canada
- Centre de Recherche en Biologie Structurale (CRBS), McGill University, Quebec, H3G 0B1 Canada
- McGill Research Center on Complex Traits, McGill University, Quebec, H3G 0B1 Canada
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Quebec, H3A 1A3 Canada
- Department of Oncology, McGill University, Quebec, H4A 3T2 Canada
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Grindheim AK, Patil SS, Nebigil CG, Désaubry L, Vedeler A. The flavagline FL3 interferes with the association of Annexin A2 with the eIF4F initiation complex and transiently stimulates the translation of annexin A2 mRNA. Front Cell Dev Biol 2023; 11:1094941. [PMID: 37250892 PMCID: PMC10214161 DOI: 10.3389/fcell.2023.1094941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/28/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction: Annexin A2 (AnxA2) plays a critical role in cell transformation, immune response, and resistance to cancer therapy. Besides functioning as a calcium- and lipidbinding protein, AnxA2 also acts as an mRNA-binding protein, for instance, by interacting with regulatory regions of specific cytoskeleton-associated mRNAs. Methods and Results: Nanomolar concentrations of FL3, an inhibitor of the translation factor eIF4A, transiently increases the expression of AnxA2 in PC12 cells and stimulates shortterm transcription/translation of anxA2 mRNA in the rabbit reticulocyte lysate. AnxA2 regulates the translation of its cognate mRNA by a feed-back mechanism, which can partly be relieved by FL3. Results obtained using the holdup chromatographic retention assay results suggest that AnxA2 interacts transiently with eIF4E (possibly eIF4G) and PABP in an RNA-independent manner while cap pulldown experiments indicate a more stable RNA-dependent interaction. Short-term (2 h) treatment of PC12 cells with FL3 increases the amount of eIF4A in cap pulldown complexes of total lysates, but not of the cytoskeletal fraction. AnxA2 is only present in cap analogue-purified initiation complexes from the cytoskeletal fraction and not total lysates confirming that AnxA2 binds to a specific subpopulation of mRNAs. Discussion: Thus, AnxA2 interacts with PABP1 and subunits of the initiation complex eIF4F, explaining its inhibitory effect on translation by preventing the formation of the full eIF4F complex. This interaction appears to be modulated by FL3. These novel findings shed light on the regulation of translation by AnxA2 and contribute to a better understanding of the mechanism of action of eIF4A inhibitors.
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Affiliation(s)
- Ann Kari Grindheim
- Department of Biomedicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Sudarshan S. Patil
- Department of Biomedicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Canan G. Nebigil
- Regenerative Nanomedicine Laboratory (UMR1260), Faculty of Medicine, FMTS, INSERM-University of Strasbourg, Strasbourg, France
| | - Laurent Désaubry
- Regenerative Nanomedicine Laboratory (UMR1260), Faculty of Medicine, FMTS, INSERM-University of Strasbourg, Strasbourg, France
| | - Anni Vedeler
- Department of Biomedicine, Faculty of Medicine, University of Bergen, Bergen, Norway
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40
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Bartish M, Abraham MJ, Gonçalves C, Larsson O, Rolny C, Del Rincón SV. The role of eIF4F-driven mRNA translation in regulating the tumour microenvironment. Nat Rev Cancer 2023; 23:408-425. [PMID: 37142795 DOI: 10.1038/s41568-023-00567-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/06/2023]
Abstract
Cells can rapidly adjust their proteomes in dynamic environments by regulating mRNA translation. There is mounting evidence that dysregulation of mRNA translation supports the survival and adaptation of cancer cells, which has stimulated clinical interest in targeting elements of the translation machinery and, in particular, components of the eukaryotic initiation factor 4F (eIF4F) complex such as eIF4E. However, the effect of targeting mRNA translation on infiltrating immune cells and stromal cells in the tumour microenvironment (TME) has, until recently, remained unexplored. In this Perspective article, we discuss how eIF4F-sensitive mRNA translation controls the phenotypes of key non-transformed cells in the TME, with an emphasis on the underlying therapeutic implications of targeting eIF4F in cancer. As eIF4F-targeting agents are in clinical trials, we propose that a broader understanding of their effect on gene expression in the TME will reveal unappreciated therapeutic vulnerabilities that could be used to improve the efficacy of existing cancer therapies.
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Affiliation(s)
- Margarita Bartish
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada
- Science for Life Laboratory, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Madelyn J Abraham
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada
| | - Christophe Gonçalves
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada
| | - Ola Larsson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Rolny
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Sonia V Del Rincón
- Department of Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada.
- Segal Cancer Center, Lady Davis Institute and Jewish General Hospital, Montreal, QC, Canada.
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Shiraishi C, Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 2023; 14:2131. [PMID: 37080962 PMCID: PMC10119107 DOI: 10.1038/s41467-023-37838-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.
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Affiliation(s)
- Chisa Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Taishi Yamamoto
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Shouji Matsushima
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiroyuki Tsutsui
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
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Coupe S, Fakhri N. ATP-induced crosslinking of a biomolecular condensate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.535486. [PMID: 37131735 PMCID: PMC10153144 DOI: 10.1101/2023.04.18.535486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DEAD-box helicases are important regulators of biomolecular condensates. However, the mechanisms through which these enzymes affect the dynamics of biomolecular condensates have not been systematically explored. Here, we demonstrate the mechanism by which mutation of a DEAD-box helicase’s catalytic core alters ribonucleoprotein condensate dynamics in the presence of ATP. Through altering RNA length within the system, we are able to attribute the altered biomolecular dynamics and material properties to physical crosslinking of RNA facilitated by the mutant helicase. These results suggest the mutant condensates approach a gel transition when RNA length is increased to lengths comparable to eukaryotic mRNA. Lastly, we show that this crosslinking effect is tunable with ATP concentration, uncovering a system whose RNA mobility and material properties vary with enzyme activity. More generally, these findings point to a fundamental mechanism for modulating condensate dynamics and emergent material properties through nonequilibrium, molecular-scale interactions. Significance Biomolecular condensates are membraneless organelles which organize cellular biochemistry. These structures have a diversity of material properties and dynamics which are crucial to their function. How condensate properties are determined by biomolecular interactions and enzyme activity remain open questions. DEAD-box helicases have been identified as central regulators of many protein-RNA condensates, though their specific mechanistic roles are ill-defined. In this work, we demonstrate that a DEAD-box helicase mutation crosslinks condensate RNA in an ATP-dependent fashion via protein-RNA clamping. Protein and RNA diffusion can be tuned with ATP concentration, corresponding to an order of magnitude change in condensate viscosity. These findings expand our understanding of control points for cellular biomolecular condensates that have implications for medicine and bioengineering.
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Affiliation(s)
- Sebastian Coupe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nikta Fakhri
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
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43
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Fedorova AD, Tierney JA, Michel AM, Baranov PV. RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2023.168043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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Naineni SK, Robert F, Nagar B, Pelletier J. Targeting DEAD-box RNA helicases: The emergence of molecular staples. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1738. [PMID: 35581936 DOI: 10.1002/wrna.1738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/29/2022]
Abstract
RNA helicases constitute a large family of proteins that play critical roles in mediating RNA function. They have been implicated in all facets of gene expression pathways involving RNA, from transcription to processing, transport and translation, and storage and decay. There is significant interest in developing small molecule inhibitors to RNA helicases as some family members have been documented to be dysregulated in neurological and neurodevelopment disorders, as well as in cancers. Although different functional properties of RNA helicases offer multiple opportunities for small molecule development, molecular staples have recently come to the forefront. These bifunctional molecules interact with both protein and RNA components to lock them together, thereby imparting novel gain-of-function properties to their targets. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Bhushan Nagar
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
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45
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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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46
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Chen M, Kumakura N, Saito H, Muller R, Nishimoto M, Mito M, Gan P, Ingolia NT, Shirasu K, Ito T, Shichino Y, Iwasaki S. A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants. eLife 2023; 12:81302. [PMID: 36852480 PMCID: PMC9977294 DOI: 10.7554/elife.81302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/12/2023] [Indexed: 03/01/2023] Open
Abstract
Plants often generate secondary metabolites as defense mechanisms against parasites. Although some fungi may potentially overcome the barrier presented by antimicrobial compounds, only a limited number of examples and molecular mechanisms of resistance have been reported. Here, we found an Aglaia plant-parasitizing fungus that overcomes the toxicity of rocaglates, which are translation inhibitors synthesized by the plant, through an amino acid substitution in a eukaryotic translation initiation factor (eIF). De novo transcriptome assembly revealed that the fungus belongs to the Ophiocordyceps genus and that its eIF4A, a molecular target of rocaglates, harbors an amino acid substitution critical for rocaglate binding. Ribosome profiling harnessing a cucumber-infecting fungus, Colletotrichum orbiculare, demonstrated that the translational inhibitory effects of rocaglates were largely attenuated by the mutation found in the Aglaia parasite. The engineered C. orbiculare showed a survival advantage on cucumber plants with rocaglates. Our study exemplifies a plant-fungus tug-of-war centered on secondary metabolites produced by host plants.
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Affiliation(s)
- Mingming Chen
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Naoyoshi Kumakura
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource ScienceYokohamaJapan
| | - Hironori Saito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Ryan Muller
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Madoka Nishimoto
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Pamela Gan
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource ScienceYokohamaJapan
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Department of Biological Science, Graduate School of Science, The University of TokyoTokyoJapan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering ResearchWakoJapan
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Saito H, Osaki T, Ikeuchi Y, Iwasaki S. High-throughput Assessment of Mitochondrial Protein Synthesis in Mammalian Cells Using Mito-FUNCAT FACS. Bio Protoc 2023; 13:e4602. [PMID: 36816992 PMCID: PMC9909305 DOI: 10.21769/bioprotoc.4602] [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: 09/12/2022] [Revised: 10/24/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023] Open
Abstract
In addition to cytosolic protein synthesis, mitochondria also utilize another translation system that is tailored for mRNAs encoded in the mitochondrial genome. The importance of mitochondrial protein synthesis has been exemplified by the diverse diseases associated with in organello translation deficiencies. Various methods have been developed to monitor mitochondrial translation, such as the classic method of labeling newly synthesized proteins with radioisotopes and the more recent ribosome profiling. However, since these methods always assess the average cell population, measuring the mitochondrial translation capacity in individual cells has been challenging. To overcome this issue, we recently developed mito-fluorescent noncanonical amino acid tagging (FUNCAT) fluorescence-activated cell sorting (FACS), which labels nascent peptides generated by mitochondrial ribosomes with a methionine analog, L-homopropargylglycine (HPG), conjugates the peptides with fluorophores by an in situ click reaction, and detects the signal in individual cells by FACS equipment. With this methodology, the hidden heterogeneity of mitochondrial translation in cell populations can be addressed.
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Affiliation(s)
- Hironori Saito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tatsuya Osaki
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
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Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
,
*For correspondence:
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48
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Li F, Fang J, Yu Y, Hao S, Zou Q, Zeng Q, Yang X. Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A. Nat Commun 2023; 14:553. [PMID: 36725859 PMCID: PMC9891901 DOI: 10.1038/s41467-023-36290-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
The quickly accumulating ribosome profiling data is an insightful resource for studying the critical details of translation regulation under various biological contexts. Rocaglamide A (RocA), an antitumor heterotricyclic natural compound, has been shown to inhibit translation initiation of a large group of mRNA species by clamping eIF4A onto poly-purine motifs in the 5' UTRs. However, reanalysis of previous ribosome profiling datasets reveals an unexpected shift of the ribosome occupancy pattern, upon RocA treatment in various types of cells, during early translation elongation for a specific group of mRNA transcripts without poly-purine motifs over-represented in their 5' UTRs. Such perturbation of translation elongation dynamics can be attributed to the blockage of translating ribosomes due to the binding of eIF4A to the poly-purine sequence in coding regions. In summary, our study presents the complete dual modes of RocA in blocking translation initiation and elongation, which underlie the potent antitumor effect of RocA.
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Affiliation(s)
- Fajin Li
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China.
| | - Jianhuo Fang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Yifan Yu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Sijia Hao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China
| | - Qin Zou
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Qinglin Zeng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing, 100084, China.
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49
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eIF4A1 Is a Prognostic Marker and Actionable Target in Human Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:ijms24032055. [PMID: 36768380 PMCID: PMC9917075 DOI: 10.3390/ijms24032055] [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: 12/10/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary liver tumor with high lethality and increasing incidence worldwide. While tumor resection or liver transplantation is effective in the early stages of the disease, the therapeutic options for advanced HCC remain limited and the benefits are temporary. Thus, novel therapeutic targets and more efficacious treatments against this deadly cancer are urgently needed. Here, we investigated the pathogenetic and therapeutic role of eukaryotic initiation factor 4A1 (eIF4A1) in this tumor type. We observed consistent eIF4A1 upregulation in HCC lesions compared with non-tumorous surrounding liver tissues. In addition, eIF4A1 levels were negatively correlated with the prognosis of HCC patients. In HCC lines, the exposure to various eIF4A inhibitors triggered a remarkable decline in proliferation and augmented apoptosis, paralleled by the inhibition of several oncogenic pathways. Significantly, anti-growth effects were achieved at nanomolar concentrations of the eIF4A1 inhibitors and were further increased by the simultaneous administration of the pan mTOR inhibitor, Rapalink-1. In conclusion, our results highlight the pathogenetic relevance of eIF4A1 in HCC and recommend further evaluation of the potential usefulness of pharmacological combinations based on eIF4A and mTOR inhibitors in treating this aggressive tumor.
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50
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Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBP α. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524343. [PMID: 36711859 PMCID: PMC9882168 DOI: 10.1101/2023.01.16.524343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor CCAAT-enhancer binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of the CEBPA transcript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identify trans-acting factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPα isoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.
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Affiliation(s)
| | - Lucas Ferguson
- Department of Molecular and Cell Biology, University of California, Berkeley
| | - Nicholas T. Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley
- Center for Computational Biology and California Institute for Quantitative Biosciences, University of California, Berkeley
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