1
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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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2
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Oblinger JL, Wang J, Wetherell GD, Agarwal G, Wilson TA, Benson NR, Fenger JM, Fuchs JR, Kinghorn AD, Chang LS. Anti-tumor effects of the eIF4A inhibitor didesmethylrocaglamide and its derivatives in human and canine osteosarcomas. Sci Rep 2024; 14:19349. [PMID: 39164287 PMCID: PMC11335891 DOI: 10.1038/s41598-024-69171-3] [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: 05/29/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Inhibition of translation initiation using eIF4A inhibitors like (-)-didesmethylrocaglamide [(-)-DDR] and (-)-rocaglamide [(-)-Roc] is a potential cancer treatment strategy as they simultaneously diminish multiple oncogenic drivers. We showed that human and dog osteosarcoma cells expressed higher levels of eIF4A1/2 compared with mesenchymal stem cells. Genetic depletion of eIF4A1 and/or 2 slowed osteosarcoma cell growth. To advance preclinical development of eIF4A inhibitors, we demonstrated the importance of (-)-chirality in DDR for growth-inhibitory activity. Bromination of DDR at carbon-5 abolished growth-inhibitory activity, while acetylating DDR at carbon-1 was tolerated. Like (-)-DDR, (±)-DDR, and (-)-Roc, (±)-DDR-acetate increased γH2A.X levels and induced G2/M arrest and apoptosis. Consistent with translation inhibition, these rocaglates decreased the levels of several mitogenic kinases, the STAT3 transcription factor, and the stress-activated protein kinase p38. However, phosphorylated p38 was greatly enhanced in treated cells, suggesting activation of stress response pathways. RNA sequencing identified RHOB as a top upregulated gene in both (-)-DDR- and (-)-Roc-treated osteosarcoma cells, but the Rho inhibitor Rhosin did not enhance the growth-inhibitory activity of (-)-DDR or (-)-Roc. Nonetheless, these rocaglates potently suppressed tumor growth in a canine osteosarcoma patient-derived xenograft model. These results suggest that these eIF4A inhibitors can be leveraged to treat both human and dog osteosarcomas.
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Affiliation(s)
- Janet L Oblinger
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Jack Wang
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Georgia D Wetherell
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Garima Agarwal
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University College of Pharmacy, Columbus, OH, 43210, USA
| | - Tyler A Wilson
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University College of Pharmacy, Columbus, OH, 43210, USA
| | - Nicole R Benson
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University College of Pharmacy, Columbus, OH, 43210, USA
| | - Joelle M Fenger
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Ethos Veterinary Health and Ethos Discovery (501c3), Woburn, MA, 01801, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University College of Pharmacy, Columbus, OH, 43210, USA
| | - A Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University College of Pharmacy, Columbus, OH, 43210, USA
| | - Long-Sheng Chang
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA.
- Departments of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
- Departments of Otolaryngology-Head & Neck Surgery, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
- Departments of Pathology, The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
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3
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Keiser PT, Zhang W, Ricca M, Wacquiez A, Grimins A, Cencic R, Patten JJ, Shah P, Padilha E, Connor JH, Pelletier J, Lyons SM, Saeed M, Brown LE, Porco JA, Davey RA. Amidino-rocaglates (ADRs), a class of synthetic rocaglates, are potent inhibitors of SARS-CoV-2 replication through inhibition of viral protein synthesis. Antiviral Res 2024; 230:105976. [PMID: 39117283 DOI: 10.1016/j.antiviral.2024.105976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/12/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
Coronaviruses are highly transmissible respiratory viruses that cause symptoms ranging from mild congestion to severe respiratory distress. The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has underscored the need for new antivirals with broad-acting mechanisms to combat increasing emergence of new variants. Currently, there are only a few antivirals approved for treatment of SARS-CoV-2. Previously, the rocaglate natural product silvestrol and synthetic rocaglates such as CR-1-31b were shown to have antiviral effects by inhibiting eukaryotic translation initiation factor 4A1 (eIF4A) function and virus protein synthesis. In this study, we evaluated amidino-rocaglates (ADRs), a class of synthetic rocaglates with the most potent eIF4A-inhibitory activity to-date, for inhibition of SARS-CoV-2 infection. This class of compounds showed low nanomolar potency against multiple SARS-CoV-2 variants and in multiple cell types, including human lung-derived cells, with strong inhibition of virus over host protein synthesis and low cytotoxicity. The most potent ADRs were also shown to be active against two highly pathogenic and distantly related coronaviruses, SARS-CoV and MERS-CoV. Mechanistically, cells with mutations of eIF4A1, which are known to reduce rocaglate interaction displayed reduced ADR-associated loss of cellular function, consistent with targeting of protein synthesis. Overall, ADRs and derivatives may offer new potential treatments for SARS-CoV-2 with the goal of developing a broad-acting anti-coronavirus agent.
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Affiliation(s)
- Patrick T Keiser
- Department of Virology, Immunology, and Microbiology, Boston University Medical School, Boston, MA, 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, MA, 02118, USA
| | - Wenhan Zhang
- Boston University Center for Molecular Discovery (BU-CMD), Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Michael Ricca
- Boston University Center for Molecular Discovery (BU-CMD), Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Alan Wacquiez
- National Emerging Infectious Diseases Laboratories, Boston University, MA, 02118, USA; Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, 02118, USA
| | - Autumn Grimins
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, 02118, USA
| | - Regina Cencic
- Department of Biochemistry, Department of Oncology and Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada, H3G 1Y6
| | - J J Patten
- Department of Virology, Immunology, and Microbiology, Boston University Medical School, Boston, MA, 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, MA, 02118, USA
| | - Pranav Shah
- National Institutes of Health, National Center for Advancing Translational Sciences, Bethesda, MD, 20892, USA
| | - Elias Padilha
- National Institutes of Health, National Center for Advancing Translational Sciences, Bethesda, MD, 20892, USA
| | - John H Connor
- Department of Virology, Immunology, and Microbiology, Boston University Medical School, Boston, MA, 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, MA, 02118, USA
| | - Jerry Pelletier
- Department of Biochemistry, Department of Oncology and Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada, H3G 1Y6
| | - Shawn M Lyons
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, 02118, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories, Boston University, MA, 02118, USA; Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, 02118, USA
| | - Lauren E Brown
- Boston University Center for Molecular Discovery (BU-CMD), Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - John A Porco
- Boston University Center for Molecular Discovery (BU-CMD), Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Robert A Davey
- Department of Virology, Immunology, and Microbiology, Boston University Medical School, Boston, MA, 02118, USA; National Emerging Infectious Diseases Laboratories, Boston University, MA, 02118, USA.
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4
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Oblinger J, Wang J, Wetherell G, Agarwal G, Wilson T, Benson N, Fenger J, Fuchs J, Kinghorn AD, Chang L. Anti-tumor Effects of the eIF4A Inhibitor Didesmethylrocaglamide and Its Derivatives in Human and Canine Osteosarcomas. RESEARCH SQUARE 2024:rs.3.rs-4494024. [PMID: 38947012 PMCID: PMC11213195 DOI: 10.21203/rs.3.rs-4494024/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Inhibition of translation initiation using eIF4A inhibitors like (-)-didesmethylrocaglamide [(-)-DDR] and (-)-rocaglamide [(-)-Roc] is a potential cancer treatment strategy as they simultaneously diminish multiple oncogenic drivers. We showed that human and dog osteosarcoma cells expressed high levels of eIF4A1/2, particularly eIF4A2. Genetic depletion of eIF4A1 and/or 2 slowed osteosarcoma cell growth. To advance preclinical development of eIF4A inhibitors, we demonstrated the importance of (-)-chirality in DDR for growth-inhibitory activity. Bromination of DDR at carbon-5 abolished growth-inhibitory activity, while acetylating DDR at carbon-1 was tolerated. Like DDR and Roc, DDR-acetate increased the γH2A.X levels and induced G2/M arrest and apoptosis. Consistent with translation inhibition, these rocaglates decreased the levels of several mitogenic kinases, the STAT3 transcription factor, and the stress-activated protein kinase p38. However, phosphorylated p38 was greatly enhanced in treated cells, suggesting activation of stress response pathways. RNA sequencing identified RHOB as a top upregulated gene in both DDR- and Roc-treated osteosarcoma cells, but the Rho inhibitor Rhosin did not enhance the growth-inhibitory activity of (-)-DDR or (-)-Roc. Nonetheless, these rocaglates potently suppressed tumor growth in a canine osteosarcoma patient-derived xenograft model. These results suggest that these eIF4A inhibitors can be leveraged to treat both human and dog osteosarcomas.
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Affiliation(s)
- Janet Oblinger
- Abigail Wexner Research Institute at Nationwide Children's Hospital
| | - Jack Wang
- Abigail Wexner Research Institute at Nationwide Children's Hospital
| | | | | | | | | | | | | | | | - Long Chang
- Abigail Wexner Research Institute at Nationwide Children's Hospital
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5
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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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6
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Thirman HL, Hayes MJ, Brown LE, Porco JA, Irish JM. Single Cell Profiling Distinguishes Leukemia-Selective Chemotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.591362. [PMID: 38826485 PMCID: PMC11142275 DOI: 10.1101/2024.05.01.591362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
A central challenge in chemical biology is to distinguish molecular families in which small structural changes trigger large changes in cell biology. Such families might be ideal scaffolds for developing cell-selective chemical effectors - for example, molecules that activate DNA damage responses in malignant cells while sparing healthy cells. Across closely related structural variants, subtle structural changes have the potential to result in contrasting bioactivity patterns across different cell types. Here, we tested a 600-compound Diversity Set of screening molecules from the Boston University Center for Molecular Discovery (BU-CMD) in a novel phospho-flow assay that tracked fundamental cell biological processes, including DNA damage response, apoptosis, M-phase cell cycle, and protein synthesis in MV411 leukemia cells. Among the chemotypes screened, synthetic congeners of the rocaglate family were especially bioactive. In follow-up studies, 37 rocaglates were selected and deeply characterized using 12 million additional cellular measurements across MV411 leukemia cells and healthy peripheral blood mononuclear cells. Of the selected rocaglates, 92% displayed significant bioactivity in human cells, and 65% selectively induced DNA damage responses in leukemia and not healthy human blood cells. Furthermore, the signaling and cell-type selectivity were connected to structural features of rocaglate subfamilies. In particular, three rocaglates from the rocaglate pyrimidinone (RP) structural subclass were the only molecules that activated exceptional DNA damage responses in leukemia cells without activating a detectable DNA damage response in healthy cells. These results indicate that the RP subset should be extensively characterized for anticancer therapeutic potential as it relates to the DNA damage response. This single cell profiling approach advances a chemical biology platform to dissect how systematic variations in chemical structure can profoundly and differentially impact basic functions of healthy and diseased cells.
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Affiliation(s)
- Hannah L. Thirman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN, USA
| | - Madeline J. Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren E. Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Therapeutic targeting of eukaryotic initiation factor (eIF) 4E. Biochem Soc Trans 2023; 51:113-124. [PMID: 36661272 DOI: 10.1042/bst20220285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023]
Abstract
Fundamental studies unraveled the role of eukaryotic initiation factor (eIF) 4E in mRNA translation and its control. Under physiological conditions, regulation of translation by eIF4E is essential to cellular homeostasis. Under stress, gene flow information is parsed by eIF4E to support adaptive mechanisms that favor cell survival. Dysregulated eIF4E activity fuels tumor formation and progression and modulates response to therapy. Thus, there has been heightened interest in understanding eIF4E function in controlling gene expression as well as developing strategies to block its activity to treat disease.
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17
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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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18
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Fooks K, Galicia-Vazquez G, Gife V, Schcolnik-Cabrera A, Nouhi Z, Poon WWL, Luo V, Rys RN, Aloyz R, Orthwein A, Johnson NA, Hulea L, Mercier FE. EIF4A inhibition targets bioenergetic homeostasis in AML MOLM-14 cells in vitro and in vivo and synergizes with cytarabine and venetoclax. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:340. [PMID: 36482393 PMCID: PMC9733142 DOI: 10.1186/s13046-022-02542-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is an aggressive hematological cancer resulting from uncontrolled proliferation of differentiation-blocked myeloid cells. Seventy percent of AML patients are currently not cured with available treatments, highlighting the need of novel therapeutic strategies. A promising target in AML is the mammalian target of rapamycin complex 1 (mTORC1). Clinical inhibition of mTORC1 is limited by its reactivation through compensatory and regulatory feedback loops. Here, we explored a strategy to curtail these drawbacks through inhibition of an important effector of the mTORC1signaling pathway, the eukaryotic initiation factor 4A (eIF4A). METHODS We tested the anti-leukemic effect of a potent and specific eIF4A inhibitor (eIF4Ai), CR-1-31-B, in combination with cytosine arabinoside (araC) or the BCL2 inhibitor venetoclax. We utilized the MOLM-14 human AML cell line to model chemoresistant disease both in vitro and in vivo. In eIF4Ai-treated cells, we assessed for changes in survival, apoptotic priming, de novo protein synthesis, targeted intracellular metabolite content, bioenergetic profile, mitochondrial reactive oxygen species (mtROS) and mitochondrial membrane potential (MMP). RESULTS eIF4Ai exhibits anti-leukemia activity in vivo while sparing non-malignant myeloid cells. In vitro, eIF4Ai synergizes with two therapeutic agents in AML, araC and venetoclax. EIF4Ai reduces mitochondrial membrane potential (MMP) and the rate of ATP synthesis from mitochondrial respiration and glycolysis. Furthermore, eIF4i enhanced apoptotic priming while reducing the expression levels of the antiapoptotic factors BCL2, BCL-XL and MCL1. Concomitantly, eIF4Ai decreases intracellular levels of specific metabolic intermediates of the tricarboxylic acid cycle (TCA cycle) and glucose metabolism, while enhancing mtROS. In vitro redox stress contributes to eIF4Ai cytotoxicity, as treatment with a ROS scavenger partially rescued the viability of eIF4A inhibition. CONCLUSIONS We discovered that chemoresistant MOLM-14 cells rely on eIF4A-dependent cap translation for survival in vitro and in vivo. EIF4A drives an intrinsic metabolic program sustaining bioenergetic and redox homeostasis and regulates the expression of anti-apoptotic proteins. Overall, our work suggests that eIF4A-dependent cap translation contributes to adaptive processes involved in resistance to relevant therapeutic agents in AML.
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Affiliation(s)
- Katie Fooks
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada
| | | | - Victor Gife
- grid.414216.40000 0001 0742 1666Maisonneuve-Rosemont Hospital Research Centre, Montreal, Canada ,grid.14848.310000 0001 2292 3357Present Address: Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, Canada
| | | | - Zaynab Nouhi
- grid.414216.40000 0001 0742 1666Maisonneuve-Rosemont Hospital Research Centre, Montreal, Canada
| | - William W. L. Poon
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada
| | - Vincent Luo
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada
| | - Ryan N. Rys
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Physiology, McGill University, Montreal, Canada
| | - Raquel Aloyz
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Alexandre Orthwein
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada ,grid.189967.80000 0001 0941 6502Present Address: Department of Radiation Oncology, Emory School of Medicine, Atlanta, USA
| | - Nathalie A. Johnson
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Laura Hulea
- grid.414216.40000 0001 0742 1666Maisonneuve-Rosemont Hospital Research Centre, Montreal, Canada ,grid.14848.310000 0001 2292 3357Present Address: Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, Canada ,grid.14848.310000 0001 2292 3357Département de Médecine, Université de Montréal, Montreal, Canada
| | - Francois E. Mercier
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Medicine, McGill University, Montreal, Canada
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Applications and mechanisms of the cyclin-dependent kinase 4/6 inhibitor, PD-0332991, in solid tumors. Cell Oncol (Dordr) 2022; 45:1053-1071. [PMID: 36087253 DOI: 10.1007/s13402-022-00714-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2022] [Indexed: 01/10/2023] Open
Abstract
Abnormal CDK4/6-Rb-E2F signal transduction is a common finding in tumors and is a driving factor for the excessive proliferation of various tumor cells. PD-0332991, a highly specific, small molecule inhibitor for CDK4 and 6, has been shown to inhibit tumor growth by abrogating the phosphorylating capacity of CDK4/6 and suppressing Rb phosphorylation. It has been promoted for the treatment of breast cancer and potentially for other tumor types such as liver cancers, lung cancers and sarcomas. Due to the risk of monotherapy resistance, PD-0332991 is commonly used in combination with other drugs. Such combination treatments have proved able to inhibit tumor proliferation more effectively, induce stronger senescence and apoptosis, and enhance the efficiency of immunotherapy. Therefore, tumor cells with senescence induced by PD-0332991 are now used as ideal screening tools of cytolytic drugs with more efficient and thorough anti-tumor properties. With more extensive understandings about the branching points between senescence and apoptosis, it is possible to refine the dosage of PD-0332991. Better characterization of resistant cells, of inhibitors and of adverse effects such as leukopenia are needed to overcome obstacles in the use of PD-0332991. In this review of PD-0332991 research, we hope to provide guidance of transitions from laboratory findings to clinical applications of PD-0332991 and to facilitate PD-0332991-based multi-inhibitor combination therapies for various tumors.
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20
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Pedroni L, Dellafiora L, Varrà MO, Galaverna G, Ghidini S. In silico study on the Hepatitis E virus RNA Helicase and its inhibition by silvestrol, rocaglamide and other flavagline compounds. Sci Rep 2022; 12:15512. [PMID: 36109625 PMCID: PMC9477874 DOI: 10.1038/s41598-022-19818-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
Hepatitis E Virus (HEV) follows waterborne or zoonotic/foodborne transmission. Genotype 3 HEV infections are worldwide spread, especially in swine populations, representing an emerging threat for human health, both for farm workers and pork meat consumers. Unfortunately, HEV in vitro culture and analysis are still difficult, resulting in a poor understanding of its biology and hampering the implementation of counteracting strategies. Indeed, HEV encodes for only one non-structural multifunctional and multidomain protein (ORF1), which might be a good candidate for anti-HEV drugging strategies. In this context, an in silico molecular modelling approach that consisted in homology modelling to derive the 3D model target, docking study to simulate the binding event, and molecular dynamics to check complex stability over time was used. This workflow succeeded to describe ORF1 RNA Helicase domain from a molecular standpoint allowing the identification of potential inhibitory compounds among natural plant-based flavagline-related molecules such as silvestrol, rocaglamide and derivatives thereof. In the context of scouting potential anti-viral compounds and relying on the outcomes presented, further dedicated investigations on silvestrol, rocaglamide and a promising oxidized derivative have been suggested. For the sake of data reproducibility, the 3D model of HEV RNA Helicase has been made publicly available.
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21
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Lehman SL, Wechsler T, Schwartz K, Brown LE, Porco JA, Devine WG, Pelletier J, Shankavaram UT, Camphausen K, Tofilon PJ. Inhibition of the Translation Initiation Factor eIF4A Enhances Tumor Cell Radiosensitivity. Mol Cancer Ther 2022; 21:1406-1414. [PMID: 35732578 PMCID: PMC9452469 DOI: 10.1158/1535-7163.mct-22-0037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/12/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
A fundamental component of cellular radioresponse is the translational control of gene expression. Because a critical regulator of translational control is the eukaryotic translation initiation factor 4F (eIF4F) cap binding complex, we investigated whether eIF4A, the RNA helicase component of eIF4F, can serve as a target for radiosensitization. Knockdown of eIF4A using siRNA reduced translational efficiency, as determined from polysome profiles, and enhanced tumor cell radiosensitivity as determined by clonogenic survival. The increased radiosensitivity was accompanied by a delayed dispersion of radiation-induced γH2AX foci, suggestive of an inhibition of DNA double-strand break repair. Studies were then extended to (-)-SDS-1-021, a pharmacologic inhibitor of eIF4A. Treatment of cells with the rocaglate (-)-SDS-1-021 resulted in a decrease in translational efficiency as well as protein synthesis. (-)-SDS-1-021 treatment also enhanced the radiosensitivity of tumor cell lines. This (-)-SDS-1-021-induced radiosensitization was accompanied by a delay in radiation-induced γH2AX foci dispersal, consistent with a causative role for the inhibition of double-strand break repair. In contrast, although (-)-SDS-1-021 inhibited translation and protein synthesis in a normal fibroblast cell line, it had no effect on radiosensitivity of normal cells. Subcutaneous xenografts were then used to evaluate the in vivo response to (-)-SDS-1-021 and radiation. Treatment of mice bearing subcutaneous xenografts with (-)-SDS-1-021 decreased tumor translational efficiency as determined by polysome profiles. Although (-)-SDS-1-021 treatment alone had no effect on tumor growth, it significantly enhanced the radiation-induced growth delay. These results suggest that eIF4A is a tumor-selective target for radiosensitization.
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Affiliation(s)
| | | | | | - Lauren E Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts
| | - John A Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts
| | - William G Devine
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts
| | - Jerry Pelletier
- Department of Biochemistry, Oncology and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
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22
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Li M, Huang F, Xie Z, Hong H, Xu Q, Peng Z. Identification of three small nucleolar RNAs (snoRNAs) as potential prognostic markers in diffuse large B-cell lymphoma. Cancer Med 2022; 12:3812-3829. [PMID: 36812125 PMCID: PMC9939161 DOI: 10.1002/cam4.5115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a non-Hodgkin lymphoma with high mortality rates. Small nucleolar RNAs (snoRNAs) are tumor-specific biological markers, but there are few studies on the role of snoRNAs in DLBCL. MATERIALS AND METHODS Survival-related snoRNAs were selected to construct a specific snoRNA-based signature via computational analyses (Cox regression and independent prognostic analyses) to predict the prognosis of DLBCL patients. To assist in clinical applications, a nomogram was built by combining the risk model and other independent prognostic factors. Pathway analysis, gene ontology analysis, transcription factor enrichment, protein-protein interactions, and single nucleotide variant analysis were used to explore the potential biological mechanisms of co-expressed genes. RESULTS Twelve prognosis-correlated snoRNAs were selected from the DLBCL patient cohort of microarray profiles, and a three-snoRNA signature consisting of SNORD1A, SNORA60, and SNORA66 was constructed. DLBCL patients could be divided into high-risk and low-risk cohorts using the risk model, and the high-risk group and activated B cell-like (ABC) type DLBCL were linked with disappointing survival. In addition, SNORD1A co-expressed genes were inseparably linked to the biological functions of the ribosome and mitochondria. Potential transcriptional regulatory networks have also been identified. MYC and RPL10A were the most mutated SNORD1A co-expressed genes in DLBCL. CONCLUSION Put together, our findings explored the potential biological effects of snoRNAs in DLBCL, and provided a new predictor for DLBCL prediction.
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Affiliation(s)
- Mei‐wei Li
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Feng‐xiang Huang
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Zu‐cheng Xie
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Hao‐yuan Hong
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Qing‐yuan Xu
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Zhi‐gang Peng
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
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23
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Compounds for selective translational inhibition. Curr Opin Chem Biol 2022; 69:102158. [DOI: 10.1016/j.cbpa.2022.102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/04/2022] [Accepted: 04/17/2022] [Indexed: 11/23/2022]
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24
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Praditya DF, Klöhn M, Brüggemann Y, Brown LE, Porco JA, Zhang W, Kinast V, Kirschning A, Vondran FWR, Todt D, Steinmann E. Identification of structurally re-engineered rocaglates as inhibitors against hepatitis E virus replication. Antiviral Res 2022; 204:105359. [PMID: 35728703 PMCID: PMC9731315 DOI: 10.1016/j.antiviral.2022.105359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/16/2022] [Accepted: 06/06/2022] [Indexed: 11/19/2022]
Abstract
Hepatitis E virus (HEV) infections are a leading cause of acute viral hepatitis in humans and pose a considerable threat to public health. Current standard of care treatment is limited to the off-label use of nucleoside-analog ribavirin (RBV) and PEGylated interferon-α, both of which are associated with significant side effects and provide limited efficacy. In the past few years, a promising natural product compound class of eukaryotic initiation factor 4A (eIF4A) inhibitors (translation initiation inhibitors), called rocaglates, were identified as antiviral agents against RNA virus infections. In the present study, we evaluated a total of 205 synthetic rocaglate derivatives from the BU-CMD compound library for their antiviral properties against HEV. At least eleven compounds showed inhibitory activities against the HEV genotype 3 (HEV-3) subgenomic replicon below 30 nM (EC50 value) as determined by Gaussia luciferase assay. Three amidino-rocaglates (ADRs) (CMLD012073, CMLD012118, and CMLD012612) possessed antiviral activity against HEV with EC50 values between 1 and 9 nM. In addition, these three selected compounds inhibited subgenomic replicons of different genotypes (HEV-1 [Sar55], wild boar HEV-3 [83-2] and human HEV-3 [p6]) in a dose-dependent manner and at low nanomolar concentrations. Furthermore, tested ADRs tend to be better tolerated in primary hepatocytes than hepatoma cancer cell lines and combination treatment of CMLD012118 with RBV and interferon-α (IFN-α) showed that CMLD012118 acts additive to RBV and IFN-α treatment. In conclusion, our results indicate that ADRs, especially CMLD012073, CMLD012118, and CMLD012612 may prove to be potential therapeutic candidates for the treatment of HEV infections and may contribute to the discovery of pan-genotypic inhibitors in the future.
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Affiliation(s)
- Dimas F Praditya
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany; Research Center for Vaccine and Drugs, The National Research and Innovation Agency, Cibinong, Indonesia.
| | - Mara Klöhn
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany.
| | - Yannick Brüggemann
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany.
| | - Lauren E Brown
- Department of Chemistry, Boston University, Boston, MA, 02215, USA; Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA.
| | - John A Porco
- Department of Chemistry, Boston University, Boston, MA, 02215, USA; Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA.
| | - Wenhan Zhang
- Department of Chemistry, Boston University, Boston, MA, 02215, USA; Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA.
| | - Volker Kinast
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany; Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany.
| | - Florian W R Vondran
- ReMediES, Department of General, Visceral and Transplantation Surgery, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany.
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743, Jena, Germany.
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany; German Centre for Infection Research (DZIF), External Partner Site, Bochum, Germany.
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25
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Çetin B, O’Leary SE. mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation. Nucleic Acids Res 2022; 50:8240-8261. [PMID: 35871304 PMCID: PMC9371892 DOI: 10.1093/nar/gkac631] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
mRNA 5′ cap recognition by eIF4F is a key element of eukaryotic translational control. Kinetic differences in eIF4F–mRNA interactions have long been proposed to mediate translation-efficiency differences between mRNAs, and recent transcriptome-wide studies have revealed significant heterogeneity in eIF4F engagement with differentially-translated mRNAs. However, detailed kinetic information exists only for eIF4F interactions with short model RNAs. We developed and applied single-molecule fluorescence approaches to directly observe real-time Saccharomyces cerevisiae eIF4F subunit interactions with full-length polyadenylated mRNAs. We found that eIF4E–mRNA association rates linearly anticorrelate with mRNA length. eIF4G–mRNA interaction accelerates eIF4E–mRNA association in proportion to mRNA length, as does an eIF4F-independent activity of eIF4A, though cap-proximal secondary structure still plays an important role in defining the final association rates. eIF4F–mRNA interactions remained dominated by effects of eIF4G, but were modulated to different extents for different mRNAs by the presence of eIF4A and ATP. We also found that eIF4A-catalyzed ATP hydrolysis ejects eIF4E, and likely eIF4E•eIF4G from the mRNA after initial eIF4F•mRNA complex formation, suggesting a mechanism to prepare the mRNA 5′ end for ribosome recruitment. Our results support a role for mRNA-specific, factor-driven eIF4F association rates in kinetically controlling translation.
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Affiliation(s)
- Burak Çetin
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
| | - Seán E O’Leary
- Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside , Riverside, CA 92521, USA
- Department of Biochemistry, University of California Riverside , Riverside, CA 92521, USA
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26
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Wei W, Liu C, Wang M, Jiang W, Wang C, Zhang S. Prognostic Signature and Tumor Immune Landscape of N7-Methylguanosine-Related lncRNAs in Hepatocellular Carcinoma. Front Genet 2022; 13:906496. [PMID: 35938009 PMCID: PMC9354608 DOI: 10.3389/fgene.2022.906496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 01/15/2023] Open
Abstract
Despite great advances in the treatment of liver hepatocellular carcinoma (LIHC), such as immunotherapy, the prognosis remains extremely poor, and there is an urgent need to develop novel diagnostic and prognostic markers. Recently, RNA methylation-related long non-coding RNAs (lncRNAs) have been demonstrated to be novel potential biomarkers for tumor diagnosis and prognosis as well as immunotherapy response, such as N6-methyladenine (m6A) and 5-methylcytosine (m5C). N7-Methylguanosine (m7G) is a widespread RNA modification in eukaryotes, but the relationship between m7G-related lncRNAs and prognosis of LIHC patients as well as tumor immunotherapy response is still unknown. In this study, based on the LIHC patients’ clinical and transcriptomic data from TCGA database, a total of 992 m7G-related lncRNAs that co-expressed with 22 m7G regulatory genes were identified using Pearson correlation analysis. Univariate regression analysis was used to screen prognostic m7G-related lncRNAs, and the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression were applied to construct a 9-m7G-related-lncRNA risk model. The m7G-related lncRNA risk model was validated to exhibit good prognostic performance through Kaplan–Meier analysis and ROC analysis. Together with the clinicopathological features, the m7G-related lncRNA risk score was found to be an independent prognostic factor for LIHC. Furthermore, the high-risk group of LIHC patients was unveiled to have a higher tumor mutation burden (TMB), and their tumor microenvironment was more prone to the immunosuppressive state and exhibited a lower response rate to immunotherapy. In addition, 47 anti-cancer drugs were identified to exhibit a difference in drug sensitivity between the high-risk and low-risk groups. Taken together, the m7G-related lncRNA risk model might display potential value in predicting prognosis, immunotherapy response, and drug sensitivity in LIHC patients.
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Affiliation(s)
- Wei Wei
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chao Liu
- Department of Vascular Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wei Jiang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Caihong Wang
- Department of Pathology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Shuqun Zhang,
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27
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Zhuang Y, Che J, Wu M, Guo Y, Xu Y, Dong X, Yang H. Altered pathways and targeted therapy in double hit lymphoma. J Hematol Oncol 2022; 15:26. [PMID: 35303910 PMCID: PMC8932183 DOI: 10.1186/s13045-022-01249-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
High-grade B-cell lymphoma with translocations involving MYC and BCL2 or BCL6, usually referred to as double hit lymphoma (DHL), is an aggressive hematological malignance with distinct genetic features and poor clinical prognosis. Current standard chemoimmunotherapy fails to confer satisfying outcomes and few targeted therapeutics are available for the treatment against DHL. Recently, the delineating of the genetic landscape in tumors has provided insight into both biology and targeted therapies. Therefore, it is essential to understand the altered signaling pathways of DHL to develop treatment strategies with better clinical benefits. Herein, we summarized the genetic alterations in the two DHL subtypes (DHL-BCL2 and DHL-BCL6). We further elucidate their implications on cellular processes, including anti-apoptosis, epigenetic regulations, B-cell receptor signaling, and immune escape. Ongoing and potential therapeutic strategies and targeted drugs steered by these alterations were reviewed accordingly. Based on these findings, we also discuss the therapeutic vulnerabilities that coincide with these genetic changes. We believe that the understanding of the DHL studies will provide insight into this disease and capacitate the finding of more effective treatment strategies.
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Affiliation(s)
- Yuxin Zhuang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Meijuan Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Yu Guo
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
| | - Yongjin Xu
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, People’s Republic of China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, People’s Republic of China
- Cancer Center, Zhejiang University, Hangzhou, People’s Republic of China
| | - Haiyan Yang
- Department of Lymphoma, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, People’s Republic of China
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Rocaglates as Antivirals: Comparing the Effects on Viral Resistance, Anti-Coronaviral Activity, RNA-Clamping on eIF4A and Immune Cell Toxicity. Viruses 2022; 14:v14030519. [PMID: 35336926 PMCID: PMC8950828 DOI: 10.3390/v14030519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
Rocaglates are potent broad-spectrum antiviral compounds with a promising safety profile. They inhibit viral protein synthesis for different RNA viruses by clamping the 5′-UTRs of mRNAs onto the surface of the RNA helicase eIF4A. Apart from the natural rocaglate silvestrol, synthetic rocaglates like zotatifin or CR-1-31-B have been developed. Here, we compared the effects of rocaglates on viral 5′-UTR-mediated reporter gene expression and binding to an eIF4A-polypurine complex. Furthermore, we analyzed the cytotoxicity of rocaglates on several human immune cells and compared their antiviral activities in coronavirus-infected cells. Finally, the potential for developing viral resistance was evaluated by passaging human coronavirus 229E (HCoV-229E) in the presence of increasing concentrations of rocaglates in MRC-5 cells. Importantly, no decrease in rocaglate-sensitivity was observed, suggesting that virus escape mutants are unlikely to emerge if the host factor eIF4A is targeted. In summary, all three rocaglates are promising antivirals with differences in cytotoxicity against human immune cells, RNA-clamping efficiency, and antiviral activity. In detail, zotatifin showed reduced RNA-clamping efficiency and antiviral activity compared to silvestrol and CR-1-31-B, but was less cytotoxic for immune cells. Our results underline the potential of rocaglates as broad-spectrum antivirals with no indications for the emergence of escape mutations in HCoV-229E.
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Genetic and Histopathological Heterogeneity of Neuroblastoma and Precision Therapeutic Approaches for Extremely Unfavorable Histology Subgroups. Biomolecules 2022; 12:biom12010079. [PMID: 35053227 PMCID: PMC8773700 DOI: 10.3390/biom12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
Peripheral neuroblastic tumors (neuroblastoma, ganglioneuroblastoma and ganglioneuroma) are heterogeneous and their diverse and wide range of clinical behaviors (spontaneous regression, tumor maturation and aggressive progression) are closely associated with genetic/molecular properties of the individual tumors. The International Neuroblastoma Pathology Classification, a biologically relevant and prognostically significant morphology classification distinguishing the favorable histology (FH) and unfavorable histology (UH) groups in this disease, predicts survival probabilities of the patients with the highest hazard ratio. The recent advance of neuroblastoma research with precision medicine approaches demonstrates that tumors in the UH group are also heterogeneous and four distinct subgroups—MYC, TERT, ALT and null—are identified. Among them, the first three subgroups are collectively named extremely unfavorable histology (EUH) tumors because of their highly aggressive clinical behavior. As indicated by their names, these EUH tumors are individually defined by their potential targets detected molecularly and immunohistochemically, such as MYC-family protein overexpression, TERT overexpression and ATRX (or DAXX) loss. In the latter half on this paper, the current status of therapeutic targeting of these EUH tumors is discussed for the future development of effective treatments of the patients.
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Translation Inhibitors Activate Autophagy Master Regulators TFEB and TFE3. Int J Mol Sci 2021; 22:ijms222112083. [PMID: 34769510 PMCID: PMC8584619 DOI: 10.3390/ijms222112083] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023] Open
Abstract
The autophagy-lysosome pathway is a major protein degradation pathway stimulated by multiple cellular stresses, including nutrient or growth factor deprivation, hypoxia, misfolded proteins, damaged organelles, and intracellular pathogens. Recent studies have revealed that transcription factor EB (TFEB) and transcription factor E3 (TFE3) play a pivotal role in the biogenesis and functions of autophagosome and lysosome. Here we report that three translation inhibitors (cycloheximide, lactimidomycin, and rocaglamide A) can facilitate the nuclear translocation of TFEB/TFE3 via dephosphorylation and 14-3-3 dissociation. In addition, the inhibitor-mediated TFEB/TFE3 nuclear translocation significantly increases the transcriptional expression of their downstream genes involved in the biogenesis and function of autophagosome and lysosome. Furthermore, we demonstrated that translation inhibition increased autophagosome biogenesis but impaired the degradative autolysosome formation because of lysosomal dysfunction. These results highlight the previously unrecognized function of the translation inhibitors as activators of TFEB/TFE3, suggesting a novel biological role of translation inhibition in autophagy regulation.
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31
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Ho JJD, Cunningham TA, Manara P, Coughlin CA, Arumov A, Roberts ER, Osteen A, Kumar P, Bilbao D, Krieger JR, Lee S, Schatz JH. Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome. Cell Rep 2021; 37:109806. [PMID: 34644561 PMCID: PMC8558842 DOI: 10.1016/j.celrep.2021.109806] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
Tactical disruption of protein synthesis is an attractive therapeutic strategy, with the first-in-class eIF4A-targeting compound zotatifin in clinical evaluation for cancer and COVID-19. The full cellular impact and mechanisms of these potent molecules are undefined at a proteomic level. Here, we report mass spectrometry analysis of translational reprogramming by rocaglates, cap-dependent initiation disruptors that include zotatifin. We find effects to be far more complex than simple “translational inhibition” as currently defined. Translatome analysis by TMT-pSILAC (tandem mass tag-pulse stable isotope labeling with amino acids in cell culture mass spectrometry) reveals myriad upregulated proteins that drive hitherto unrecognized cytotoxic mechanisms, including GEF-H1-mediated anti-survival RHOA/JNK activation. Surprisingly, these responses are not replicated by eIF4A silencing, indicating a broader translational adaptation than currently understood. Translation machinery analysis by MATRIX (mass spectrometry analysis of active translation factors using ribosome density fractionation and isotopic labeling experiments) identifies rocaglate-specific dependence on specific translation factors including eEF1ε1 that drive translatome remodeling. Our proteome-level interrogation reveals that the complete cellular response to these historical “translation inhibitors” is mediated by comprehensive translational landscape remodeling. Tactical protein synthesis inhibition is actively pursued as a cancer therapy that bypasses signaling redundancies limiting current strategies. Ho et al. show that rocaglates, first identified as inhibitors of eIF4A activity, globally reprogram cellular translation at both protein synthesis machinery and translatome levels, inducing cytotoxicity through anti-survival GEF-H1/RHOA/JNK signaling.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Tyler A Cunningham
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Paola Manara
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Caroline A Coughlin
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Artavazd Arumov
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Evan R Roberts
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ashanti Osteen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Preet Kumar
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Bilbao
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | - Stephen Lee
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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Sieber-Frank J, Stark HJ, Kalteis S, Prigge ES, Köhler R, Andresen C, Henkel T, Casari G, Schubert T, Fischl W, Li-Weber M, Krammer PH, von Knebel Doeberitz M, Kopitz J, Kloor M, Ahadova A. Treatment resistance analysis reveals GLUT-1-mediated glucose uptake as a major target of synthetic rocaglates in cancer cells. Cancer Med 2021; 10:6807-6822. [PMID: 34546000 PMCID: PMC8495295 DOI: 10.1002/cam4.4212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022] Open
Abstract
Rocaglates are natural compounds that have been extensively studied for their ability to inhibit translation initiation. Rocaglates represent promising drug candidates for tumor treatment due to their growth‐inhibitory effects on neoplastic cells. In contrast to natural rocaglates, synthetic analogues of rocaglates have been less comprehensively characterized, but were also shown to have similar effects on the process of protein translation. Here, we demonstrate an enhanced growth‐inhibitory effect of synthetic rocaglates when combined with glucose anti‐metabolite 2‐deoxy‐D‐glucose (2DG) in different cancer cell lines. Moreover, we unravel a new aspect in the mechanism of action of synthetic rocaglates involving reduction of glucose uptake mediated by downregulation or abrogation of glucose transporter GLUT‐1 expression. Importantly, cells with genetically induced resistance to synthetic rocaglates showed substantially less pronounced treatment effect on glucose metabolism and did not demonstrate GLUT‐1 downregulation, pointing at the crucial role of this mechanism for the anti‐tumor activity of the synthetic rocaglates. Transcriptome profiling revealed glycolysis as one of the major pathways differentially regulated in sensitive and resistant cells. Analysis of synthetic rocaglate efficacy in a 3D tissue context with a co‐culture of tumor and normal cells demonstrated a selective effect on tumor cells and substantiated the mechanistic observations obtained in cancer cell lines. Increased glucose uptake and metabolism is a universal feature across different tumor types. Therefore, targeting this feature by synthetic rocaglates could represent a promising direction for exploitation of rocaglates in novel anti‐tumor therapies.
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Affiliation(s)
- Julia Sieber-Frank
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Jürgen Stark
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Kalteis
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elena-Sophie Prigge
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Richard Köhler
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolin Andresen
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | | | - Min Li-Weber
- Tumor Immunology Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter H Krammer
- Tumor Immunology Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,Collaboration Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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A forward genetic screen identifies modifiers of rocaglate responsiveness. Sci Rep 2021; 11:18516. [PMID: 34531456 PMCID: PMC8445955 DOI: 10.1038/s41598-021-97765-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
Rocaglates are a class of eukaryotic translation initiation inhibitors that are being explored as chemotherapeutic agents. They function by targeting eukaryotic initiation factor (eIF) 4A, an RNA helicase critical for recruitment of the 40S ribosome (and associated factors) to mRNA templates. Rocaglates perturb eIF4A activity by imparting a gain-of-function activity to eIF4A and mediating clamping to RNA. To appreciate how rocaglates could best be enabled in the clinic, an understanding of resistance mechanisms is important, as this could inform on strategies to bypass such events as well as identify responsive tumor types. Here, we report on the results of a positive selection, ORFeome screen aimed at identifying cDNAs capable of conferring resistance to rocaglates. Two of the most potent modifiers of rocaglate response identified were the transcription factors FOXP3 and NR1I3, both of which have been implicated in ABCB1 regulation-the gene encoding P-glycoprotein (Pgp). Pgp has previously been implicated in conferring resistance to silvestrol, a naturally occurring rocaglate, and we show here that this extends to additional synthetic rocaglate derivatives. In addition, FOXP3 and NR1I3 impart a multi-drug resistant phenotype that is reversed upon inhibition of Pgp, suggesting a potential therapeutic combination strategy.
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34
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Wilmore S, Rogers-Broadway KR, Taylor J, Lemm E, Fell R, Stevenson FK, Forconi F, Steele AJ, Coldwell M, Packham G, Yeomans A. Targeted inhibition of eIF4A suppresses B-cell receptor-induced translation and expression of MYC and MCL1 in chronic lymphocytic leukemia cells. Cell Mol Life Sci 2021; 78:6337-6349. [PMID: 34398253 PMCID: PMC8429177 DOI: 10.1007/s00018-021-03910-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/09/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022]
Abstract
Signaling via the B-cell receptor (BCR) is a key driver and therapeutic target in chronic lymphocytic leukemia (CLL). BCR stimulation of CLL cells induces expression of eIF4A, an initiation factor important for translation of multiple oncoproteins, and reduces expression of PDCD4, a natural inhibitor of eIF4A, suggesting that eIF4A may be a critical nexus controlling protein expression downstream of the BCR in these cells. We, therefore, investigated the effect of eIF4A inhibitors (eIF4Ai) on BCR-induced responses. We demonstrated that eIF4Ai (silvestrol and rocaglamide A) reduced anti-IgM-induced global mRNA translation in CLL cells and also inhibited accumulation of MYC and MCL1, key drivers of proliferation and survival, respectively, without effects on upstream signaling responses (ERK1/2 and AKT phosphorylation). Analysis of normal naïve and non-switched memory B cells, likely counterparts of the two main subsets of CLL, demonstrated that basal RNA translation was higher in memory B cells, but was similarly increased and susceptible to eIF4Ai-mediated inhibition in both. We probed the fate of MYC mRNA in eIF4Ai-treated CLL cells and found that eIF4Ai caused a profound accumulation of MYC mRNA in anti-IgM treated cells. This was mediated by MYC mRNA stabilization and was not observed for MCL1 mRNA. Following drug wash-out, MYC mRNA levels declined but without substantial MYC protein accumulation, indicating that stabilized MYC mRNA remained blocked from translation. In conclusion, BCR-induced regulation of eIF4A may be a critical signal-dependent nexus for therapeutic attack in CLL and other B-cell malignancies, especially those dependent on MYC and/or MCL1.
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MESH Headings
- Antibodies, Anti-Idiotypic/pharmacology
- Benzofurans/pharmacology
- Cells, Cultured
- Eukaryotic Initiation Factor-4A/antagonists & inhibitors
- Eukaryotic Initiation Factor-4A/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/metabolism
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Protein Biosynthesis/drug effects
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA Stability/drug effects
- RNA, Messenger/metabolism
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/drug effects
- Triterpenes/pharmacology
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Affiliation(s)
- Sarah Wilmore
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Karly-Rai Rogers-Broadway
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Joe Taylor
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Elizabeth Lemm
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Rachel Fell
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Freda K Stevenson
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Francesco Forconi
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Andrew J Steele
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
| | - Mark Coldwell
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK.
| | - Alison Yeomans
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Somers Building, Southampton, SO16 6YD, UK
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35
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Ingolia NT. eIF4A inhibitors PatA and RocA stack the deck against translation. Structure 2021; 29:638-639. [PMID: 34214439 DOI: 10.1016/j.str.2021.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In Cell Chemical Biology, Naineni et al. (2021) report the structure of a synthetic analog of the translation inhibitor pateamine A bound to initiation factor eIF4A and RNA. The drug stacks with RNA bases in the same pocket where unrelated rocaglate compounds bind, highlighting a druggable site for DEAD-box proteins.
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Affiliation(s)
- Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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37
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Burgers LD, Fürst R. Natural products as drugs and tools for influencing core processes of eukaryotic mRNA translation. Pharmacol Res 2021; 170:105535. [PMID: 34058326 DOI: 10.1016/j.phrs.2021.105535] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022]
Abstract
Eukaryotic protein synthesis is the highly conserved, complex mechanism of translating genetic information into proteins. Although this process is essential for cellular homoeostasis, dysregulations are associated with cellular malfunctions and diseases including cancer and diabetes. In the challenging and ongoing search for adequate treatment possibilities, natural products represent excellent research tools and drug leads for new interactions with the translational machinery and for influencing mRNA translation. In this review, bacterial-, marine- and plant-derived natural compounds that interact with different steps of mRNA translation, comprising ribosomal assembly, translation initiation and elongation, are highlighted. Thereby, the exact binding and interacting partners are unveiled in order to accurately understand the mode of action of each natural product. The pharmacological relevance of these compounds is furthermore assessed by evaluating the observed biological activities in the light of translational inhibition and by enlightening potential obstacles and undesired side-effects, e.g. in clinical trials. As many of the natural products presented here possess the potential to serve as drug leads for synthetic derivatives, structural motifs, which are indispensable for both mode of action and biological activities, are discussed. Evaluating the natural products emphasises the strong diversity of their points of attack. Especially the fact that selected binding partners can be set in direct relation to different diseases emphasises the indispensability of natural products in the field of drug development. Discovery of new, unique and unusual interacting partners again renders them promising tools for future research in the field of eukaryotic mRNA translation.
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Affiliation(s)
- Luisa D Burgers
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt, Germany
| | - Robert Fürst
- Institute of Pharmaceutical Biology, Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University, Frankfurt, Germany; LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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38
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Hong HJ, Guevara MG, Lin E, O'Leary SE. Single-Molecule Dynamics of SARS-CoV-2 5' Cap Recognition by Human eIF4F. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34075378 DOI: 10.1101/2021.05.26.445185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coronaviruses initiate translation through recognition of the viral RNA 5' m 7 GpppA m cap by translation factor eIF4F. eIF4F is a heterotrimeric protein complex with cap-binding, RNA-binding, and RNA helicase activities. Modulating eIF4F function through cellular regulation or small-molecule inhibition impacts coronavirus replication, including for SARS-CoV-2. Translation initiation involves highly coordinated dynamics of translation factors with messenger or viral RNA. However, how the eIF4F subunits coordinate on the initiation timescale to define cap-binding efficiency remains incompletely understood. Here we report that translation supported by the SARS-CoV-2 5'-UTR is highly sensitive to eIF4A inhibition by rocaglamide. Through a single-molecule fluorescence approach that reports on eIF4E-cap interaction, we dissect how eIF4F subunits contribute to cap-recognition efficiency on the SARS-CoV-2 5' UTR. We find that free eIF4A enhances cap accessibility for eIF4E binding, but eIF4G alone does not change the kinetics of eIF4E-RNA interaction. Conversely, formation of the full eIF4F complex significantly alters eIF4E-cap interaction, suggesting that coordinated eIF4E and eIF4A activities establish the net eIF4F-cap recognition efficiency. Moreover, the eIF4F complex formed with phosphomimetic eIF4E(S209D) binds the viral UTR more efficiently than with wild-type eIF4E. These results highlight a dynamic interplay of eIF4F subunits and mRNA that determines cap-recognition efficiency.
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39
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Chen M, Asanuma M, Takahashi M, Shichino Y, Mito M, Fujiwara K, Saito H, Floor SN, Ingolia NT, Sodeoka M, Dodo K, Ito T, Iwasaki S. Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A. Cell Chem Biol 2021; 28:475-486.e8. [PMID: 33296667 PMCID: PMC8052261 DOI: 10.1016/j.chembiol.2020.11.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022]
Abstract
The translation inhibitor rocaglamide A (RocA) has shown promising antitumor activity because it uniquely clamps eukaryotic initiation factor (eIF) 4A onto polypurine RNA for selective translational repression. As eIF4A has been speculated to be a unique target of RocA, alternative targets have not been investigated. Here, we reveal that DDX3 is another molecular target of RocA. Proximity-specific fluorescence labeling of an O-nitrobenzoxadiazole-conjugated derivative revealed that RocA binds to DDX3. RocA clamps the DDX3 protein onto polypurine RNA in an ATP-independent manner. Analysis of a de novo-assembled transcriptome from the plant Aglaia, a natural source of RocA, uncovered the amino acid critical for RocA binding. Moreover, ribosome profiling showed that because of the dominant-negative effect of RocA, high expression of eIF4A and DDX3 strengthens translational repression in cancer cells. This study indicates that sequence-selective clamping of DDX3 and eIF4A, and subsequent dominant-negative translational repression by RocA determine its tumor toxicity.
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Affiliation(s)
- Mingming Chen
- 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
| | - Miwako Asanuma
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Mari Takahashi
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Koichi Fujiwara
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hironori Saito
- 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
| | - Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Mikiko Sodeoka
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Japan
| | - Kosuke Dodo
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan; AMED-CREST, Japan Agency for Medical Research and Development, 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; AMED-CREST, Japan Agency for Medical Research and Development, Japan.
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40
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DiVita DJ, Kearse MG. A double on the Rocs with a twist: Rocaglamide A targets multiple DEAD-box helicases to inhibit translation initiation. Cell Chem Biol 2021; 28:431-433. [PMID: 33861954 PMCID: PMC11295116 DOI: 10.1016/j.chembiol.2021.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In this issue of Cell Chemical Biology, Chen et al. (2020) expand the target repertoire of rocaglamide A (RocA) to now include eIF4A2 and DDX3X, converting DEAD-box helicases into dominant-negative translation repressors. These results also highlight how cancer cell sensitivity to RocA is dependent on eIF4A and DDX3X levels.
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Affiliation(s)
- Daisy J DiVita
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Kearse
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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41
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Targeting the DEAD-Box RNA Helicase eIF4A with Rocaglates-A Pan-Antiviral Strategy for Minimizing the Impact of Future RNA Virus Pandemics. Microorganisms 2021; 9:microorganisms9030540. [PMID: 33807988 PMCID: PMC8001013 DOI: 10.3390/microorganisms9030540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022] Open
Abstract
The increase in pandemics caused by RNA viruses of zoonotic origin highlights the urgent need for broad-spectrum antivirals against novel and re-emerging RNA viruses. Broad-spectrum antivirals could be deployed as first-line interventions during an outbreak while virus-specific drugs and vaccines are developed and rolled out. Viruses depend on the host’s protein synthesis machinery for replication. Several natural compounds that target the cellular DEAD-box RNA helicase eIF4A, a key component of the eukaryotic translation initiation complex eIF4F, have emerged as potential broad-spectrum antivirals. Rocaglates, a group of flavaglines of plant origin that clamp mRNAs with highly structured 5′ untranslated regions (5′UTRs) onto the surface of eIF4A through specific stacking interactions, exhibit the largest selectivity and potential therapeutic indices among all known eIF4A inhibitors. Their unique mechanism of action limits the inhibitory effect of rocaglates to the translation of eIF4A-dependent viral mRNAs and a minor fraction of host mRNAs exhibiting stable RNA secondary structures and/or polypurine sequence stretches in their 5′UTRs, resulting in minimal potential toxic side effects. Maintaining a favorable safety profile while inducing efficient inhibition of a broad spectrum of RNA viruses makes rocaglates into primary candidates for further development as pan-antiviral therapeutics.
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42
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Knowles CM, McIntyre KM, Panepinto JC. Tools for Assessing Translation in Cryptococcus neoformans. J Fungi (Basel) 2021; 7:jof7030159. [PMID: 33668175 PMCID: PMC7995980 DOI: 10.3390/jof7030159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022] Open
Abstract
Cryptococcus neoformans is a ubiquitous environmental fungus capable of establishing an infection in a human host. Rapid changes in environments and exposure to the host immune system results in a significant amount of cellular stress, which is effectively combated at the level of translatome reprogramming. Repression of translation following stress allows for the specific reallocation of limited resources. Understanding the mechanisms involved in regulating translation in C. neoformans during host infection is critical in the development of new antifungal drugs. In this review, we discuss the main tools available for assessing changes in translation state and translational output during cellular stress.
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43
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Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A. Cell Chem Biol 2021; 28:825-834.e6. [PMID: 33412110 DOI: 10.1016/j.chembiol.2020.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/15/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022]
Abstract
Interfacial inhibitors exert their biological effects through co-association with two macromolecules. The pateamine A (PatA) class of molecules function by stabilizing eukaryotic initiation factor (eIF) 4A RNA helicase onto RNA, resulting in translation initiation inhibition. Here, we present the crystal structure of an eIF4A1:RNA complex bound to an analog of the marine sponge-derived natural product PatA, C5-desmethyl PatA (DMPatA). One end of this small molecule wedges itself between two RNA bases while the other end is cradled by several protein residues. Strikingly, DMPatA interacts with the eIF4A1:RNA complex in an almost identical fashion as rocaglamide A (RocA), despite being completely unrelated from a structural standpoint. The structural data rationalize the ability of PatA analogs to target a wider range of RNA substrates compared to RocA. We define the molecular basis of how DMPatA is able to clamp eIF4A1 onto RNA, imparting potent inhibitory properties to this molecule.
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44
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Steinberger J, Shen L, J Kiniry S, Naineni SK, Cencic R, Amiri M, Aboushawareb SAE, Chu J, Maïga RI, Yachnin BJ, Robert F, Sonenberg N, Baranov PV, Pelletier J. Identification and characterization of hippuristanol-resistant mutants reveals eIF4A1 dependencies within mRNA 5' leader regions. Nucleic Acids Res 2020; 48:9521-9537. [PMID: 32766783 PMCID: PMC7515738 DOI: 10.1093/nar/gkaa662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Hippuristanol (Hipp) is a natural product that selectively inhibits protein synthesis by targeting eukaryotic initiation factor (eIF) 4A, a DEAD-box RNA helicase required for ribosome recruitment to mRNA templates. Hipp binds to the carboxyl-terminal domain of eIF4A, locks it in a closed conformation, and inhibits its RNA binding. The dependencies of mRNAs for eIF4A during initiation is contingent on the degree of secondary structure within their 5′ leader region. Interest in targeting eIF4A therapeutically in cancer and viral-infected settings stems from the dependencies that certain cellular (e.g. pro-oncogenic, pro-survival) and viral mRNAs show towards eIF4A. Using a CRISPR/Cas9-based variomics screen, we identify functional EIF4A1 Hipp-resistant alleles, which in turn allowed us to link the translation-inhibitory and cytotoxic properties of Hipp to eIF4A1 target engagement. Genome-wide translational profiling in the absence or presence of Hipp were undertaken and our validation studies provided insight into the structure-activity relationships of eIF4A-dependent mRNAs. We find that mRNA 5′ leader length, overall secondary structure and cytosine content are defining features of Hipp-dependent mRNAs.
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Affiliation(s)
- Jutta Steinberger
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Leo Shen
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Mehdi Amiri
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | | | - Jennifer Chu
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | | | - Brahm J Yachnin
- Department of Chemistry & Chemical Biology & the Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway 08854, NJ
| | - Francis Robert
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada.,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal H3A 1A3, Canada
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal H3G 1Y6, Canada.,Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal H3G 1Y6, Canada
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Nebigil CG, Moog C, Vagner S, Benkirane-Jessel N, Smith DR, Désaubry L. Flavaglines as natural products targeting eIF4A and prohibitins: From traditional Chinese medicine to antiviral activity against coronaviruses. Eur J Med Chem 2020; 203:112653. [PMID: 32693294 PMCID: PMC7362831 DOI: 10.1016/j.ejmech.2020.112653] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
Flavaglines are cyclopenta[b]benzofurans found in plants of the genus Aglaia, several species of which are used in traditional Chinese medicine. These compounds target the initiation factor of translation eIF4A and the scaffold proteins prohibitins-1 and 2 (PHB1/2) to exert various pharmacological activities, including antiviral effects against several types of viruses, including coronaviruses. This review is focused on the antiviral effects of flavaglines and their therapeutic potential against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Canan G Nebigil
- INSERM U 1260, Regenerative Nanomedicine (RNM), FMTS, 11 Rue Humann, 67000, Strasbourg, France
| | - Christiane Moog
- INSERM U1109, LabEx TRANSPLANTEX, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
| | - Nadia Benkirane-Jessel
- INSERM U 1260, Regenerative Nanomedicine (RNM), FMTS, 11 Rue Humann, 67000, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, Hôpitaux Universitaires de Strasbourg, 8 Rue de Ste Elisabeth, 67000, Strasbourg, France
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand
| | - Laurent Désaubry
- INSERM U 1260, Regenerative Nanomedicine (RNM), FMTS, 11 Rue Humann, 67000, Strasbourg, France.
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46
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Webb TE, Davies M, Maher J, Sarker D. The eIF4A inhibitor silvestrol sensitizes T-47D ductal breast carcinoma cells to external-beam radiotherapy. Clin Transl Radiat Oncol 2020; 24:123-126. [PMID: 32875125 PMCID: PMC7451755 DOI: 10.1016/j.ctro.2020.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/12/2020] [Accepted: 07/14/2020] [Indexed: 01/05/2023] Open
Abstract
Treatment of T-47D breast cancer cells with silvestrol sensitised them to radiation. 1 nM silvestrol caused a 34% reduction in cells exposed to 2 Gy. Clonogenic assays revealed silvestrol had a dose modifying factor of 1.4. Radiation was delivered to the tissue culture plate using a clinical LINAC machine.
Purpose eIF4A is an RNA helicase that forms part of the machinery of translation initiation. Proteomic analysis demonstrated eIF4A expression to be at least two-fold greater in a radioresistant derivative of T-47D breast cancer cells compared to parental cells. Inhibition of eIF4A has previously been shown to re-sensitize lymphomas to chemotherapeutic agents that cause DNA damage. The objective of this work is to investigate whether inhibition of eIF4A using silvestrol sensitizes breast cancer cells to radiotherapy in tissue culture, using T-47D as a model system. Methods and materials T-47D cells were incubated in medium containing 0 nM to 1 nM silvestrol either for 24 h prior to irradiation at 0 Gy to 10 Gy, delivered by linear accelerator (LINAC) or continually for six days post irradiation. MTT viability and clonogenic assays were used to quantify response. Results Pre-treatment of T-47D cells with 1 nM silvestrol caused a 34% reduction (p = 0.014) in viability on irradiation at 2 Gy compared to treatment with a DMSO control, as assessed by MTT assay. Maintenance of cells in 1 nM silvestrol for six days following irradiation at 2 Gy caused a 58% reduction (p = <0.001) in tumor cell viability. Clonogenic assays performed on cells maintained in 1 nM silvestrol following irradiation showed a dose modifying factor (DMF) of 1.4 (p = <0.001, one-way ANOVA). Conclusions Low concentrations of silvestrol sensitize T-47D breast cancer cells to radiation with minimal effects on unirradiated cells. This highlights the possible usefulness of eIF4A inhibition in potentiating radiation-induced damage at the tumor site without causing systemic toxicity.
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Affiliation(s)
- Thomas E Webb
- Guy's and St Thomas' NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK
| | - Marc Davies
- Research Oncology, Comprehensive Cancer Centre, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze, Pond Road, London SE1 9RT, UK.,King's College London, School of Cancer and Pharmaceutical Sciences, Guy's Cancer Centre, Great Maze, Pond, London SE1 9RT, UK
| | - John Maher
- King's College London, School of Cancer and Pharmaceutical Sciences, Guy's Cancer Centre, Great Maze, Pond, London SE1 9RT, UK.,Department of Clinical Immunology and Allergy, King's College Hospital NHS Foundation Trust, Denmark, Hill, London SE5 9RS, UK.,Department of Immunology, Eastbourne Hospital, Kings Drive, Eastbourne, East Sussex BN21 2UD, UK
| | - Debashis Sarker
- Research Oncology, Comprehensive Cancer Centre, 3rd Floor Bermondsey Wing, Guy's Hospital, Great Maze, Pond Road, London SE1 9RT, UK.,Department of Medical Oncology, Guy's & St Thomas' NHS Trust, London SE1 9RT, UK
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Yurugi H, Zhuang Y, Siddiqui FA, Liang H, Rosigkeit S, Zeng Y, Abou-Hamdan H, Bockamp E, Zhou Y, Abankwa D, Zhao W, Désaubry L, Rajalingam K. A subset of flavaglines inhibits KRAS nanoclustering and activation. J Cell Sci 2020; 133:jcs244111. [PMID: 32501281 DOI: 10.1242/jcs.244111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/30/2020] [Indexed: 08/31/2023] Open
Abstract
The RAS oncogenes are frequently mutated in human cancers and among the three isoforms (KRAS, HRAS and NRAS), KRAS is the most frequently mutated oncogene. Here, we demonstrate that a subset of flavaglines, a class of natural anti-tumour drugs and chemical ligands of prohibitins, inhibit RAS GTP loading and oncogene activation in cells at nanomolar concentrations. Treatment with rocaglamide, the first discovered flavagline, inhibited the nanoclustering of KRAS, but not HRAS and NRAS, at specific phospholipid-enriched plasma membrane domains. We further demonstrate that plasma membrane-associated prohibitins directly interact with KRAS, phosphatidylserine and phosphatidic acid, and these interactions are disrupted by rocaglamide but not by the structurally related flavagline FL1. Depletion of prohibitin-1 phenocopied the rocaglamide-mediated effects on KRAS activation and stability. We also demonstrate that flavaglines inhibit the oncogenic growth of KRAS-mutated cells and that treatment with rocaglamide reduces non-small-cell lung carcinoma (NSCLC) tumour nodules in autochthonous KRAS-driven mouse models without severe side effects. Our data suggest that it will be promising to further develop flavagline derivatives as specific KRAS inhibitors for clinical applications.
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Affiliation(s)
- Hajime Yurugi
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yinyin Zhuang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Farid A Siddiqui
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, Mcgovern Medical School, UT Health, 6431 Fannin St. MSE R382, Houston, TX 77030, USA
| | - Sebastian Rosigkeit
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yongpeng Zeng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Hussein Abou-Hamdan
- Therapeutic Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, University of Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg, France
| | - Ernesto Bockamp
- Institute for Translational Immunology and Research Center for Immunotherapy, University Medical Center, Johannes Gutenberg University, D 55131 Mainz, Germany
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, Mcgovern Medical School, UT Health, 6431 Fannin St. MSE R382, Houston, TX 77030, USA
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit University of Luxembourg, L 4362 Esch-sur-Alzette, Luxembourg
| | - Wenting Zhao
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637457 Singapore
| | - Laurent Désaubry
- Therapeutic Laboratory of Cardio-Oncology and Medicinal Chemistry (FRE 2033), CNRS, University of Strasbourg, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg, France
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center Mainz, Johannes Gutenberg University, D 55131 Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, D 55131 Mainz, Germany
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48
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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