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Mars JC, Culjkovic-Kraljacic B, Borden KL. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 PMCID: PMC11185188 DOI: 10.1080/19491034.2024.2360196] [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: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.
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Affiliation(s)
- Jean-Clément Mars
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Katherine L.B. Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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2
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Shen Y, Zhang L, Yang T, Li X, Liu C, Li H, Hu Y, Shen H, Li H, Orlov YL, Zhou S, Shen Y. Monosome Stalls the Translation Process Mediated by IGF2BP in Arcuate Nucleus for Puberty Onset Delay. Mol Neurobiol 2024:10.1007/s12035-024-04450-8. [PMID: 39235646 DOI: 10.1007/s12035-024-04450-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 08/09/2024] [Indexed: 09/06/2024]
Abstract
Puberty onset through hypothalamic-pituitary-gonad (HPG) axis as an important reproductive event in postnatal development is initiated from hypothalamic arcuate nucleus (ARC). The growing evidence indicates that translational control also plays an essential role in the final expression of gonadotropin genes. To investigate the role of protein translation and behavior of ribosomes in pubertal onset, the global profiles of transcriptome, single ribosome (monosome), polysome, and tandem mass tag proteome were comprehensively investigated in rat hypothalamic ARCs of different pubertal stages using RNA sequencing, polyribo sequencing, and mass spectrum. Transcriptome-wide enrichments of N6-methyladenosine and IGF2BP2 were investigated using meRIP and RIP sequencing. Monosome was robustly enriched on a large proportion of mRNA in early puberty rats (postnatal day (PND)-25) compared to late puberty (PND-35 and PND-45). Monosome-enriched mRNAs, including HPG axis-related genes, had a large number of upstream ORFs (uORF, < 100 nt) and displayed translational repression in early puberty. Furthermore, insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) could particularly interact with and facilitate monosome to bind with mRNA in early puberty. Finally, ectopic over-expression of IGF2BP2 in hypothalamic ARC via lateral ventricle injection in vivo could recruit monosome to aggregate on mRNA and delay puberty onset. We uncovered a novel regulatory mechanism of IGF2BP2 and monosome for translational control in puberty onset, which shed light on the neuroendocrine regulatory network involved in HPG axis activation.
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Affiliation(s)
- Yifen Shen
- Central Laboratory, Suzhou Bay Clinical College, Xuzhou Medical University, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215200, Jiangsu, China
| | - Le Zhang
- Jiangsu Province Engineering Research Center of Molecular Target Therapy and Companion Diagnostics in Oncology, Suzhou Vocational Health College, Suzhou, 215009, Jiangsu, China
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Yang
- Department of Medical Cosmetology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215200, Jiangsu, China
| | - Xiaosong Li
- Department of Anorectal Surgery, Suzhou Ninth People's Hospital, Suzhou, 215200, Jiangsu, China
| | - Chao Liu
- Central Laboratory, Suzhou Bay Clinical College, Xuzhou Medical University, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215200, Jiangsu, China
| | - Hongmei Li
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200023, China
| | - Yanping Hu
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, Henan, China
| | - Hao Shen
- Clinical Laboratory, Suzhou Ninth People's Hospital, Suzhou, 215200, Jiangsu, China
| | - Hua Li
- Jiangsu Province Engineering Research Center of Molecular Target Therapy and Companion Diagnostics in Oncology, Suzhou Vocational Health College, Suzhou, 215009, Jiangsu, China.
| | - Yuriy L Orlov
- The Digital Health Center, Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, 119991, Russia.
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Shasha Zhou
- Department of Endocrinology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200040, China.
| | - Yihang Shen
- Central Laboratory, Suzhou Bay Clinical College, Xuzhou Medical University, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215200, Jiangsu, China.
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3
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Ulfig A, Jakob U. Cellular oxidants and the proteostasis network: balance between activation and destruction. Trends Biochem Sci 2024; 49:761-774. [PMID: 39168791 DOI: 10.1016/j.tibs.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024]
Abstract
Loss of protein homeostasis (proteostasis) is a common hallmark of aging and age-associated diseases. Considered as the guardian of proteostasis, the proteostasis network (PN) acts to preserve the functionality of proteins during their lifetime. However, its activity declines with age, leading to disease manifestation. While reactive oxygen species (ROS) were traditionally considered culprits in this process, recent research challenges this view. While harmful at high concentrations, moderate ROS levels protect the cell against age-mediated onset of proteotoxicity by activating molecular chaperones, stress response pathways, and autophagy. This review explores the nuanced roles of ROS in proteostasis and discusses the most recent findings regarding the redox regulation of the PN and its potential in extending healthspan and delaying age-related pathologies.
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Affiliation(s)
- Agnes Ulfig
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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4
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Gugnoni M, Lorenzini E, Torricelli F, Donati B, Manicardi V, Vitale E, Muccioli S, Piana S, Lococo F, Zamponi R, Gandellini P, Ciarrocchi A. Linc00941 fuels ribogenesis and protein synthesis by supporting robust cMYC translation in malignant pleural mesothelioma. Cancer Lett 2024; 592:216950. [PMID: 38729555 DOI: 10.1016/j.canlet.2024.216950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Malignant pleural mesothelioma is a rare and lethal cancer caused by exposure to asbestos. The highly inflammatory environment caused by fibers accumulation forces cells to undergo profound adaptation to gain survival advantages. Prioritizing the synthesis of essential transcripts is an efficient mechanism coordinated by multiple molecules, including long non-coding RNAs. Enhancing the knowledge about these mechanisms is an essential weapon in combating mesothelioma. Linc00941 correlates to bad prognosis in various cancers, but it is reported to partake in distinct and apparently irreconcilable processes. In this work, we report that linc00941 supports the survival and aggressiveness of mesothelioma cells by influencing protein synthesis and ribosome biogenesis. Linc00941 binds to the translation initiation factor eIF4G, promoting the selective protein synthesis of cMYC, which, in turn, enhances the expression of key genes involved in translation. We analyzed a retrospective cohort of 97 mesothelioma patients' samples from our institution, revealing that linc00941 expression strongly correlates with reduced survival probability. This discovery clarifies linc00941's role in mesothelioma and proposes a unified mechanism of action for this lncRNA involving the selective translation of essential oncogenes, reconciling the discrepancies about its function.
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Affiliation(s)
- Mila Gugnoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy.
| | - Eugenia Lorenzini
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy; Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Italy
| | - Silvia Muccioli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy; Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Italy
| | | | - Filippo Lococo
- Università Cattolica del Sacro Cuore, Rome, Italy; UOC Chirurgia Toracica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Raffaella Zamponi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy.
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5
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Lebedeva M, Nikonova E, Babakov A, Kolesnikova V, Razhina O, Zlobin N, Taranov V, Nikonov O. Interaction of Solanum tuberosum L. translation initiation factors eIF4E with potato virus Y VPg: Apprehend and avoid. Biochimie 2024; 219:1-11. [PMID: 37562705 DOI: 10.1016/j.biochi.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Potato virus Y (PVY) is one of the most dangerous agricultural pathogens that causes substantial harm to vegetative propagated crops, such as potatoes (Solanum tuberosum L.). A necessary condition for PVY infection is an interaction between the plant cap-binding translation initiation factors eIF4E and a viral protein VPg, which mimics the cap-structure. In this study, we identified the point mutations in potato eIF4E1 and eIF4E2 that disrupt VPg binding while preserving the functional activity. For the structural interpretation of the obtained results, molecular models of all the studied forms of eIF4E1 and eIF4E2 were constructed and analyzed via molecular dynamics. The results of molecular dynamics simulations corresponds to the biochemical results and suggests that the β1β2 loop plays a key role in the stabilization of both eIF4E-cap and eIF4E-VPg complexes.
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Affiliation(s)
- Marina Lebedeva
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia.
| | - Ekaterina Nikonova
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - Alexey Babakov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Victoria Kolesnikova
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia; Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - Oksana Razhina
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Nikolay Zlobin
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Vasiliy Taranov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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7
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Borden KLB. The eukaryotic translation initiation factor eIF4E unexpectedly acts in splicing thereby coupling mRNA processing with translation: eIF4E induces widescale splicing reprogramming providing system-wide connectivity between splicing, nuclear mRNA export and translation. Bioessays 2024; 46:e2300145. [PMID: 37926700 PMCID: PMC11021180 DOI: 10.1002/bies.202300145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
Recent findings position the eukaryotic translation initiation factor eIF4E as a novel modulator of mRNA splicing, a process that impacts the form and function of resultant proteins. eIF4E physically interacts with the spliceosome and with some intron-containing transcripts implying a direct role in some splicing events. Moreover, eIF4E drives the production of key components of the splicing machinery underpinning larger scale impacts on splicing. These drive eIF4E-dependent reprogramming of the splicing signature. This work completes a series of studies demonstrating eIF4E acts in all the major mRNA maturation steps whereby eIF4E drives production of the RNA processing machinery and escorts some transcripts through various maturation steps. In this way, eIF4E couples the mRNA processing-export-translation axis linking nuclear mRNA processing to cytoplasmic translation. eIF4E elevation is linked to worse outcomes in acute myeloid leukemia patients where these activities are dysregulated. Understanding these effects provides new insight into post-transcriptional control and eIF4E-driven cancers.
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Affiliation(s)
- Katherine L. B. Borden
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell BiologyUniversity of MontrealMontrealQuebecCanada
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Xie J, Mo T, Li R, Zhang H, Liang G, Ma T, Chen J, Xie H, Wen X, Hu T, Xian Z, Pan W. The m 7G Reader NCBP2 Promotes Pancreatic Cancer Progression by Upregulating MAPK/ERK Signaling. Cancers (Basel) 2023; 15:5454. [PMID: 38001714 PMCID: PMC10670634 DOI: 10.3390/cancers15225454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
PDAC is one of the most common malignant tumors worldwide. The difficulty of early diagnosis and lack of effective treatment are the main reasons for its poor prognosis. Therefore, it is urgent to identify novel diagnostic and therapeutic targets for PDAC patients. The m7G methylation is a common type of RNA modification that plays a pivotal role in regulating tumor development. However, the correlation between m7G regulatory genes and PDAC progression remains unclear. By integrating gene expression and related clinical information of PDAC patients from TCGA and GEO cohorts, m7G binding protein NCBP2 was found to be highly expressed in PDAC patients. More importantly, PDAC patients with high NCBP2 expression had a worse prognosis. Stable NCBP2-knockdown and overexpression PDAC cell lines were constructed to further perform in-vitro and in-vivo experiments. NCBP2-knockdown significantly inhibited PDAC cell proliferation, while overexpression of NCBP2 dramatically promoted PDAC cell growth. Mechanistically, NCBP2 enhanced the translation of c-JUN, which in turn activated MEK/ERK signaling to promote PDAC progression. In conclusion, our study reveals that m7G reader NCBP2 promotes PDAC progression by activating MEK/ERK pathway, which could serve as a novel therapeutic target for PDAC patients.
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Affiliation(s)
- Jiancong Xie
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
| | - Taiwei Mo
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China;
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
| | - Ruibing Li
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Hao Zhang
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
| | - Guanzhan Liang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Tao Ma
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
| | - Jing Chen
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Hanlin Xie
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Xiaofeng Wen
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Tuo Hu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Zhenyu Xian
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Weidong Pan
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
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9
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Zhong S, Chen S, Lin H, Luo Y, He J. Selection of M7G-related lncRNAs in kidney renal clear cell carcinoma and their putative diagnostic and prognostic role. BMC Urol 2023; 23:186. [PMID: 37968670 PMCID: PMC10652602 DOI: 10.1186/s12894-023-01357-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is a common malignant tumor of the urinary system. This study aims to develop new biomarkers for KIRC and explore the impact of biomarkers on the immunotherapeutic efficacy for KIRC, providing a theoretical basis for the treatment of KIRC patients. METHODS Transcriptome data for KIRC was obtained from the The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Weighted gene co-expression network analysis identified KIRC-related modules of long noncoding RNAs (lncRNAs). Intersection analysis was performed differentially expressed lncRNAs between KIRC and normal control samples, and lncRNAs associated with N(7)-methylguanosine (m7G), resulting in differentially expressed m7G-associated lncRNAs in KIRC patients (DE-m7G-lncRNAs). Machine Learning was employed to select biomarkers for KIRC. The prognostic value of biomarkers and clinical features was evaluated using Kaplan-Meier (K-M) survival analysis, univariate and multivariate Cox regression analysis. A nomogram was constructed based on biomarkers and clinical features, and its efficacy was evaluated using calibration curves and decision curves. Functional enrichment analysis was performed to investigate the functional enrichment of biomarkers. Correlation analysis was conducted to explore the relationship between biomarkers and immune cell infiltration levels and common immune checkpoint in KIRC samples. RESULTS By intersecting 575 KIRC-related module lncRNAs, 1773 differentially expressed lncRNAs, and 62 m7G-related lncRNAs, we identified 42 DE-m7G-lncRNAs. Using XGBoost and Boruta algorithms, 8 biomarkers for KIRC were selected. Kaplan-Meier survival analysis showed significant survival differences in KIRC patients with high and low expression of the PTCSC3 and RP11-321G12.1. Univariate and multivariate Cox regression analyses showed that AP000696.2, PTCSC3 and clinical characteristics were independent prognostic factors for patients with KIRC. A nomogram based on these prognostic factors accurately predicted the prognosis of KIRC patients. The biomarkers showed associations with clinical features of KIRC patients, mainly localized in the cytoplasm and related to cytokine-mediated immune response. Furthermore, immune feature analysis demonstrated a significant decrease in immune cell infiltration levels in KIRC samples compared to normal samples, with a negative correlation observed between the biomarkers and most differentially infiltrating immune cells and common immune checkpoints. CONCLUSION In summary, this study discovered eight prognostic biomarkers associated with KIRC patients. These biomarkers showed significant correlations with clinical features, immune cell infiltration, and immune checkpoint expression in KIRC patients, laying a theoretical foundation for the diagnosis and treatment of KIRC.
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Affiliation(s)
- Shuangze Zhong
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Shangjin Chen
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Hansheng Lin
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
- Department of Urology, Yangjiang People's Hospital affiliated to Guangdong Medical University, Yangjiang, 42 Dongshan Road, Jiangcheng District, Guangdong Province, 529500, China
| | - Yuancheng Luo
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Jingwei He
- Department of Urology, Yangjiang People's Hospital affiliated to Guangdong Medical University, Yangjiang, 42 Dongshan Road, Jiangcheng District, Guangdong Province, 529500, China.
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10
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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11
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Zucko D, Boris-Lawrie K. Blocking tri-methylguanosine synthase 1 (TGS1) stops anchorage-independent growth of canine sarcomas. Cancer Gene Ther 2023; 30:1274-1284. [PMID: 37386121 PMCID: PMC10501901 DOI: 10.1038/s41417-023-00636-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 07/01/2023]
Abstract
Tri methylguanosine synthase 1 (TGS1) is the enzyme that hyper methylates the hallmark 7-methyl-guanosine cap (m7G-cap) appended to the transcription start site of RNAs. The m7G-cap and the eIF4E-cap binding protein guide canonical cap-dependent translation of mRNAs, whereas hyper methylated cap, m2,2,7G-cap (TMG) lacks adequate eIF4E affinity and licenses entry into a different translation initiation pathway. The potential role for TGS1 and TMG-capped mRNA in neoplastic growth is unknown. Canine sarcoma has high translational value to the human disease. Cumulative downregulation of protein synthesis in osteosarcoma OSCA-40 was achieved cooperatively by siTGS1 and Torin-1. Torin-1 inhibited the proliferation of three canine sarcoma explants in a reversible manner that was eliminated by siRNA-downregulation of TGS1. TGS1 failure prevented the anchorage-independent growth of osteo- and hemangio-sarcomas and curtailed sarcoma recovery from mTOR inhibition. RNA immunoprecipitation studies identified TMG-capped mRNAs encoding TGS1, DHX9 and JUND. TMG-tgs1 transcripts were downregulated by leptomycin B and TGS1 failure was compensated by eIF4E mRNP-dependent tgs1 mRNA translation affected by mTOR. The evidence documents TMG-capped mRNAs are hallmarks of the investigated neoplasms and synergy between TGS1 specialized translation and canonical translation is involved in sarcoma recovery from mTOR inhibition. Therapeutic targeting of TGS1 activity in cancer is ripe for future exploration.
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Affiliation(s)
- Dora Zucko
- University of Minnesota - Twin Cities, Department of Veterinary and Biomedical Sciences, Saint Paul, MN, 55108, USA
| | - Kathleen Boris-Lawrie
- University of Minnesota - Twin Cities, Department of Veterinary and Biomedical Sciences, Saint Paul, MN, 55108, USA.
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12
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Liang M, Hody C, Yammine V, Soin R, Sun Y, Lin X, Tian X, Meurs R, Perdrau C, Delacourt N, Oumalis M, Andris F, Conrard L, Kruys V, Gueydan C. eIF4EHP promotes Ldh mRNA translation in and fruit fly adaptation to hypoxia. EMBO Rep 2023; 24:e56460. [PMID: 37144276 PMCID: PMC10328074 DOI: 10.15252/embr.202256460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Hypoxia induces profound modifications in the gene expression program of eukaryotic cells due to lowered ATP supply resulting from the blockade of oxidative phosphorylation. One significant consequence of oxygen deprivation is the massive repression of protein synthesis, leaving a limited set of mRNAs to be translated. Drosophila melanogaster is strongly resistant to oxygen fluctuations; however, the mechanisms allowing specific mRNA to be translated into hypoxia are still unknown. Here, we show that Ldh mRNA encoding lactate dehydrogenase is highly translated into hypoxia by a mechanism involving a CA-rich motif present in its 3' untranslated region. Furthermore, we identified the cap-binding protein eIF4EHP as a main factor involved in 3'UTR-dependent translation under hypoxia. In accordance with this observation, we show that eIF4EHP is necessary for Drosophila development under low oxygen concentrations and contributes to Drosophila mobility after hypoxic challenge. Altogether, our data bring new insight into mechanisms contributing to LDH production and Drosophila adaptation to oxygen variations.
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Affiliation(s)
- Manfei Liang
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
- Present address:
Medical Science and Technology Innovation CenterShandong First Medical UniversityJinanChina
| | - Clara Hody
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Vanessa Yammine
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Yuqiu Sun
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xing Lin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xiaoying Tian
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romane Meurs
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Camille Perdrau
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Nadège Delacourt
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Marina Oumalis
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Fabienne Andris
- Laboratoire d'Immunobiologie, Faculté des SciencesUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Louise Conrard
- Center of Microscopy and Molecular Imaging (CMMI)Université libre de Bruxelles (ULB)GosseliesBelgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
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13
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Zhang Y, Gan W, Ru N, Xue Z, Chen W, Chen Z, Wang H, Zheng X. Comprehensive multi-omics analysis reveals m7G-related signature for evaluating prognosis and immunotherapy efficacy in osteosarcoma. J Bone Oncol 2023; 40:100481. [PMID: 37139222 PMCID: PMC10149372 DOI: 10.1016/j.jbo.2023.100481] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Background Osteosarcoma is one of the most prevalent bone malignancies with a poor prognosis. The N7-methylguanosine (m7G) modification facilitates the modification of RNA structure and function tightly associated with cancer. Nonetheless, there is a lack of joint exploration of the relationship between m7G methylation and immune status in osteosarcoma. Methods With the support of TARGET and GEO databases, we performed consensus clustering to characterize molecular subtypes based on m7G regulators in all osteosarcoma patients. The least absolute shrinkage and selection operator (LASSO) method, Cox regression, and receiver operating characteristic (ROC) curves were employed to construct and validate m7G-related prognostic features and derived risk scores. In addition, GSVA, ssGSEA, CIBERSORT, ESTIMATE, and gene set enrichment analysis were conducted to characterize biological pathways and immune landscapes. We explored the relationship between risk scores and drug sensitivity, immune checkpoints, and human leukocyte antigens by correlation analysis. Finally, the roles of EIF4E3 in cell function were verified through external experiments. Results Two molecular isoforms based on regulator genes were identified, which presented significant discrepancies in terms of survival and activated pathways. Moreover, the six m7G regulators most associated with prognosis in osteosarcoma patients were identified as independent predictors for the construction of prognostic signature. The model was well stabilized and outperformed traditional clinicopathological features to reliably predict 3-year (AUC = 0.787) and 5-year (AUC = 0.790) survival in osteosarcoma cohorts. Patients with increased risk scores had a poorer prognosis, higher tumor purity, lower checkpoint gene expression, and were in an immunosuppressive microenvironment. Furthermore, enhanced expression of EIF4E3 indicated a favorable prognosis and affected the biological behavior of osteosarcoma cells. Conclusions We identified six prognostic relevant m7G modulators that may provide valuable indicators for the estimation of overall survival and the corresponding immune landscape in patients with osteosarcoma.
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14
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Loan Young T, Chang Wang K, James Varley A, Li B. Clinical Delivery of Circular RNA: Lessons Learned from RNA Drug Development. Adv Drug Deliv Rev 2023; 197:114826. [PMID: 37088404 DOI: 10.1016/j.addr.2023.114826] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Circular RNAs (circRNA) represent a distinct class of covalently closed-loop RNA molecules, which play diverse roles in regulating biological processes and disease states. The enhanced stability of synthetic circRNAs compared to their linear counterparts has recently garnered considerable research interest, paving the way for new therapeutic applications. While clinical circRNA technology is still in its early stages, significant advancements in mRNA technology offer valuable insights into its potential future applications. Two primary obstacles that must be addressed are the development of efficient production methods and the optimization of delivery systems. To expedite progress in this area, this review aims to provide an overview of the current state of knowledge on circRNA structure and function, outline recent techniques for synthesizing circRNAs, highlight key delivery strategies and applications, and discuss the current challenges and future prospects in the field of circRNA-based therapeutics.
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Affiliation(s)
- Tiana Loan Young
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Kevin Chang Wang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Andrew James Varley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Bowen Li
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3M2, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada.
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15
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Korneeva N, Khalil MI, Ghosh I, Fan R, Arnold T, De Benedetti A. SARS-CoV-2 viral protein Nsp2 stimulates translation under normal and hypoxic conditions. Virol J 2023; 20:55. [PMID: 36998012 PMCID: PMC10060939 DOI: 10.1186/s12985-023-02021-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractWhen viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.
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16
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Ghram M, Morris G, Culjkovic-Kraljacic B, Mars JC, Gendron P, Skrabanek L, Revuelta MV, Cerchietti L, Guzman ML, Borden KLB. The eukaryotic translation initiation factor eIF4E reprograms alternative splicing. EMBO J 2023; 42:e110496. [PMID: 36843541 PMCID: PMC10068332 DOI: 10.15252/embj.2021110496] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
Aberrant splicing is typically attributed to splice-factor (SF) mutation and contributes to malignancies including acute myeloid leukemia (AML). Here, we discovered a mutation-independent means to extensively reprogram alternative splicing (AS). We showed that the dysregulated expression of eukaryotic translation initiation factor eIF4E elevated selective splice-factor production, thereby impacting multiple spliceosome complexes, including factors mutated in AML such as SF3B1 and U2AF1. These changes generated a splicing landscape that predominantly supported altered splice-site selection for ~800 transcripts in cell lines and ~4,600 transcripts in specimens from high-eIF4E AML patients otherwise harboring no known SF mutations. Nuclear RNA immunoprecipitations, export assays, polysome analyses, and mutational studies together revealed that eIF4E primarily increased SF production via its nuclear RNA export activity. By contrast, eIF4E dysregulation did not induce known SF mutations or alter spliceosome number. eIF4E interacted with the spliceosome and some pre-mRNAs, suggesting its direct involvement in specific splicing events. eIF4E induced simultaneous effects on numerous SF proteins, resulting in a much larger range of splicing alterations than in the case of mutation or dysregulation of individual SFs and providing a novel paradigm for splicing control and dysregulation.
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Affiliation(s)
- Mehdi Ghram
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Gavin Morris
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Jean-Clement Mars
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.,Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Maria Victoria Revuelta
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Leandro Cerchietti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Monica L Guzman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada.,Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, Canada
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17
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Muthmann N, Albers M, Rentmeister A. CAPturAM, a Chemo-Enzymatic Strategy for Selective Enrichment and Detection of Physiological CAPAM-Targets. Angew Chem Int Ed Engl 2023; 62:e202211957. [PMID: 36282111 PMCID: PMC10107118 DOI: 10.1002/anie.202211957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Modified nucleotides impact all aspects of eukaryotic mRNAs and contribute to regulation of gene expression at the transcriptional and translational level. At the 5' cap, adenosine as first transcribed nucleotide is often N6 -methyl-2'-O-methyl adenosine (m6 Am ). This modification is tissue dependent and reversible, pointing to a regulatory function. CAPAM was recently identified as methyltransferase responsible for m6 Am formation, however, the direct assignment of its target transcripts proves difficult. Antibodies do not discriminate between internal N6 -methyl adenosine (m6 A) and m6 Am . Here we present CAPturAM, an antibody-free chemical biology approach for direct enrichment and probing of physiological CAPAM-targets. We harness CAPAM's cosubstrate promiscuity to install propargyl groups on its targets. Subsequent functionalization with an affinity handle allows for their enrichment. Using wildtype and CAPAM-/- cells, we successfully applied CAPturAM to confirm or disprove CAPAM-targets, facilitating the verification and identification of CAPAM targets.
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Affiliation(s)
- Nils Muthmann
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| | - Marvin Albers
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
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18
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Yang J, Liu M, Fang X, Zhang H, Ren Q, Zheng Y, Wang Y, Zhou Y. Advances in peptides encoded by non-coding RNAs: A cargo in exosome. Front Oncol 2022; 12:1081997. [PMID: 36620552 PMCID: PMC9822543 DOI: 10.3389/fonc.2022.1081997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.
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Affiliation(s)
- Jing Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengxiao Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xidong Fang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qian Ren
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
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19
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Song Z, Lin J, Su R, Ji Y, Jia R, Li S, Shan G, Huang C. eIF3j inhibits translation of a subset of circular RNAs in eukaryotic cells. Nucleic Acids Res 2022; 50:11529-11549. [PMID: 36330957 PMCID: PMC9723666 DOI: 10.1093/nar/gkac980] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Increasing studies have revealed that a subset of circular RNAs (circRNAs) harbor an open reading frame and can act as protein-coding templates to generate functional proteins that are closely associated with multiple physiological and disease-relevant processes, and thus proper regulation of synthesis of these circRNA-derived proteins is a fundamental cellular process required for homeostasis maintenance. However, how circRNA translation initiation is coordinated by different trans-acting factors remains poorly understood. In particular, the impact of different eukaryotic translation initiation factors (eIFs) on circRNA translation and the physiological relevance of this distinct regulation have not yet been characterized. In this study, we screened all 43 Drosophila eIFs and revealed the conflicting functions of eIF3 subunits in the translational control of the translatable circRNA circSfl: eIF3 is indispensable for circSfl translation, while the eIF3-associated factor eIF3j is the most potent inhibitor. Mechanistically, the binding of eIF3j to circSfl promotes the disassociation of eIF3. The C-terminus of eIF3j and an RNA regulon within the circSfl untranslated region (UTR) are essential for the inhibitory effect of eIF3j. Moreover, we revealed the physiological relevance of eIF3j-mediated circSfl translation repression in response to heat shock. Finally, additional translatable circRNAs were identified to be similarly regulated in an eIF3j-dependent manner. Altogether, our study provides a significant insight into the field of cap-independent translational regulation and undiscovered functions of eIF3.
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Affiliation(s)
| | | | - Rui Su
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yu Ji
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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20
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Borden KL. Cancer cells hijack RNA processing to rewrite the message. Biochem Soc Trans 2022; 50:1447-1456. [PMID: 36282006 PMCID: PMC9704515 DOI: 10.1042/bst20220621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Typically, cancer is thought to arise due to DNA mutations, dysregulated transcription and/or aberrant signalling. Recently, it has become clear that dysregulated mRNA processing, mRNA export and translation also contribute to malignancy. RNA processing events result in major modifications to the physical nature of mRNAs such as the addition of the methyl-7-guanosine cap, the removal of introns and the addition of polyA tails. mRNA processing is a critical determinant for the protein-coding capacity of mRNAs since these physical changes impact the efficiency by which a given transcript can be exported to the cytoplasm and translated into protein. While many of these mRNA metabolism steps were considered constitutive housekeeping activities, they are now known to be highly regulated with combinatorial and multiplicative impacts i.e. one event will influence the capacity to undergo others. Furthermore, alternative splicing and/or cleavage and polyadenylation can produce transcripts with alternative messages and new functionalities. The coordinated processing of groups of functionally related RNAs can potently re-wire signalling pathways, modulate survival pathways and even re-structure the cell. As postulated by the RNA regulon model, combinatorial regulation of these groups is achieved by the presence of shared cis-acting elements (known as USER codes) which recruit machinery for processing, export or translation. In all, dysregulated RNA metabolism in cancer gives rise to an altered proteome that in turn elicits biological responses related to malignancy. Studies of these events in cancer revealed new mechanisms underpinning malignancies and unearthed novel therapeutic opportunities. In all, cancer cells coopt RNA processing, export and translation to support their oncogenic activity.
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Affiliation(s)
- Katherine L.B. Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC H3C 3J7, Canada
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21
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Cruz A, Joseph S. Interaction of the Influenza A Virus NS1 Protein with the 5'-m7G-mRNA·eIF4E·eIF4G1 Complex. Biochemistry 2022; 61:1485-1494. [PMID: 35797022 PMCID: PMC10164398 DOI: 10.1021/acs.biochem.2c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influenza A virus (IAV) is responsible for seasonal epidemics that result in hundreds of thousands of deaths worldwide annually. The non-structural protein 1 (NS1) of the IAV inflicts various antagonistic processes on the host during infection. These processes include inhibition of the host interferon system, inhibition of the apoptotic response, and enhancement of viral mRNA translation, all of which contribute to the overall virulence of the IAV. Although the mechanism by which NS1 stimulates translation is unknown, NS1 has been shown to bind both poly-A binding Protein 1 and eukaryotic initiation factor 4 gamma 1 (eIF4G1), two proteins necessary for cap-dependent translation. We directly analyzed the interaction between NS1 and eIF4G1 within the context of the 5'-m7G-mRNA·eIF4E·eIF4G1 complex. Interestingly, our studies show that NS1 can bind this complex in the presence or absence of 5'-m7G-mRNA. Additionally, we were interested in investigating whether NS1 interacts with eIF4E directly. Our results indicate that NS1 can bind to eIF4E only in the absence of 5'-m7G-mRNA. Considering previous data, we propose that NS1 stimulates translation by binding to eIF4G1 and recruiting the 43S pre-translation initiation complex to the mRNA.
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Affiliation(s)
- Alejandro Cruz
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314 United States
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0314 United States
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22
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Borden K. The search for genetic dark matter and lessons learned from the journey. Biochem Cell Biol 2022; 100:276-281. [DOI: 10.1139/bcb-2022-0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this review, I describe our scientific journey to unearth the impact of RNA metabolism in cancer using the eukaryotic translation initiation factor eIF4E as an exemplar. This model allowed us to discover new structural, biochemical, and molecular features of RNA processing, and to reveal their substantial impact on cell physiology. This led us to develop proof-of-principle strategies to target these pathways in cancer patients leading to clinical benefit. I discuss the important role that the unexpected plays in research and the necessity of embracing the data even when it clashes with dogma. I also touch on the importance of equity, diversity and inclusion to the success of the scientific enterprise.
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Affiliation(s)
- Katherine Borden
- University of Montreal, 5622, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
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23
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Boris-Lawrie K, Singh G, Osmer PS, Zucko D, Staller S, Heng X. Anomalous HIV-1 RNA, How Cap-Methylation Segregates Viral Transcripts by Form and Function. Viruses 2022; 14:935. [PMID: 35632676 PMCID: PMC9145092 DOI: 10.3390/v14050935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022] Open
Abstract
The acquisition of m7G-cap-binding proteins is now recognized as a major variable driving the form and function of host RNAs. This manuscript compares the 5'-cap-RNA binding proteins that engage HIV-1 precursor RNAs, host mRNAs, small nuclear (sn)- and small nucleolar (sno) RNAs and sort into disparate RNA-fate pathways. Before completion of the transcription cycle, the transcription start site of nascent class II RNAs is appended to a non-templated guanosine that is methylated (m7G-cap) and bound by hetero-dimeric CBP80-CBP20 cap binding complex (CBC). The CBC is a nexus for the co-transcriptional processing of precursor RNAs to mRNAs and the snRNA and snoRNA of spliceosomal and ribosomal ribonucleoproteins (RNPs). Just as sn/sno-RNAs experience hyper-methylation of m7G-cap to trimethylguanosine (TMG)-cap, so do select HIV RNAs and an emerging cohort of mRNAs. TMG-cap is blocked from Watson:Crick base pairing and disqualified from participating in secondary structure. The HIV TMG-cap has been shown to license select viral transcripts for specialized cap-dependent translation initiation without eIF4E that is dependent upon CBP80/NCBP3. The exceptional activity of HIV precursor RNAs secures their access to maturation pathways of sn/snoRNAs, canonical and non-canonical host mRNAs in proper stoichiometry to execute the retroviral replication cycle.
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Affiliation(s)
- Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Seth Staller
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
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24
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Osborne MJ, Volpon L, Memarpooryazdi M, Pillay S, Thambipillai A, Czarnota S, Culjkovic-Kraljacic B, Trahan C, Oeffinger M, Cowling VH, L B Borden K. Identification and characterization of the interaction between the methyl-7-guanosine cap maturation enzyme RNMT and the cap-binding protein eIF4E. J Mol Biol 2022; 434:167451. [PMID: 35026230 DOI: 10.1016/j.jmb.2022.167451] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022]
Abstract
The control of RNA metabolism is an important aspect of molecular biology with wide-ranging impacts on cells. Central to processing of coding RNAs is the addition of the methyl-7 guanosine (m7G) "cap" on their 5' end. The eukaryotic translation initiation factor eIF4E directly binds the m7G cap and through this interaction plays key roles in many steps of RNA metabolism including nuclear RNA export and translation. eIF4E also stimulates capping of many transcripts through its ability to drive the production of the enzyme RNMT which methylates the G-cap to form the mature m7G cap. Here, we found that eIF4E also physically associated with RNMT in human cells. Moreover, eIF4E directly interacted with RNMT in vitro. eIF4E is only the second protein reported to directly bind the methyltransferase domain of RNMT, the first being its co-factor RAM. We combined high-resolution NMR methods with biochemical studies to define the binding interfaces for the RNMT-eIF4E complex. Further, we found that eIF4E competes for RAM binding to RNMT and conversely, RNMT competes for binding of well-established eIF4E-binding partners such as the 4E-BPs. RNMT uses novel structural means to engage eIF4E. Finally, we observed that m7G cap-eIF4E-RNMT trimeric complexes form, and thus RNMT-eIF4E complexes may be employed so that eIF4E captures newly capped RNA. In all, we show for the first time that the cap-binding protein eIF4E directly binds to the cap-maturation enzyme RNMT.
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Affiliation(s)
- Michael J Osborne
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada
| | - Mina Memarpooryazdi
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada
| | - Subhadra Pillay
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada; Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aksharh Thambipillai
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada
| | - Sylwia Czarnota
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada
| | - Christian Trahan
- Department for Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Marlene Oeffinger
- Department for Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK, DD1 5EH
| | - Katherine L B Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Pavilion Marcelle-Coutu, Chemin Polytechnique, Montréal, QC H3T 1J4, Canada.
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25
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HIV-1 hypermethylated guanosine cap licenses specialized translation unaffected by mTOR. Proc Natl Acad Sci U S A 2022; 119:2105153118. [PMID: 34949712 PMCID: PMC8740576 DOI: 10.1073/pnas.2105153118] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/29/2022] Open
Abstract
The proliferation of viral pathogens is restricted by hosts, but resilient pathogens antagonize the restriction by hosts. Findings explain that HIV-1 blocked mono-methylated guanosine cap by hypermethylation and engaged novel cap-binding complex for virion protein translation unaffected by global translation inhibition. The hypermethylated cap activity required RNA-structure-dependent binding of RNA helicase A/DHX9. eIF4E interaction proceeded on completely spliced HIV messenger RNA templates encoding viral regulatory proteins, thus eIF4E inactivation by catalytic site mTOR inhibitor suppressed regulatory protein translation, while structural/accessory protein translation was maintained. Two mutually exclusive translation pathways antagonize hosts and facilitate HIV-1 proliferation in primary CD4+ T cells to the detriment of hosts. eIF4E inactivation imposed an operational rheostat that suppressed regulatory proteins, while maintaining virion production in immune cells. Appended to the 5′ end of nascent RNA polymerase II transcripts is 7-methyl guanosine (m7G-cap) that engages nuclear cap-binding complex (CBC) to facilitate messenger RNA (mRNA) maturation. Mature mRNAs exchange CBC for eIF4E, the rate-limiting translation factor that is controlled through mTOR. Experiments in immune cells have now documented HIV-1 incompletely processed transcripts exhibited hypermethylated m7G-cap and that the down-regulation of the trimethylguanosine synthetase-1–reduced HIV-1 infectivity and virion protein synthesis by several orders of magnitude. HIV-1 cap hypermethylation required nuclear RNA helicase A (RHA)/DHX9 interaction with the shape of the 5′ untranslated region (UTR) primer binding site (PBS) segment. Down-regulation of RHA or the anomalous shape of the PBS segment abrogated hypermethylated caps and derepressed eIF4E binding for virion protein translation during global down-regulation of host translation. mTOR inhibition was detrimental to HIV-1 proliferation and attenuated Tat, Rev, and Nef synthesis. This study identified mutually exclusive translation pathways and the calibration of virion structural/accessory protein synthesis with de novo synthesis of the viral regulatory proteins. The hypermethylation of select, viral mRNA resulted in CBC exchange to heterodimeric CBP80/NCBP3 that expanded the functional capacity of HIV-1 in immune cells.
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26
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Mars JC, Ghram M, Culjkovic-Kraljacic B, Borden KLB. The Cap-Binding Complex CBC and the Eukaryotic Translation Factor eIF4E: Co-Conspirators in Cap-Dependent RNA Maturation and Translation. Cancers (Basel) 2021; 13:6185. [PMID: 34944805 PMCID: PMC8699206 DOI: 10.3390/cancers13246185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022] Open
Abstract
The translation of RNA into protein is a dynamic process which is heavily regulated during normal cell physiology and can be dysregulated in human malignancies. Its dysregulation can impact selected groups of RNAs, modifying protein levels independently of transcription. Integral to their suitability for translation, RNAs undergo a series of maturation steps including the addition of the m7G cap on the 5' end of RNAs, splicing, as well as cleavage and polyadenylation (CPA). Importantly, each of these steps can be coopted to modify the transcript signal. Factors that bind the m7G cap escort these RNAs through different steps of maturation and thus govern the physical nature of the final transcript product presented to the translation machinery. Here, we describe these steps and how the major m7G cap-binding factors in mammalian cells, the cap binding complex (CBC) and the eukaryotic translation initiation factor eIF4E, are positioned to chaperone transcripts through RNA maturation, nuclear export, and translation in a transcript-specific manner. To conceptualize a framework for the flow and integration of this genetic information, we discuss RNA maturation models and how these integrate with translation. Finally, we discuss how these processes can be coopted by cancer cells and means to target these in malignancy.
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Affiliation(s)
- Jean-Clement Mars
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
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27
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He L, Man C, Xiang S, Yao L, Wang X, Fan Y. Circular RNAs' cap-independent translation protein and its roles in carcinomas. Mol Cancer 2021; 20:119. [PMID: 34526007 PMCID: PMC8442428 DOI: 10.1186/s12943-021-01417-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs a kind of covalently closed RNA and widely expressed in eukaryotes. CircRNAs are involved in a variety of physiological and pathological processes, but their regulatory mechanisms are not fully understood. Given the development of the RNA deep-sequencing technology and the improvement of algorithms, some CircRNAs are discovered to encode proteins through the cap-independent mechanism and participate in the important process of tumorigenesis and development. Based on an overview of CircRNAs, this paper summarizes its translation mechanism and research methods, and reviews the research progress of CircRNAs translation in the field of oncology in recent years. Moreover, this paper aims to provide new ideas for tumor diagnosis and treatment through CircRNAs translation.
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Affiliation(s)
- Lian He
- Cancer Institue, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China
| | - Changfeng Man
- Cancer Institue, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China
| | - Shouyan Xiang
- Cancer Institue, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China
| | - Lin Yao
- Cancer Institue, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China
| | - Xiaoyan Wang
- Department of Gastroenterology, Affiliated Suqian First People's Hospital of Nanjing Medical University, No 120, Suzhi Road, Suqian, Jiangsu Province, 223812, People's Republic of China.
| | - Yu Fan
- Cancer Institue, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China.
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28
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Borden K, Culjkovic-Kraljacic B, Cowling VH. To cap it all off, again: dynamic capping and recapping of coding and non-coding RNAs to control transcript fate and biological activity. Cell Cycle 2021; 20:1347-1360. [PMID: 34241559 PMCID: PMC8344758 DOI: 10.1080/15384101.2021.1930929] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The addition of the methyl-7-guanosine (m7G) “cap” on the 5' ends of coding and some non-coding RNAs is essential for their protein coding capacity and biochemical activity, respectively. It was previously considered that capping was a constitutive process that generates a complete cap on all transcripts at steady-state. However, development of new methodologies demonstrated that steady-state capping is a dynamic and regulatable feature of many coding and non-coding RNAs. Indeed, capping status of specific RNAs can flux during differentiation and development, thereby impacting on their protein-coding capacity and activity. Moreover, in some primary cancer specimens, capping can be elevated for transcripts encoding proteins involved in proliferation and survival corresponding to their increased protein levels. Overexpression of one of the capping enzymes (RNMT), the transcription factor MYC or the eukaryotic translation initiation factor eIF4E all led to increased levels of steady-state capping of selected transcripts. Additionally, transcripts can be decapped and recapped, allowing these to be sequestered until needed. This review provides a summary of the major advances in enzymatic and affinity-based approaches to quantify m7G capping. Further, we summarize the evidence for regulation of capping. Capping has emerged as a significant regulatory step in RNA metabolism which is poised to impact a myriad of biological processes.
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Affiliation(s)
- Klb Borden
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer, University of Montreal, Montreal, Canada
| | - B Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer, University of Montreal, Montreal, Canada
| | - V H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK, UK
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29
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Gindina S, Botsford B, Cowansage K, LeDoux J, Klann E, Hoeffer C, Ostroff L. Upregulation of eIF4E, but not other translation initiation factors, in dendritic spines during memory formation. J Comp Neurol 2021; 529:3112-3126. [PMID: 33864263 DOI: 10.1002/cne.25158] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/27/2021] [Accepted: 04/11/2021] [Indexed: 11/09/2022]
Abstract
Local translation can provide a rapid, spatially targeted supply of new proteins in distal dendrites to support synaptic changes that underlie learning. Learning and memory are especially sensitive to manipulations of translational control mechanisms, particularly those that target the initiation step, and translation initiation at synapses could be a means of maintaining synapse specificity during plasticity. Initiation predominantly occurs via recruitment of ribosomes to the 5' mRNA cap by complexes of eukaryotic initiation factors (eIFs), and the interaction between eIF4E and eIF4G1 is a particularly important target of translational control pathways. Pharmacological inhibition of eIF4E-eIF4G1 binding impairs formation of memory for aversive Pavlovian conditioning as well as the accompanying increase in polyribosomes in the heads of dendritic spines in the lateral amygdala (LA). This is consistent with a role for initiation at synapses in memory formation, but whether eIFs are even present near synapses is unknown. To determine whether dendritic spines contain eIFs and whether eIF distribution is affected by learning, we combined immunolabeling with serial section transmission electron microscopy (ssTEM) volume reconstructions of LA dendrites after Pavlovian conditioning. Labeling for eIF4E, eIF4G1, and eIF2α-another key target of regulation-occurred in roughly half of dendritic spines, but learning effects were only found for eIF4E, which was upregulated in the heads of dendritic spines. Our results support the possibility of regulated translation initiation as a means of synapse-specific protein targeting during learning and are consistent with the model of eIF4E availability as a central point of control.
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Affiliation(s)
- Sofya Gindina
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, New York, USA
| | - Benjamin Botsford
- Center for Neural Science, New York University, New York, New York, USA
| | - Kiriana Cowansage
- Center for Neural Science, New York University, New York, New York, USA
| | - Joseph LeDoux
- Center for Neural Science, New York University, New York, New York, USA.,Nathan Kline Institute for Psychiatric Research, Orangeburg, New York, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, New York, USA
| | - Charles Hoeffer
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| | - Linnaea Ostroff
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
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30
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Hernández G, García A, Sonenberg N, Lasko P. Unorthodox Mechanisms to Initiate Translation Open Novel Paths for Gene Expression. J Mol Biol 2020; 432:166702. [PMID: 33166539 DOI: 10.1016/j.jmb.2020.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/24/2022]
Abstract
Translation in eukaryotes is dependent on the activity of translation initiation factor (eIF) 4G family of proteins, a scaffold protein that, during the initiation step, coordinates the activity of other eIFs to recruit the 40S ribosomal subunit to the mRNA. Three decades of research on protein synthesis and its regulation has provided a wealth of evidence supporting the crucial role of cap-dependent translation initiation, which involves eIF4G. However, the recent discovery of a surprising variety of alternative mechanisms to initiate translation in the absence of eIF4G has stirred the orthodox view of how protein synthesis is performed. These mechanisms involve novel interactions among known eIFs, or between known eIFs and other proteins not previously linked to translation. Thus, a new picture is emerging in which the unorthodox translation initiation complexes contribute to the diversity of mechanisms that regulate gene expression in eukaryotes.
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Affiliation(s)
- Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Ave., Tlalpan, 14080 Mexico City, Mexico.
| | - Alejandra García
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Ave., Tlalpan, 14080 Mexico City, Mexico
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Paul Lasko
- Department of Biology, McGill University, Montreal, Québec, Canada; Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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31
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Culjkovic-Kraljacic B, Skrabanek L, Revuelta MV, Gasiorek J, Cowling VH, Cerchietti L, Borden KLB. The eukaryotic translation initiation factor eIF4E elevates steady-state m 7G capping of coding and noncoding transcripts. Proc Natl Acad Sci U S A 2020; 117:26773-26783. [PMID: 33055213 PMCID: PMC7604501 DOI: 10.1073/pnas.2002360117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Methyl-7-guanosine (m7G) "capping" of coding and some noncoding RNAs is critical for their maturation and subsequent activity. Here, we discovered that eukaryotic translation initiation factor 4E (eIF4E), itself a cap-binding protein, drives the expression of the capping machinery and increased capping efficiency of ∼100 coding and noncoding RNAs. To quantify this, we developed enzymatic (cap quantification; CapQ) and quantitative cap immunoprecipitation (CapIP) methods. The CapQ method has the further advantage that it captures information about capping status independent of the type of 5' cap, i.e., it is not restricted to informing on m7G caps. These methodological advances led to unanticipated revelations: 1) Many RNA populations are inefficiently capped at steady state (∼30 to 50%), and eIF4E overexpression increased this to ∼60 to 100%, depending on the RNA; 2) eIF4E physically associates with noncoding RNAs in the nucleus; and 3) approximately half of eIF4E-capping targets identified are noncoding RNAs. eIF4E's association with noncoding RNAs strongly positions it to act beyond translation. Coding and noncoding capping targets have activities that influence survival, cell morphology, and cell-to-cell interaction. Given that RNA export and translation machineries typically utilize capped RNA substrates, capping regulation provides means to titrate the protein-coding capacity of the transcriptome and, for noncoding RNAs, to regulate their activities. We also discovered a cap sensitivity element (CapSE) which conferred eIF4E-dependent capping sensitivity. Finally, we observed elevated capping for specific RNAs in high-eIF4E leukemia specimens, supporting a role for cap dysregulation in malignancy. In all, levels of capping RNAs can be regulated by eIF4E.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Lucy Skrabanek
- Applied Bioinformatics Core, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Maria V Revuelta
- Division of Hematology & Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Jadwiga Gasiorek
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Leandro Cerchietti
- Division of Hematology & Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Katherine L B Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC H3T 1J4, Canada;
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