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Prusty AB, Hirmer A, Sierra-Delgado JA, Huber H, Guenther UP, Schlosser A, Dybkov O, Yildirim E, Urlaub H, Meyer KC, Jablonka S, Erhard F, Fischer U. RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis. Cell Rep 2024; 43:113802. [PMID: 38368610 DOI: 10.1016/j.celrep.2024.113802] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
RNA helicases constitute a large protein family implicated in cellular RNA homeostasis and disease development. Here, we show that the RNA helicase IGHMBP2, linked to the neuromuscular disorder spinal muscular atrophy with respiratory distress type 1 (SMARD1), associates with polysomes and impacts translation of mRNAs containing short, GC-rich, and structured 5' UTRs. The absence of IGHMBP2 causes ribosome stalling at the start codon of target mRNAs, leading to reduced translation efficiency. The main mRNA targets of IGHMBP2-mediated regulation encode for components of the THO complex (THOC), linking IGHMBP2 to mRNA production and nuclear export. Accordingly, failure of IGHMBP2 regulation of THOC causes perturbations of the transcriptome and its encoded proteome, and ablation of THOC subunits phenocopies these changes. Thus, IGHMBP2 is an upstream regulator of THOC. Of note, IGHMBP2-dependent regulation of THOC is also observed in astrocytes derived from patients with SMARD1 disease, suggesting that deregulated mRNA metabolism contributes to SMARD1 etiology and may enable alternative therapeutic avenues.
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Affiliation(s)
| | - Anja Hirmer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Hannes Huber
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Andreas Schlosser
- Rudolf-Virchow-Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Ezgi Yildirim
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Kathrin C Meyer
- Nationwide Children's Hospital, Center for Gene Therapy, Columbus, OH 43205, USA; Department of Pediatrics, Ohio State University, Columbus, OH 43210, USA
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany; Faculty for Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany.
| | - Utz Fischer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany.
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2
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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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3
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Das A, Liu T, Li H, Husain S. The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei. mSphere 2023; 8:e0027323. [PMID: 37581443 PMCID: PMC10654194 DOI: 10.1128/msphere.00273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 08/16/2023] Open
Abstract
RNA-binding proteins (RBPs) are key players in coordinated post-transcriptional regulation of functionally related genes, defined as RNA regulons. RNA regulons play particularly critical roles in parasitic trypanosomes, which exhibit unregulated co-transcription of long unrelated gene arrays. In this report, we present a systematic analysis of an essential RBP, RBP42, in the mammalian-infective bloodstream form of African trypanosome and show that RBP42 is a key regulator of parasite's central carbon and energy metabolism. Using individual-nucleotide resolution UV cross-linking and immunoprecipitation to identify genome-wide RBP42-RNA interactions, we show that RBP42 preferentially binds within the coding region of mRNAs encoding core metabolic enzymes. Global quantitative transcriptomic and proteomic analyses reveal that loss of RBP42 reduces the abundance of target mRNA-encoded proteins, but not target mRNA, suggesting a positive translational regulatory role of RBP42. Significant changes in central carbon metabolic intermediates, following loss of RBP42, further support its critical role in cellular energy metabolism. Trypanosoma brucei infection, transmitted through the bite of blood-feeding tsetse flies, causes deadly diseases in humans and livestock. This disease, if left untreated, is almost always fatal. Existing therapies are toxic and difficult to administer. During T. brucei's lifecycle in two different host environments, the parasite progresses through distinctive life stages with major morphological and metabolic changes, requiring precise alteration of parasite gene expression program. In the absence of regulated transcription, post-transcriptional processes mediated by RNA-binding proteins play critical roles in T. brucei gene regulation. In this study, we show that the RNA-binding protein RBP42 plays crucial roles in cellular energy metabolic regulation of this important human pathogen. Metabolic dysregulation observed in RBP42 knockdown cells offers a breadth of potential interest to researchers studying parasite biology and can also impact research in general eukaryotic biology.
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Affiliation(s)
- Anish Das
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Tong Liu
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Hong Li
- Center for Advanced Proteomics Research, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - Seema Husain
- Genomics Center, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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4
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Kershaw CJ, Nelson MG, Castelli LM, Jennings MD, Lui J, Talavera D, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP. Translation factor and RNA binding protein mRNA interactomes support broader RNA regulons for posttranscriptional control. J Biol Chem 2023; 299:105195. [PMID: 37633333 PMCID: PMC10562868 DOI: 10.1016/j.jbc.2023.105195] [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: 07/07/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023] Open
Abstract
The regulation of translation provides a rapid and direct mechanism to modulate the cellular proteome. In eukaryotes, an established model for the recruitment of ribosomes to mRNA depends upon a set of conserved translation initiation factors. Nevertheless, how cells orchestrate and define the selection of individual mRNAs for translation, as opposed to other potential cytosolic fates, is poorly understood. We have previously found significant variation in the interaction between individual mRNAs and an array of translation initiation factors. Indeed, mRNAs can be separated into different classes based upon these interactions to provide a framework for understanding different modes of translation initiation. Here, we extend this approach to include new mRNA interaction profiles for additional proteins involved in shaping the cytoplasmic fate of mRNAs. This work defines a set of seven mRNA clusters, based on their interaction profiles with 12 factors involved in translation and/or RNA binding. The mRNA clusters share both physical and functional characteristics to provide a rationale for the interaction profiles. Moreover, a comparison with mRNA interaction profiles from a host of RNA binding proteins suggests that there are defined patterns in the interactions of functionally related mRNAs. Therefore, this work defines global cytoplasmic mRNA binding modules that likely coordinate the synthesis of functionally related proteins.
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Affiliation(s)
- Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Michael G Nelson
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Jennifer Lui
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, The University of Manchester, Manchester, UK
| | - Chris M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK.
| | - Simon J Hubbard
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK.
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK.
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5
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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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6
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Trkulja KL, Manji F, Kuruvilla J, Laister RC. Nuclear Export in Non-Hodgkin Lymphoma and Implications for Targeted XPO1 Inhibitors. Biomolecules 2023; 13:111. [PMID: 36671496 PMCID: PMC9855521 DOI: 10.3390/biom13010111] [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: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023] Open
Abstract
Exportin-1 (XPO1) is a key player in the nuclear export pathway and is overexpressed in almost all cancers. This is especially relevant for non-Hodgkin lymphoma (NHL), where high XPO1 expression is associated with poor prognosis due to its oncogenic role in exporting proteins and RNA that are involved in cancer progression and treatment resistance. Here, we discuss the proteins and RNA transcripts that have been identified as XPO1 cargo in NHL lymphoma including tumour suppressors, immune modulators, and transcription factors, and their implications for oncogenesis. We then highlight the research to date on XPO1 inhibitors such as selinexor and other selective inhibitors of nuclear export (SINEs), which are used to treat some cases of non-Hodgkin lymphoma. In vitro, in vivo, and clinical studies investigating the anti-cancer effects of SINEs from bench to bedside, both as a single agent and in combination, are also reported. Finally, we discuss the limitations of the current research landscape and future directions to better understand and improve the clinical utility of SINE compounds in NHL.
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Affiliation(s)
- Kyla L. Trkulja
- Institute of Medical Science, University of Toronto, 27 King’s College Circle, Toronto, ON M5S 1A1, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
| | - Farheen Manji
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
| | - John Kuruvilla
- Institute of Medical Science, University of Toronto, 27 King’s College Circle, Toronto, ON M5S 1A1, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
| | - Rob C. Laister
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
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7
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Zhang C, Liu J, Guo H, Hong D, Ji J, Zhang Q, Guan Q, Ren Q. m6A RNA methylation regulators were associated with the malignancy and prognosis of ovarian cancer. Bioengineered 2021; 12:3159-3176. [PMID: 34187307 PMCID: PMC8806923 DOI: 10.1080/21655979.2021.1946305] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
N6-methyladenosine (m6A) RNA methylation regulators play a regulatory role in tumor pathogenesis and development. However, the role of m6A regulator genes in ovarian cancer (OC) has not been fully elucidated. This study aims to investigate the mRNA expressions, clinicopathological features, and prognostic values of m6A regulators in OC. Here, we demonstrate that the 17 m6A RNA methylation regulators are differentially expressed in ovarian cancer and normal tissues. By using consensus clustering, all ovarian cancer patients can be divided into two subgroups (cluster 1 and 2) based on the expression of 17 m6A RNA methylation regulators. Using Gene Set Enrichment Analysis, we identified that cluster 1 was most connected to oxidative phosphorylation pathways. Regression models identified that prognosis is associated with HNRNPA2B1, KIAA1429, and WTAP. qRT-PCR result show that the expression trends of HNRNPA2B1 and KIAA1429 are consistent with the predicted results. Multivariate Cox regression analysis results show that the risk score was an independent predictive factor in OV. The overall survival of high-risk patients was significantly shorter than that of low-risk patients. ROC curve analysis showed that the prognostic signature precisely predicted the 5-year survival of OV patients. A nomogram was developed to predict each patient's survival probability and well calibrated and showed a satisfactory discrimination. Dendritic fraction, macrophage fraction, and neutrophil fraction showed higher fraction in high-risk patients. In conclusion, m6A RNA methylation regulators are vital participants in ovarian cancer pathology, and three-gene mRNA levels are valuable factors for prognosis predictions.
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Affiliation(s)
- Cheng Zhang
- Department of Gynecology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029 Jiangsu, China
| | - JinHui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu, China
| | - Hongyu Guo
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu, China
| | - Dandan Hong
- Department of Gynecology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029 Jiangsu, China
| | - Jing Ji
- Department of Gynecology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029 Jiangsu, China
| | - Qin Zhang
- Department of Gynecology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029 Jiangsu, China
| | - Qun Guan
- Department of Gynecology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029 Jiangsu, China
| | - Qingling Ren
- Department of Gynecology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029 Jiangsu, China
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8
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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9
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Ran LY, Xiang J, Zeng XX, Tang JL, Dong YT, Zhang F, Yu WF, Qi XL, Xiao Y, Zou J, Deng J, Guan ZZ. Integrated transcriptomic and proteomic analysis indicated that neurotoxicity of rats with chronic fluorosis may be in mechanism involved in the changed cholinergic pathway and oxidative stress. J Trace Elem Med Biol 2021; 64:126688. [PMID: 33260044 DOI: 10.1016/j.jtemb.2020.126688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/16/2020] [Accepted: 11/16/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND To reveal the underling molecular mechanism in brain damage induced by chronic fluorosis, the neurotoxicity and its correlation were investigated by transcriptomics and proteomics. METHODS Sprague-Dawley rats were treated with fluoride at different concentrations (0, 5, 50 and 100 ppm, prepared by NaF) for 3 months. Spatial learning and memory were evaluated by Morris water maze test; neuronal morphological change in the hippocampus was observed using Nissl staining; and the level of oxidative stress including reactive oxygen species (ROS), malondialdehyde (MDA) and superoxide dismutase (SOD) were detected by biological methods. The high-throughput transcriptome sequencing (RNA-Seq) and tandem mass tag (TMT) proteomic sequencing were performed to detect the expression of differentially expressed genes and proteins, respectively. RESULTS The results showed that compared with control group, rats exposed to high-dose fluoride exhibited declined abilities of learning and memory, decreased SOD activity and increased ROS and MDA levels, with lighter colored Nissl bodies. A total of 28 important differentially expressed genes (DEGs) were screened out by transcriptomics. Then, functional enrichment analyses showed that upregulated proteins enriched in cellular transport, while downregulated proteins enriched in synapse-related pathways. Thirteen corresponding DEGs and DAPs (cor-DEGs-DAPs) were identified by differential expressions selected with positively correlated genes/proteins, most of which were related to neurodegenerative changes and oxidative stress response. CONCLUSION These results provide new omics evidence that rats chronically exposed to high-dose fluoride can induce neurotoxicity in the brains through changes in the cholinergic pathway and oxidative stress.
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Affiliation(s)
- Long-Yan Ran
- Departments of Pathology at Guizhou Medical University and the Affiliated Hospital of Guizhou Medical University, and Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University) of the Ministry of Education, PR China; Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Jie Xiang
- Departments of Pathology at Guizhou Medical University and the Affiliated Hospital of Guizhou Medical University, and Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University) of the Ministry of Education, PR China; Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Xiao-Xiao Zeng
- Departments of Pathology at Guizhou Medical University and the Affiliated Hospital of Guizhou Medical University, and Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University) of the Ministry of Education, PR China; Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Jing-Ling Tang
- Clinical Research Center, Affiliated Hospital of Guizhou Medical University, Guizhou, PR China
| | - Yang-Ting Dong
- Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Feng Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Wen-Feng Yu
- Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Xiao-Lan Qi
- Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Yan Xiao
- Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Jian Zou
- Departments of Pathology at Guizhou Medical University and the Affiliated Hospital of Guizhou Medical University, and Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University) of the Ministry of Education, PR China; Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Jie Deng
- Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China
| | - Zhi-Zhong Guan
- Departments of Pathology at Guizhou Medical University and the Affiliated Hospital of Guizhou Medical University, and Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University) of the Ministry of Education, PR China; Provincial Key Laboratory of Medical Molecular Biology, Guiyang, Guizhou, PR China.
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10
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Yergert KM, Doll CA, O’Rouke R, Hines JH, Appel B. Identification of 3' UTR motifs required for mRNA localization to myelin sheaths in vivo. PLoS Biol 2021; 19:e3001053. [PMID: 33439856 PMCID: PMC7837478 DOI: 10.1371/journal.pbio.3001053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 01/26/2021] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
Myelin is a specialized membrane produced by oligodendrocytes that insulates and supports axons. Oligodendrocytes extend numerous cellular processes, as projections of the plasma membrane, and simultaneously wrap multiple layers of myelin membrane around target axons. Notably, myelin sheaths originating from the same oligodendrocyte are variable in size, suggesting local mechanisms regulate myelin sheath growth. Purified myelin contains ribosomes and hundreds of mRNAs, supporting a model that mRNA localization and local protein synthesis regulate sheath growth and maturation. However, the mechanisms by which mRNAs are selectively enriched in myelin sheaths are unclear. To investigate how mRNAs are targeted to myelin sheaths, we tested the hypothesis that transcripts are selected for myelin enrichment through consensus sequences in the 3' untranslated region (3' UTR). Using methods to visualize mRNA in living zebrafish larvae, we identified candidate 3' UTRs that were sufficient to localize mRNA to sheaths and enriched near growth zones of nascent membrane. We bioinformatically identified motifs common in 3' UTRs from 3 myelin-enriched transcripts and determined that these motifs are required and sufficient in a context-dependent manner for mRNA transport to myelin sheaths. Finally, we show that 1 motif is highly enriched in the myelin transcriptome, suggesting that this sequence is a global regulator of mRNA localization during developmental myelination.
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Affiliation(s)
- Katie M. Yergert
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Caleb A. Doll
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Rebecca O’Rouke
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jacob H. Hines
- Department of Biology, Winona State University, Winona, Minnesota, United States of America
| | - Bruce Appel
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- * E-mail:
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11
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The Nuclear Pore Complex and mRNA Export in Cancer. Cancers (Basel) 2020; 13:cancers13010042. [PMID: 33375634 PMCID: PMC7796397 DOI: 10.3390/cancers13010042] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Export of mRNAs from the nucleus to the cytoplasm is a key regulatory step in the expression of proteins. mRNAs are transported through the nuclear pore complex (NPC). Export of mRNAs responds to a variety of cellular stimuli and stresses. Revelations of the specific effects elicited by NPC components and associated co-factors provides a molecular basis for the export of selected RNAs, independent of bulk mRNA export. Aberrant RNA export has been observed in primary human cancer specimens. These cargo RNAs encode factors involved in nearly all facets of malignancy. Indeed, the NPC components involved in RNA export as well as the RNA export machinery can be found to be dysregulated, mutated, or impacted by chromosomal translocations in cancer. The basic mechanisms associated with RNA export with relation to export machinery and relevant NPC components are described. Therapeutic strategies targeting this machinery in clinical trials is also discussed. These findings firmly position RNA export as a targetable feature of cancer along with transcription and translation.
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12
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Xi PW, Zhang X, Zhu L, Dai XY, Cheng L, Hu Y, Shi L, Wei JF, Ding Q. Oncogenic action of the exosome cofactor RBM7 by stabilization of CDK1 mRNA in breast cancer. NPJ Breast Cancer 2020; 6:58. [PMID: 33145401 PMCID: PMC7603334 DOI: 10.1038/s41523-020-00200-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/01/2020] [Indexed: 12/22/2022] Open
Abstract
RNA exosome can target the specific RNAs for their processing/degradation by distinct exosome cofactors. As a key component in exosome cofactors, RNA binding motif protein 7 (RBM7) shows the binding specificity for uridine-rich sequences in mRNAs via its RNA recognition motifs. However, the specific function of RBM7 in human breast cancer remains unclear. In vitro, experiments revealed that knockdown of RBM7 dramatically inhibited breast cancer cell proliferation, while inducing G1 cell cycle arrest; the opposite was true when RBM7 was overexpressed. Meanwhile, experiments in vivo confirmed the oncogenic function of RBM7 in breast cancer. RNA sequencing and the following pathway analysis found that cyclin-dependent kinase1 (CDK1) was one of the main gene regulated by RBM7. Overexpression of RBM7 increased CDK1 expression, while RBM7 knockdown decreased it. RIP assays additionally found that RBM7 bound directly to CDK1 mRNA. It was also showed that RBM7 could directly bind to the AU-rich elements (AREs) in 3'-UTR of CDK1 mRNA, which contributed to the stability of CDK1 mRNA by lengthening its half-life. More importantly, the oncogenic activity reduced by knockdown of RBM7 could be rescued by overexpression of CDK1 both in vitro and in vivo, but mutant CDK1 failed. All the evidences implied RBM7 promoted breast cancer cell proliferation by stabilizing CDK1 mRNA via binding to AREs in its 3'-UTR. As we knew, it was the first attempt to connect the RNA exosome to the tumor development, providing new insights into the mechanisms of RNA exosome-linked diseases.
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Affiliation(s)
- Pei-Wen Xi
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Xu Zhang
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Lei Zhu
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Xin-Yuan Dai
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Lin Cheng
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Yue Hu
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Liang Shi
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Qiang Ding
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
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13
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Borden KLB, Volpon L. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. RNA Biol 2020; 17:1239-1251. [PMID: 32496897 PMCID: PMC7549709 DOI: 10.1080/15476286.2020.1766179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Translation initiation is a critical facet of gene expression with important impacts that underlie cellular responses to stresses and environmental cues. Its dysregulation in many diseases position this process as an important area for the development of new therapeutics. The gateway translation factor eIF4E is typically considered responsible for ‘global’ or ‘canonical’ m7G cap-dependent translation. However, eIF4E impacts translation of specific transcripts rather than the entire translatome. There are many alternative cap-dependent translation mechanisms that also contribute to the translation capacity of the cell. We review the diversity of these, juxtaposing more recently identified mechanisms with eIF4E-dependent modalities. We also explore the multiplicity of functions played by translation factors, both within and outside protein synthesis, and discuss how these differentially contribute to their ultimate physiological impacts. For comparison, we discuss some modalities for cap-independent translation. In all, this review highlights the diverse mechanisms that engage and control translation in eukaryotes.
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Affiliation(s)
- Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
| | - Laurent Volpon
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal , Montreal, Québec, Canada
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14
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Ghram M, Bonnet-Magnaval F, Hotea DI, Doran B, Ly S, DesGroseillers L. Staufen1 is Essential for Cell-Cycle Transitions and Cell Proliferation Via the Control of E2F1 Expression. J Mol Biol 2020; 432:3881-3897. [DOI: 10.1016/j.jmb.2020.04.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
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15
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Tang S, Yu S, Cheng J, Zhang Y, Huang X. The versatile roles and clinical implications of exosomal mRNAs and microRNAs in cancer. Int J Biol Markers 2020; 35:3-19. [PMID: 32389046 DOI: 10.1177/1724600820920293] [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] [Indexed: 12/29/2022]
Abstract
Extracellular vesicles (EVs), which include exosomes, microvesicles, and apoptotic bodies, are nanosized structures that are secreted by various cells and act as important mediators in intercellular communication. Recent studies have shown that exosomes carrying bioactive molecules are generated from multivesicular bodies and are present in various body fluids. mRNAs and microRNAs (miRNAs) are encapsulated in exosomes and have been found to be involved in multiple pathophysiological processes. Here, we provide a review of tumor-associated exosomal mRNAs and miRNAs and their roles in metastasis and drug resistance. In particular, we emphasize their clinical application potential as diagnostic and prognostic biomarkers of cancer and in cancer therapy.
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Affiliation(s)
- Shuli Tang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Siming Yu
- Department of Pharmacy, Drug Clinical Trails Institution, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jianan Cheng
- Institute of immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Xiaoyi Huang
- Biotherapy Center, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
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16
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García-Cárdenas JM, Guerrero S, López-Cortés A, Armendáriz-Castillo I, Guevara-Ramírez P, Pérez-Villa A, Yumiceba V, Zambrano AK, Leone PE, Paz-y-Miño C. Post-transcriptional Regulation of Colorectal Cancer: A Focus on RNA-Binding Proteins. Front Mol Biosci 2019; 6:65. [PMID: 31440515 PMCID: PMC6693420 DOI: 10.3389/fmolb.2019.00065] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/23/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a major health problem with an estimated 1. 8 million new cases worldwide. To date, most CRC studies have focused on DNA-related aberrations, leaving post-transcriptional processes under-studied. However, post-transcriptional alterations have been shown to play a significant part in the maintenance of cancer features. RNA binding proteins (RBPs) are uprising as critical regulators of every cancer hallmark, yet little is known regarding the underlying mechanisms and key downstream oncogenic targets. Currently, more than a thousand RBPs have been discovered in humans and only a few have been implicated in the carcinogenic process and even much less in CRC. Identification of cancer-related RBPs is of great interest to better understand CRC biology and potentially unveil new targets for cancer therapy and prognostic biomarkers. In this work, we reviewed all RBPs which have a role in CRC, including their control by microRNAs, xenograft studies and their clinical implications.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - César Paz-y-Miño
- Facultad de Ciencias de la Salud Eugenio Espejo, Centro de Investigación Genética y Genómica, Universidad UTE, Quito, Ecuador
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